title: MCF7, Paraxanthine_500uM, 6h, rep3, G9

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-G9


title: Delta cells control #1

status: Public on Jan 11 2023

type: SRA

city: Paris

first: Masaya

last: OSHIMA

address: 123 boulevard de Port Royal

country: France

institute: INSERM U1016

library_source: transcriptomic

data_processing:
Sequencing reads were mapped to the mouse genome (Ensembl GRCm38 release 101) using STAR v2.5.2b. Transcripts were quantified using the RSEM software tool.
Normalization and differential gene expression DGE analyses were performed with R package DESeq2 v1.32.0.
Assembly: GRCm38 from Ensembl release 101

molecule: total RNA

organism: Mus musculus

source_name: Pancreas

extract_protocol:
RNA was isolated using the RNeasy Micro kit ( #74004, Qiagen)
For library construction, 5 ng of high quality (RIN >7) total RNA was processed using an Ovation Solo RNA-seq Kit.

tag: tissue

value: Pancreas

tag: strain

tag: cell type

value: Delta cells

tag: treatment

value: Control


title: MCF7, Butylparaben_500uM, 6h, rep3, G7

city: Mason

first: Yuqing

last: Shan

state: Ohio

address: 8700 mason montgomery road

country: USA

institute: Procter & Gamble

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-G7

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R.
The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample.
Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user.
The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Assembly: hWTv2
Supplementary files format and content: txt file

organism: Homo sapiens

source_name: Breast; Mammary gland

extract_protocol:
6h after treatment, 100uL of TempoSeq lysis buffer used to lyse cells per 96-well, which were then frozen and 2ul used for TempO-Seq library building
In TempO-Seq, each Detector Oligo (DO) consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

tag: cell line

value: Breast; Mammary gland

tag: genotype

value: epithelial cell

value: Adenocarcinoma

tag: time

value: 6h exposure of chemical


title: Germinal Center B cell, rep4

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

description:
Follicular_vs_GC.xlsx
TPM_values.xlsx
GCB_4_S8

data_processing:
Kallisto (v.0.46) was used to map sequence reads to Mus musculus transcriptome (GRCm38/ Ensembl release 99). Kallisto TPM values were converted to absolute counts using tximport (v1.12.3) R package and DESeq2 (v.1.24.0) [3] was utilized for differential expression analysis.
Assembly: mm10
Supplementary files format and content: Excel files with TPM expression abundance and differential expression

source_name: B cells

extract_protocol:
RNA was isolated using RNAClean XP Beads (Beckman Coulter, A63987). Near full-length mRNA was reverse transcribed as previously described (Islam et al., 2014) (Trombetta et al., 2014).
Multiplexed libraries were prepared for sequencing using a Nextera XT DNA Library Preparation Kit (Illumina). Libraries were sequenced on an Illumina NextSeq 500 at the Rockefeller University Genomics Core.

treatment_protocol: Cells were sorted directly into a solution of 1% 2-β-mercaptoethanol (Sigma) in TCL Buffer (Qiagen, 1031576).

value: lymph node

value: Germinal Center B cell


title: MCF7, 4-Hydroxybenzoic acid_500uM, 6h, rep3, G6

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-G6


title: Germinal Center B cell, rep3

description:
Follicular_vs_GC.xlsx
TPM_values.xlsx
GCB_3_S7


title: F-LF-KO-4

city: Chicago

first: Jose

last: Cordoba-Chacon

state: IL

address: 835 S Wolcott Ave

department: Medicine

institute: University of Illinois at Chicago

data_processing:
Sequencing Ilumina HiSeq PE150 Platform 6G/sample Q3>95%
Mapping with STAR v 2.6.1
Analysis of gene expression Htseq v0.6.1
Differential expression analysis DESeq2 R package v2_1.26.0
Enrichment analysis clusterProfiler R package v3.8.1
Assembly: Mouse reference genome sequence (GRCm38/mm10)
Supplementary files format and content: These files are the differential expression analysis. The columns are: Gene ID; Values of each mouse; log2FoldChange; p-value; p adjusted; Gene Name; Chromosome; Strand; Start; End; Gene Length; Gene Description; Values of each mouse (reads counts); Values of each  mouse (FPKM)

source_name: Liver

growth_protocol: Adult mice were fed a LF diet (LF, D12450J, Research Diets) or a HF diet (HF, D12492, Research Diets) for 18 weeks. Half of the mice fed the HF diet were either maintained on the same diet or switched to the HFCF diet (HFCF, D16010101, Research Diets).

extract_protocol:
Whole liver RNA was extracted using Trizol reagent.
250-300bp insert cDNA libraries non strand specific.

treatment_protocol: Half of the PPARg floxed mice fed the LF or HF diet after 16 weeks were given AAV8-TBG-Cre to generate  hepatocyte-specific PPARgamma knockout mice. The remaining mice were given AAV8-TBG-null to generate control mice.

