title: cell-free DNA, Healthy pregnancy DNA124142

description:
Library name: DNA124142
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: EDTA


title: Colon tumor, Control for Carmofur, rep3

status: Public on Jan 01 2026

type: SRA

city: CAMBRIDGE

first: Qiming

last: Zhang

state: MA

address: 88 Ames Street

country: USA

institute: Koch institute

description: Library name: nAKP.Control.201109.intCt

library_source: transcriptomic

data_processing:
The reads were used to quantify transcripts from the mm10 mouse assembly with the Ensembl version 101 annotation using Salmon version 1.3.0 and gene level summaries were prepared using tximport version 1.16.1
Assembly: mm10
Supplementary files format and content: Tab-delimited csv file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Colon

extract_protocol:
RNA was extracted from organoids using TRIzol and Ambion PureLink RNA Mini Kit (Thermo Fisher Scientific, 12-183-018 A) according to the manufacturer’s instructions
NEBNext Ultra II Directional RNA preparation with poly(A) selection is used to selectively capture mRNA from total RNA and barcoded libraries were generated

tag: tissue

value: Colon

tag: cell type

value: tumor

tag: genotype

value: AKP

tag: treatment

value: Control


title: cell-free DNA, Healthy pregnancy DNA124158

city: Ghent

first: Bram

last: Van Gaever

address: C. Heymanlsaan 10

country: Belgium

institute: Ghent University

description:
Library name: DNA124158
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

library_source: genomic

data_processing:
Demultiplexing was performed using bcl-convert on standard settings
fastq files were processed with the bismark workflow of the nf-core/methylseq pipeline https://github.com/nf-core/methylseq/
the --rrbs flag was enabled for processing.
further data processing code can be found in the following git repo:https://github.com/bravgaev/ExPECT-analysis
Assembly: hg38
Supplementary files format and content: bismark coverage file

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood plasma

extract_protocol:
Cell-free DNA (cfDNA) was extracted using the Maxwell RSC LV ccfDNA kit (Promega) according to the manufacturer’s instructions
The cfRRBS protocol was followed as described by De Koker et al.  and adapted by Van Paemel et al. https://doi.org/10.1080/15592294.2020.1790950 the EZ DNA Lightning kit (ZymoResearch) was used.

value: Blood plasma

tag: disease state

value: Healthy

tag: blood tube_type

tag: patient id

tag: gestational age_(weeks)

tag: sequencing batch


title: Colon tumor, Control for Carmofur, rep1

description: Library name: nAKP.Control.201107.intCt


title: Colon tumor, Carmofur, rep7

description: Library name: nAKP.Carm.201125.intCt

value: Carmofur


title: Colon tumor, Carmofur, rep3

description: Library name: nAKP.Carm.201115.intCt


title: cell-free DNA, Healthy pregnancy DNA124136

description:
Library name: DNA124136
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124141

description:
Library name: DNA124141
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124143

description:
Library name: DNA124143
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124144

description:
Library name: DNA124144
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124135

description:
Library name: DNA124135
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: PAXgene DNA


title: Colon tumor, Control for Carmofur, rep2

description: Library name: nAKP.Control.201108.intCt


title: Colon tumor, Carmofur, rep6

description: Library name: nAKP.Carm.201118.intCt


title: cell-free DNA, Healthy pregnancy DNA124138

description:
Library name: DNA124138
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, PA batch1, rep2

description: Library name: PA_2

value: Palmitic acid


title: Colon tumor, Control for PA, rep3

description: Library name: Ctrl_3


title: cell-free DNA, Healthy pregnancy DNA124133

description:
Library name: DNA124133
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124131

description:
Library name: DNA124131
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124132

description:
Library name: DNA124132
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, Serine-free HFD, rep5

description: Library name: 239053.intCt

value: Wild type

value: Serine-free HFD


title: cell-free DNA, Healthy pregnancy DNA124130

description:
Library name: DNA124130
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, PA batch1, rep1

description: Library name: PA_1


title: Colon, Serine-free HFD, rep1

description: Library name: 239049.intCt


title: Colon, Serine-free HFD, rep3

description: Library name: 239051.intCt


title: cell-free DNA, Healthy pregnancy DNA124127

description:
Library name: DNA124127
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124123

description:
Library name: DNA124123
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, Control for PA, rep1

description: Library name: Ctrl_1


title: Colon, Serine-free CD, rep5

description: Library name: 239048.intCt

value: Serine-free CD


title: cell-free DNA, Healthy pregnancy DNA124126

description:
Library name: DNA124126
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, Serine-free CD, rep3

description: Library name: 239046.intCt


title: cell-free DNA, Healthy pregnancy DNA124129

description:
Library name: DNA124129
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, Serine-free CD, rep4

description: Library name: 239047.intCt


title: Colon, Serine-free HFD, rep4

description: Library name: 239052.intCt


title: cell-free DNA, Healthy pregnancy DNA124110

description:
Library name: DNA124110
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, Control for PA, rep2

description: Library name: Ctrl_2


title: cell-free DNA, Healthy pregnancy DNA124113

description:
Library name: DNA124113
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, Serine-free HFD, rep2

description: Library name: 239050.intCt


title: cell-free DNA, Healthy pregnancy DNA124108

description:
Library name: DNA124108
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124122

description:
Library name: DNA124122
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124125

description:
Library name: DNA124125
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124134

description:
Library name: DNA124134
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124106

description:
Library name: DNA124106
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, PA batch1, rep3

description: Library name: PA_3


title: Colon, Serine-free CD, rep2

description: Library name: 239045.intCt


title: Colon, CD, rep2

description: Library name: G1.165007.intCt

value: Control diet


title: Colon, Serine-free CD, rep1

description: Library name: 239044.intCt


title: Colon, CD, rep1

description: Library name: G1.165002.intCt


title: cell-free DNA, Healthy pregnancy DNA124102

description:
Library name: DNA124102
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124128

description:
Library name: DNA124128
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124124

description:
Library name: DNA124124
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, GFP-P, rep11

description: Library name: 7968-GFP-P.239043.intCt

value: GFP-positive


title: cell-free DNA, Healthy pregnancy DNA124112

description:
Library name: DNA124112
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124101

description:
Library name: DNA124101
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, GFP-P, rep8

description: Library name: 40-1-GFP-P-2.239040.intCt


title: Colon, HFD, rep4

description: Library name: G1.165018.intCt

value: High fat diet


title: Colon, HFD, rep3

description: Library name: G1.165016.intCt


title: Colon, GFP-P, rep7

description: Library name: 61-1-GFP-P-2.239038.intCt


title: cell-free DNA, Healthy pregnancy DNA124096

description:
Library name: DNA124096
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124097

description:
Library name: DNA124097
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124109

description:
Library name: DNA124109
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124107

description:
Library name: DNA124107
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, HFD, rep1

description: Library name: G1.165013.intCt


title: cell-free DNA, Healthy pregnancy DNA124093

description:
Library name: DNA124093
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, CD, rep3

description: Library name: G1.165008.intCt


title: Colon, GFP-N, rep10

description: Library name: 7907-GFP-N.239034.intCt

value: GFP-negative


title: cell-free DNA, Healthy pregnancy DNA124099

description:
Library name: DNA124099
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: EDTA


title: Colon, HFD, rep2

description: Library name: G1.165014.intCt

value: Colon


title: Colon, GFP-N, rep8

description: Library name: 61-1-GFP-N.239031.intCt


title: cell-free DNA, Healthy pregnancy DNA124105

description:
Library name: DNA124105
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124103

description:
Library name: DNA124103
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124104

description:
Library name: DNA124104
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, GFP-P, rep5

description: Library name: 7421-GFP-P.239017.intCt


title: cell-free DNA, Healthy pregnancy DNA109804

description:
Library name: DNA109804
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124100

description:
Library name: DNA124100
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, GFP-P, rep10

description: Library name: 7914-GFP-P.239042.intCt


title: Colon, GFP-P, rep9

description: Library name: 7907-GFP-P.239041.intCt


title: Colon, GFP-P, rep3

description: Library name: 7789-7795-GFP-P.239013.intCt


title: cell-free DNA, Healthy pregnancy DNA109803

description:
Library name: DNA109803
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA109802

description:
Library name: DNA109802
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Preeclampsia


title: Colon, GFP-P, rep2

description: Library name: 61-1-GFP-P.239012.intCt


title: cell-free DNA, Healthy pregnancy DNA124095

description:
Library name: DNA124095
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, GFP-N, rep11

description: Library name: 7914-GFP-N.239035.intCt


title: cell-free DNA, Healthy pregnancy DNA109800

description:
Library name: DNA109800
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA109807

description:
Library name: DNA109807
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA109805

