title: 3b_CD19B

description: B-cell DNA from pedigree 3 twin b

source_name: Twin 3b B-cells


title: 6a_CD19B

status: Public on Mar 19 2018

type: genomic

city: Evry

first: Jorg

last: Tost

address: 2 rue Gaston Cremieux

country: France

institute: CEA-Institut de Genomique, Centre National de Genotypage

description: B-cell DNA from pedigree 6 twin a

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium Human Methylation 450 K bead arrays (Illumina Inc., San Diego, CA). Processing was done according to the manufacturer’s protocol using an automated pipeline.  of bisulfite-treated DNA was analyzed using the Infinium  Human Methylation 450 K bead arrays spanning approximately  over 480,000 CpG sites/sample (Illumina Inc., San  Diego, CA). Processing was done according to the manufacturer’s  protocol using an automated pipeline, and the  arrays were scanned on an Illumina iScan platform (Illumina  Inc., San Diego, CA) established at the Life & Brain  Center (Bonn, Germany)

data_processing: Subset quantile normalization, revised version of Touleimat & tost, Epigenomics 2012

label: Cy5, Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Twin 6a B-cells

label_protocol: Standard Illumina Protocol

extract_protocol: Peripheral blood was processed using density gradient centrifugation and the granulocyte fraction was preserved. Serial cell sorting was performed on the mononuclear cell fraction using a RoboSep device (StemCell Technologies), using first a CD14 positive selection, then a CD4 positive selection and finally a B cell enrichment. Genomic DNA was extracted and purified from monocytes, CD4+ T-cells, B-cells and granulocytes using the AllPrep DNA/RNA/miRNA Universal kit (Qiagen) following the manufacturer's instructions

tag: status

value: Systemic lupus erythematosus (SLE)

tag: cell type

value: B-cells

tag: gender

value: Female

tag: zygosity

value: Same-sex dizygotic


title: 8a_CD19B

description: B-cell DNA from pedigree 8 twin a

scan_protocol: the arrays were scanned on an Illumina iScan platform

source_name: Twin 8a B-cells

value: Monozygotic


title: 5b_CD19B

description: B-cell DNA from pedigree 5 twin b

source_name: Twin 5b B-cells

value: Co-twin


title: 5a_CD19B

description: B-cell DNA from pedigree 5 twin a

source_name: Twin 5a B-cells


title: G0058_1

type: RNA

city: Atlanta

first: Anna

middle: K

last: Knight

state: Georgia

address: 101 Woodruff Circle NE

country: USA

institute: Emory University

description: Human HT12-v4 - standard protocol

data_processing: BeadStudio

label: biotin

molecule: total RNA

source_name: PBMC

extract_protocol: AllPrep RNA/DNA Mini Kit (Qiagen)

tag: Sex

tag: race

value: African American

tag: sample type

value: PBMC

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: G0148_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection


title: G0081_2

description: Human HT12-v4 - standard protocol

tag: maternal age

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7


title: G0058_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: E0587_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection


title: E0579_1

description: Human HT12-v4 - standard protocol

tag: maternal age


title: E0594_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8


title: 1b_CD19B

description: B-cell DNA from pedigree 1 twin b

source_name: Twin 1b B-cells

tag: status

tag: cell type

tag: gender

tag: zygosity


title: 3a_CD19B

description: B-cell DNA from pedigree 3 twin a

source_name: Twin 3a B-cells

value: Male


title: 1a_CD19B

description: B-cell DNA from pedigree 1 twin a

source_name: Twin 1a B-cells


title: G0151_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance


title: E0579_2

description: Human HT12-v4 - standard protocol

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: E0550_1

description: Human HT12-v4 - standard protocol


title: G0096_1

description: Human HT12-v4 - standard protocol


title: 15a_CD14M

description: Monocyte DNA from pedigree 15 twin a

source_name: Twin 15a monocytes

value: Monocytes


title: G0064_2

description: Human HT12-v4 - standard protocol


title: 9a_CD19B

description: B-cell DNA from pedigree 9 twin a

source_name: Twin 9a B-cells

value: Opposite-sex dizygotic


title: G0151_2

description: Human HT12-v4 - standard protocol


title: 15b_CD14M

description: Monocyte DNA from pedigree 15 twin b

source_name: Twin 15b monocytes


title: 14a_CD14M

description: Monocyte DNA from pedigree 14 twin a

source_name: Twin 14a monocytes


title: 1b_CD4T

description: CD4+ T-cell DNA from pedigree 1 twin b

source_name: Twin 1b CD4+ T-cells

value: CD4+ T-cells


title: 14b_CD14M

description: Monocyte DNA from pedigree 14 twin b

source_name: Twin 14b monocytes


title: G0088_1

description: Human HT12-v4 - standard protocol


title: 13a_CD14M

description: Monocyte DNA from pedigree 13 twin a

source_name: Twin 13a monocytes


title: G0075_1

description: Human HT12-v4 - standard protocol


title: 12b_CD14M

description: Monocyte DNA from pedigree 12 twin b

source_name: Twin 12b monocytes


title: 11a_CD14M

description: Monocyte DNA from pedigree 11 twin a

source_name: Twin 11a monocytes


title: 12a_CD14M

description: Monocyte DNA from pedigree 12 twin a

source_name: Twin 12a monocytes


title: 6b_CD19B

description: B-cell DNA from pedigree 6 twin b

source_name: Twin 6b B-cells


title: 13b_CD14M

description: Monocyte DNA from pedigree 13 twin b

source_name: Twin 13b monocytes


title: 10b_CD14M

description: Monocyte DNA from pedigree 10 twin b

source_name: Twin 10b monocytes


title: 10a_CD14M

description: Monocyte DNA from pedigree 10 twin a

source_name: Twin 10a monocytes


title: G0148_2

description: Human HT12-v4 - standard protocol

source_name: PBMC


title: 9b_CD14M

description: Monocyte DNA from pedigree 9 twin b

source_name: Twin 9b monocytes


title: E0592_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: G0084_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance


title: E0591_1

description: Human HT12-v4 - standard protocol

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 1

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8


title: 11b_CD14M

description: Monocyte DNA from pedigree 11 twin b

source_name: Twin 11b monocytes

tag: status

tag: cell type

tag: gender

tag: zygosity


title: E0592_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: 7a_CD14M

description: Monocyte DNA from pedigree 7 twin a

source_name: Twin 7a monocytes


title: G0064_1

description: Human HT12-v4 - standard protocol

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: G0102_1

description: Human HT12-v4 - standard protocol

tag: Sex


title: E0591_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8


title: 7b_CD14M

description: Monocyte DNA from pedigree 7 twin b

source_name: Twin 7b monocytes

tag: status

tag: cell type

tag: gender

tag: zygosity


title: G0102_2

description: Human HT12-v4 - standard protocol

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit


title: G0088_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: 9a_CD14M

description: Monocyte DNA from pedigree 9 twin a

source_name: Twin 9a monocytes


title: E0570_2

description: Human HT12-v4 - standard protocol


title: 6b_CD14M

description: Monocyte DNA from pedigree 6 twin b

source_name: Twin 6b monocytes


title: E0570_1

description: Human HT12-v4 - standard protocol


title: G0125_1

description: Human HT12-v4 - standard protocol


title: E0568_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: G0043_1

description: Human HT12-v4 - standard protocol

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit


title: G0125_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: 6a_CD14M

description: Monocyte DNA from pedigree 6 twin a

source_name: Twin 6a monocytes

tag: status

tag: cell type

tag: gender

tag: zygosity


title: 5b_CD14M

description: Monocyte DNA from pedigree 5 twin b

source_name: Twin 5b monocytes


title: 8a_CD14M

description: Monocyte DNA from pedigree 8 twin a

source_name: Twin 8a monocytes


title: E0568_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12


title: E0565_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: G0110_2

description: Human HT12-v4 - standard protocol


title: 5a_CD14M

description: Monocyte DNA from pedigree 5 twin a

source_name: Twin 5a monocytes

tag: status

tag: cell type

tag: gender

tag: zygosity


title: G0034_1

description: HumanMethylation450 BeadChip - standard protocol

scan_protocol: BeadStudio

data_processing: Any CpG site with low signal or missing data for greater than 10% of samples was removed, and any sample with missing data for greater than 5% of CpG sites was removed. BMIQ.