value: Liver

tag: gender

value: female

value: Hepatocyte-specfic KO of PPARgamma in hepatocyte after 16 weeks of control diet

tag: diet

value: control diet (34 weeks)

tag: disease state

value: Healthy mouse


title: F-HF-C-2

value: Control mouse

value: High fat diet (34 weeks)

value: Liver steatosis


title: F-HF-C-3


title: F-LF-KO-3


title: Germinal Center B cell, rep2

description:
Follicular_vs_GC.xlsx
TPM_values.xlsx
GCB_2_S6


title: F-LF-KO-2


title: MCF7, Butylparaben_50uM, 6h, rep3, F8

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-F8


title: Germinal Center B cell, rep1

description:
Follicular_vs_GC.xlsx
TPM_values.xlsx
GCB_1_S5


title: F-HF-C-1


title: F-LF-KO-1


title: MCF7, Theobromine_500uM, 6h, rep3, F7

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-F7


title: MCF7, DMSO, 6h, rep3, F9

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-F9

value: vehicle control


title: MCF7, Methylparaben_1uM, 6h, rep3, F4

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-F4


title: Follicular B cell, rep4

description:
Follicular_vs_GC.xlsx
TPM_values.xlsx
FoB_4_S4

value: Follicular B cell


title: F-LF-C-3


title: Follicular B cell, rep2

description:
Follicular_vs_GC.xlsx
TPM_values.xlsx
FoB_2_S2


title: Follicular B cell, rep3

description:
Follicular_vs_GC.xlsx
TPM_values.xlsx
FoB_3_S3


title: MCF7, Ethylparaben_50uM, 6h, rep3, F12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-F12


title: Follicular B cell, rep1

description:
Follicular_vs_GC.xlsx
TPM_values.xlsx
FoB_1_S1


title: MCF7, Propylparaben_500uM, 6h, rep3, E9

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-E9


title: F-LF-C-1


title: F-LF-C-2


title: F-LF-C-4


title: MCF7, Caffeine_500uM, 6h, rep3, E7

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-E7


title: MCF7, DMSO, 6h, rep3, E5

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-E5


title: TOV21g-mAB2-63 [RSA.0000107293]

city: Boston

first: Evanthia

last: Pashos

state: MA

address: 1 Portland St

institute: Pfizer Inc

data_processing:
QuickRNAseq pipeline
STAR alignment (mm10)
FeatureCounts
Assembly: mm10
Supplementary files format and content: Tab delimited, count data

source_name: Gastroc muscle

growth_protocol: TOV21G cells were maintained in a 1:1 mixture of MCDB 105 medium containing a final concentration of 1.5 g/L sodium bicarbonate and Medium 199 containing a final concentration of 2.2 g/L sodium bicarbonate and supplemented with 15% fetal bovine serum and 1% penicillin/streptomycin in incubators at 37 °C and 5% CO2.

extract_protocol:
RNA was extracted and purified with QIAzol lysis reagent and RNeasy kits (Qiagen Inc., Germantown, MD, USA) from snap-frozen muscle tissues. 1ug of total RNA was used for library construction.
RNA was converted into sequencing libraries using an Illumina TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA, USA) with Sciclone G3 NGSx workstation (PerkinElmer, Waltham, MA, USA).

treatment_protocol: immunoglobulin G (IgG) control or an anti-GDF15 monoclonal antibody (mAB2) was initiated when tumor-bearing mice had 5%–7% average body weight loss from the animal’s baseline. The treatment was 10mg/kg, once per week.

value: Gastroc muscle

tag: Sex

value: SCID CB17 ICR-Prkdc


title: MCF7, Paraxanthine_1000uM, 6h, rep3, E2

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-E2

value: Breast; Mammary gland

value: epithelial cell


title: M-N-KO-5

value: male

value: Hepatocyte-specfic KO of PPARgamma in hepatocyte after 16 weeks of high fat diet

value: High fat diet (18 weeks) followed by 16 weeks of high fat, cholestrol, fructose diet

value: Non-alcoholic steatohepatitis


title: TOV21g-mAB2-62 [RSA.0000107292]

value: female


title: M-N-KO-6

value: Liver


title: MCF7, Methylparaben_50uM, 6h, rep3, E12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-E12

value: Adenocarcinoma

value: 6h exposure of chemical


title: TOV21g-mAB2-77 [RSA.0000107294]


title: M-N-KO-4


title: M-N-KO-3


title: TOV21g-mAB2-20 [RSA.0000107290]


title: cell-free DNA from serum ME8

type: genomic

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

hyb_protocol: bisulphite converted DNA was amplified  fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000)  using standard recommended Illumina scanner setting

data_processing: Data were processed using R studio (R v4.0.3)

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Cell-free DNA was extracted and purified from seum samples using QIAmp® MinElute® ccfDNA Mini Kit (Qiagen) according to standard instructions

value: Female

tag: sample type

value: Serum

value: MTLE


title: M-N-KO-2


title: TOV21g-mAB2-16 [RSA.0000107288]


title: MCF7, Theobromine_1000uM, 6h, rep3, D9

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-D9


title: cell-free DNA from serum ME12


title: cell-free DNA from serum ME10


title: M-N-KO-1


title: MCF7, Methylparaben_500uM, 6h, rep3, D8

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-D8


title: TOV21g-mAB2-9 [RSA.0000107287]


title: TOV21g-mAB2-56 [RSA.0000107291]


title: ChIPseq-TCFL5-testis

city: Worcester

first: Tianxiong

last: Yu

address: 364 Plantation St

institute: Umass Med

library_source: genomic

data_processing:
For small RNA-seq data, after removing 3′ adaptor sequence from the reads, we filtered reads whose PHRED score was <5. Those reads that passed the quality check were then mapped to mouse genome (mm10) using piPipes that uses bowtie 2.2.5 allowing one mismatch.  For RNA-seq data, we first removed rRNA reads using bowtie 2.2.5 with default parameters and then the unaligned reads were further mapped to mouse genome (mm10) using STAR. Mapped results were generated as SAM format that was further transformed into duplication removed sorted BAM format using SAMtools 1.8 and Umitools. For ChIP-seq data, raw reads were mapped to mapped to mouse genome (mm10) using Bowtie 2.2.5 with parameter —very-sensitive —no-unal —no-mixed —no-discordant. We then removed duplicate reads using SAMtools. Normalized genome coverage files in bigWig format were generated using homemade script. For CUT&RUN data, Raw reads were mapped to mapped to mouse genome (mm10) using Bowtie 2.2.5 with parameter —very-sensitive —no-unal —no-mixed —no-discordant. We presented the data in bigWig file that was reported as unique mapping reads as read depth per million reads (rpm).
Genome_build: mm10; rheMac8
Supplementary_files_format_and_content: bigWig