description:
Library name: DNA109805
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, GFP-N, rep7

description: Library name: 5780-GFP-N.239030.intCt


title: Colon, GFP-N, rep12

description: Library name: 7968-GFP-N.239036.intCt


title: Colon, HFD, rep5

description: Library name: G1.165019.intCt

value: tumor


title: cell-free DNA, Healthy pregnancy DNA109797

description:
Library name: DNA109797
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, GFP-N, rep5

description: Library name: 8045-GFP-N.239008.intCt


title: Colon, GFP-N, rep9

description: Library name: 40-1-GFP-N-2.239033.intCt


title: cell-free DNA, Healthy pregnancy DNA109808

description:
Library name: DNA109808
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA109793

description:
Library name: DNA109793
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124094

description:
Library name: DNA124094
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA109798

description:
Library name: DNA109798
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA109791

description:
Library name: DNA109791
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, GFP-P, rep1

description: Library name: 3034-GFP-P.239011.intCt


title: Colon, GFP-P, rep4

description: Library name: 8045-8050-GFP-P.239015.intCt


title: cell-free DNA, Preeclampsia pregnancy DNA109787

description:
Library name: DNA109787
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Degs1-KO, clone2, colon tumor, rep9

description: Library name: X20.4.21.201055.intCt

value: epithelial

value: AKP


title: Degs1-KO, clone2, colon tumor, rep8

description: Library name: X20.4.21.201054.intCt


title: cell-free DNA, Healthy pregnancy DNA109795

description:
Library name: DNA109795
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy


title: Colon, GFP-N, rep1

description: Library name: 3034-GFP-N.239001.intCt


title: cell-free DNA, Healthy pregnancy DNA109799

description:
Library name: DNA109799
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA109786

description:
Library name: DNA109786
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, GFP-N, rep4

description: Library name: 8050-GFP-N.239007.intCt


title: Degs1-KO, clone2, colon tumor, rep6

description: Library name: X20.4.21.201052.intCt


title: cell-free DNA, Healthy pregnancy DNA109782

description:
Library name: DNA109782
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA109789

description:
Library name: DNA109789
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Degs1-KO, clone2, colon tumor, rep3

description: Library name: X20.4.21.201049.intCt


title: cell-free DNA, Healthy pregnancy DNA109794

description:
Library name: DNA109794
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, GFP-P, rep6

description: Library name: 5780-GFP-P.239037.intCt


title: Degs1-KO, clone2, colon tumor, rep4

description: Library name: X20.4.21.201050.intCt


title: cell-free DNA, Preeclampsia pregnancy DNA109777

description:
Library name: DNA109777
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Degs1-KO, clone2, colon tumor, rep7

description: Library name: X20.4.21.201053.intCt


title: cell-free DNA, Preeclampsia pregnancy DNA109776

description:
Library name: DNA109776
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: PAXgene DNA


title: Colon, GFP-N, rep6

description: Library name: 7789-7795-GFP-N.239009.intCt


title: Degs1-KO, clone1, colon tumor, rep6

description: Library name: X20.4.18.201043.intCt


title: Colon, GFP-N, rep3

description: Library name: 7082-GFP-N.239004.intCt


title: NHP C, 21 DPI

status: Public on Jan 06 2026

city: Galveston

first: Jacquelyn

last: Turcinovic

state: TX

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

description: Library name: sample31

data_processing:
Raw FASTQ files were aligned to the combined M. fascicularis (Ensembl 102 v5.0) and BOMV (OK633884.1) genomes using STAR aligner v2.7.11b.
Transcript-aligning reads were quantified with Rsubread featureCounts v2.20.0.
Sequencing batch effect was regressed using SVA ComBat-seq v3.54.0.
Postexposure samples were binned by day (DPI) and compared to baseline (-8 DPI) using DESeq2 v1.46.0.
Assembly: M. fascicularis (Ensembl 102 v5.0) and BOMV (OK633884.1)
Supplementary files format and content: counts.tsv is the raw count matrix output from featureCounts

organism: Macaca fascicularis

source_name: Blood

extract_protocol:
Total RNA extracted from TRIzol LS using chloroform phase separation according to the manufacturer's specifications. RNA cleanup was performed via QIAGEN RNeasy cleanup columns, and DNA was digested on-column during cleanup.
Globin and ribosomal RNA were removed via the NEBNext Globin and rRNA Depletion Kit, and sequencing libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit.

value: Blood

tag: batch

value: A


title: cell-free DNA, Healthy pregnancy DNA109784

description:
Library name: DNA109784
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA109781

description:
Library name: DNA109781
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA109780

description:
Library name: DNA109780
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Degs1-KO, clone2, colon tumor, rep2

description: Library name: X20.4.21.201048.intCt


title: Degs1-KO, clone2, colon tumor, rep5

description: Library name: X20.4.21.201051.intCt


title: cell-free DNA, Preeclampsia pregnancy DNA109766

description:
Library name: DNA109766
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Degs1-KO, clone1, colon tumor, rep3

description: Library name: X20.4.18.201040.intCt


title: Degs1-KO, clone1, colon tumor, rep8

description: Library name: X20.4.18.201045.intCt


title: Colon, GFP-N, rep2

description: Library name: 7421-GFP-N.239003.intCt


title: cell-free DNA, Preeclampsia pregnancy DNA109775

description:
Library name: DNA109775
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Degs1-KO, clone1, colon tumor, rep9

description: Library name: X20.4.18.201046.intCt


title: cell-free DNA, Preeclampsia pregnancy DNA109765

description:
Library name: DNA109765
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA109762

description:
Library name: DNA109762
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Degs1-KO, clone1, colon tumor, rep2

description: Library name: X20.4.18.201039.intCt


title: Degs1-KO, clone1, colon tumor, rep5

description: Library name: X20.4.18.201042.intCt


title: cell-free DNA, Preeclampsia pregnancy DNA109774

description:
Library name: DNA109774
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Degs1-KO, clone1, colon tumor, rep4

description: Library name: X20.4.18.201041.intCt


title: cell-free DNA, Preeclampsia pregnancy DNA109770

description:
Library name: DNA109770
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA109761

description:
Library name: DNA109761
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA109779

description:
Library name: DNA109779
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA109769

description:
Library name: DNA109769
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Scrambled, colon tumor, rep1

description: Library name: X9.0.Scr.201035.intCt

value: Scrambled


title: Degs1-KO, clone1, colon tumor, rep7

description: Library name: X20.4.18.201044.intCt


title: Degs1-KO, clone2, colon tumor, rep1

description: Library name: X20.4.21.201047.intCt


title: cell-free DNA, Healthy pregnancy DNA109752

description:
Library name: DNA109752
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA109751

description:
Library name: DNA109751
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA109749

description:
Library name: DNA109749
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: shControl, colon tumor, rep9

description: Library name: Scramble.sh.201030.intCt

value: Control


title: cell-free DNA, Healthy pregnancy DNA109757

description:
Library name: DNA109757
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA109778

description:
Library name: DNA109778
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Degs1-KO, clone1, colon tumor, rep1

description: Library name: X20.4.18.201038.intCt


title: shControl, colon tumor, rep7

description: Library name: Scramble.sh.201028.intCt


title: cell-free DNA, Healthy pregnancy DNA109753

description:
Library name: DNA109753
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: shControl, colon tumor, rep8

description: Library name: Scramble.sh.201029.intCt


title: shControl, colon tumor, rep6

description: Library name: Scramble.sh.201027.intCt


title: shControl, colon tumor, rep5

description: Library name: Scramble.sh.201026.intCt


title: shYAP, colon tumor, rep3

description: Library name: Sh.Yap.4.201034.intCt

value: shYAP


title: Scrambled, colon tumor, rep3

description: Library name: X9.0.Scr.201037.intCt


title: cell-free DNA, Healthy pregnancy DNA088246

description:
Library name: DNA088246
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Scrambled, colon tumor, rep2

description: Library name: X9.0.Scr.201036.intCt


title: shControl, colon tumor, rep4

description: Library name: Scramble.sh.201016.intCt


title: cell-free DNA, Preeclampsia pregnancy DNA109760

description:
Library name: DNA109760
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: shYAP, colon tumor, rep2

description: Library name: Sh.Yap.4.201033.intCt


title: cell-free DNA, Healthy pregnancy DNA109755

description:
Library name: DNA109755
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: shControl, colon tumor, rep10

description: Library name: Scramble.sh.201031.intCt


title: cell-free DNA, Healthy pregnancy DNA088241

description:
Library name: DNA088241
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, HFD rep2, scRNAseq

