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.gitattributes

@@ -57,3 +57,11 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+controls/GSE40279/GSE40279_RAW/GPL13534_HumanMethylation450_15017482_v.1.2.bpm filter=lfs diff=lfs merge=lfs -text
+controls/GSE40279/GSE40279_RAW/GPL13534_HumanMethylation450_15017482_v.1.1.csv filter=lfs diff=lfs merge=lfs -text
+controls/GSE40279/GSE40279_RAW/GPL13534_HumanMethylation450_15017482_v.1.1.bpm.txt filter=lfs diff=lfs merge=lfs -text
+controls/GSE112905/GSE112905_non-normalized.txt filter=lfs diff=lfs merge=lfs -text
+controls/GSE42861/GSE42861_methylation_signal_matrix_SUBSETS/GSE42861_methylation_signal_matrix_2of13.txt filter=lfs diff=lfs merge=lfs -text
+controls/GSE42861/GSE42861_methylation_signal_matrix_SUBSETS/GSE42861_methylation_signal_matrix_3of13.txt filter=lfs diff=lfs merge=lfs -text
+controls/GSE42861/GSE42861_methylation_signal_matrix_SUBSETS/GSE42861_methylation_signal_matrix_11of13.txt filter=lfs diff=lfs merge=lfs -text
+controls/GSE40279/GSE40279_average_beta_GSM990464-GSM990627.txt filter=lfs diff=lfs merge=lfs -text

controls/GSE112905/GSE112905_non-normalized.txt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:005b977bb104ae015703a68bd8daa1aa637f53635644777c4ee515f5b022b63e
+size 214167648

controls/GSE112905/meta/GSE112905_family.xml/GSE112905_family.xml

@@ -0,0 +1,1638 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+
+<MINiML
+   xmlns="http://www.ncbi.nlm.nih.gov/geo/info/MINiML"
+   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+   xsi:schemaLocation="http://www.ncbi.nlm.nih.gov/geo/info/MINiML http://www.ncbi.nlm.nih.gov/geo/info/MINiML.xsd"
+   version="0.5.0" >
+
+  <Contributor iid="contrib1">
+    <Person><First>Lubov</First><Last>Nathanson</Last></Person>
+    <Email>[email protected]</Email>
+    <Department>INIM</Department>
+    <Organization>Nova Southeastern University</Organization>
+    <Address>
+      <Line>3321 College Ave.</Line>
+      <City>Fort Lauderdale</City>
+      <State>Florida</State>
+      <Zip-Code>33314</Zip-Code>
+      <Country>USA</Country>
+    </Address>
+  </Contributor>
+
+  <Contributor iid="contrib2">
+    <Organization>Illumina Inc.</Organization>
+    <Email>[email protected], [email protected]</Email>
+    <Phone>1 800 809 4566 </Phone>
+    <Organization>Illumina Inc.</Organization>
+    <Address>
+      <Line>9885 Towne Centre Drive</Line>
+      <City>San Diego</City>
+      <State>CA</State>
+      <Zip-Code>92121</Zip-Code>
+      <Country>USA</Country>
+    </Address>
+    <Web-Link>www.illumina.com</Web-Link>
+  </Contributor>
+
+  <Contributor iid="contrib3">
+    <Person><First>Malav</First><Middle>S</Middle><Last>Trivedi</Last></Person>
+  </Contributor>
+
+  <Contributor iid="contrib4">
+    <Person><First>Maria</First><Last>Abreu</Last></Person>
+  </Contributor>
+
+  <Contributor iid="contrib5">
+    <Person><First>Leonor</First><Last>Sarria</Last></Person>
+  </Contributor>
+
+  <Contributor iid="contrib6">
+    <Person><First>Natasha</First><Last>Rose</Last></Person>
+  </Contributor>
+
+  <Contributor iid="contrib7">
+    <Person><First>Vladimir</First><Last>Beljanski</Last></Person>
+  </Contributor>
+
+  <Contributor iid="contrib8">
+    <Person><First>Mary</First><Middle>A</Middle><Last>Fletcher</Last></Person>
+  </Contributor>
+
+  <Contributor iid="contrib9">
+    <Person><First>Nancy</First><Middle>G</Middle><Last>Klimas</Last></Person>
+  </Contributor>
+
+  <Database iid="GEO">
+    <Name>Gene Expression Omnibus (GEO)</Name>
+    <Public-ID>GEO</Public-ID>
+    <Organization>NCBI NLM NIH</Organization>
+    <Web-Link>http://www.ncbi.nlm.nih.gov/geo</Web-Link>
+    <Email>[email protected]</Email>
+  </Database>
+
+  <Platform iid="GPL21145">
+    <Status database="GEO">
+      <Submission-Date>2015-11-16</Submission-Date>
+      <Release-Date>2015-11-16</Release-Date>
+      <Last-Update-Date>2019-01-20</Last-Update-Date>
+    </Status>
+    <Title>Infinium MethylationEPIC</Title>
+    <Accession database="GEO">GPL21145</Accession>
+    <Technology>oligonucleotide beads</Technology>
+    <Distribution>commercial</Distribution>
+    <Organism taxid="9606">Homo sapiens</Organism>
+    <Manufacturer>Illumina, Inc.</Manufacturer>
+    <Manufacture-Protocol>
+See manufacturer's website
+    </Manufacture-Protocol>
+    <Contact-Ref ref="contrib2" />
+    <Supplementary-Data type="CSV">
+ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL21nnn/GPL21145/suppl/GPL21145_MethylationEPIC_15073387_v-1-0.csv.gz
+    </Supplementary-Data>
+    <Relation type="Alternative to" target="GPL23976" />
+    <Data-Table>
+      <Column position="1">
+        <Name>ID</Name>
+        <Description>IlmnID</Description>
+      </Column>
+      <Column position="2">
+        <Name>SPOT_ID</Name>
+      </Column>
+      <Column position="3">
+        <Name>AddressA_ID</Name>
+      </Column>
+      <Column position="4">
+        <Name>AlleleA_ProbeSeq</Name>
+      </Column>
+      <Column position="5">
+        <Name>AddressB_ID</Name>
+      </Column>
+      <Column position="6">
+        <Name>AlleleB_ProbeSeq</Name>
+      </Column>
+      <Column position="7">
+        <Name>Infinium_Design_Type</Name>
+      </Column>
+      <Column position="8">
+        <Name>Next_Base</Name>
+      </Column>
+      <Column position="9">