organism: Macaca mulatta

source_name: testis

extract_protocol:
In brief, testis frozen tissues were cut into small pieces on dry ice and collected to 1.7 ml tubes containing cold PBS in which samples were cross-linked with 2% (w/v) formaldehyde at room temperature for 30 min using end-over-end tumbler. We then crushed fixed tissues in the presence of ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) by 40 strokes with a Dounce homogenizer pestle “B” (Kimble-Chase, Vineland, USA). To shear the chromatin into 150 to 200 bp, lysed samples were sonicated using Covaris ultrasonicator (Covaris, E220). Sonicated lysate was then diluted 1:10 with ChIP dilution buffer (0.01% SDS, 1.1% Triton X-1001.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl) and we performed immunoprecipitation using 5 µg anti-TCFL5 antibody (Sigma, HPA055223, lot # 000000907). Following the immunoprecipitation of the chromatin, we extracted DNA by phenol:chloroform:isoamyl alcohol (25:24:1) (pH 8).
Library construction for anti-TCFL5 DNA was performed after DNA extraction as previously described (Zhang, Z., Theurkauf, W.E., Weng, Z., and Zamore, P.D. (2012). Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence 3, 9.).

tag: antibody

value: rabbit anti TCFL5 antibody; Sigma, HPA055223

value: Macaca Mulatta

tag: Stage

value: adult


title: M-N-C-6

value: Control mouse


title: cell-free DNA from serum ME9


title: TOV21g-IgG-84 [RSA.0000107286]

value: Gastroc muscle

value: SCID CB17 ICR-Prkdc


title: cell-free DNA from serum ME11


title: MCF7, Theophylline_500uM, 6h, rep3, D6

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-D6

value: Breast; Mammary gland

value: epithelial cell


title: daf-18(ok480) male3

city: Kaifeng

first: Shanqing

last: Zheng

address: 1 Jinming Avenue North, Longting District,  School of Basic Medical Sciences, Henan University

country: China

institute: Henan university

description:
Caenorhabditis elegans,20℃,young adult,rep3
Herm-Male-fpkm.txt

data_processing:
Illumina Casava1.7 software used for base-calling
Sequenced reads were trimmed for adaptor sequence. and masked for low-complexity or low-quality sequence. then mapped to WBcel235 whole genome using bowtie v0.12.2 with parameters
The transcript abundances for each sample was estimated with StringTie（1.3.3）
the FPKM value for gene and transcript level was calculated through a protocol from Chepelev et al., Nucleic Acids Research,2009.
Assembly: C. elegans genome version WBcel235 was used as the reference.
Supplementary files format and content: The txt format file contains the FPKM value of  expression gene

organism: Caenorhabditis elegans

source_name: daf-18 loss worms

growth_protocol: Harvest worms and collect eggs simultaneously. The eggs were cultured in M9 and incubated at 20℃ until L1. Feeding to young adult in NGM plates, a large number of hermaphroditic and male worms were isolated for RNA preparation.

extract_protocol: RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1ug of total RNA for the construction

treatment_protocol: After the synchronization of contorl and daf-18(ok480) mutants, worms were cultured to young adult  , and a large number of hermaphroditics and males were separated.

value: whole body

tag: developmental stage

value: young adult

value: male


title: ChIPseq-Input-testis

extract_protocol:
In brief, testis frozen tissues were cut into small pieces on dry ice and collected to 1.7 ml tubes containing cold PBS in which samples were cross-linked with 2% (w/v) formaldehyde at room temperature for 30 min using end-over-end tumbler. We then crushed fixed tissues in the presence of ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) by 40 strokes with a Dounce homogenizer pestle “B” (Kimble-Chase, Vineland, USA). To shear the chromatin into 150 to 200 bp, lysed samples were sonicated using Covaris ultrasonicator (Covaris, E220). Sonicated lysate was then diluted 1:10 with ChIP dilution buffer (0.01% SDS, 1.1% Triton X-1001.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl) and we performed immunoprecipitation using 5 µg anti-TCFL5 antibody (Sigma, HPA055223, lot # 000000907). Following the immunoprecipitation of the chromatin, we extracted DNA by phenol:chloroform:isoamyl alcohol (25:24:1) (pH 8).
Library construction for input DNA was performed after DNA extraction as previously described (Zhang, Z., Theurkauf, W.E., Weng, Z., and Zamore, P.D. (2012). Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence 3, 9.).