description: Library name: HFD-colon2

library_source: transcriptomic single cell

data_processing:
The Cell Ranger toolkit (version 3.1.0) provided by 10x Genomics was applied to aggregate raw data, filter low-quality reads, align reads to mouse reference genome (GRCm39), assign cell barcodes, and generate the unique molecular identifier (UMI) matrix. An R-based toolkit, Seurat (version 4.0.1), was used for analyzing the scRNA-seq data.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

extract_protocol:
Based on FACS analysis, alive cells from colon tumor or normal colon of mice fed with control and high-fat diets were sorted into 1.5 ml low-binding tubes with 500 ul FACS buffer. Single cells were processed through the GemCode Single Cell Platform using the GemCode Gel Bead, Chip and Library Kits (10x Genomics, Pleasanton) as per the manufacturer’s protocol. The loading cell number is 18,000 for each sample The cells were then partitioned into Gel Beads in Emulsion in the GemCode instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification. Amplified cDNA was then used for 3’ gene expression library construction
Amplified cDNA was fragmented and end-repaired, double-sided size-selected, PCR-amplified with sample indexing primers, and double-sided size-selected

value: Alive cell

tag: Sex

value: Male


title: cell-free DNA, Healthy pregnancy DNA088248

description:
Library name: DNA088248
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA109747

description:
Library name: DNA109747
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA088247

description:
Library name: DNA088247
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA088245

description:
Library name: DNA088245
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: shControl, colon tumor, rep2

description: Library name: Scramble.sh.201014.intCt


title: cell-free DNA, Healthy pregnancy DNA088238

description:
Library name: DNA088238
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA088243

description:
Library name: DNA088243
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA109746

description:
Library name: DNA109746
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA088234

description:
Library name: DNA088234
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, HFD rep3, scRNAseq

description: Library name: HFD-CT3

source_name: Colon tumor

value: Colon tumor

value: High fat diet


title: cell-free DNA, Healthy pregnancy DNA088233

description:
Library name: DNA088233
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, HFD rep2, scRNAseq

description: Library name: HFD-CT2


title: Colon tumor, CD rep1, scRNAseq

description: Library name: CD-CT1


title: cell-free DNA, Healthy pregnancy DNA088244

description:
Library name: DNA088244
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: EDTA


title: shControl, colon tumor, rep3

description: Library name: Scramble.sh.201015.intCt

value: Colon


title: shControl, colon tumor, rep1

description: Library name: Scramble.sh.201013.intCt


title: shYAP, colon tumor, rep1

description: Library name: Sh.Yap.4.201032.intCt


title: cell-free DNA, Healthy pregnancy DNA088242

description:
Library name: DNA088242
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA088236

description:
Library name: DNA088236
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA088240

description:
Library name: DNA088240
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon, HFD rep1, scRNAseq

description: Library name: HFD-colon1


title: cell-free DNA, Healthy pregnancy DNA088239

description:
Library name: DNA088239
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA088231

description:
Library name: DNA088231
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA088237

description:
Library name: DNA088237
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA088232

description:
Library name: DNA088232
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, CD rep2, scRNAseq

description: Library name: CD-CT2


title: Colon, CD rep1, scRNAseq

description: Library name: CD-colon1


title: Colon tumor, CD rep3, scRNAseq

description: Library name: CD-CT3


title: PW5_1

city: Xiamen

first: Liangxiang

last: Xiao

address: No. 201-209, Hubin South Road

country: China

institute: Zhongshan Hospital of Xiamen University

description:
Library name: sample6
PW5_fpkm

data_processing:
Reads were further filtered by fastp (version 0.18.0). The parameters were as follows:  1) removing reads containing adapters;  2) removing reads containing more than 10% of unknown nucleotides (N);  3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: mm10
Supplementary files format and content: FPKM values and counts for each Sample

source_name: Kidney

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB#7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000.

value: Kidney

tag: cell line

value: tissue

value: Overexpression of Wnt1 gene in mice

value: treated with the Wnt1 plasmid


title: Colon, CD rep2, scRNAseq

description: Library name: CD-colon2


title: cell-free DNA, Healthy pregnancy DNA088235

description:
Library name: DNA088235
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy


title: C6_1

description:
Library name: sample3
C6_fpkm

value: control

value: treated with the empty vector (pcDNA3)


title: PW2_1

description:
Library name: sample4
PW2_fpkm


title: Foxa1 WildType overexpression (scRNA-seq)

city: New York

first: Erik

last: Ladewig

state: New York

address: 435 East 65th Street

institute: MSKCC

description:
Library name: WT_multiome snRNA
10x Genomics
WT_multiome_barcodes.tsv.gz
WT_multiome_features.tsv.gz
WT_multiome_matrix.mtx.gz

data_processing:
[scATAC-seq]  The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
[scATAC-seq]  Peaks were called using MACS v2.1.0 with the significance cut-off q-value <=0.01
[scATAC-seq]  bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
[scATAC-seq]  bigWig, narrowPeak (except for Input sample)
[scRNA-seq]  Multiome-seq: Single nuclei were extracted from mouse prostate organoids. Joint scRNA- and scATAC libraries were prepared using the 10x Genomics platform.
[scRNA-seq]  The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: prostate

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
For scATAC-seq, mouse prostates were freshly dissociated (described above), and flow sorted for live single cells using DAPI. Fresh nuclei were isolated before processing for 10X Genomics Chromium single cell multiome ATAC + gene expression sequencing following manufacture’s instructions.
[scATAC-seq]  Mouse prostates were harvested and subsequently digested with collagenase type II (Gibco) for 2 hrs at 37 °C, followed by TrypLE (Gibco) digestion at 37 °C until a single-cell suspension was obtained. Digestions were supplemented with Y-27632 (10 μM) to inhibit anoikis and filtered to obtain single cell suspension.
[scATAC-seq]  Murine prostate organoid culture was established and maintained under standard conditions. Briefly, dissociated prostatic epithelial cells were embedded in 20-µl drops of Matrigel (Corning) and overlaid with mouse prostate organoid medium.
[scRNA-seq]  Mouse prostate organoids cultured in medium and single cell were sorted for 10X multiome sequencing
[scRNA-seq]  Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: epithelial

value: prostate

value: Organoid

tag: strain


title: PW3_1

description:
Library name: sample5
PW3_fpkm


title: Foxa1 M253K (scRNA-seq)

description:
Library name: M2_multiome snRNA
10x Genomics
M2_multiome_barcodes.tsv.gz
M2_multiome_features.tsv.gz
M2_multiome_matrix.mtx.gz


title: C3_1

description:
Library name: sample2
C3_fpkm


title: Colon tumor, HFD rep1, scRNAseq

description: Library name: HFD-CT1

value: Alive cell


title: cell-free DNA, Healthy pregnancy DNA088229

description:
Library name: DNA088229
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Foxa1 H247Y (scRNA-seq)

description:
Library name: H2_multiome snRNA
10x Genomics
H2_multiome_barcodes.tsv.gz
H2_multiome_features.tsv.gz
H2_multiome_matrix.mtx.gz


title: cell-free DNA, Healthy pregnancy DNA088225

description:
Library name: DNA088225
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA088227

description:
Library name: DNA088227
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: C1_1

description:
Library name: sample1
C1_fpkm


title: cell-free DNA, Healthy pregnancy DNA088230

description:
Library name: DNA088230
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Foxa1 G275X (scRNA-seq)

description:
Library name: G2_multiome snRNA
10x Genomics
G2_multiome_barcodes.tsv.gz
G2_multiome_features.tsv.gz
G2_multiome_matrix.mtx.gz


title: cell-free DNA, Preeclampsia pregnancy DNA088223

description:
Library name: DNA088223
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Preeclampsia


title: cell-free DNA, Healthy pregnancy DNA088224

description:
Library name: DNA088224
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA088226

description:
Library name: DNA088226
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA088220

description:
Library name: DNA088220
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: PAXgene DNA


title: Foxa1 FE255 (scRNA-seq)

description:
Library name: FE_multiome snRNA
10x Genomics
FE_multiome_barcodes.tsv.gz
FE_multiome_features.tsv.gz
FE_multiome_matrix.mtx.gz


title: WildType overexpression Day5 (scRNA-seq)

description:
Library name: AN-1411_WT_Day5_multiome snRNA
10x Genomics
AN-1411_WT_Day5_multiome_barcodes.tsv.gz
AN-1411_WT_Day5_multiome_features.tsv.gz
AN-1411_WT_Day5_multiome_matrix.mtx.gz


title: cell-free DNA, Preeclampsia pregnancy DNA088221

description:
Library name: DNA088221
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA088217

description:
Library name: DNA088217
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA088222

description:
Library name: DNA088222
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WildType overexpression Day1 (scRNA-seq)