+        <Name>Color_Channel</Name>
+      </Column>
+      <Column position="10">
+        <Name>Forward_Sequence</Name>
+      </Column>
+      <Column position="11">
+        <Name>Genome_Build</Name>
+      </Column>
+      <Column position="12">
+        <Name>CHR</Name>
+      </Column>
+      <Column position="13">
+        <Name>MAPINFO</Name>
+      </Column>
+      <Column position="14">
+        <Name>SourceSeq</Name>
+      </Column>
+    <External-Data rows="868564">
+GPL21145-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Platform>
+
+  <Sample iid="GSM3090983">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA Healthy Control [HC] 1</Title>
+    <Accession database="GEO">GSM3090983</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>HC PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+HC subject 1
+      </Characteristics>
+      <Characteristics tag="disease state">
+Healthy Control [HC]
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from HC subject 1
+10H
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090983/suppl/GSM3090983_200526590034_R02C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090983/suppl/GSM3090983_200526590034_R02C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090983-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3090984">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA Healthy Control [HC] 2</Title>
+    <Accession database="GEO">GSM3090984</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>HC PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+HC subject 2
+      </Characteristics>
+      <Characteristics tag="disease state">
+Healthy Control [HC]
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from HC subject 2
+34H
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090984/suppl/GSM3090984_200526580039_R02C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090984/suppl/GSM3090984_200526580039_R02C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090984-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3090985">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA Healthy Control [HC] 3</Title>
+    <Accession database="GEO">GSM3090985</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>HC PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+HC subject 3
+      </Characteristics>
+      <Characteristics tag="disease state">
+Healthy Control [HC]
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from HC subject 3
+46H
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090985/suppl/GSM3090985_200526580053_R06C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090985/suppl/GSM3090985_200526580053_R06C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090985-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3090986">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA Healthy Control [HC] 4</Title>
+    <Accession database="GEO">GSM3090986</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>HC PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+HC subject 4
+      </Characteristics>
+      <Characteristics tag="disease state">
+Disease state:Healthy Control [HC]
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from HC subject 4
+58H
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090986/suppl/GSM3090986_200526580069_R02C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090986/suppl/GSM3090986_200526580069_R02C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090986-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3090987">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA GWI 1</Title>
+    <Accession database="GEO">GSM3090987</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>GWI PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+GWI subject 1
+      </Characteristics>
+      <Characteristics tag="disease state">
+Gulf War Illness (GWI)
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from GWI subject 1
+67G
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090987/suppl/GSM3090987_200526580034_R03C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090987/suppl/GSM3090987_200526580034_R03C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090987-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3090988">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA Healthy Control [HC] 5</Title>
+    <Accession database="GEO">GSM3090988</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>HC PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+HC subject 5
+      </Characteristics>
+      <Characteristics tag="disease state">
+Healthy Control [HC]
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from HC subject 5
+82H
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090988/suppl/GSM3090988_200526580035_R02C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090988/suppl/GSM3090988_200526580035_R02C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090988-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3090989">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA GWI 2</Title>
+    <Accession database="GEO">GSM3090989</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>GWI PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+GWI subject 2
+      </Characteristics>
+      <Characteristics tag="disease state">
+Gulf War Illness (GWI)
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from GWI subject 2