value: Input


title: daf-18(ok480) male2

description:
Caenorhabditis elegans,20℃,young adult,rep2
Herm-Male-fpkm.txt


title: M-N-C-5

value: Liver

value: High fat diet (18 weeks) followed by 16 weeks of high fat, cholestrol, fructose diet

value: Non-alcoholic steatohepatitis


title: MCF7, Ethylparaben_1uM, 6h, rep3, D3

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-D3

value: Adenocarcinoma

value: 6h exposure of chemical


title: M-N-C-4


title: TOV21g-IgG-75 [RSA.0000107285]

value: female


title: cell-free DNA from serum ME2

value: Male

value: Serum

value: MTLE


title: TOV21g-IgG-65 [RSA.0000107284]

value: Gastroc muscle


title: cell-free DNA from serum ME6

value: Female


title: daf-18(ok480) male1

description:
Caenorhabditis elegans,20℃,young adult,rep1
Male-fpkm.txt


title: cell-free DNA from serum ME5


title: M-N-C-3

value: Control mouse


title: cell-free DNA from serum ME7


title: TOV21g-IgG-64 [RSA.0000107283]

value: SCID CB17 ICR-Prkdc


title: cell-free DNA from serum ME1


title: cell-free DNA from serum C11

value: Healthy control


title: cell-free DNA from serum ME3


title: MCF7, DMSO, 6h, rep3, D10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-D10

value: Breast; Mammary gland

value: epithelial cell

value: vehicle control


title: TOV21g-IgG-10 [RSA.0000107282]


title: control  male2

source_name: control

value: whole body

value: young adult

value: male


title: TOV21g-IgG-8 [RSA.0000107281]


title: MCF7, Paraxanthine_50uM, 6h, rep3, D4

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-D4

value: Adenocarcinoma


title: MCF7, Theophylline_50uM, 6h, rep3, E10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-E10

value: 6h exposure of chemical


title: cell-free DNA from serum C9


title: cell-free DNA from serum ME4


title: cell-free DNA from serum C6


title: cell-free DNA from serum C10


title: MCF7, DMSO, 6h, rep3, D2

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-D2


title: M-N-C-2

value: Liver

value: High fat diet (18 weeks) followed by 16 weeks of high fat, cholestrol, fructose diet

value: Non-alcoholic steatohepatitis


title: M-HF-KO-6

value: Hepatocyte-specfic KO of PPARgamma in hepatocyte after 16 weeks of high fat diet

value: High fat diet (34 weeks)

value: Liver steatosis


title: M-N-C-1

value: Control mouse


title: MCF7, DMSO, 6h, rep3, C7

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-C7


title: cell-free DNA from serum C7

value: Female

value: Serum


title: cell-free DNA from serum C8

value: Healthy control


title: MCF7, Theophylline_1000uM, 6h, rep3, C5

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-C5

value: Breast; Mammary gland

value: epithelial cell


title: M-HF-KO-5


title: control  male1

value: whole body


title: NTB-87 [RSA.0000107279]

value: Gastroc muscle

value: female

value: SCID CB17 ICR-Prkdc

value: Non-tumor bearing


title: daf-18(ok480) hermaphrodite2

value: young adult

value: hermaphrodite


title: MCF7, Theobromine_50uM, 6h, rep3, C4

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-C4

value: Adenocarcinoma

value: 6h exposure of chemical


title: M-HF-KO-4

value: Liver

value: male

value: Hepatocyte-specfic KO of PPARgamma in hepatocyte after 16 weeks of high fat diet

value: High fat diet (34 weeks)


title: MCF7, DMSO, 6h, rep3, B6

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-B6

value: vehicle control


title: NTB-82 [RSA.0000107278]


title: cell-free DNA from serum C4

value: Female

value: Serum

value: Healthy control


title: NTB-88 [RSA.0000107280]


title: M-HF-KO-3

value: Liver steatosis


title: NTB-78 [RSA.0000107277]

value: Gastroc muscle


title: daf-18(ok480) hermaphrodite3

value: whole body


title: MCF7, 4-Hydroxybenzoic acid_50uM, 6h, rep3, A9

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-A9

value: Breast; Mammary gland

value: epithelial cell


title: cell-free DNA from serum C3

value: Male


title: control hermaphrodite3

value: young adult

value: hermaphrodite


title: control  male3


title: cell-free DNA from serum C5


title: MCF7, Propylparaben_50uM, 6h, rep3, A8

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-A8

value: Adenocarcinoma

value: 6h exposure of chemical


title: daf-18(ok480) hermaphrodite1

description:
Caenorhabditis elegans,20℃,young adult,rep1
Herm-fpkm.txt


title: M-HF-KO-2

value: Liver

value: male


title: NTB-59 [RSA.0000107276]

value: female

value: SCID CB17 ICR-Prkdc

value: Non-tumor bearing


title: control hermaphrodite2


title: MCF7, Caffeine_50uM, 6h, rep3, A6

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-A6


title: NTB-58 [RSA.0000107275]


title: control hermaphrodite1


title: M-HF-C-6

value: Control mouse

value: High fat diet (34 weeks)


title: MCF7, Caffeine_1000uM, 6h, rep3, A2

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-A2


title: M-HF-KO-1

value: Hepatocyte-specfic KO of PPARgamma in hepatocyte after 16 weeks of high fat diet

value: Liver steatosis


title: cell-free DNA from serum C1

value: Female

value: Serum

value: Healthy control


title: MCF7, DMSO, 6h, rep3, A11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-A11

value: Breast; Mammary gland

value: epithelial cell

value: vehicle control


title: TOV21g-mAB2-49 [RSA.0000107313]

value: Gastroc muscle


title: M-HF-C-5


title: MCF7, Butylparaben_1uM, 6h, rep3, A10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW913A-A10

value: Adenocarcinoma

value: 6h exposure of chemical


title: TOV21g-mAB2-46 [RSA.0000107312]