description:
Library name: AN-1411_WT_Day1_multiome snRNA
10x Genomics
AN-1411_WT_Day1_multiome_barcodes.tsv.gz
AN-1411_WT_Day1_multiome_features.tsv.gz
AN-1411_WT_Day1_multiome_matrix.mtx.gz


title: cell-free DNA, Preeclampsia pregnancy DNA088219

description:
Library name: DNA088219
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: G275X Day0 (scRNA-seq)

description:
Library name: AN-1411_GX_Day0_multiome snRNA
10x Genomics
AN-1411_GX_Day0_multiome_barcodes.tsv.gz
AN-1411_GX_Day0_multiome_features.tsv.gz
AN-1411_GX_Day0_multiome_matrix.mtx.gz


title: cell-free DNA, Healthy pregnancy DNA088228

description:
Library name: DNA088228
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Empty Vector control (scRNA-seq)

description:
Library name: EV_multiome snRNA
10x Genomics
EV_multiome_barcodes.tsv.gz
EV_multiome_features.tsv.gz
EV_multiome_matrix.mtx.gz


title: cell-free DNA, Preeclampsia pregnancy DNA088212

description:
Library name: DNA088212
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA088215

description:
Library name: DNA088215
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: G275X Day5 (scRNA-seq)

description:
Library name: AN-1411_GX_Day5_multiome snRNA
10x Genomics
AN-1411_GX_Day5_multiome_barcodes.tsv.gz
AN-1411_GX_Day5_multiome_features.tsv.gz
AN-1411_GX_Day5_multiome_matrix.mtx.gz


title: WildType overexpression Day0 (scRNA-seq)

description:
Library name: AN-1411_WT_Day0_multiome snRNA
10x Genomics
AN-1411_WT_Day0_multiome_barcodes.tsv.gz
AN-1411_WT_Day0_multiome_features.tsv.gz
AN-1411_WT_Day0_multiome_matrix.mtx.gz


title: cell-free DNA, Preeclampsia pregnancy DNA088216

description:
Library name: DNA088216
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA076393

description:
Library name: DNA076393
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Foxa1 G275X Pou2f1 KO in Pou2f1/Gata3 experiment (scRNA-seq)

description:
Library name: AN-1398_GX-pou2f1_KO_multiome snRNA
10x Genomics
AN-1398_GX-pou2f1_KO_multiome_barcodes.tsv.gz
AN-1398_GX-pou2f1_KO_multiome_features.tsv.gz
AN-1398_GX-pou2f1_KO_multiome_matrix.mtx.gz


title: cell-free DNA, Preeclampsia pregnancy DNA088214

description:
Library name: DNA088214
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA088210

description:
Library name: DNA088210
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA088209

description:
Library name: DNA088209
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Foxa1 G275X in Pou2f1/Gata3 experiment (scRNA-seq)

description:
Library name: AN-1398_GX_multiome snRNA
10x Genomics
AN-1398_GX_multiome_barcodes.tsv.gz
AN-1398_GX_multiome_features.tsv.gz
AN-1398_GX_multiome_matrix.mtx.gz


title: G275X Day1 (scRNA-seq)

description:
Library name: AN-1411_GX_Day1_multiome snRNA
10x Genomics
AN-1411_GX_Day1_multiome_barcodes.tsv.gz
AN-1411_GX_Day1_multiome_features.tsv.gz
AN-1411_GX_Day1_multiome_matrix.mtx.gz


title: Foxa1 M253K (snATAC-seq)

description:
Library name: M2_multiome snATAC
10x Genomics snATAC
M2_multiome_barcodes.tsv.gz
M2_multiome_features.tsv.gz
M2_multiome_matrix.mtx.gz

library_source: genomic single cell


title: cell-free DNA, Healthy pregnancy DNA076384

description:
Library name: DNA076384
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA088213

description:
Library name: DNA088213
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Foxa1 FE255 (snATAC-seq)

description:
Library name: FE_multiome snATAC
10x Genomics snATAC
FE_multiome_barcodes.tsv.gz
FE_multiome_features.tsv.gz
FE_multiome_matrix.mtx.gz


title: cell-free DNA, Preeclampsia pregnancy DNA088218

description:
Library name: DNA088218
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA088211

description:
Library name: DNA088211
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA076383

description:
Library name: DNA076383
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Empty Vector control (snATAC-seq)

description:
Library name: EV_multiome snATAC
10x Genomics snATAC
EV_multiome_barcodes.tsv.gz
EV_multiome_features.tsv.gz
EV_multiome_matrix.mtx.gz


title: Empty Vector Day5 (scRNA-seq)

description:
Library name: AN-1411_EV_Day5_multiome snRNA
10x Genomics
AN-1411_EV_Day5_multiome_barcodes.tsv.gz
AN-1411_EV_Day5_multiome_features.tsv.gz
AN-1411_EV_Day5_multiome_matrix.mtx.gz


title: Empty Vector Day1 (scRNA-seq)

description:
Library name: AN-1411_EV_Day1_multiome snRNA
10x Genomics
AN-1411_EV_Day1_multiome_barcodes.tsv.gz
AN-1411_EV_Day1_multiome_features.tsv.gz
AN-1411_EV_Day1_multiome_matrix.mtx.gz


title: cell-free DNA, Healthy pregnancy DNA076381

description:
Library name: DNA076381
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Foxa1 G275X Gata3 KO in Pou2f1/Gata3 experiment (scRNA-seq)

description:
Library name: AN-1398_GX-gata3_KO_multiome snRNA
10x Genomics
AN-1398_GX-gata3_KO_multiome_barcodes.tsv.gz
AN-1398_GX-gata3_KO_multiome_features.tsv.gz
AN-1398_GX-gata3_KO_multiome_matrix.mtx.gz


title: Empty Vector control in Pou2f1/Gata3 experiment (scRNA-seq)

description:
Library name: AN-1398_EV_1_multiome snRNA
10x Genomics
AN-1398_EV_1_multiome_barcodes.tsv.gz
AN-1398_EV_1_multiome_features.tsv.gz
AN-1398_EV_1_multiome_matrix.mtx.gz


title: Empty Vector Day0 (scRNA-seq)

description:
Library name: AN-1411_EV_Day0_multiome snRNA
10x Genomics
AN-1411_EV_Day0_multiome_barcodes.tsv.gz
AN-1411_EV_Day0_multiome_features.tsv.gz
AN-1411_EV_Day0_multiome_matrix.mtx.gz


title: cell-free DNA, Preeclampsia pregnancy DNA076391

description:
Library name: DNA076391
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA076378

description:
Library name: DNA076378
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WildType overexpression Day1 (snATAC-seq)

description:
Library name: AN-1411_WT_Day1_multiome snATAC
10x Genomics snATAC
AN-1411_WT_Day1_multiome_barcodes.tsv.gz
AN-1411_WT_Day1_multiome_features.tsv.gz
AN-1411_WT_Day1_multiome_matrix.mtx.gz


title: Foxa1 WildType overexpression (snATAC-seq)

description:
Library name: WT_multiome snATAC
10x Genomics snATAC
WT_multiome_barcodes.tsv.gz
WT_multiome_features.tsv.gz
WT_multiome_matrix.mtx.gz


title: G275X Day5 (snATAC-seq)

description:
Library name: AN-1411_GX_Day5_multiome snATAC
10x Genomics snATAC
AN-1411_GX_Day5_multiome_barcodes.tsv.gz
AN-1411_GX_Day5_multiome_features.tsv.gz
AN-1411_GX_Day5_multiome_matrix.mtx.gz


title: Foxa1 H247Y (snATAC-seq)

description:
Library name: H2_multiome snATAC
10x Genomics snATAC
H2_multiome_barcodes.tsv.gz
H2_multiome_features.tsv.gz
H2_multiome_matrix.mtx.gz


title: WildType overexpression Day0 (snATAC-seq)

description:
Library name: AN-1411_WT_Day0_multiome snATAC
10x Genomics snATAC
AN-1411_WT_Day0_multiome_barcodes.tsv.gz
AN-1411_WT_Day0_multiome_features.tsv.gz
AN-1411_WT_Day0_multiome_matrix.mtx.gz


title: cell-free DNA, Preeclampsia pregnancy DNA076392

description:
Library name: DNA076392
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA076372

description:
Library name: DNA076372
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: G275X Day1 (snATAC-seq)

description:
Library name: AN-1411_GX_Day1_multiome snATAC
10x Genomics snATAC
AN-1411_GX_Day1_multiome_barcodes.tsv.gz
AN-1411_GX_Day1_multiome_features.tsv.gz
AN-1411_GX_Day1_multiome_matrix.mtx.gz


title: cell-free DNA, Healthy pregnancy DNA076382

description:
Library name: DNA076382
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Foxa1 G275X (snATAC-seq)