+91G
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090989/suppl/GSM3090989_200526580088_R03C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090989/suppl/GSM3090989_200526580088_R03C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090989-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3090990">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA Healthy Control [HC] 6</Title>
+    <Accession database="GEO">GSM3090990</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>HC PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+HC subject 6
+      </Characteristics>
+      <Characteristics tag="disease state">
+Healthy Control [HC]
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from HC subject 6
+94H
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090990/suppl/GSM3090990_200526580088_R06C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090990/suppl/GSM3090990_200526580088_R06C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090990-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3090991">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA GWI 3</Title>
+    <Accession database="GEO">GSM3090991</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>GWI PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+GWI subject 3
+      </Characteristics>
+      <Characteristics tag="disease state">
+Gulf War Illness (GWI)
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from GWI subject 3
+103G
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090991/suppl/GSM3090991_200134080024_R07C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090991/suppl/GSM3090991_200134080024_R07C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090991-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3090992">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA Healthy Control [HC] 7</Title>
+    <Accession database="GEO">GSM3090992</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>HC PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+HC subject 7
+      </Characteristics>
+      <Characteristics tag="disease state">
+Healthy Control [HC]
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from HC subject 7
+106H
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090992/suppl/GSM3090992_200526580062_R02C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090992/suppl/GSM3090992_200526580062_R02C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090992-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3090993">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA GWI 4</Title>
+    <Accession database="GEO">GSM3090993</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>GWI PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+GWI subject 4
+      </Characteristics>
+      <Characteristics tag="disease state">
+Gulf War Illness (GWI)
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from GWI subject 4
+127G
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090993/suppl/GSM3090993_200526580071_R07C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090993/suppl/GSM3090993_200526580071_R07C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090993-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3090994">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA Healthy Control [HC] 8</Title>
+    <Accession database="GEO">GSM3090994</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>HC PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+HC subject 8
+      </Characteristics>
+      <Characteristics tag="disease state">
+Healthy Control [HC]
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from HC subject 8
+142H
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090994/suppl/GSM3090994_200526580078_R06C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090994/suppl/GSM3090994_200526580078_R06C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090994-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3090995">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA GWI 5</Title>
+    <Accession database="GEO">GSM3090995</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>GWI PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+GWI subject 5
+      </Characteristics>
+      <Characteristics tag="disease state">
+Gulf War Illness (GWI)
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from GWI subject 5
+151G
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090995/suppl/GSM3090995_200526580083_R07C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090995/suppl/GSM3090995_200526580083_R07C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090995-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3090996">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA GWI 6</Title>
+    <Accession database="GEO">GSM3090996</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>GWI PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+GWI subject 6
+      </Characteristics>
+      <Characteristics tag="disease state">
+Gulf War Illness (GWI)
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from GWI subject 6
+163G
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090996/suppl/GSM3090996_200134080026_R03C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090996/suppl/GSM3090996_200134080026_R03C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090996-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3090997">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA GWI 7</Title>