tag: age

tag: ga sample


title: G0110_1

description: Human HT12-v4 - standard protocol


title: 3a_CD14M

description: Monocyte DNA from pedigree 3 twin a

source_name: Twin 3a monocytes


title: 8b_CD14M

description: Monocyte DNA from pedigree 8 twin b

source_name: Twin 8b monocytes


title: 1a_CD14M

description: Monocyte DNA from pedigree 1 twin a

source_name: Twin 1a monocytes


title: G0072_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: 1b_CD14M

description: Monocyte DNA from pedigree 1 twin b

source_name: Twin 1b monocytes

tag: status

tag: cell type

tag: gender

tag: zygosity


title: G0072_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 12


title: E0572_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: G0082_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection


title: G0084_2

description: Human HT12-v4 - standard protocol

tag: maternal age


title: E0502_1

tag: age

tag: ga sample


title: E0572_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 12


title: E0504_2

tag: Sex

tag: race

tag: sample type

tag: fetal intolerance


title: E0569_2

tag: visit

tag: pregnancy complication


title: G0123_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age


title: E0525_1

tag: age

tag: ga sample


title: G0123_1

description: Human HT12-v4 - standard protocol


title: E0577_1

description: Human HT12-v4 - standard protocol


title: E0502_2


title: G0013_1


title: G0076_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: E0504_1

tag: Sex

tag: race

tag: sample type

tag: fetal intolerance

tag: visit


title: 3b_CD14M

description: Monocyte DNA from pedigree 3 twin b

source_name: Twin 3b monocytes

tag: status

tag: cell type

tag: gender

tag: zygosity


title: E0511_1

tag: age

tag: ga sample

tag: pregnancy complication


title: G0059_2


title: G0059_1


title: G0046_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age


title: G0035_1


title: G0046_1

description: Human HT12-v4 - standard protocol


title: G0076_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14


title: E0511_2

tag: Sex

tag: race

tag: sample type

tag: fetal intolerance

tag: visit

tag: age

tag: ga sample

tag: pregnancy complication


title: G0071_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 15


title: E0566_1

tag: Sex

tag: race


title: G0022_1

tag: sample type

tag: fetal intolerance


title: G0099_1

description: Human HT12-v4 - standard protocol

tag: visit


title: G0099_2

description: Human HT12-v4 - standard protocol


title: G0022_2

tag: age

tag: ga sample


title: G0035_2

tag: pregnancy complication


title: G0070_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14


title: G0130_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: maternal age


title: E0566_2

tag: sample type

tag: fetal intolerance

tag: visit


title: G0070_1

description: Human HT12-v4 - standard protocol

tag: pregnancy complication

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 15


title: G0130_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection


title: G0042_1

tag: age

tag: ga sample


title: G0042_2

tag: Sex

tag: race


title: G0028_2

tag: sample type


title: E0562_2

description: Human HT12-v4 - standard protocol

tag: fetal intolerance

tag: maternal age

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14


title: G0006_1

tag: visit

tag: pregnancy complication


title: G0100_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 15


title: G0100_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: fetal intolerance

tag: maternal age

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9


title: E0562_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: visit

tag: pregnancy complication

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14


title: G0020_1

tag: age

tag: ga sample


title: G0003_2

tag: Sex

tag: race


title: G0079_1

description: Human HT12-v4 - standard protocol

tag: sample type

tag: fetal intolerance

tag: weeks gestation at sample collection


title: G0020_2


title: G0079_2

description: Human HT12-v4 - standard protocol

tag: maternal age


title: G0098_2

description: Human HT12-v4 - standard protocol


title: G0098_1

description: Human HT12-v4 - standard protocol


title: G0023_2


title: E0575_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 15


title: E0508_1

tag: visit

tag: age

tag: ga sample

tag: pregnancy complication


title: G0006_2

tag: Sex

tag: race

tag: sample type

tag: fetal intolerance


title: G0071_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14


title: E0508_2

tag: visit

tag: age


title: G0028_1

tag: ga sample

tag: pregnancy complication


title: E0575_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 15


title: E0524_2

tag: sample type

tag: fetal intolerance


title: G0023_1


title: E0574_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age


title: E0513_2

tag: visit

tag: age

tag: ga sample


title: E0538_2

tag: Sex

tag: race

tag: pregnancy complication


title: E0524_1


title: E0574_2

description: Human HT12-v4 - standard protocol


title: G0003_1


title: G0077_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14


title: E0513_1

tag: sample type

tag: fetal intolerance


title: G0077_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: visit

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 15


title: E0541_1

tag: Sex

tag: race

tag: age

tag: ga sample

tag: pregnancy complication


title: E0538_1


title: G0015_2


title: G0015_1


title: E0541_2


title: E0515_1


title: G0104_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14


title: G0014_1

tag: sample type

tag: fetal intolerance

tag: visit


title: G0078_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 15


title: G0078_1

description: Human HT12-v4 - standard protocol

tag: pregnancy complication

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 10

tag: surrogate variable 11


title: G0134_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: fetal intolerance

tag: visit


title: LSD1_day_2

type: SRA

city: Kumamoto

first: Kotaro

last: Anan

state: Kumamoto

address: 2-2-1, Honjo, Chuo-ku

department: Department of Medicall Cell Biology

country: Japan

institute: Kumamoto University

library_source: genomic

data_processing:
Basecalls and conversion to FASTQ files were performed using BaseSpace Onsite (Illumina)
Sequence data were alignmened onto the mouse reference genome mm9 using the Bowtie 2 algorithm.
Duplicate reads and low read/mapping quality reads were trimmed out with Galaxy.
Peak detection was done using the MACS algorithm. LSD1 binding sites were detected based on the LSD1 peaks significantly enriched over input peaks at a cutoff value of p=10^-5.
Number of reads in LSD1-ChIP samples was normalized to RPKM to generate coverage score using bamCoverage tool in Galaxy.
Genome_build: mm9
Supplementary_files_format_and_content: The BED files were generated using MACS algorithm.
Supplementary_files_format_and_content: The BIGWIG files were generated using bamCoverage tool in Galaxy.

organism: Mus musculus

source_name: differentiating C2C12 cells

growth_protocol: Cells were grown in DMEM containing 25mM glucose and 10% FBS.

extract_protocol:
Cells were crosslinked with formaldehyde and disuccinimidyl glutarate. Cell lysates were subjected to two-step DNA fragmentation by a probe-type sonifier and a water bath sonifier, and chromatin-DNA complexes were pulled down using the specific antibody.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs) according to the manufacturer's instructions. Briefly, ChIP DNA was end-repaired using an end prep enzyme. After adapter ligation, DNA was PCR amplified with NEB Index primers for 8-10 cycles. The purified DNA was checked for quality on Agilent TapeStation instrument with an Agilent High Sensitivity D1000 kit. The library DNA was approximately 170–500 bp in length. Libraries ware quantified using quantitative real-time PCR with the Kapa Library Quantification Kit. Diluted library DNA was subjected NextSeq sequencers (Illumina) according to the manufacturer's protocols.

treatment_protocol: For myogenic induction, medium was changed to DMEM containing 25mM glucose and 2% horse serum, then incubated for 48 or 120 hours.

tag: cell status

value: differentiating

tag: antibody

value: Anti-LSD1 polyclonal antibody (Abcam:ab177721)

tag: time point


title: LSD1_day_5

source_name: differentiated C2C12 cells

value: differentiated


title: input_day_2


title: input_day_5


title: G0104_2

description: Human HT12-v4 - standard protocol

source_name: PBMC

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: G0097_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: pregnancy complication


title: E0537_2

tag: fetal intolerance

tag: visit

tag: age

tag: ga sample


title: E0576_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age


title: E0576_1

description: Human HT12-v4 - standard protocol


title: G0026_1


title: G0134_1

description: Human HT12-v4 - standard protocol


title: G0061_2


title: E0581_1

description: Human HT12-v4 - standard protocol


title: exp2_S2101_H3K4me3

data_processing:
Basecalls and conversion to FASTQ files were performed using BaseSpace Onsite (Illumina)
Sequence data were alignmened onto the mouse reference genome mm9 using the Bowtie 2 algorithm.
Duplicate reads and low read/mapping quality reads were trimmed out with Galaxy.
Peak detection was done using the MACS algorithm. Modified histone binding sites were detected based on the peaks significantly enriched over input peaks at a cutoff value of p=10^-10.
Number of reads in modified histone-ChIP samples was normalized to RPKM to generate coverage score using bamCoverage tool in Galaxy.
Genome_build: mm9
Supplementary_files_format_and_content: The BED files were generated using MACS algorithm.
Supplementary_files_format_and_content: The BIGWIG files were generated using bamCoverage tool in Galaxy.

extract_protocol:
Cells were crosslinked with formaldehyde. Cell lysates were subjected to two-step DNA fragmentation by a probe-type sonifier and a water bath sonifier, and chromatin-DNA complexes were pulled down using the specific antibody.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs) according to the manufacturer's instructions. Briefly, ChIP DNA was end-repaired using an end prep enzyme. After adapter ligation, DNA was PCR amplified with NEB Index primers for 8-10 cycles. The purified DNA was checked for quality on Agilent TapeStation instrument with an Agilent High Sensitivity D1000 kit. The library DNA was approximately 170–500 bp in length. Libraries ware quantified using quantitative real-time PCR with the Kapa Library Quantification Kit. Diluted library DNA was subjected NextSeq sequencers (Illumina) according to the manufacturer's protocols.

treatment_protocol: For myogenic induction, medium was changed to DMEM containing 25mM glucose and 2% horse serum and LSD1 inhibitor S2101 (10uM), or vehicle control, then incubated for 48 hours.