description:
Library name: G2_multiome snATAC
10x Genomics snATAC
G2_multiome_barcodes.tsv.gz
G2_multiome_features.tsv.gz
G2_multiome_matrix.mtx.gz


title: Empty Vector Day5 (snATAC-seq)

description:
Library name: AN-1411_EV_Day5_multiome snATAC
10x Genomics snATAC
AN-1411_EV_Day5_multiome_barcodes.tsv.gz
AN-1411_EV_Day5_multiome_features.tsv.gz
AN-1411_EV_Day5_multiome_matrix.mtx.gz


title: cell-free DNA, Healthy pregnancy DNA076376

description:
Library name: DNA076376
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA076380

description:
Library name: DNA076380
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA076370

description:
Library name: DNA076370
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WildType overexpression Day5 (snATAC-seq)

description:
Library name: AN-1411_WT_Day5_multiome snATAC
10x Genomics snATAC
AN-1411_WT_Day5_multiome_barcodes.tsv.gz
AN-1411_WT_Day5_multiome_features.tsv.gz
AN-1411_WT_Day5_multiome_matrix.mtx.gz


title: cell-free DNA, Healthy pregnancy DNA076369

description:
Library name: DNA076369
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA076377

description:
Library name: DNA076377
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA076379

description:
Library name: DNA076379
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Empty Vector Day0 (snATAC-seq)

description:
Library name: AN-1411_EV_Day0_multiome snATAC
10x Genomics snATAC
AN-1411_EV_Day0_multiome_barcodes.tsv.gz
AN-1411_EV_Day0_multiome_features.tsv.gz
AN-1411_EV_Day0_multiome_matrix.mtx.gz


title: Foxa1 G275X Pou2f1 KO in Pou2f1/Gata3 experiment (snATAC-seq)

description:
Library name: AN-1398_GX-pou2f1_KO_multiome snATAC
10x Genomics snATAC
AN-1398_GX-pou2f1_KO_multiome_barcodes.tsv.gz
AN-1398_GX-pou2f1_KO_multiome_features.tsv.gz
AN-1398_GX-pou2f1_KO_multiome_matrix.mtx.gz


title: cell-free DNA, Healthy pregnancy DNA076366

description:
Library name: DNA076366
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: stim5days

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

description:
Library name: A_S011
In vitro cultured CD8 T cells 5 days post stimulation

data_processing:
The fastqs were aligned to hg19 using bowtie2.
Unmapped, unpaired, and mitochondrial reads were removed using samtools.
ENCODE Blacklist regions were removed.
PCR duplicates were removed using Picard.
Peak calling was performed with MACS2 with a FDR q-value < 0.001
Assembly: hg19
Supplementary files format and content: Accessibility Counts text file for all samples

source_name: PBMC

growth_protocol: A total of 40,000 cells were sorted and processed for ATAC-seq. Nuclei were isolated by lysing cells in a buffer containing 10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, and 0.1%Tween-20. Immediately following isolation, nuclei were subjected to DNA tagmentation by 50μl Tn5 transposase reaction mix

extract_protocol:
Fragmented DNA were purified by Qiagen MinElute Enzyme Reaction Cleanup Kit (Qiagen, 28204) per the manufacture’s protocol. ATAC-seq libraries were prepared by PCR amplification of DNA fragments using Nextera Index Kit
Transposed DNA was prepared with Tn5 (Illumina #FC-121-1031) as described in Buenrostro et al. 2013 using 0.1% Tween 20 instead of IGEPAL CA-630.Libraries were barcoded with Nextera Index Kit (Illumina # FC-121-1012) ,Libraries were quantified using the KAPA Library Quantification Kit (Roche, KK4824) and sequenced on a NextSeq 550 platform

value: PBMC


title: cell-free DNA, Healthy pregnancy DNA076373

description:
Library name: DNA076373
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: G275X Day0 (snATAC-seq)

description:
Library name: AN-1411_GX_Day0_multiome snATAC
10x Genomics snATAC
AN-1411_GX_Day0_multiome_barcodes.tsv.gz
AN-1411_GX_Day0_multiome_features.tsv.gz
AN-1411_GX_Day0_multiome_matrix.mtx.gz


title: NaïveCD8s

description:
Library name: A_S002
Naïve CD8 T cells from fresh PBMC


title: Empty Vector Day1 (snATAC-seq)

description:
Library name: AN-1411_EV_Day1_multiome snATAC
10x Genomics snATAC
AN-1411_EV_Day1_multiome_barcodes.tsv.gz
AN-1411_EV_Day1_multiome_features.tsv.gz
AN-1411_EV_Day1_multiome_matrix.mtx.gz


title: cell-free DNA, Healthy pregnancy DNA076368

description:
Library name: DNA076368
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: EDTA


title: stim48hours

description:
Library name: A_S009
In vitro cultured CD8 T cells 48 hours post stimulation


title: cell-free DNA, Healthy pregnancy DNA076365

description:
Library name: DNA076365
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: CD8

description:
Library name: A_S001
Total CD8 T cells from fresh PBMC


title: RH iAP2XI-3 +IAA rep2

city: Wuhan

first: Fan

last: Fuqiang

address: 1 Shizishan St

institute: Huazhong Agricultural University

description: Library name: RH iAP2XI-3 +IAA rep2

data_processing:
To identify transcript changes in AP2XI-3 depleted strain, raw data were trimmed and quality controlled by SeqPrep and Sickle with default parameters. Then, clean data were mapped to reference genome GT1 (ToxoDB, version 68) using TopHat. The transcript per million reads (TPM) method was used to calculate the transcript levels of each gene. Differentially expressed gene (DEG) analysis was performed by Deseq2 with a p-value cutoff of 0.05 and a minimum fold change of 2.
Assembly: ToxoDB TGGT1 v68
Supplementary files format and content: RH_AP2XI-3.tpm.counts.txt

organism: Toxoplasma gondii

source_name: Toxoplasma

growth_protocol: All parasites strain used in this study were cultured in human foreskin fibroblast cells in high-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 unit/mL penicillin, and 100 mg/mL streptomycin at 37 °C with 5% CO2.

extract_protocol:
RNA extraction was performed using TRIzol Reagent according to the manufacturer’s instructions (TransGen Biotech, China) following addition of RNase-free DNaseI to remove genomic DNA.
RNA libraries were prepared using the KCTM Stranded mRNA Library Prep Kit (Wuhan Seqhealth Co. Ltd. China) and 2 μg total RNA was used for each sample. PCR products with the sizes of 200–500 bps were enriched, quantified, and sequenced on the DNBSEQ-T7 sequencer (MGI Tech Co. Ltd., China) with the PE150 model.

treatment_protocol: To prepare RNA samples, tachyzoites were allowed to grow in T25 flasks for 40 h and IAA or ethanol was added 24 h before sample collection. 3 × 10^7 tachyzoites were calculated for each sample and at least three replicates were prepared for each strain.

value: Toxoplasma

value: RH iAP2XI-3-mAID-3HA

value: with IAA


title: Wildtype, no stress

city: Vienna

first: Jian Yi

last: Kok

address: Dr.-Bohr-Gasse 3

country: Austria

institute: GMI - Gregor Mendel Institute of Molecular Plant Biology

description: Library name: library1

data_processing:
Iso-Seq4
mini-map2 -ax splice:hq -uf
tama collapse -a 100 –m 100 –x no_cap
Assembly: PombBase ASM294v2
Supplementary files format and content: Provided are bed files with transcripts from tama collapse

organism: Schizosaccharomyces pombe

growth_protocol: Cells were revived from frozen (-70 ºC) stocks on YES plates at 32 ºC. Cells were then grown to saturation in YES at 32 ºC, subcultured and grown to mid-log (OD600 ~ 0.5) before being harvested.

extract_protocol:
Total RNA was extracted from yeast cells using a standard hot acid phenol protocol, followed by phenol-chloroform-isopropanol (PCI) extraction and DNase digestion
SMRTbell Barcoded Adapter Plate 3.0

treatment_protocol: Cells were either not treated, treated with 14 mM Caffeine, or treated with 200 ng/ml Clotrimazole.