title: MCF7, DMSO, 6h, rep2, H8

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-H8


title: M-HF-C-4

value: Liver

value: male


title: M-HF-C-3


title: TOV21g-mAB2-21 [RSA.0000107311]

value: female

value: SCID CB17 ICR-Prkdc


title: MCF7, Propylparaben_50uM, 6h, rep2, H6

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-H6


title: M-HF-C-2

value: Control mouse


title: M-HF-C-1

value: High fat diet (34 weeks)


title: MCF7, Caffeine_50uM, 6h, rep2, H4

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-H4


title: TOV21g-mAB2-55 [RSA.0000107314]


title: TOV21g-IgG-52 [RSA.0000107310]


title: MCF7, Ethylparaben_1uM, 6h, rep2, H12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-H12


title: TOV21g-IgG-47 [RSA.0000107309]


title: TOV21g-IgG-31 [RSA.0000107308]


title: MCF7, Butylparaben_1uM, 6h, rep2, H1

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-H1


title: cell-free DNA from serum C2


title: COVID_2_SPLEEN

city: Athens

first: Spyros

last: Foutadakis

address: Soranou

country: Greece

institute: Biomedical Research Foundation Academy of Athens

data_processing:
The quality of sequencing reads was evaluated using FastQC (Galaxy Version 0.73+galaxy0)
Reads were aligned to the mouse genome using HISAT2 (Galaxy Version 2.2.1+galaxy0)
Sequencing counts for each gene were calculated using htseq-count (Galaxy version 0.9.1)
Differential expression between conditions was calculated using DEseq2 (Galaxy Version 2.11.40.7+galaxy1)
Assembly: mm9
Supplementary files format and content: 2 Excel file containing DESeq results for spleen and lung tissues separately, and 2 excel files containing normalised counts

source_name: Spleen of animals challenged with plasma from COVID-19

growth_protocol: Mice were intravenously injected with 100μl of plasma from adults with COVID-19 pneumonia and severe respiratory failure once daily for three serial days. Mice were sacrificed 24 hours after the last injection

extract_protocol:
Tissue segments were aseptically removed following animal sacrifice.
RNA-seq libraries were prepared with the NebNext Ultra II directional RNA library prep kit for Illumina.

treatment_protocol: Control mice were intravenously injected with 100μl of plasma from healthy adults once daily for three serial days. Mice were sacrificed 24 hours after the last injection

value: Spleen

value: challenged with plasma from COVID-19


title: COVID_3_SPLEEN


title: MCF7, Theophylline_1000uM, 6h, rep2, G4

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-G4


title: TOV21g-IgG-28 [RSA.0000107307]


title: TOV21g-IgG-26 [RSA.0000107306]


title: COVID_3_LUNG

source_name: Lung of animals challenged with plasma from COVID-19

value: Lung


title: TOV21g-IgG-25 [RSA.0000107305]


title: HEALTHY_1_LUNG

source_name: Lung of animals challenged with plasma from healthy individuals


title: MCF7, Theophylline_50uM, 6h, rep2, G2

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-G2


title: HEALTHY_3_SPLEEN

source_name: Spleen of animals challenged with plasma from healthy individuals


title: MCF7, 4-Hydroxybenzoic acid_500uM, 6h, rep2, G1

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-G1


title: HEALTHY_3_LUNG

value: challenged with plasma from healthy individuals


title: M2 BMDMs replicate 3

type: RNA

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Gene-level signal were derived from CEL files using sst-RMA algorithm implemente in Affymetrix Expression Console software

label: biotin

source_name: M2 BMDMs_

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Affymetrix).

extract_protocol: RNA was extracted with miRNeasy FFPE kit (Qiagen) in accordance with the manufacture's protocol.

value: M2 BMDMs


title: TOV21g-IgG-19 [RSA.0000107304]


title: MCF7, DMSO, 6h, rep2, F9

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-F9

value: Breast; Mammary gland


title: BMDMs treated with Calu-1 conditioned medium replicate 2

source_name: Calu1-CM BMDMs_


title: M2 BMDMs replicate 2


title: M1 BMDMs replicate 2

source_name: M1 BMDMs_

value: M1 BMDMs


title: M2 BMDMs replicate 1


title: M1 BMDMs replicate 1


title: BMDMs treated with Calu-1 conditioned medium replicate 4


title: BMDMs treated with Calu-1 conditioned medium replicate 3


title: M1 BMDMs replicate 3


title: MCF7, Methylparaben_50uM, 6h, rep2, G3

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-G3

value: epithelial cell


title: HEALTHY_2_SPLEEN


title: NTB-57 [RSA.0000107302]

value: Gastroc muscle

value: Non-tumor bearing


title: BMDMs treated with Calu-1 conditioned medium replicate 1


title: BMDMs treated with NCI-H1299 conditioned medium replicate 3

source_name: H1299-CM BMDMs_


title: BMDMs treated with NCI-H1299 conditioned medium replicate 4


title: NTB-50 [RSA.0000107301]


title: HEALTHY_1_SPLEEN


title: MCF7, Propylparaben_500uM, 6h, rep2, F7

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-F7

value: Adenocarcinoma

value: 6h exposure of chemical


title: MCF7, Theophylline_500uM, 6h, rep2, F5

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-F5


title: HEALTHY_2_LUNG


title: MCF7, Methylparaben_1uM, 6h, rep2, F2

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-F2


title: TOV21g-IgG-18 [RSA.0000107303]


title: COVID_2_LUNG


title: NTB-40 [RSA.0000107298]


title: NTB-44 [RSA.0000107300]