tag: cell type

value: differentiating myoblasts

tag: antibody

value: Anti-tri-methylated histone H3K4 (Millipore:07-473)

tag: drug

value: LSD1 inhibitor, S2101


title: exp2_S2101_H3

value: differentiated myoblasts

value: Anti-pan histone H3 (Abcam:ab1791)


title: exp2_S2101_input


title: G0001_1

value: Female


title: G0080_1

description: Human HT12-v4 - standard protocol


title: exp2_Control_H3

value: vehicle


title: G0026_2


title: exp2_Control_H3K4me3


title: G0014_2


title: exp2_Control_input


title: G0080_2

description: Human HT12-v4 - standard protocol


title: E0551_2


title: exp1_S2101_input


title: exp1_S2101_H3K4me1

value: Anti-mono-methylated histone H3K4 (Abcam:ab8895)


title: exp1_Control_H3K4me2

value: Anti-di-methylated histone H3K4 (Millipore:07-030)


title: G0108_1

description: Human HT12-v4 - standard protocol

value: African American

value: PBMC

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13


title: G0040_2

tag: Sex

tag: race

tag: sample type

tag: fetal intolerance

tag: visit

tag: age

tag: ga sample

tag: pregnancy complication


title: exp1_Control_H3K4me1

tag: cell type

tag: antibody

tag: drug


title: G0048_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age


title: G0061_1


title: G0108_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 14

tag: surrogate variable 15


title: exp1_Control_input

tag: cell type

tag: drug


title: G0060_2

tag: Sex

tag: race

tag: sample type

tag: fetal intolerance

tag: visit

tag: age

tag: ga sample

tag: pregnancy complication


title: E0528_2


title: Naïve (alum alone)

city: Mahasset

first: Andrew

last: Shih

state: NY

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

library_source: transcriptomic

data_processing:
The raw image files from the NextSeq sequencer was de-multiplexed and converted to fastq files using Illumina's the bcl2fastq BaseSpace App.
Adapter sequences and low quality bass reads were trimmed from fastq files using cutadapt.
Genes quantification from the fastq files was done using Kallisto
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files with TPM per gene

source_name: Dorsal Root Ganglion

extract_protocol:
Dorsal root ganglion (DRG)  were harvested from the thoracic and lumbar regions of mice immediately following euthanasia, as described previously (Malin et al 2007, Nat. Protoc. 2: 152–160). To enrich for DRG neurons, DRGs were digested with 1µg/mL collagenase/dispase (Roche) in neurobasal medium (Gibco, Thermo Fisher Scientific, Waltham MA) for 1 hour at 37°C on a rotator-shaker.  Following digestion, DRGs were washed with HBSS (Gibco) and filtered through a 70µM strainer.  The cell suspension was layered on a 15% BSA in HBSS, and centrifuged at 800rpm for 20 minutes without brake.  The cell pellet was re-suspended in neurobasal medium. B lymphocytes were depleted from cell preparations using DynabeadsTM mouse pan B purification kit (Invitrogen, USA).
RNA libraries were prepared for sequencing using the Truseq Stranded mRNA prep kit following standard Illumina protocols

tag: strain

tag: tissue

value: Dorsal Root Ganglion


title: Alum+KLH


title: exp1_S2101_H3K4me2

tag: antibody


title: E0547_1


title: G0016_1


title: E0583_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 12

tag: surrogate variable 13


title: E0588_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: fetal intolerance

tag: visit

tag: pregnancy complication


title: G0160_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age


title: E0583_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 11

tag: surrogate variable 14

tag: surrogate variable 15


title: E0582_2

description: Human HT12-v4 - standard protocol

tag: Sex


title: G0160_1

description: Human HT12-v4 - standard protocol

tag: race


title: E0547_2

tag: sample type

tag: age

tag: ga sample


title: G0062_2

description: Human HT12-v4 - standard protocol

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 12

tag: surrogate variable 13


title: G0029_1


title: G0007_2


title: G0143_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age


title: G0066_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race


title: E0582_1

description: Human HT12-v4 - standard protocol

tag: sample type


title: G0081_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 11

tag: surrogate variable 14

tag: surrogate variable 15


title: E0523_1

tag: fetal intolerance

tag: visit

tag: age

tag: ga sample

tag: pregnancy complication


title: G0062_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 12

tag: surrogate variable 13


title: G0060_1

tag: Sex

tag: race

tag: sample type


title: E0514_1

description: Human HT12-v4 - standard protocol

tag: fetal intolerance

tag: visit


title: E0554_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 11

tag: surrogate variable 14

tag: surrogate variable 15


title: E0554_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9


title: G0107_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: fetal intolerance

tag: visit

tag: surrogate variable 10

tag: surrogate variable 12

tag: surrogate variable 13


title: E0556_1

tag: age

tag: ga sample


title: E0531_1

tag: pregnancy complication


title: E0556_2


title: G0095_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection


title: G0055_1


title: G0107_1

description: Human HT12-v4 - standard protocol

tag: maternal age

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 11

tag: surrogate variable 14

tag: surrogate variable 15


title: G0055_2

tag: Sex

tag: race

tag: sample type

tag: fetal intolerance

tag: visit


title: G0065_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: pregnancy complication

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 12

tag: surrogate variable 13


title: E0545_2

description: Human HT12-v4 - standard protocol

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6


title: E0526_1

tag: Sex

tag: race

tag: sample type

tag: fetal intolerance

tag: visit

tag: age

tag: ga sample


title: E0523_2

tag: pregnancy complication


title: E0545_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: G0054_1

tag: Sex

tag: race


title: G0146_1

description: Human HT12-v4 - standard protocol

tag: sample type

tag: fetal intolerance

tag: weeks gestation at sample collection

tag: maternal age


title: E0553_2

tag: visit

tag: age

tag: ga sample

tag: pregnancy complication


title: G0153_2

description: Human HT12-v4 - standard protocol

tag: experienced labor


title: G0065_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10


title: G0047_1

tag: Sex

tag: race

tag: sample type

tag: fetal intolerance


title: G0044_1

tag: visit

tag: age

tag: ga sample


title: G0053_2

tag: pregnancy complication


title: G0047_2


title: G0054_2


title: E0553_1


title: G0153_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age


title: E0597_1

description: Human HT12-v4 - standard protocol


title: E0548_2


title: E0598_1

description: Human HT12-v4 - standard protocol


title: G0044_2


title: G0039_1


title: G0154_2

description: Human HT12-v4 - standard protocol


title: G0017_1


title: E0548_1


title: G0154_1

description: Human HT12-v4 - standard protocol


title: E0597_2

description: Human HT12-v4 - standard protocol


title: E0600_2

description: Human HT12-v4 - standard protocol


title: E0600_1

description: Human HT12-v4 - standard protocol


title: G0027_2


title: CST-KO rep2

city: La Jolla

first: Nick

last: Webster

state: CA

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

description: RNA from 4 independent mice for 4 replicates

hyb_protocol: Hybridized using Nimblegen Hybridization System 4 following standard porotocols

scan_protocol: Scanned on Genepix 4000B scanner

data_processing: Data extracted using Arraystar 4

source_name: left cardiac ventricle

label_protocol: Labeled using Nimblegen One-color labeling kit

growth_protocol: Mice maintained on normal chow with a 12 h light/dark cycle.

extract_protocol: Total RNA extracted with Rneasy (Qiagen) according to manufacturers instructions

tag: tissue

value: left cardiac ventricle

tag: genotype

value: CST knockout


title: CST-KO rep3


title: G0030_2


title: G0033_1


title: G0030_1


title: G0033_2


title: E0578_1

description: Human HT12-v4 - standard protocol


title: G0027_1


title: E0544_1

description: Human HT12-v4 - standard protocol


title: G0093_2

description: Human HT12-v4 - standard protocol


title: G0010_2


title: G0025_1


title: CHGA-KO rep4

value: CHGA knockout


title: G0039_2


title: CHGA-KO rep2


title: G0024_1

description: Human HT12-v4 - standard protocol


title: G0009_2


title: G0025_2


title: G0010_1


title: G0093_1

description: Human HT12-v4 - standard protocol


title: G0146_2

description: Human HT12-v4 - standard protocol


title: CHGA-KO rep3


title: E0549_2


title: WT rep4

value: Wild-type


title: WT rep3


title: CHGA-KO rep1


title: G0009_1


title: CST-KO rep1


title: E0517_1


title: E0561_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: E0561_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10


title: G0068_2

description: Human HT12-v4 - standard protocol

tag: weeks gestation at sample collection

tag: maternal age


title: G0068_1

description: Human HT12-v4 - standard protocol


title: G0019_1

tag: age

tag: ga sample


title: WT rep2

tag: tissue

tag: genotype


title: E0549_1


title: E0517_2


title: E0543_2


title: CST-KO rep4


title: G0129_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: WT rep1


title: G0021_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: G0180_1

description: Human HT12-v4 - standard protocol


title: G0121_2

description: Human HT12-v4 - standard protocol


title: E0543_1

tag: age

tag: ga sample


title: E0617_1

description: Human HT12-v4 - standard protocol


title: E0542_1


title: PBMC, Day 44, PID 8

city: Rixensart

first: Laurane

last: De Mot

address: Rue de l'Institut 89

country: Belgium

institute: GSK Vaccines

description: PBMC sample, 14 days after 2nd vaccination

hyb_protocol: After fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on GeneChip_ Human Genome U133 Plus 2.0 arrays following standard procedures.