+    <Accession database="GEO">GSM3090997</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>GWI PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+GWI subject 7
+      </Characteristics>
+      <Characteristics tag="disease state">
+Gulf War Illness (GWI)
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from GWI subject 7
+181G
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090997/suppl/GSM3090997_200526580044_R05C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090997/suppl/GSM3090997_200526580044_R05C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090997-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3090998">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA Healthy Control [HC] 9</Title>
+    <Accession database="GEO">GSM3090998</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>HC PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+HC subject 9
+      </Characteristics>
+      <Characteristics tag="disease state">
+Healthy Control [HC]
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from HC subject 9
+196H
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090998/suppl/GSM3090998_200526580051_R04C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090998/suppl/GSM3090998_200526580051_R04C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090998-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3090999">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA GWI 8</Title>
+    <Accession database="GEO">GSM3090999</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>GWI PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+GWI subject 8
+      </Characteristics>
+      <Characteristics tag="disease state">
+Gulf War Illness (GWI)
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from GWI subject 8
+205G
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090999/suppl/GSM3090999_200526580080_R05C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3090nnn/GSM3090999/suppl/GSM3090999_200526580080_R05C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3090999-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3091000">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA GWI 9</Title>
+    <Accession database="GEO">GSM3091000</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>GWI PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+GWI subject 9
+      </Characteristics>
+      <Characteristics tag="disease state">
+Gulf War Illness (GWI)
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from GWI subject 9
+214G
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3091nnn/GSM3091000/suppl/GSM3091000_200526580037_R06C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3091nnn/GSM3091000/suppl/GSM3091000_200526580037_R06C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3091000-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3091001">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA Healthy Control [HC] 10</Title>
+    <Accession database="GEO">GSM3091001</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>HC PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+HC subject 10
+      </Characteristics>
+      <Characteristics tag="disease state">
+Healthy Control [HC]
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from HC subject 10
+217H
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3091nnn/GSM3091001/suppl/GSM3091001_200526580007_R01C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3091nnn/GSM3091001/suppl/GSM3091001_200526580007_R01C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3091001-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Sample iid="GSM3091002">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-03-15</Last-Update-Date>
+    </Status>
+    <Title>PBMC genomic DNA GWI 10</Title>
+    <Accession database="GEO">GSM3091002</Accession>
+    <Type>genomic</Type>
+    <Channel-Count>1</Channel-Count>
+    <Channel position="1">
+      <Source>GWI PBMC</Source>
+      <Organism taxid="9606">Homo sapiens</Organism>
+      <Characteristics tag="gender">
+male
+      </Characteristics>
+      <Characteristics tag="subject id">
+GWI subject 10
+      </Characteristics>
+      <Characteristics tag="disease state">
+Gulf War Illness (GWI)
+      </Characteristics>
+      <Characteristics tag="cell type">
+peripheral blood mononuclear cells (PBMC)
+      </Characteristics>
+      <Molecule>genomic DNA</Molecule>
+      <Extract-Protocol>
+genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Blood &amp; Tissue Kit according to manufacturer instructions
+      </Extract-Protocol>
+      <Label>Cy3, Cy5</Label>
+      <Label-Protocol>
+Standard Illumina Protocol
+      </Label-Protocol>
+    </Channel>
+    <Hybridization-Protocol>
+bisulphite converted DNA was hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol
+    </Hybridization-Protocol>
+    <Scan-Protocol>
+Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
+    </Scan-Protocol>
+    <Description>
+PBMC genomic DNA from GWI subject 10
+223G
+    </Description>
+    <Data-Processing>
+Illumina Genome Studio; Matrix signal intensities contains unmethylated and methylated signal intensities; Matrix processed contains non-normalized average beta values.