title: COVID_1_LUNG


title: MCF7, Theobromine_50uM, 6h, rep2, E6

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-E6


title: NTB-38 [RSA.0000107297]


title: MCF7, DMSO, 6h, rep2, E5

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-E5

value: vehicle control


title: NTB-37 [RSA.0000107296]

value: female


title: BMDMs treated with A549 conditioned medium replicate 3

source_name: A549-CM BMDMs_


title: BMDMs treated with NCI-H1299 conditioned medium replicate 1


title: BMDMs treated with A549 conditioned medium replicate 4


title: MCF7, Caffeine_1000uM, 6h, rep2, E9

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-E9


title: MCF7, 4-Hydroxybenzoic acid_50uM, 6h, rep2, E3

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-E3


title: NTB-42 [RSA.0000107299]

value: SCID CB17 ICR-Prkdc


title: MCF7, Propylparaben_1uM, 6h, rep2, E2

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-E2


title: RT input for BAT H3K27Ac ChIPseq, rep 3

city: Grand Rapids

first: Ning

last: Wu

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

data_processing:
Reads were trimmed using TrimGalore v0.6.0 (https://github.com/FelixKrueger/TrimGalore) with default settings.
Trimmed reads were aligned to the GRCm38.p6 reference genome from GENCODE vM24 using bwa mem v0.7.17 (Li, 2013). In the case of the C/EBPA and wildtype cold/RT H3K27ac datasets, the reference was concatenated with decoy sequences (Zhang et al., 2021).
Duplicates were marked using SAMBLASTER v 0.1.24 (Faust and Hall, 2014). Alignments were filtered using SAMtools view v1.9 (Li et al., 2009) with the parameters ‘-q 30 -F 2828’ and ‘-f 2’ for paired-end reads.
Peaks were called using macs2 v2.2.7.1 (Zhang et al., 2008) with the parameters ‘-g mm -q 0.05’ and ‘-f BAMPE’ for paired-end reads, using the corresponding input sample as the control.
Bigwig files were generated using deepTools bamCoverage v3.4.3 (Ramirez et al., 2016) with the parameters ‘--binSize 10 --normalizeUsing “CPM” --samFlagExclude 1024’, specifying the ENCODE v2 blacklist using ‘--blackListFileName’; for paired-end reads, the parameters ‘--samFlagInclude 64 --extendReads’ were added.
Assembly: GRCm38.p6
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

source_name: BAT

extract_protocol:
BAT was fixed with 0.8% formaldehyde for 12min (H3K27Ac ChIP) or with 2mM DSG for 25min followed by 0.8% formaldehyde for 12min (other ChIPs). Sonication was done with Diagenode Bioruptor UCD-200, 5" on and 5" off for 3x3min.
Libraries for Input and IP samples were prepared by the Van Andel Genomics Core form 10 ng of input material and all available IP material using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems, Wilmington, MA USA). Prior to PCR amplification, end repaired and A-tailed DNA fragments were ligated to uniquely barcoded dual indexes (IDT, Coralville, IA USA).

value: BAT

tag: chip antibody

value: WT

value: RT


title: BAT H3K27Ac ChIP at RT, rep 3

value: Cell Signaling Tech 8173


title: MCF7, Paraxanthine_1000uM, 6h, rep2, E10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-E10

source_name: Breast; Mammary gland


title: NTB-24 [RSA.0000107295]


title: BMDMs treated with NCI-H1299 conditioned medium replicate 2


title: A6_Air WT 3

city: Clayton

first: Jan

last: Schroeder

state: VIC

address: Building 75 Innovation Walk

department: Anatomy & Developmental Biology

country: Australia

institute: Monash University

data_processing:
NOTE: The experiment was multiplexed with other data, and split the two experiments, then selected the cell bar codes from to filter the aligned bam file, and revert that into FASTQ
Cellranger (v1.3.1) to map reads against mouse/human compbined reference (m/h38)
Split library by mouse/human cells for demultiplexing
Filter low quality cells
Genome_build: mm10
Supplementary_files_format_and_content: counts matrix (csv) and metadata table (csv)

extract_protocol:
Lungs from 5 day-old pups were isolated and immediately cryopreserved in 10% DMSO and 90% FCS at -80°C. Samples were thawed and stained by flow cytometry to sort for endothelial, epithelial and immune cells.
8 single cell RNA libraries were constructed using a Chromium controller (10X Genomics Chromium Sinlge Cell 3' V3.1 chemistry).
A total of 12 cDNA amplification cycles and 15 cycles of library amplification were used. Sequencing was carried out using an Illumina Novaseq 6000 SP Reagent Kit v1.5 (100 cycles)

treatment_protocol: Neonatal mice were exposed to antenatal LPS at day 14 of gestation and then immediately after birth were exposed to 65% O2 (hyperoxia/BPD) or 21% O2 (air/healthy).