scan_protocol: Data acquisition was performed using GeneChip Operating Software (Affymetrix).

data_processing: The data were analyzed with R/Bioconductor using GCRMA as summarization/normalization method

source_name: PBMC samples from subject 8 at Day 44

label_protocol: Biotinylated cDNA were prepared according to NuGen Ovation RNA amplification system V2 (+ Ovation WB reagent) protocol from 50ng total RNA

extract_protocol: Total RNA was isolated by RNeasy™ Minikit (Qiagen) according to the manufacturer’s protocol. A DNAse treatment was applied on the RNeasy column to avoid genomic DNA contamination. RNA was quantified by Nanodrop DO.

treatment_protocol: PBMC were thawed in RPMI medium, centrifuged and resuspended in RLT buffer (106 cells/350µl of lysis buffer - Qiagen).

tag: tissue

value: Peripheral Blood Mononuclear Cells (PBMC)

tag: subject id

tag: sample day


title: E0542_2


title: E0539_2


title: PBMC, Day 31, PID 9

description: PBMC sample, 1 day after 2nd vaccination

source_name: PBMC samples from subject 9 at Day 31


title: PBMC, Day 31, PID 11

source_name: PBMC samples from subject 11 at Day 31


title: G0129_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13


title: PBMC, Day 31, PID 8

source_name: PBMC samples from subject 8 at Day 31


title: G0066_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: PBMC, Day 44, PID 11

source_name: PBMC samples from subject 11 at Day 44

tag: tissue

tag: subject id

tag: sample day


title: PBMC, Day 0, PID 11

description: PBMC sample, Day of 1st vaccination, before vaccination

source_name: PBMC samples from subject 11 at Day 0


title: PBMC, Day 0, PID 9

source_name: PBMC samples from subject 9 at Day 0


title: E0617_2

description: Human HT12-v4 - standard protocol


title: PBMC, Day 0, PID 8

source_name: PBMC samples from subject 8 at Day 0


title: E0535_2

tag: age

tag: ga sample


title: E0535_1


title: G0124_1

description: Human HT12-v4 - standard protocol


title: G0127_2

description: Human HT12-v4 - standard protocol


title: PBMC, Day 44, PID 12

source_name: PBMC samples from subject 12 at Day 44


title: E0530_2


title: G0127_1

description: Human HT12-v4 - standard protocol


title: G0121_1

description: Human HT12-v4 - standard protocol


title: G0109_1

description: Human HT12-v4 - standard protocol


title: G0124_2

description: Human HT12-v4 - standard protocol


title: E0534_1


title: PBMC, Day 44, PID 4

source_name: PBMC samples from subject 4 at Day 44


title: E0534_2


title: PBMC, Day 31, PID 4

source_name: PBMC samples from subject 4 at Day 31


title: E0527_1


title: PBMC, Day 0, PID 4

source_name: PBMC samples from subject 4 at Day 0


title: PBMC, Day 31, PID 12

source_name: PBMC samples from subject 12 at Day 31


title: E0530_1


title: E0585_1

description: Human HT12-v4 - standard protocol


title: E0614_1

description: Human HT12-v4 - standard protocol


title: G0103_1

description: Human HT12-v4 - standard protocol


title: PBMC, Day 44, PID 10

source_name: PBMC samples from subject 10 at Day 44


title: E0527_2

source_name: PBMC


title: G0089_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 14

tag: surrogate variable 15


title: G0067_2

tag: Sex

tag: race

tag: sample type

tag: fetal intolerance

tag: visit

tag: pregnancy complication


title: G0067_1

tag: age

tag: ga sample


title: PBMC, Day 0, PID 10

source_name: PBMC samples from subject 10 at Day 0

tag: tissue

tag: subject id

tag: sample day


title: G0063_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age


title: E0521_2


title: E0522_2


title: PBMC, Day 31, PID 10

source_name: PBMC samples from subject 10 at Day 31


title: E0522_1


title: G0089_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13


title: G0103_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: fetal intolerance

tag: visit

tag: pregnancy complication


title: PBMC, Day 44, PID 18

source_name: PBMC samples from subject 18 at Day 44

tag: tissue

tag: subject id

tag: sample day


title: E0521_1

tag: age

tag: ga sample


title: PBMC, Day 0, PID 18

source_name: PBMC samples from subject 18 at Day 0


title: PBMC, Day 0, PID 12

source_name: PBMC samples from subject 12 at Day 0


title: PBMC, Day 31, PID 18

source_name: PBMC samples from subject 18 at Day 31


title: siI3_rep3

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

country: Germany

institute: Martin Luther University Halle-Wittenberg

description: small RNA

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.6) with parameters -q 10 -m 15
Trimmed reads were mapped against the human genome (hg19 UCSC) using Bowtie2 (v 2.2.4) with parameters  -N 0
Mapped reads were summarized using featureCounts (v 1.4.6) with parameters -M -t miRNA -g ID and annotated using miRBase (v 20)
Differential gene expression was assessed using R/edgeR (v 3.12) using TMM normalization
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated text file including CPM, log2 fold change and false discovery rate values for each sample

source_name: ovarian cancer derived cell line

growth_protocol: ES-2 cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
500 ng of total RNA was used in the small RNA protocol with the TruSeq™ Small RNA sample prepkit v2 (Illumina) according to the instructions of the manufacturer. The barcoded libraries were size restricted between 140 and 165bp, purified and quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems) according to the instructions of the manufacturer. A pool of up to 10 libraries was used for cluster generation at a concentration of 10nM using an Illumina cBot. Sequencing of 51 bp was performed with an IlluminaHighScan-SQ sequencer at the sequencing core facility of the IZKF Leipzig (Faculty of Medicine, University Leipzig)  using version 3 chemistry and flowcell according to the instructions of the manufacturer.

treatment_protocol: Parental ES-2 cells were seeded for RNA extraction.

tag: cell type

value: ovarian cancer derived cell line

tag: cell line

tag: sirna

value: siRNA pool against IGF2BP3


title: E0601_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age


title: E0518_2

tag: Sex


title: G0063_1

description: Human HT12-v4 - standard protocol

tag: race


title: E0509_1

tag: sample type


title: siI3_rep2

description: small RNA


title: PBMC, Day 44, PID 14

source_name: PBMC samples from subject 14 at Day 44


title: siI3_rep1

description: small RNA


title: siI2_rep1

description: small RNA

value: siRNA pool against IGF2BP2


title: siI2_rep2

description: small RNA


title: siI2_rep3

description: small RNA


title: mRNA_siI3_rep3

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.6) with parameters -q 10 -O 7 -m 20
Trimmed reads were mapped against the human genome (hg19 UCSC) using TopHat2 (v 2.0.13) with parameters  -p 6 -g 20 --b2-N 1
Mapped reads were summarized using featureCounts (v 1.4.6) with parameters -p  -M -t exon -g gene_id and Ensembl gene annotations (GRCh 37.75)
Differential gene expression was assessed using R/edgeR (v 3.12) using TMM normalization
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated text file including FPM, log2 fold change and false discovery rate values for each sample

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
500 ng of total RNA was depleted of ribosomal RNA using the Ribo-Zero rRNA removal kit (Epicentre) according to the instructions of the manufacturer. Depleted RNA was then fragmented by addition of 5  fragmentation buffer (200 mM Tris acetate, pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate) and heating at 94 °C for 3 min in a thermocycler followed by ethanol precipitation with ammonium acetate and GlycoBlue (Life Technologies) as carrier. Fragmented RNA was then reversed transcribed using random hexamer and Superscript III (Life Technologies). The second strand was synthesized using the TargetAmp kit (Epicentre) according to the instructions of the manufacturer. The final steps of library preparation, e.g. blunt end repair, adapter ligation, adapter fill-in and amplification were done according to Meyer and Kircher (2010, PMID: 20516186). The barcoded libraries were purified and quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems) according to the instructions of the manufacturer. A pool of up to 10 libraries was used for cluster generation at a concentration of 10nM using an Illumina cBot. Sequencing of 2x101 bp was performed with an IlluminaHighScan-SQ sequencer at the sequencing core facility of the IZKF Leipzig (Faculty of Medicine, University Leipzig) using version 3 chemistry and flowcell according to the instructions of the manufacturer.