+    </Data-Processing>
+    <Platform-Ref ref="GPL21145" />
+    <Contact-Ref ref="contrib1" />
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3091nnn/GSM3091002/suppl/GSM3091002_200526580007_R07C01_Grn.idat.gz
+    </Supplementary-Data>
+    <Supplementary-Data type="IDAT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3091nnn/GSM3091002/suppl/GSM3091002_200526580007_R07C01_Red.idat.gz
+    </Supplementary-Data>
+    <Data-Table>
+      <Column position="1">
+        <Name>ID_REF</Name>
+      </Column>
+      <Column position="2">
+        <Name>VALUE</Name>
+        <Description>Average Beta</Description>
+      </Column>
+      <Column position="3">
+        <Name>Detection Pval</Name>
+      </Column>
+    <External-Data rows="866895">
+GSM3091002-tbl-1.txt
+    </External-Data>
+    </Data-Table>
+  </Sample>
+
+  <Series iid="GSE112905">
+    <Status database="GEO">
+      <Submission-Date>2018-04-10</Submission-Date>
+      <Release-Date>2019-03-15</Release-Date>
+      <Last-Update-Date>2019-06-14</Last-Update-Date>
+    </Status>
+    <Title>Changes in DNA methylation patterns associated with Gulf War Illness</Title>
+    <Accession database="GEO">GSE112905</Accession>
+    <Pubmed-ID>30920300</Pubmed-ID>
+    <Summary>
+Gulf War Illness (GWI) is a complex condition that involves multiple organ systems and is characterized by an abrupt or delayed onset of persistent/relapsing symptomatology such as memory and other neurological problems, muscle and joint pain, gastrointestinal issues, hormonal imbalance, immune dysfunction and debilitating fatigue. Currently, treatment of the condition relies solely on management of symptomatology and improvement in quality of life due to a lack of knowledgeof the underlying mechanisms of disease onset and progression. An improved understanding of the key mechanisms of GWI and dysfunction within regulatory systems will lead to more objective diagnosis methods and adequate management of patients by providing targeted approaches to treatment. Disruption of DNA methylation patterns has been tied to various immune, neurological and endocrine disease states; however, the status of this epigenetic mark in GWI remains uncertain. This study aimed at identifying biomarkers of GWI by gaining knowledge on DNA methylation patterns of GWI in an effort to determine therapeutic targets of disease activity and provide insight into disease onset and progression.  Methods: Genomic DNA from 10 GWI patients and 10 healthy controls [HC] (“experimental cohort”) prepared from PBMCs was analyzed with ELISA-based DNA methylation assays and Illumina MethylationEPIC microarrays. These arrays allow measuring the methylation status at 850,000 CpG sites. Methylation changes in promoter regions were separately analyzed and used as input data in ingenuity pathway analysis software to identify altered functional pathways. Relevant differentially methylated CpG sites (DMS) were validated by pyrosequencing.  Results: Global DNA methylation levels using the ELISA-based assay on the DNA isolated from PBMCs of GWI patients were similar to those of HC. However, deeper evaluation using microarray-based genome-wide technology allowed detection of DMS in GWI patients with respect to HC. As an overall 10,767 CpG sites presented with differential DNA methylation levels across promoters, gene regulatory elements and within coding regions of genes. Majority of these DMS were hypermethylated in GWI patients as compared to the HC, and more than half of these sites localized to promoters and gene regulatory elements, relative to distribution of DMSin the network as a whole, indicating gene regulatory potential. Functional pathway analysis of the 776 genes with differentially methylated promoters (DMPs) fulfilling FDR≤0.2 criteriafollowing a genomic region-based approachlinks GWI to defects in at least 15 different pathways mostly related to cell signaling with a strong immune component.  Conclusions: This is the first study that has explored genome-wide epigenetic changes associated with GWI using the new MethylationEPIC microarrays covering about 850,000 CpG sites; which builds on previous methylation preliminary reports. The data obtained are consistent with previous evidence for dysregulation of the immune system in GWI and suggests a role of this epigenetic modification on the DNA pathobiology of GWI. They are also consistent with previous reports showing a Th1- to Th2-mediated immune response shift in GWI in addition to altered immune system function. Future validation studies in larger cohorts of GWI patients and evaluation of the effects of these methylation patterns on gene expression regulation are granted.