value: no


title: cell-free DNA, Healthy pregnancy DNA076367

description:
Library name: DNA076367
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: RH iAP2XI-3 +IAA rep3

description: Library name: RH iAP2XI-3 +IAA rep3


title: Foxa1 G275X in Pou2f1/Gata3 experiment (snATAC-seq)

description:
Library name: AN-1398_GX_multiome snATAC
10x Genomics snATAC
AN-1398_GX_multiome_barcodes.tsv.gz
AN-1398_GX_multiome_features.tsv.gz
AN-1398_GX_multiome_matrix.mtx.gz


title: EMRA

description:
Library name: A_S007
Terminal effector memory CD8 T cells expressing CD45RA from fresh PBMC


title: Stress induced pool

description: Library name: library2

value: pool; h+ ade6-M216 ura4-D18 leu1-32; h+ ade6-M216 ura4-D18 leu1-32 hrp1del::kanMX hrp3del

value: pool; no, caffeine, clotrimazole


title: 94

city: East Lansing

first: Tim

last: Zacharewski

state: Michigan

address: 1129 Farm Ln

department: Biochemistry and Molecular Biology, Integrative Toxicological Sciences

institute: Michigan State University

description:
Library name: P176_M_94
Adult male mouse dosed every 4 days for 84 days

data_processing:
Read quality was assessed using FastQC v0.12.1 and adapter trimming was performed using Trimmomatic v0.39.
Alignment was performed with STAR v2.7.11b. Genome indices were created using Mus_musculus.GRCm39.dna.chromosome.fa and Mus_musculus.GRCm39.104.gtf.
Gene counts were determined using STAR v2.7.3a.
Assembly: mm10 (build 39)
Supplementary files format and content: STAR-aligned counts were transformed with the variance stabilizing transformation method in DESeq2.
Supplementary files format and content: Tab-delimited text files represent the number of aligned PE reads to each gene.

source_name: Gastrocnemius

extract_protocol:
Frozen muscle (~100 mg) was homogenized in 1 mL of TriZOL with chrome-steel beads using a Mixer Mill 300 (Life Sciences, Carlsbad, CA) for 4 minutes. Following, total RNA was extracted per the manufacturer’s instructions with an additional 5:1 phenol:chloroform extraction step (Sigma Aldrich, St. Louis, MO). RNA purity (260/280 ratio) and concentration (ng/µL) were assessed with a NanoDrop 1000 spectrophotometer. RNA quality was determined using an Agilent 2100 Bioanalyzer. All RNA samples had RNA integrity numbers (RINs) ≥7.
Library preparation was performed using an mRNA-seq Lib Prep Kit for Illumina (RK20302).

treatment_protocol: Mice were orally gavaged with TCDD in sesame oil vehicle every 4 days for 84 days. Half of the mice were exposed to simvastatin in their diet.

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Tap

tag: name

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

tag: formula

tag: vendor

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

tag: dose

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: CM

description:
Library name: A_S004
Central memory CD8 T cells from fresh PBMC

tag: tissue

value: PBMC


title: 95

description:
Library name: P176_M_95
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)


title: cell-free DNA, Preeclampsia pregnancy DNA076360

description:
Library name: DNA076360
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Preeclampsia

value: EDTA


title: RH iAP2XI-3 +IAA rep1

description: Library name: RH iAP2XI-3 +IAA rep1

tag: cell type

value: Toxoplasma

tag: genotype

value: RH iAP2XI-3-mAID-3HA

tag: treatment

value: with IAA


title: Foxa1 G275X Gata3 KO in Pou2f1/Gata3 experiment (snATAC-seq)

description:
Library name: AN-1398_GX-gata3_KO_multiome snATAC
10x Genomics snATAC
AN-1398_GX-gata3_KO_multiome_barcodes.tsv.gz
AN-1398_GX-gata3_KO_multiome_features.tsv.gz
AN-1398_GX-gata3_KO_multiome_matrix.mtx.gz

value: epithelial

value: prostate

value: Organoid


title: stim24hours

description:
Library name: A_S008
In vitro cultured CD8 T cells 24 hours post stimulation

value: PBMC


title: RH Tir1 +IAA rep2

description: Library name: RH Tir1 +IAA rep2

value: RH Tir1


title: Empty Vector control in Pou2f1/Gata3 experiment (snATAC-seq)

description:
Library name: AN-1398_EV_1_multiome snATAC
10x Genomics snATAC
AN-1398_EV_1_multiome_barcodes.tsv.gz
AN-1398_EV_1_multiome_features.tsv.gz
AN-1398_EV_1_multiome_matrix.mtx.gz


title: cell-free DNA, Healthy pregnancy DNA076364

description:
Library name: DNA076364
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: disease state

value: Healthy

tag: blood tube_type

tag: patient id


title: EM1

description:
Library name: A_S005
Effector memory CD8T cells from fresh PBMC


title: stim72hours

description:
Library name: A_S010
In vitro cultured CD8 T cells 72 hours post stimulation


title: Non-naiveCD8s

description:
Library name: A_S003
Non-Naïve CD8 T cells from fresh PBMC


title: cell-free DNA, Preeclampsia pregnancy DNA076357

description:
Library name: DNA076357
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: gestational age_(weeks)

tag: sequencing batch


title: Editing_Squ-Warm-1_1.fastq.gz

city: Cambridge

first: Rishav

last: Mitra

state: Massachusetts

address: 16 Divinity Avenue

institute: Harvard University

description: Library name: Editing_Squ-Warm-1_1.fastq.gz

data_processing:
FastQC
TrimGalore
Trinity
TransDecoder
Kallisto
RNA editing analysis using JACUSA
Assembly: de-novo transcriptome assembly using Trinity
Supplementary files format and content: csv
Supplementary files format and content: Kallisto count files, JACUSA output file

organism: Euprymna berryi

source_name: Arm

growth_protocol: California two-spot octopuses (O. bimaculoides) were wild-caught male and female adults (aged 1-2 years, Aquatic Research Consultants) and fed a daily diet of fiddler crabs (Leptuca pugilator, Northeast Brine Shrimp, Oak Hill, FL). Adult (aged 6-8 months) hummingbird bobtail squid (E. berryi) were laboratory cultured (Marine Biological Laboratory, Woods Hole, MA) and fed daily with grass shrimp (Palaemonetes pugio, Aquatic Indicators). All cephalopods were euthanized using established methods with sedation in 15% ethanol followed by pithing for tissue harvesting. All housed animals were kept under a 12 h–12 h light/dark cycle in filtered natural seawater.

extract_protocol:
Tissues were dissected, stored in RNALater, and immediately flash frozen in loquid nitrogen. Samples were stored at -80C until they were shipped on dry ice. All subsequent steps were performed by Azenta (Genewiz)
Poly(A) selected mRNA was used for library prep by Azenta (Genewiz)

value: Arm

value: WT

value: Control


title: 89

description:
Library name: P176_M_89
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

tag: Sex

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: EM2

description:
Library name: A_S006
Effector memory CD8 T cells from fresh PBMC

value: PBMC


title: RH Tir1 +IAA rep3

description: Library name: RH Tir1 +IAA rep3

value: Toxoplasma

value: RH Tir1

value: with IAA


title: 88

description:
Library name: P176_M_88
Adult male mouse dosed every 4 days for 84 days

tag: strain

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad


title: cell-free DNA, Preeclampsia pregnancy DNA076363

description:
Library name: DNA076363
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Preeclampsia

value: EDTA


title: 92

description:
Library name: P176_M_92
Adult male mouse dosed every 4 days for 84 days

tag: bedding

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: cell-free DNA, Preeclampsia pregnancy DNA076358

description:
Library name: DNA076358
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: RH Tir1 +IAA rep1

description: Library name: RH Tir1 +IAA rep1

value: Toxoplasma

value: RH Tir1

value: with IAA


title: 91

description:
Library name: P176_M_91
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad


title: Squ-Arm-2_1.fastq.gz

description: Library name: Squ-Arm-2_1.fastq.gz

value: Arm

value: WT


title: cell-free DNA, Healthy pregnancy DNA076225

description:
Library name: DNA076225
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

value: PAXgene DNA


title: Editing_Squ-Warm-2_1.fastq.gz

description: Library name: Editing_Squ-Warm-2_1.fastq.gz

value: Control


title: cell-free DNA, Preeclampsia pregnancy DNA076356

description:
Library name: DNA076356
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Preeclampsia

value: EDTA


title: Editing_Squ-Cold-2_1.fastq.gz

description: Library name: Editing_Squ-Cold-2_1.fastq.gz

value: Cold acclimation


title: RedCloverExtract3

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

description: Library name: A9

data_processing:
Adaptor sequences and low quality reads removed
Mapped to A suum genome (version PRJNA62057)
DEG determined using DESeq2
Assembly: PRJNA62057
Supplementary files format and content: excel file with count data and gene symbol for each sample

organism: Ascaris suum

source_name: Whole organism

extract_protocol:
total RNA was extracted using TRIZOL reagent, followed by chrloroform treatment and isopropanol precipiation
standard Illumina

value: Whole organism

value: RedCloverExtract


title: Squ-Arm-1_1.fastq.gz

description: Library name: Squ-Arm-1_1.fastq.gz


title: 86

description:
Library name: P176_M_86
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