title: PBMC, Day 0, PID 17

source_name: PBMC samples from subject 17 at Day 0


title: E0601_1

description: Human HT12-v4 - standard protocol

tag: fetal intolerance


title: G0090_2

description: Human HT12-v4 - standard protocol

tag: visit

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: G0038_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: PBMC, Day 0, PID 14

source_name: PBMC samples from subject 14 at Day 0

tag: tissue

tag: subject id

tag: sample day


title: mRNA_siI3_rep2

tag: cell line

tag: cell type

tag: sirna


title: mRNA_siI3_rep1


title: PBMC, Day 31, PID 14

source_name: PBMC samples from subject 14 at Day 31


title: G0090_1

description: Human HT12-v4 - standard protocol

tag: visit

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13


title: PBMC, Day 31, PID 17

source_name: PBMC samples from subject 17 at Day 31

tag: tissue

tag: subject id

tag: sample day


title: G0138_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: PBMC, Day 44, PID 17

source_name: PBMC samples from subject 17 at Day 44


title: PBMC, Day 44, PID 7

source_name: PBMC samples from subject 7 at Day 44


title: E0546_2

tag: age

tag: ga sample


title: G0038_2

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 14

tag: surrogate variable 15


title: PBMC, Day 31, PID 7

source_name: PBMC samples from subject 7 at Day 31

tag: tissue

tag: subject id

tag: sample day


title: PBMC, Day 0, PID 7

source_name: PBMC samples from subject 7 at Day 0


title: E0505_2

source_name: PBMC

tag: Sex

tag: race

tag: sample type

tag: fetal intolerance

tag: visit

tag: age

tag: ga sample

tag: pregnancy complication


title: mRNA_siI2_rep3

tag: cell line

tag: cell type

tag: sirna


title: E0546_1


title: G0142_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: weeks gestation at sample collection

tag: maternal age


title: G0138_2

description: Human HT12-v4 - standard protocol


title: mRNA_siI1_rep2

value: siRNA pool against IGF2BP1


title: mRNA_siI2_rep1


title: mRNA_siI2_rep2


title: mRNA_siI1_rep1


title: mRNA_siC_rep3

value: Control siRNA


title: mRNA_siI1_rep3


title: G0141_1

description: Human HT12-v4 - standard protocol

value: Female


title: E0503_2


title: G0005_1

description: Human HT12-v4 - standard protocol


title: E0633_2

description: Human HT12-v4 - standard protocol


title: G0105_2

description: Human HT12-v4 - standard protocol


title: PBMC, Day 44, PID 15

source_name: PBMC samples from subject 15 at Day 44

tag: tissue


title: G0155_2

description: Human HT12-v4 - standard protocol


title: PBMC, Day 31, PID 15

source_name: PBMC samples from subject 15 at Day 31

tag: subject id


title: PBMC, Day 0, PID 15

source_name: PBMC samples from subject 15 at Day 0

tag: sample day


title: PBMC, Day 44, PID 13

source_name: PBMC samples from subject 13 at Day 44


title: mRNA_siC_rep2


title: E0633_1

description: Human HT12-v4 - standard protocol

tag: Sex


title: mRNA_siC_rep1


title: E0519_1

description: Human HT12-v4 - standard protocol

tag: race


title: PBMC, Day 44, PID 1

source_name: PBMC samples from subject 1 at Day 44


title: E0505_1

tag: sample type


title: G0094_1

description: Human HT12-v4 - standard protocol

tag: fetal intolerance


title: PBMC, Day 31, PID 13

source_name: PBMC samples from subject 13 at Day 31


title: PBMC, Day 0, PID 13

source_name: PBMC samples from subject 13 at Day 0


title: PBMC, Day 31, PID 1

source_name: PBMC samples from subject 1 at Day 31


title: E0518_1

tag: visit


title: siI1_rep1

description: small RNA


title: E0616_1

description: Human HT12-v4 - standard protocol


title: siC_rep2

description: small RNA


title: siC_rep1

description: small RNA


title: siI1_rep2

description: small RNA


title: PBMC, Day 44, PID 2

source_name: PBMC samples from subject 2 at Day 44


title: PBMC, Day 0, PID 2

source_name: PBMC samples from subject 2 at Day 0


title: G0045_1

description: Human HT12-v4 - standard protocol


title: PBMC, Day 31, PID 2

source_name: PBMC samples from subject 2 at Day 31


title: G0069_1

description: Human HT12-v4 - standard protocol


title: E0565_2

description: Human HT12-v4 - standard protocol


title: PBMC, Day 44, PID 6

source_name: PBMC samples from subject 6 at Day 44


title: E0580_1

description: Human HT12-v4 - standard protocol


title: G0050_1

description: Human HT12-v4 - standard protocol


title: G0052_1

description: Human HT12-v4 - standard protocol


title: G0139_1

description: Human HT12-v4 - standard protocol


title: PBMC, Day 44, PID 3

source_name: PBMC samples from subject 3 at Day 44


title: PBMC, Day 0, PID 6

source_name: PBMC samples from subject 6 at Day 0


title: PBMC, Day 0, PID 3

source_name: PBMC samples from subject 3 at Day 0


title: G0050_2

description: Human HT12-v4 - standard protocol


title: PBMC, Day 31, PID 6

source_name: PBMC samples from subject 6 at Day 31


title: G0011_2

description: Human HT12-v4 - standard protocol

source_name: PBMC

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: E0671_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: pregnancy complication

tag: weeks gestation at sample collection

tag: maternal age


title: G0011_1

description: Human HT12-v4 - standard protocol

tag: visit

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7


title: PBMC, Day 31, PID 3

source_name: PBMC samples from subject 3 at Day 31

tag: tissue

tag: subject id

tag: sample day


title: PBMC, Day 44, PID 5

source_name: PBMC samples from subject 5 at Day 44


title: G0139_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type


title: E0671_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: fetal intolerance

tag: pregnancy complication

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: WB, Day 30, PID 8

description: WB sample, Day of 2nd vaccination, before vaccination

source_name: WB samples from subject 8 at Day 30

label_protocol: Biotinylated cDNA were prepared according to NuGen Ovation WB amplification protocol from 50ng total RNA

extract_protocol: Total RNA was isolated by PAXgene Blood RNA kit (Qiagen) according to the manufacturer’s protocol. A DNAse treatment was applied on the PAXgene RNA spin column to avoid genomic DNA contamination. RNA was quantified by UV-spectrophotometry.

treatment_protocol: PAXgene preserved whole blood samples were centrifuged, resuspended in lysis buffer and treated with proteinase K.

tag: tissue

value: Whole Blood (WB)


title: PBMC, Day 31, PID 5

source_name: PBMC samples from subject 5 at Day 31

tag: subject id


title: E0688_2

description: Human HT12-v4 - standard protocol

tag: visit

tag: weeks gestation at sample collection

tag: maternal age


title: PBMC, Day 0, PID 1

source_name: PBMC samples from subject 1 at Day 0

tag: sample day


title: E0688_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor


title: G0056_2

description: Human HT12-v4 - standard protocol

tag: fetal intolerance

tag: pregnancy complication


title: WB, Day 0, PID 14

description: WB sample, Day of 1st vaccination, before vaccination

source_name: WB samples from subject 14 at Day 0


title: WB, Day 0, PID 7

source_name: WB samples from subject 7 at Day 0


title: G0169_2

description: Human HT12-v4 - standard protocol


title: PBMC, Day 0, PID 5

source_name: PBMC samples from subject 5 at Day 0


title: G0145_1

description: Human HT12-v4 - standard protocol


title: WB, Day 37, PID 7

description: WB sample, 7 days after 2nd vaccination

source_name: WB samples from subject 7 at Day 37


title: WB, Day 47, PID 4

description: WB sample, 17 days after 2nd vaccination

source_name: WB samples from subject 4 at Day 47


title: G0145_2

description: Human HT12-v4 - standard protocol


title: WB, Day 44, PID 1

description: WB sample, 14 days after 2nd vaccination

source_name: WB samples from subject 1 at Day 44


title: WB, Day 44, PID 15

source_name: WB samples from subject 15 at Day 44


title: WB, Day 37, PID 11

description: WB sample, 7 days after 2nd vaccination

source_name: WB samples from subject 11 at Day 37


title: WB, Day 30, PID 18

source_name: WB samples from subject 18 at Day 30


title: G0086_1

description: Human HT12-v4 - standard protocol


title: E0618_1

description: Human HT12-v4 - standard protocol


title: G0137_2

description: Human HT12-v4 - standard protocol


title: E0618_2

description: Human HT12-v4 - standard protocol


title: WB, Day 0, PID 5

source_name: WB samples from subject 5 at Day 0


title: G0137_1

description: Human HT12-v4 - standard protocol


title: G0086_2

description: Human HT12-v4 - standard protocol


title: WB, Day 44, PID 8

source_name: WB samples from subject 8 at Day 44


title: WB, Day 44, PID 13

source_name: WB samples from subject 13 at Day 44


title: WB, Day 0, PID 6

source_name: WB samples from subject 6 at Day 0


title: WB, Day 30, PID 7

source_name: WB samples from subject 7 at Day 30


title: G0037_1

description: Human HT12-v4 - standard protocol

source_name: PBMC


title: G0037_2

description: Human HT12-v4 - standard protocol


title: G0159_1

description: Human HT12-v4 - standard protocol


title: G0106_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11


title: G0073_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: visit

tag: weeks gestation at sample collection

tag: maternal age


title: WB, Day 0, PID 9

source_name: WB samples from subject 9 at Day 0

tag: tissue

tag: subject id

tag: sample day


title: WB, Day 30, PID 17

source_name: WB samples from subject 17 at Day 30


title: G0106_2

description: Human HT12-v4 - standard protocol

tag: race

tag: sample type

tag: experienced labor

tag: fetal intolerance

tag: pregnancy complication

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: E0615_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: visit