+    </Summary>
+    <Overall-Design>
+Genomic DNA from 20 peripheral blood mononuclear cells (PBMC) samples (10 GWI, 10 controls) were bisulfite-converted and hybridised to the Illumina MethylationEPIC microarrays. GenomeStudio idat files were generated and the data was analyzed using the RnBeads R package.
+    </Overall-Design>
+    <Type>Methylation profiling by array</Type>
+    <Contributor-Ref ref="contrib3" position="1" />
+    <Contributor-Ref ref="contrib4" position="2" />
+    <Contributor-Ref ref="contrib5" position="3" />
+    <Contributor-Ref ref="contrib6" position="4" />
+    <Contributor-Ref ref="contrib7" position="5" />
+    <Contributor-Ref ref="contrib8" position="6" />
+    <Contributor-Ref ref="contrib9" position="7" />
+    <Contributor-Ref ref="contrib1" position="8" />
+    <Contact-Ref ref="contrib1" />
+    <Sample-Ref ref="GSM3090983" />
+    <Sample-Ref ref="GSM3090984" />
+    <Sample-Ref ref="GSM3090985" />
+    <Sample-Ref ref="GSM3090986" />
+    <Sample-Ref ref="GSM3090987" />
+    <Sample-Ref ref="GSM3090988" />
+    <Sample-Ref ref="GSM3090989" />
+    <Sample-Ref ref="GSM3090990" />
+    <Sample-Ref ref="GSM3090991" />
+    <Sample-Ref ref="GSM3090992" />
+    <Sample-Ref ref="GSM3090993" />
+    <Sample-Ref ref="GSM3090994" />
+    <Sample-Ref ref="GSM3090995" />
+    <Sample-Ref ref="GSM3090996" />
+    <Sample-Ref ref="GSM3090997" />
+    <Sample-Ref ref="GSM3090998" />
+    <Sample-Ref ref="GSM3090999" />
+    <Sample-Ref ref="GSM3091000" />
+    <Sample-Ref ref="GSM3091001" />
+    <Sample-Ref ref="GSM3091002" />
+    <Supplementary-Data type="TAR">
+ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112905/suppl/GSE112905_RAW.tar
+    </Supplementary-Data>
+    <Supplementary-Data type="TXT">
+ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112905/suppl/GSE112905_non-normalized.txt.gz
+    </Supplementary-Data>
+    <Relation type="BioProject" target="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA449457" />
+  </Series>
+
+</MINiML>

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+<sst xmlns="http://schemas.openxmlformats.org/spreadsheetml/2006/main" count="76" uniqueCount="75"><si><t>Description</t></si><si><t>Column Name</t></si><si><t>Defines Assay type - Infinium I or Infinium II</t></si><si><t>Base added at SBE step - Infinium I assays only</t></si><si><t>Color of the incorporated base  (Red or Green) - Infinium I assays only</t></si><si><t>Genome build on which forward sequence is based</t></si><si><t>Chromosome - genome build 37</t></si><si><t>Coordinates - genome build 37</t></si><si><t>Chromosome - genome build 36</t></si><si><t>Coordinates - genome build 36</t></si><si><t>Assays with SNPs present within probe ≤10bp from query site (HM27 carryover or recently discovered)</t></si><si><t>Present or absent on HumanMethylation27 array</t></si><si><t>Relationship to Canonical CpG Island: Shores - 0-2 kb from CpG island; Shelves - 2-4 kb from CpG island.