tag: name

value: Yes

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: Squ-Brain-3_1.fastq.gz

description: Library name: Squ-Brain-3_1.fastq.gz

source_name: Brain

value: Brain

value: WT


title: Editing_Squ-Cold-3_1.fastq.gz

description: Library name: Editing_Squ-Cold-3_1.fastq.gz

value: Arm

value: Cold acclimation


title: cell-free DNA, Healthy pregnancy DNA076354

description:
Library name: DNA076354
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

value: EDTA


title: Editing_Squ-Warm-3_1.fastq.gz

description: Library name: Editing_Squ-Warm-3_1.fastq.gz

value: Control


title: Squ-Brain-1_1.fastq.gz

description: Library name: Squ-Brain-1_1.fastq.gz


title: Editing_Squ-Cold-1_1.fastq.gz

description: Library name: Editing_Squ-Cold-1_1.fastq.gz


title: BiochaninA3

description: Library name: A6

value: Whole organism

value: BiochaninA


title: cell-free DNA, Healthy pregnancy DNA076355

description:
Library name: DNA076355
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Squ-Brain-2_1.fastq.gz

description: Library name: Squ-Brain-2_1.fastq.gz


title: cell-free DNA, Healthy pregnancy DNA076222

description:
Library name: DNA076222
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: PAXgene DNA


title: 85

description:
Library name: P176_M_85
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

tag: formula

value: Accustandard

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram


title: Unmated, Whole gut, Replicate 2

status: Public on Jan 05 2026

city: Salt Lake City

first: Tahmineh

last: Kandelouei

state: Utah

address: 1950 Circle of Hope Dr.

institute: Huntsman Cancer Institute

description: Library name: 19464X6

data_processing:
The sample reads were aligned to the latest genome assembly (BDGP 6.94) using the STAR Aligner.
The aligned reads were then assigned to genes using HTSeq in 'Union' mode.
Raw scores derived from this process were then used for differential expression analysis using the DESeq2 algorithm.
Genes that met the criteria of an absolute log2 fold change ≥1 and an adjusted p-value <0.05 were identified as significantly differentially expressed.
Assembly: dm6
Supplementary files format and content: tab-delimited text files include raw counts for each sample.

organism: Drosophila melanogaster

source_name: gut

extract_protocol:
RNAwas extracted from dissected midguts using RNAqueous®-Micro Total RNA Isolation Kit.
NEBNext® Ultra™ II Directional RNA Library Prep with polyA mRNA isolation.

value: gut


title: 82

description:
Library name: P176_M_82
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

tag: vendor

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: cell-free DNA, Healthy pregnancy DNA076226

description:
Library name: DNA076226
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

value: PAXgene DNA


title: 80

description:
Library name: P176_M_80
Adult male mouse dosed every 4 days for 84 days

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard

tag: dose


title: Squ-Arm-3_1.fastq.gz

description: Library name: Squ-Arm-3_1.fastq.gz

tag: tissue

value: Arm

value: WT


title: cell-free DNA, Healthy pregnancy DNA076224

description:
Library name: DNA076224
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: EDTA


title: RedCloverExtract1

description: Library name: A7

value: Whole organism

value: RedCloverExtract


title: BiochaninA2

description: Library name: A5

value: BiochaninA


title: AMA17 LB + B12 replicate 2

city: Fullerton

first: M. S.

last: Ramirez

state: CA

address: 800 N. State College Blvd

institute: California State University Fullerton

description: Library name: AMA17_B12_2

data_processing:
Low-quality reads were removed using Trimmomatic v0.39
Reads were aligned witth Burrows Wheeler Alignment software (BWA) v0.7.17
Bigwig files were generated with custom bash scripts and BEDtools
Read counts per gene were determined using featureCounts (Subread package v2.0.3)
RNA-seq differential expression analysis was performed using DESeq2
Assembly: NZ_CP008706.1 and NZ_VYTP01000001.1
Supplementary files format and content: .txt files containing the output of featureCounts of each sample

organism: Acinetobacter baumannii

source_name: bacterial culture

extract_protocol:
RNA was extracted using Direct-zol RNA Kit (Zymo Research, Irvine, CA, USA)
Illumina RNA-seq

value: bacterial culture


title: Control3

description: Library name: A3

value: Control


title: 79

description:
Library name: P176_M_79
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: RedCloverExtract2

description: Library name: A8

value: Whole organism

value: RedCloverExtract


title: 78

description:
Library name: P176_M_78
Adult male mouse dosed every 4 days for 84 days

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard


title: 76

description:
Library name: P176_M_76
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage


title: 77

description:
Library name: P176_M_77
Adult male mouse dosed every 4 days for 84 days

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: BiochaninA1

description: Library name: A4

value: Whole organism

value: BiochaninA


title: AMA17 LB replicate 2

description: Library name: AMA17_2

value: bacterial culture


title: cell-free DNA, Healthy pregnancy DNA076223

description:
Library name: DNA076223
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

value: PAXgene DNA


title: 73

description:
Library name: P176_M_73
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard


title: cell-free DNA, Healthy pregnancy DNA076221

description:
Library name: DNA076221
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: EDTA


title: Control2

description: Library name: A2

value: Whole organism

value: Control


title: Control1

description: Library name: A1


title: cell-free DNA, Healthy pregnancy DNA076217

description:
Library name: DNA076217
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy


title: cell-free DNA, Healthy pregnancy DNA076216

description:
Library name: DNA076216
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: 74

description:
Library name: P176_M_74
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: AMA17 LB + B12 replicate 1

description: Library name: AMA17_B12_1

value: bacterial culture


title: AMA17 LB replicate 1

description: Library name: AMA17_1


title: AB5075 LB + B12 replicate 2

description: Library name: AB5075_B12_2


title: cell-free DNA, Healthy pregnancy DNA076215

description:
Library name: DNA076215
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: EDTA


title: 72

description:
Library name: P176_M_72
Adult male mouse dosed every 4 days for 84 days

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard


title: AB5075 LB replicate 2

description: Library name: AB5075_2


title: AB5075 LB replicate 1

description: Library name: AB5075_1


title: cell-free DNA, Healthy pregnancy DNA076214

description:
Library name: DNA076214
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

value: PAXgene DNA


title: 71

description:
Library name: P176_M_71
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: cell-free DNA, Healthy pregnancy DNA076211

description:
Library name: DNA076211
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: EDTA


title: H-3

city: Nanjing

first: can

last: xiong

address: 101 Longmian Avenue, Jiangning District

department: Basic Medical Sciences

institute: Nanjing Medical University

description:
Library name: H-3
H-3

data_processing:
fastp(v0.23.4)
HISAT2(v2.2.1)
StringTie(v2.2.1)
HTSeq(v0.13.5)
Assembly: hg38

source_name: cell

extract_protocol:
RNAprep Pure Tissue Kit(TIANGEN，DP431)
AT4221-U-mRNAseq Library Prep Kit（KAITAI-Bio, AT4221）

value: cell

tag: cell line

value: Cardiomyocyte cell line

tag: cell type

value: Treat the cells with high glucose


title: H-2

description:
Library name: H-2
H-2

tag: treatment


title: 70

description:
Library name: P176_M_70
Adult male mouse dosed every 4 days for 84 days

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard


title: Bai-2

description:
Library name: Bai-2
Bai-2

value: Treat the cells with a combination of high glucose and chrysin


title: AB5075 LB + B12 replicate 1

description: Library name: AB5075_B12_1

value: bacterial culture


title: L-2

description:
Library name: L-2
L-2

value: Treat the cells with low glucose


title: H-1

description:
Library name: H-1
H-1

value: cell


title: 67

description:
Library name: P176_M_67
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: cell-free DNA, Healthy pregnancy DNA076210

description:
Library name: DNA076210
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

tag: disease state

value: Healthy

value: EDTA


title: 65

description:
Library name: P176_M_65
Adult male mouse dosed every 4 days for 84 days