title: WB, Day 44, PID 7

source_name: WB samples from subject 7 at Day 44


title: WB, Day 31, PID 14

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 14 at Day 31


title: WB, Day 44, PID 9

source_name: WB samples from subject 9 at Day 44


title: WB, Day 31, PID 6

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 6 at Day 31


title: E0615_2

description: Human HT12-v4 - standard protocol

tag: weeks gestation at sample collection

tag: maternal age


title: G0140_1

description: Human HT12-v4 - standard protocol


title: G0185_2

description: Human HT12-v4 - standard protocol


title: G0140_2

description: Human HT12-v4 - standard protocol


title: G0185_1

description: Human HT12-v4 - standard protocol


title: WB, Day 0, PID 13

source_name: WB samples from subject 13 at Day 0

tag: tissue

tag: subject id


title: E0599_2

description: Human HT12-v4 - standard protocol

tag: race


title: G0174_2

description: Human HT12-v4 - standard protocol

tag: sample type


title: WB, Day 44, PID 2

source_name: WB samples from subject 2 at Day 44

tag: sample day


title: WB, Day 47, PID 1

source_name: WB samples from subject 1 at Day 47


title: WB, Day 44, PID 5

source_name: WB samples from subject 5 at Day 44


title: WB, Day 31, PID 12

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 12 at Day 31


title: WB, Day 44, PID 11

source_name: WB samples from subject 11 at Day 44


title: E0589_1

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: fetal intolerance


title: WB, Day 31, PID 5

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 5 at Day 31


title: E0512_2

description: Human HT12-v4 - standard protocol

tag: pregnancy complication


title: G0174_1

description: Human HT12-v4 - standard protocol


title: E0624_1

description: Human HT12-v4 - standard protocol


title: WB, Day 30, PID 2

source_name: WB samples from subject 2 at Day 30


title: WB, Day 44, PID 17

source_name: WB samples from subject 17 at Day 44


title: WB, Day 31, PID 18

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 18 at Day 31


title: WB, Day 0, PID 15

source_name: WB samples from subject 15 at Day 0


title: E0626_1

description: Human HT12-v4 - standard protocol

source_name: PBMC


title: G0144_1

description: Human HT12-v4 - standard protocol


title: WB, Day 31, PID 17

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 17 at Day 31


title: G0111_2

description: Human HT12-v4 - standard protocol


title: WB, Day 40, PID 6

description: WB sample, 10 days after 2nd vaccination

source_name: WB samples from subject 6 at Day 40


title: G0144_2

description: Human HT12-v4 - standard protocol


title: G0111_1

description: Human HT12-v4 - standard protocol


title: WB, Day 0, PID 4

source_name: WB samples from subject 4 at Day 0


title: G0057_1

description: Human HT12-v4 - standard protocol


title: E0624_2

description: Human HT12-v4 - standard protocol


title: WB, Day 47, PID 11

source_name: WB samples from subject 11 at Day 47


title: WB, Day 30, PID 4

source_name: WB samples from subject 4 at Day 30


title: G0101_1

description: Human HT12-v4 - standard protocol


title: G0031_1

description: Human HT12-v4 - standard protocol


title: E0529_1

description: Human HT12-v4 - standard protocol


title: WB, Day 40, PID 7

source_name: WB samples from subject 7 at Day 40


title: WB, Day 40, PID 16

source_name: WB samples from subject 16 at Day 40


title: E0619_2

description: Human HT12-v4 - standard protocol


title: WB, Day 0, PID 11

source_name: WB samples from subject 11 at Day 0


title: E0619_1

description: Human HT12-v4 - standard protocol


title: G0101_2

description: Human HT12-v4 - standard protocol


title: WB, Day 47, PID 9

source_name: WB samples from subject 9 at Day 47


title: WB, Day 31, PID 8

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 8 at Day 31


title: WB, Day 40, PID 4

source_name: WB samples from subject 4 at Day 40


title: WB, Day 31, PID 4

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 4 at Day 31


title: WB, Day 0, PID 1

source_name: WB samples from subject 1 at Day 0


title: WB, Day 44, PID 6

source_name: WB samples from subject 6 at Day 44


title: WB, Day 30, PID 14

source_name: WB samples from subject 14 at Day 30


title: E0567_1

description: Human HT12-v4 - standard protocol

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11


title: WB, Day 0, PID 8

source_name: WB samples from subject 8 at Day 0

tag: tissue

tag: subject id


title: WB, Day 40, PID 11

source_name: WB samples from subject 11 at Day 40

tag: sample day


title: WB, Day 40, PID 9

source_name: WB samples from subject 9 at Day 40


title: G0132_1

description: Human HT12-v4 - standard protocol

source_name: PBMC

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: visit

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 12

tag: surrogate variable 13

tag: surrogate variable 14

tag: surrogate variable 15


title: E0563_2

description: Human HT12-v4 - standard protocol

tag: fetal intolerance

tag: pregnancy complication

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 8

tag: surrogate variable 9


title: WB, Day 37, PID 10

description: WB sample, 7 days after 2nd vaccination

source_name: WB samples from subject 10 at Day 37

tag: tissue

tag: subject id

tag: sample day


title: E0563_1

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: visit

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 10

tag: surrogate variable 11

tag: surrogate variable 12

tag: surrogate variable 13


title: G0132_2

description: Human HT12-v4 - standard protocol

tag: fetal intolerance

tag: pregnancy complication

tag: surrogate variable 1

tag: surrogate variable 2

tag: surrogate variable 3

tag: surrogate variable 4

tag: surrogate variable 5

tag: surrogate variable 6

tag: surrogate variable 7

tag: surrogate variable 14

tag: surrogate variable 15


title: WB, Day 44, PID 10

source_name: WB samples from subject 10 at Day 44

tag: tissue

tag: subject id

tag: sample day


title: E0567_2

description: Human HT12-v4 - standard protocol

tag: Sex

tag: race

tag: sample type

tag: experienced labor

tag: visit

tag: weeks gestation at sample collection

tag: maternal age

tag: surrogate variable 8

tag: surrogate variable 9

tag: surrogate variable 10

tag: surrogate variable 11


title: WB, Day 47, PID 13

source_name: WB samples from subject 13 at Day 47


title: WB, Day 30, PID 5

source_name: WB samples from subject 5 at Day 30


title: WB, Day 31, PID 2

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 2 at Day 31


title: subject_53 week4

city: Milan

first: Melissa

last: Sorosina

address: via Olgettina 58

department: INSPE

country: Italy

institute: IRCCS San Raffaele Hospital

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
Quantification was performed at the probe level with quantile normalization as implemented by Bioconductor package lumi within R statistical enviroment
normalized signal intensity generated using with the package lumi within R statistical enviroment

source_name: MS patient_whole blood_Nabiximols_4 wks

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep kit for Illumina arrays.

extract_protocol: whole blood was collected in PaxGene tubes (PreAnalytix) and total RNA was extracted using the PaxGene Blood miRNA kit (PreAnalytix) according to manufacturer instructions.