value: lung

tag: condition

value: Air

value: Healthy


title: A4_Hyp WT 5

tag: tissue

value: Hyperoxia

value: BPD


title: COVID_1_SPLEEN

value: Spleen

value: challenged with plasma from COVID-19


title: A5_Hyp WT 3

tag: strain


title: MCF7, Ethylparaben_50uM, 6h, rep2, D8

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-D8

value: Breast; Mammary gland

tag: cell type

value: epithelial cell


title: A8_Air WT 4


title: A3_Air WT 1


title: RT input for BAT H3K27Ac ChIPseq, rep 2

tag: treatment


title: BAT H3K27Ac ChIP at RT, rep 2


title: MCF7, DMSO, 6h, rep2, D2

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-D2

tag: cell line

value: Adenocarcinoma


title: BMDMs treated with A549 conditioned medium replicate 1


title: MCF7, Methylparaben_500uM, 6h, rep2, D12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-D12

tag: genotype

value: 6h exposure of chemical


title: MCF7, DMSO, 6h, rep2, D10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-D10

tag: time

value: vehicle control


title: RT input for BAT H3K27Ac ChIPseq, rep 1


title: A1_Air WT 2


title: BAT H3K27Ac ChIP at RT, rep 1


title: MCF7, DMSO, 6h, rep2, C7

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-C7


title: cold input for BAT H3K27Ac ChIPseq, rep 3

value: 4h cold stress


title: A2_Hyp WT 2


title: BAT H3K27Ac ChIP after 4h cold stress, rep 3

value: BAT


title: cold input for BAT H3K27Ac ChIPseq, rep 2

value: WT


title: MCF7, Ethylparaben_500uM, 6h, rep2, C11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-C11


title: MCF7, Paraxanthine_500uM, 6h, rep2, C8

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-C8


title: x22

city: Xinxiang

first: Deming

last: Li

state: Henan

address: 46# East of Construction Road

department: College of Life Science

institute: Henan Normal University

data_processing:
Basecalls performed using CASAVA version 1.8
Raw sequencing data were first demultiplexed by bcl2fastq and then trimmed by fastp 0.19.4
The qualified reads were mapped onto the reference genome (UCSC mm9) using the bisulfite sequence aligner Bismark 0.22.1
The methylKit package (version 1.8.1) was used to identify Differential Methylation Sites (DMS) in R (version 3.5.2). CpG with a minimum coverage ≥ 10 in all samples were considered.
The edmr package was used to identify Differential Methylation Regions (DMR) .Enrichment analysis was conducted based on Perl module using fisher test. Figures were plotted based on ggplot2 3.3.2.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: tab-delimited text files include pvalue,qvalue and meth.diff

source_name: liver tissue

growth_protocol: Feeding conditions is temperature (23±2˚C), humidity (35 ± 5%) with 12 hours day/night cycle and mice are freely to get food and drinking water.

extract_protocol:
DNA was extracted with ONE-4-ALL Genomic DNA Mini-Preps Kit.
DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 10-12 weeks male mice (n=9) were intraperitoneally injected CCl4 twice a week at 10 ul/g (CCl4/olive oil, 1:4) for 4 weeks to induced hepatic fibrosis.

value: treated with CCl4 for 4 weeks

tag: age

value: 10-12 weeks


title: x23


title: x21


title: c23

value: untreated


title: MCF7, DMSO, 6h, rep2, B6

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-B6


title: cold input for BAT H3K27Ac ChIPseq, rep 1


title: MCF7, Theobromine_500uM, 6h, rep2, B4

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-B4


title: BMDMs treated with PC-9 conditioned medium replicate 3

source_name: PC9-CM BMDMs_


title: c21


title: BMDMs treated with A549 conditioned medium replicate 2


title: c22


title: BMDMs treated with NCI-H460 conditioned medium replicate 4

source_name: H460-CM BMDMs_


title: BMDMs treated with NCI-H460 conditioned medium replicate 1


title: BMDMs treated with PC-9 conditioned medium replicate 1


title: BMDMs treated with NCI-H460 conditioned medium replicate 3


title: BMDMs treated with PC-9 conditioned medium replicate 2


title: BAT H3K27Ac ChIP after 4h cold stress, rep 2

value: Cell Signaling Tech 8173


title: MCF7, Paraxanthine_50uM, 6h, rep2, B3

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-B3


title: RT input for BAT ERR1 ChIPseq

value: RT


title: Control BMDMs (M0) replicate 3

source_name: M0 BMDMs_

value: Control BMDMs (M0)


title: Control BMDMs (M0) replicate 1


title: BAT H3K27Ac ChIP after 4h cold stress, rep 1


title: BAT ERR1 ChIPseq at RT

value: Abcam Ab76228


title: MCF7, Caffeine_500uM, 6h, rep2, A8

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-A8


title: BAT ERR1 ChIPseq after 4h cold stress


title: Biological replicate of X44 X48 (miRNA-seq)

city: Winston Salem

first: Ming

last: Leung

state: NC

address: 1 Medical Center Blvd

department: Comprehensive Cancer Center

institute: Atrium Health Wake Forest

description: Biological replicate of X44

data_processing:
For each RNA-seq sample,
The sequences were trimmed using bbduk from bbtools v 36.49
The trimmed sequences were mapped using Hisat2 v 2.1.0
Read counts were extracted using HTSeq v 0.11.2
The miRNA-seq samples were analyzed using Qiagen GeneGlobe Data Analysis center

source_name: Bone healing callus

extract_protocol:
Total RNA was extreacted from frozen tissues using high salt TRIzol protocol.
For RNA-seq, cDNA libraries were prepared using the Illumina® Stranded mRNA Prep and Ligation kit (Illumina) as per manufacturer’s instructions. Briefly, poly(A) RNA was purified from 200 ng total RNA using oligo (dT) beads. The purified fraction was then subjected to fragmentation, reverse transcription, end repair, 3 adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique dual index sequences (IDT® for Illumina® RNA UD Indexes Set A, Ligation, Illumina) were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). The libraries were pooled, diluted to 3 nM using 10 mM Tris-HCl, pH 8.5, and denatured using the Illumina protocol. For miR-seq, libraries were prepared from 250 ng total RNA using the QIAseq miRNA Library Kit (QIAGEN) as per the manufacturer's instructions. This system offers a built-in Unique Molecular Identifier (UMI) application that eliminates possible PCR duplicates in sequencing datasets and, therefore, facilitates unbiased gene expression profiling. Unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. Size distribution and concentration of the final product were assessed using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled libraries were diluted to 2 nM in EB buffer (Qiagen), denatured using the Illumina protocol, and diluted to 10 pM using pre-chilled hybridization buffer.