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Tap

value: Harlan Teklad 22/5 Rodent Diet 8604

value: Harlan Teklad

value: Yes

value: Accustandard


title: Bai-3

description:
Library name: Bai-3
Bai-3

value: cell

value: Cardiomyocyte cell line

value: Treat the cells with a combination of high glucose and chrysin


title: 64

description:
Library name: P176_M_64
Adult male mouse dosed every 4 days for 84 days

value: Charles Rivers Laboratories

value: Room temperature

value: sesame oil

value: milliliter

value: oral gavage

value: microgram per kilogram

value: simvastatin

value: Millipore-Sigma

value: diet

value: milligram per kilogram per day

value: Carbon dioxide euthanasia


title: 1046-GWI-Vehicle, 1046-GWI-Toxicant, 1039-Control-Vehicle, 1039-Control-Toxicant, Mixed FLEX scRNA-seq

city: College Station

first: James

last: Cai

address: 4458 TAMU

department: Veterinary Intergrative Biosciences

institute: Texas A&M University

description:
Library name: Pool 25
scRNA-seq of pooled samples from 4 different treatment groups using 10X Chromium Flex RNA protocol

data_processing:
Raw reads from FASTQ files were mapped to the human reference genome (GRCh38-2024-A) using CellRanger (version 8.0.1) to generate raw and filtered gene expression matrices.
Assembly: GRCh38-2024-A
Supplementary files format and content: .h5 files containing mapped scRNA-seq count data

growth_protocol: First, the hiPSC colonies were dissociated in ReLeSR (Stem Cell Technologies, Vancouver, BC, Canada, 05872) for 5 min at 37°C. Following this, cells were collected then resuspended in mTeSR Plus with 5x supplement (Stem Cell Technologies, Vancouver, BC, Canada, 100-0276), 10 μM SB-4321542 at 20 ng/ml (Tocris, Bristol, United Kingdom, 1614), 5 μM dorsomorphin (Sigma-Aldrich, cat. no. P5499), and the ROCK inhibitor Y-27632 at 10 μM (Tocris, Bristol, United Kingdom, 1254) on ultra-low adherence plates (Corning, Corning, NY, United States, 3471) for embryoid body (EB) formation. The medium was replaced on day 3 and supplemented with dorsomorphin and SB-4321542. On day 6 the medium was replaced with Neurobasal Differentiation Media (NBM), consisting of Neurobasal-A media (Life Technologies, Carlsbad, CA, United States, cat. no. 10888022) with B27 supplement without vitamin A (Life Technologies, Carlsbad, CA, United States, 12587010) at 2% of the total volume and GlutaMax (Life Technologies, Carlsbad, CA, United States, cat. no. 35050–061) at 1% of the total volume. NBM was supplemented with 20 μg/ml basic fibroblast growth factor (bFGF) (PeproTech, Cranberry, NJ, United States, 100-18B) and 20 μg/ml epidermal growth factor (EGF) (PeproTech, Cranberry, NJ, United States, AF-100-115) from days 6–24. On day 11 the plates were moved to an orbital shaker (Infors HT Celltron, Annapolis Juntion, MD, United States, I69222) at 37°C set at 65 revolutions per minute. From day 26 onward the NBM was supplemented with 20 ng/ml brain-derived neurotrophic factor (BDNF) (PeproTech, Cranberry, NJ, United States, 450-02) and 20 ng/ml neurotrophin 3 (NT3) (PeproTech, Cranberry, NJ, United States, 450-03). The medium was changed every 2–3 days throughout the duration of organoid generation. *Protocol from Yates and Case et al., 2022

extract_protocol:
Next GEM Single Cell Fixed RNA Sample Preparation To fix the organoids, we utilized the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics, Pleasanton, CA, United States, 1000414). First, to dissociate the samples, the organoids were collected into a 15 mL conical tube with a wide-bore tip. Excess media was carefully removed, and the organoids were gently washed with 2 mL of sterile PBS (Gibco, Waltham, MA, United States, 10010023). Once the organoids were settled, the PBS was replaced with 2mL of prewarmed Accutase (Invitrogen, Carlsbad, California, United States, 00-4555-56) with 20 μL of DNase (Thermo Fisher Scientific, Waltham, MA, United States, EN0521). The tube was placed in the water bath at 37ºC for 2 minutes, flicked to unsettle the organoids, then incubated for an additional 2 minutes. After this period the Accutase was removed, and the organoids were briefly washed with 5 mL of neurobasal media four times. At this point, the organoids were triturated 8-10 times with a 1 mL pipette until the organoids were well dispersed in the solution. The cells were next counted with a hemocytometer (Hausser Scientific, Horsham, PA, United States) and trypan blue (Gibco, Waltham, MA, United States, 15250061). For sample fixation, the organoid samples were then spun down in a swinging-bucket rotor centrifuge (Eppendorf, Hamburg, Germany, 022628113) at 300-400 rcf for 5 minutes at 4 º C. The supernatant was then removed (careful to not disturb the pellet) and 1 mL of room temperature Fixation Buffer (recipe below) and mix five times with a 1 mL pipette then incubate overnight (16 -24 hours) at 4º C. Do not agitate or mix the sample during incubation – fixation time and temperature should be consistent across all sample collection. Following the overnight fixation, centrifuge the sample at 850 rcf for 5 minutes at room temperature then remove the supernatant without disturbing the pellet. Next, add 1 mL of chilled Quenching Buffer (recipe below) to the pellet an mix five time and place on ice. Using a hemocytometer and trypan blue, the cells were then counted to determine cell concentration. The Enhancer (10X Genomics, Pleasanton, CA, United States, PN-20000482) was thawed in a water bath for 10 minutes at 65º C for ten minutes, then briefly vortex and centrifuged. It is important to keep the enhancer warm and confirm there is no precipitate prior to use. To prepare the samples for long term storage and subsequent shipping to Texas A&M for processing, we added 100 μL of the thawed Enhancer (10X Genomics, Pleasanton, CA, United States, PN-20000482) to the fixed sample in the Quenching buffer and mixed in with a pipette. Then, the 275 μL of the 50% glycerol solution was added to the sample and gently mixed. These samples were stored in a -80º C freezer until all samples were collected. Samples can be stored this way for up to six months. Buffer Preparation (prepare fresh) Fixation Buffer -Maintain at room temperature   Nuclease Free Water : 791.9 μL 10X Conc. Fix & Prem Buffer (10X Genomics, 20000517): 100μL -Thaw at room temperature. -Vortex, check for precipitation, and centrifuge briefly   37% Formaldehyde : 108.1μL Total  -  -  1000.0μL  Quenching Buffer -Maintain at 4º C   Nuclease Free Water: 875.0μL 8X Conc. Quench Buffer (10X Genomics, 20000516): 125.0μL -Thaw at room temperature. -Vortex and centrifuge briefly.   Total  -  -  1000.0μL  Storage Buffer for fixed samples (prepare fresh): 50% glycerol solution 1. Mix equal volumes of nuclease free water (Invitrogen, Carlsbad, California, United States, 10977-015) and molecular biology grade 99% glycerol (Thermo Fisher, Waltham, MA, United States, J61059-K2).s 2. Filter the 50% glycerol solution through a 0.2 μm filter (Thermo Fisher, Waltham, MA, United States, 723-2520).
2 pools of 4 samples each were made. Libraries were then tested for quality utilizing an Agilent Bioanalyzer High Sensitivity chip (Agilent, 5067-4626) to determine the average size of the library. Library quantification was performed with the NEBNext Library Quant Kit for Illumina kit (New England Biolabs, E7630L).

treatment_protocol: A total of 2.5 months old organoids were exposed to a GW toxicant regimen adapted from established rodent models (O’Callaghan et al., 2015; Locker et al., 2017) and modified from studies on rat and human two-dimensional neuronal cultures (Rao et al., 2017; Yates et al., 2021) in order to prolong the exposure for cerebral organoids. The toxicant regimen consisted of exposing the organoids to 7 days of 2 μM hydrocortisone (Cortisol) (Sigma-Aldrich, St. Louis, MO, United States, H0888), dissolved in 10% ethanol in ddH2O, followed by 4 days of 2 μM Cortisol plus 200 nM diisopropyl fluorophosphate (DFP) (Sigma-Aldrich, St. Louis, MO, United States, D0879), dissolved in isopropanol, followed by 7 days of washout. *Protocol from Yates and Case et al., 2022

value: PBMC

value: iPSC

value: Neural

tag: genotype

value: Mixed

value: Vehicle - 10% ethanol and isopropanol; Toxicant - Cortisol (dissolved in 10% ethanol) and DFP (dissolved in isopropanol)


title: cell-free DNA, Healthy pregnancy DNA076204

description:
Library name: DNA076204
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma

value: Healthy

tag: blood tube_type

value: EDTA

tag: patient id


title: cell-free DNA, Preeclampsia pregnancy DNA076201

description:
Library name: DNA076201
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Preeclampsia

tag: gestational age_(weeks)

tag: sequencing batch


title: cell-free DNA, Healthy pregnancy DNA076209

description:
Library name: DNA076209
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: PAXgene DNA


title: cell-free DNA, Preeclampsia pregnancy DNA076202

description:
Library name: DNA076202
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: L-3

description:
Library name: L-3
L-3

value: cell

value: Cardiomyocyte cell line

value: Treat the cells with low glucose


title: Bai-1

description:
Library name: Bai-1
Bai-1

value: Treat the cells with a combination of high glucose and chrysin