value: subject 53

tag: subject status

value: Multiple Sclerosis patient

tag: weeks of nabiximols treatment

tag: disease course

value: RR

tag: concomitant disease-modifying therapy

value: Natalizumab

tag: response to the treatment

value: non-responder

value: whole blood


title: WB, Day 47, PID 17

source_name: WB samples from subject 17 at Day 47

tag: tissue

tag: subject id

tag: sample day


title: WB, Day 37, PID 2

description: WB sample, 7 days after 2nd vaccination

source_name: WB samples from subject 2 at Day 37


title: subject_6 week4

value: subject 6


title: subject_59 week4

value: subject 59

value: SP

value: Glatiramer Acetate


title: WB, Day 0, PID 16

source_name: WB samples from subject 16 at Day 0


title: subject_35 week4

value: subject 35


title: WB, Day 31, PID 15

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 15 at Day 31


title: subject_84 week4

value: subject 84


title: subject_43 week4

value: subject 43

value: Azathioprine


title: WB, Day 0, PID 17

source_name: WB samples from subject 17 at Day 0


title: subject_28 week4

value: subject 28


title: subject_55 week4

value: subject 55

value: PP


title: subject_10 week4

value: subject 10

value: responder


title: WB, Day 37, PID 18

description: WB sample, 7 days after 2nd vaccination

source_name: WB samples from subject 18 at Day 37

value: Whole Blood (WB)


title: WB, Day 40, PID 1

source_name: WB samples from subject 1 at Day 40


title: WB, Day 40, PID 15

source_name: WB samples from subject 15 at Day 40


title: subject_46 week4

value: subject 46

value: Multiple Sclerosis patient

value: RR

value: Natalizumab


title: WB, Day 0, PID 2

source_name: WB samples from subject 2 at Day 0


title: subject_14 week4

value: subject 14

value: whole blood


title: WB, Day 40, PID 12

source_name: WB samples from subject 12 at Day 40


title: WB, Day 44, PID 12

source_name: WB samples from subject 12 at Day 44


title: WB, Day 30, PID 10

source_name: WB samples from subject 10 at Day 30


title: subject_5 week4

value: subject 5

value: SP


title: WB, Day 30, PID 13

source_name: WB samples from subject 13 at Day 30


title: WB, Day 31, PID 13

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 13 at Day 31


title: subject_35 week0

source_name: MS patient_whole blood_at baseline

value: subject 35

value: 0 (at baseline)

value: non-responder


title: subject_18 week4

value: subject 18

value: Azathioprine


title: subject_6 week0

value: subject 6


title: subject_43 week0

value: subject 43


title: WB, Day 40, PID 8

source_name: WB samples from subject 8 at Day 40


title: WB, Day 40, PID 2

source_name: WB samples from subject 2 at Day 40


title: WB, Day 30, PID 11

source_name: WB samples from subject 11 at Day 30


title: WB, Day 31, PID 9

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 9 at Day 31


title: subject_28 week0

value: subject 28


title: subject_55 week0

value: subject 55

value: PP

value: Glatiramer Acetate


title: subject_46 week0

value: subject 46

value: Multiple Sclerosis patient

value: RR


title: subject_53 week0

value: subject 53

value: Natalizumab

value: whole blood


title: E0599_1

description: Human HT12-v4 - standard protocol

source_name: PBMC

tag: Sex

value: Female

tag: race

value: African American

tag: sample type

value: PBMC


title: E0626_2

description: Human HT12-v4 - standard protocol

tag: experienced labor

tag: fetal intolerance

tag: visit

tag: pregnancy complication

tag: weeks gestation at sample collection


title: subject_84 week0

value: subject 84

value: 0 (at baseline)

value: non-responder


title: subject_59 week0

value: subject 59

value: SP


title: WB, Day 44, PID 14

source_name: WB samples from subject 14 at Day 44

value: Whole Blood (WB)


title: siUPF3B_1_exp2

city: Bethesda

first: Thomas

middle: David

last: Baird

state: MD

address: 50 South Drive, Room 2339

department: Biochemistry and Biophysics

institute: NIH/NHLBI

data_processing:
Sequencing reads in FASTQ format were aligned to the reference genome hg19 using HISAT2 aligner.
Differential gene expression analysis was performed using the Kallisto and Sleuth packages.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include TPM values and fold expression change.

source_name: HEK-293 cells

growth_protocol: HEK-293 cells were maintained in DMEM supplemented with 10% FBS , 100 U/ml of penicillin, 100 μg/ml streptomycin , and 0.3 mg/ml of L-glutamine at 37°C and 5% CO2.

extract_protocol:
Qiagen RNeasy Mini RNA isolation kit
One μg of total RNA was used per sample for library preparation. Ribosomal RNA was depleted from total RNA with the Ribo-Zero rRNA Removal Kit (Epicentre), and purified RNA was then converted to cDNA with the TruSeq RNA Library Preparation Kit (Illumina).

treatment_protocol: Transient depletion for 72 hours by reverse transfection.

tag: treatment

value: Treated with UPF3B siRNA


title: siUPF3B_2_exp2


title: subject_5 week0

value: subject 5

tag: subject status

value: Azathioprine

value: responder


title: WB, Day 40, PID 14

source_name: WB samples from subject 14 at Day 40


title: siNS_2_exp2

value: Treated with non-specific (NS) siRNA


title: subject_23 week4

source_name: MS patient_whole blood_Nabiximols_4 wks

value: subject 23

value: Multiple Sclerosis patient

tag: weeks of nabiximols treatment

value: PP


title: WB, Day 30, PID 6

source_name: WB samples from subject 6 at Day 30


title: WB, Day 44, PID 18

source_name: WB samples from subject 18 at Day 44


title: subject_18 week0

value: subject 18

tag: disease course

value: whole blood


title: WB, Day 40, PID 13

source_name: WB samples from subject 13 at Day 40


title: subject_14 week0

value: subject 14

tag: concomitant disease-modifying therapy

value: Natalizumab


title: siUPF3B_3_exp2


title: WB, Day 40, PID 10

source_name: WB samples from subject 10 at Day 40


title: WB, Day 47, PID 2

source_name: WB samples from subject 2 at Day 47


title: subject_10 week0

value: subject 10

value: 0 (at baseline)

value: RR

tag: response to the treatment


title: subject_54 week4

value: subject 54

value: non-responder

tag: tissue


title: WB, Day 31, PID 11

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 11 at Day 31

value: Whole Blood (WB)

tag: subject id


title: subject_1 week4

value: subject 1

value: SP


title: siNS_3_exp2


title: WB, Day 40, PID 18

source_name: WB samples from subject 18 at Day 40

tag: sample day


title: WB, Day 47, PID 10

source_name: WB samples from subject 10 at Day 47


title: siNS_1_exp2


title: siICE1_2_exp2

value: Treated with ICE1 siRNA


title: siICE1_3_exp2


title: siICE1_1_exp2


title: WB, Day 0, PID 12

source_name: WB samples from subject 12 at Day 0


title: WB, Day 37, PID 14

description: WB sample, 7 days after 2nd vaccination

source_name: WB samples from subject 14 at Day 37


title: WB, Day 47, PID 12

source_name: WB samples from subject 12 at Day 47


title: WB, Day 37, PID 13

description: WB sample, 7 days after 2nd vaccination

source_name: WB samples from subject 13 at Day 37


title: WB, Day 30, PID 1

source_name: WB samples from subject 1 at Day 30


title: subject_45 week4

value: subject 45


title: subject_76 week4

value: subject 76

value: responder


title: subject_62 week4

value: subject 62

value: Multiple Sclerosis patient

value: PP


title: WB, Day 47, PID 14

source_name: WB samples from subject 14 at Day 47


title: subject_2 week4

value: subject 2

value: whole blood


title: WB, Day 47, PID 18

source_name: WB samples from subject 18 at Day 47


title: WB, Day 0, PID 18

source_name: WB samples from subject 18 at Day 0


title: subject_30 week4

source_name: MS patient_whole blood_Nabiximols_4 wks

value: subject 30


title: subject_15 week4

value: subject 15


title: HUH7_rep1

description: small RNA sequencing of parental HUH-7 cells

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.6) with parameters -q 20 -m 16
according to the NEXTFlex protocol the first and last 4 bases of the trimmed reads were removed using Cutadapt (v 1.6) with parameters -m 16 -u 4/-4
Trimmed reads were mapped against the human genome (hg19 UCSC) using Bowtie2 (v 2.2.4) with parameters  -N 0
Mapped reads were summarized using featureCounts (v 1.4.6) with parameters -s 1 -t miRNA -g ID and annotated using miRBase (v 20)
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated text file including CPM values

source_name: hepatocellular carcinoma derived cell line

growth_protocol: HUH-7 cells were cultured in DMEM supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.

extract_protocol:
RNA extraction was performed using TRIZOL according to manufacturer's protocol.
NEXTflex® Small RNA Sequencing Kit v3 was used for library construction according to manufacturer's protocol

treatment_protocol: Parental HUH-7 cells were seeded for RNA extraction.

tag: cell type

tag: cell line


title: WB, Day 31, PID 1

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 1 at Day 31


title: subject_4 week4

value: subject 4


title: subject_60 week4

value: subject 60


title: subject_41 week4

value: subject 41


title: WB, Day 44, PID 4

source_name: WB samples from subject 4 at Day 44

value: Whole Blood (WB)


title: subject_66 week4

value: subject 66

value: non-responder


title: WB, Day 31, PID 10

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 10 at Day 31


title: WB, Day 0, PID 10

source_name: WB samples from subject 10 at Day 0


title: subject_74 week4

value: subject 74

value: SP


title: WB, Day 37, PID 9

description: WB sample, 7 days after 2nd vaccination

source_name: WB samples from subject 9 at Day 37


title: subject_78 week4

value: subject 78


title: subject_42 week4

value: subject 42

value: responder


title: subject_33 week4

value: subject 33

value: Multiple Sclerosis patient


title: subject_80 week4

value: subject 80


title: subject_8 week4

value: subject 8

value: whole blood


title: subject_63 week4

value: subject 63


title: subject_23 week0

source_name: MS patient_whole blood_at baseline

value: subject 23

value: 0 (at baseline)

value: PP


title: WB, Day 37, PID 12

description: WB sample, 7 days after 2nd vaccination

source_name: WB samples from subject 12 at Day 37

value: Whole Blood (WB)


title: subject_1 week0

value: subject 1


title: WB, Day 30, PID 16

source_name: WB samples from subject 16 at Day 30


title: subject_66 week0

value: subject 66

value: non-responder


title: WB, Day 37, PID 5

description: WB sample, 7 days after 2nd vaccination

source_name: WB samples from subject 5 at Day 37


title: subject_62 week0

value: subject 62


title: WB, Day 31, PID 7

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 7 at Day 31


title: C2C12_shLSD1_2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Thermo Fisher Scientific).