</t></si><si><t>Index</t></si><si><t>TargetID</t></si><si><t>ProbeID_A</t></si><si><t>ProbeID_B</t></si><si><t>Identifies the probe name. Also used as a key column for data import.</t></si><si><t>IlmnID</t></si><si><t>Name</t></si><si><t>AddressA_ID</t></si><si><t>AlleleA_ProbeSeq</t></si><si><t>AddressB_ID</t></si><si><t>AlleleB_ProbeSeq</t></si><si><t>Probe Index</t></si><si><t>Illumina identifier for probe sequence A</t></si><si><t>Illumina identifier for probe sequence B</t></si><si><t>Unique CpG locus identifier from the Illumina CG database</t></si><si><t>Address of probe A</t></si><si><t>Sequence for probe A</t></si><si><r><t xml:space="preserve">Address of probe </t></r><r><rPr><b/><sz val="11"/><rFont val="Calibri"/><family val="2"/></rPr><t xml:space="preserve"> </t></r><r><rPr><sz val="11"/><rFont val="Calibri"/><family val="2"/></rPr><t>B</t></r></si><si><r><t xml:space="preserve">Sequence for probe </t></r><r><rPr><b/><sz val="11"/><rFont val="Calibri"/><family val="2"/></rPr><t>B</t></r></si><si><t>Infinium_Design_Type</t></si><si><t>Next_Base</t></si><si><t>Color_Channel</t></si><si><t>Forward_Sequence</t></si><si><t>Genome_Build</t></si><si><t>CHR</t></si><si><t>MAPINFO</t></si><si><t>SourceSeq</t></si><si><t>Chromosome_36</t></si><si><t>Coordinate_36</t></si><si><t>Strand</t></si><si><t>Probe_SNPs</t></si><si><t>Probe_SNPs_10</t></si><si><t>Random_Loci</t></si><si><t>Methyl27_Loci</t></si><si><t>UCSC_RefGene_Name</t></si><si><t>UCSC_RefGene_Accession</t></si><si><t>UCSC_RefGene_Group</t></si><si><t>UCSC_CpG_Islands_Name</t></si><si><t>Relation_to_UCSC_CpG_Island</t></si><si><t>Phantom</t></si><si><t>DMR</t></si><si><t>Enhancer</t></si><si><t>HMM_Island</t></si><si><t>Regulatory_Feature_Name</t></si><si><t>Regulatory_Feature_Group</t></si><si><t>DHS</t></si><si><t>Assays with SNPs present within probe &gt;10bp from query site</t></si><si><t>Differentially methylated region (experimentally determined)</t></si><si><t>DNAse hypersensitive site (experimentally determined)</t></si><si><t>Enhancer element (informatically-determined)</t></si><si><t>FANTOM-derived promoter</t></si><si><t>Hidden Markov Model Island</t></si><si><t>Regulatory feature (informatically determined)</t></si><si><t>Sequence (in 5'-3' orientation) flanking query site</t></si><si><t>Gene name (UCSC)</t></si><si><t>Accession number (UCSC)</t></si><si><t>Gene region feature category (UCSC)</t></si><si><t>CpG island name (UCSC)</t></si><si><t>Regulatory feature category</t></si><si><t>Loci which were chosen randomly in the design proccess</t></si><si><t>Design strand</t></si><si><t>Unconverted design sequence</t></si></sst>

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