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.4.1.46

source_name: differentiating C2C12 cells stably expressing shLSD1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3'IVT PLUS Reagent Kit, Thermo Fisher Scientific).

growth_protocol: Cells were grown in DMEM containing 25mM glucose, 10% FBS and 750 µg/mL hygromycin B (Wako). For myogenic induction, medium was changed to DMEM containing 25mM glucose and 2% horse serum.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, then total RNA was cleaned up using RNeasy Mini Kit according to manufacturer's protocol.

treatment_protocol: Cells were washed twice with PBS, and were collected in a Trizol reagent (Invitrogen).

value: differentiating myoblasts

tag: transfected with

value: shRNA against LSD1 (shLSD1)


title: C2C12_shControl_2

source_name: differentiating C2C12 cells stably expressing shControl

value: shRNA against non-targeting control (shControl)


title: subject_45 week0

value: subject 45

value: SP


title: C2C12_shLSD1_1


title: WB, Day 37, PID 17

description: WB sample, 7 days after 2nd vaccination

source_name: WB samples from subject 17 at Day 37


title: subject_54 week0

value: subject 54

value: Multiple Sclerosis patient


title: C2C12_shControl_1


title: S2101

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.3.0.187

source_name: differentiating C2C12 cells with S2101 treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3'IVT Express Kit User Manual, Affymetrix).

growth_protocol: Cells were grown in DMEM containing 25mM glucose and 10% FBS. For myogenic induction, medium was changed to DMEM containing 25mM glucose and 2% horse serum.

tag: treated with

value: LSD1 inhibitor S2101


title: WB, Day 37, PID 15

description: WB sample, 7 days after 2nd vaccination

source_name: WB samples from subject 15 at Day 37


title: Input-TSA_1 ChIP-seq

city: Oxford

first: Beth

last: Watts

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
ChIP-seq: Single end reads with a Phred score of less than 20 were removed using the the program Trimmomatic (version 0.36) and the remaining reads were aligned to the S. pombe genome (ASM294v2.25 from Pombase.org) using the short read aligner Bowtie (version 2.2.6). The BEDTools toolset was used to obtain coverage tracks that were used for peak calling using the software MACS2 2.1.1.20160309.
RNA-Seq: Paired-end reads were trimmed by quality (less than Phred score 20) and reads shorter than 20 nt were removed using Trimmomatic (Galaxy Version 0.32.3). The resulting reads were aligned to the S. pombe genome (ASM294v2.28) using TopHat (Galaxy version 0.9). Read-through was determined by counting the reads in a window 50 nt after the pA site which was normalised to counts obtained for the gene body using HTSeq (version 0.6.1.p1). In addition, bam files were converted to bed files using the deeptools tool bamtobed (option -bedpe -mate1) and the resulting file was used to generate a bed file that contains reads spanning both read pairs. This was then imported into R/Bioconductor and reads overlapping pA sites were counted and normalised to gene body expression levels as before.
Genome_build: [ChIP-seq] S. pombe genome (ASM294v2.25 from Pombase.org)
Genome_build: [RNA-Seq] S. pombe genome (ASM294v2.28)
Supplementary_files_format_and_content: ChIP-Seq: the data is provided as bigwig or bedgraph files; RNA-Seq: Bedgraph files are provided to visualize the data

organism: Schizosaccharomyces pombe

source_name: Yeast cell extract

growth_protocol: S. pombe were grown in YES medium to exponential phase at 30°C. For TSA-treated samples TSA was added 2.5 hr before harvesting

extract_protocol:
Cells were grown to mid-log phase and crosslinked using 11% formaldehyde. Cells were lysed by vortexing with glass beads and chromatin was extracted by two consecutive ultra-centrifugation steps. The DNA was sheared by sonication and DNA was extracted by phenol:chloroform.
Libraries were generated using the NEBNext fast DNA library Prep set for Ion Torrent (E6270).

tag: genotype

value: untreated

tag: chip antibody


title: Input+TSA_2 ChIP-seq

value: TSA


title: Input-TSA_2 ChIP-seq


title: TC

source_name: differentiating C2C12 cells with tranylcypromine treatment

value: LSD1 inhibitor, tranylcypromine (TC)


title: subject_78 week0

value: subject 78

value: 0 (at baseline)

value: responder

value: whole blood


title: Input+TSA_1 ChIP-seq


title: WB, Day 47, PID 8

source_name: WB samples from subject 8 at Day 47

value: Whole Blood (WB)


title: subject_8 week0

value: subject 8


title: WB, Day 31, PID 16

description: WB sample, 1 day after 2nd vaccination

source_name: WB samples from subject 16 at Day 31


title: Control_1

source_name: differentiating C2C12 cells with vehicle treatment

value: differentiating myoblasts

value: vehicle (control)


title: subject_63 week0

value: subject 63


title: WB, Day 40, PID 5

source_name: WB samples from subject 5 at Day 40


title: WB, Day 30, PID 9

source_name: WB samples from subject 9 at Day 30


title: subject_33 week0

source_name: MS patient_whole blood_at baseline

value: subject 33


title: WB, Day 47, PID 7

source_name: WB samples from subject 7 at Day 47


title: H3K14ac_IP-TSA_2 ChIP-seq

description: Crosslinked DNA

extract_protocol:
Cells were grown to mid-log phase and crosslinked using 11% formaldehyde. Cells were lysed by vortexing with glass beads and chromatin was extracted by two consecutive ultra-centrifugation steps. The DNA was sheared by sonication, histone H3K14ac was IP-ed and DNA was extracted by phenol:chloroform.
Libraries were generated using the NEBNext fast DNA library Prep set for Ion Torrent (E6270).


title: Control_2


title: H3K14ac_IP-TSA_1 ChIP-seq

description: Crosslinked DNA


title: WB, Day 30, PID 15

source_name: WB samples from subject 15 at Day 30


title: H3K14ac_IP+TSA_2 ChIP-seq

description: Crosslinked DNA


title: H3K14ac_IP+TSA_1 ChIP-seq

description: Crosslinked DNA


title: H3_IP-TSA_2 ChIP-seq

description: Crosslinked DNA

extract_protocol:
Cells were grown to mid-log phase and crosslinked using 11% formaldehyde. Cells were lysed by vortexing with glass beads and chromatin was extracted by two consecutive ultra-centrifugation steps. The DNA was sheared by sonication, histone H3 was IP-ed and DNA was extracted by phenol:chloroform.
Libraries were generated using the NEBNext fast DNA library Prep set for Ion Torrent (E6270).


title: subject_76 week0

value: subject 76

value: SP


title: H3_IP-TSA_1 ChIP-seq

description: Crosslinked DNA


title: untreated_s1

extract_protocol:
Total RNA was extracted from three separate cultures of WT and TSA treated cells grown to mid-log phase and DNase-treated.
Ribodepletion and library preparation were performed by the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics according to the TruSeq protocol. Note that with the TruSeq protocol the cDNA strand is sequenced. Thus all the strand information needs to be reversed after mapping the reads to the genome.


title: untreated_s2


title: WB, Day 47, PID 6

source_name: WB samples from subject 6 at Day 47


title: WB, Day 37, PID 4

description: WB sample, 7 days after 2nd vaccination

source_name: WB samples from subject 4 at Day 37


title: TSA_s2


title: H3_IP+TSA_2 ChIP-seq

description: Crosslinked DNA


title: subject_60 week0

value: subject 60

value: Multiple Sclerosis patient


title: H3_IP+TSA_1 ChIP-seq

description: Crosslinked DNA


title: TSA_s1


title: subject_42 week0

value: subject 42

value: PP


title: WB, Day 47, PID 16

source_name: WB samples from subject 16 at Day 47


title: subject_2 week0

value: subject 2


title: WB, Day 40, PID 17

source_name: WB samples from subject 17 at Day 40


title: subject_30 week0

value: subject 30


title: subject_74 week0

value: subject 74

value: 0 (at baseline)


title: subject_80 week0

value: subject 80

value: responder

value: whole blood


title: WB, Day 37, PID 16

description: WB sample, 7 days after 2nd vaccination

source_name: WB samples from subject 16 at Day 37

value: Whole Blood (WB)


title: subject_4 week0

value: subject 4


title: subject_41 week0

value: subject 41


title: subject_15 week0

value: subject 15