value: Bone healing callus

value: Day 14


title: MCF7, Butylparaben_500uM, 6h, rep2, A4

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-A4

value: Breast; Mammary gland


title: Biological replicate of X44 X46 (miRNA-seq)

description: Biological replicate of X44


title: MCF7, DMSO, 6h, rep2, A11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-A11

value: epithelial cell


title: MCF7, Theobromine_1000uM, 6h, rep2, C3

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-C3

value: Adenocarcinoma


title: SampleL132

city: los angeles

first: Shubhamoy

last: Ghosh

state: CA

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

library_source: other

data_processing:
Demultiplexed sequence data were imported to QIIME2 and quality filtering was performed using DADA2to ensure adequate sequence quality
A feature table along with a representative sequence table containing amplicon sequence variants (ASV) were generated and a rooted phylogenetic tree was constructed based on sequence similarity to infer the evolutionary relationship between microorganisms.
The outputs from QIIME2 (feature table, taxonomic classifications, phylogenetic tree) along with the corresponding metadata, were imported to R (version 4.2.1) and assembled into a phyloseq object using the phyloseq package (version 1.40.0)
all data visualization steps were performed using ggplot2 package in R

molecule: other

organism: Rattus norvegicus

source_name: Sprague Dawley

growth_protocol: Pregnant Sprague-Dawley rats (Charles River Laboratories, Hollister, CA) were housed in individual cages at 21-23C within 12h light/dark cycles.

extract_protocol:
fecal samples from within the intestines of Day2, Day21 and adult offspring (Day180) were collected and bacterial genomic DNA was extracted for 16S rDNA microbiota profiling
The V4 region of the 16S rRNA gene was amplified with individually barcoded universal primers. PCR amplified products were purified and pooled in equimolar concentrations and sequenced using the Illumina MiSeq platform and 2 X 250bp reagent kit for paired-end sequencing.

treatment_protocol: At gestational day 11  dams were randomized to either continue regular chow (CON group) or on a Western diet ad libitum (HFhf group)along with 25% fructose in their drinking water.The pregnant dams in the IUGR group were 50% calorie restricted beginning from gestation day (G) 10 in their access to regular chow diet until the birth of their pups.after birth, the maternal diet was switched to either regular chow accessed ad libitum forming the IUGR-RC (regular chow) group, or a HFhf diet creating the   IUGR-HFhf group

value: M

tag: age (day)

tag: collection time

value: PM

value: Sprague Dawley

tag: specimen

value: feces

tag: group

value: IUGR-RC

tag: molecule

value: 16S rDNA


title: SampleL130

tag: Sex


title: SampleL128


title: SampleL129


title: SampleL131


title: Day 14 callus  X44 (miRNA-seq)

description: Day 14 callus


title: MCF7, 4-Hydroxybenzoic acid_1uM, 6h, rep2, B10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-B10

value: 6h exposure of chemical


title: Exp8_Pax5

city: Malmö

first: Charlotte

last: Ling

address: Jan Waldenstroms gata 35

country: Sweden

institute: Lund Univesity

hyb_protocol: 2.3µg of cDNA target was hybridized to Clariom™ S Rat Arrays for 16h at 45°C under rotation in Affymetrix Gene Chip Hybridization Oven 645

scan_protocol: The fluorescent intensities were determined with Affymetrix GeneChip Scanner 3000 7G

data_processing: Processing of raw data was performed in Transcriptome Analysis Console (TAC, v4.0) using quantile normalization and gene-level SST-RMA summarization.

label: Biotin

source_name: 832/13 INS1 beta-cells transduced with Pax5 lentiviral vector

label_protocol: Labeling was done with the GeneChip® WT Plus Reagent Kit (Affymetrix) according to the manufacturers description

growth_protocol: RPMI-1640 with 11.1mM glucose, supplemented with 10% fetal calf serum, 10mM HEPES, 2mM L-glutamine, 1mM sodium pyruvate and 50uM beta-mercaptoethanol

extract_protocol: Qiagen miRNeasy extraction kit, according to the insturctions in the kit

treatment_protocol: Transduced with lentiviral vectors (MOI 1.25 in complete culture media) confering expression of GFP or Pax5 for 24h. The transduction media was then replaced with fresh complete media and culture was continued for an additional 48h

tag: overexpression


title: Biological replicate of X7 X67 (RNA-seq)

description: Biological replicate of X7

value: Day 21


title: MCF7, Ethylparaben_50uM, 6h, rep1, H7

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-H7


title: Biological replicate of X7 X66 (RNA-seq)

description: Biological replicate of X7


title: SampleL125


title: MCF7, Propylparaben_500uM, 6h, rep1, H4

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-H4


title: Day 21 callus  X7 (RNA-seq)

description: Day 21 callus


title: SampleL124

value: AM


title: MCF7, DMSO, 6h, rep1, H8

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-H8

value: vehicle control


title: MCF7, Paraxanthine_500uM, 6h, rep1, H3

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-H3


title: Exp8_GFP

source_name: 832/13 INS1 beta-cells transduced with GFP lentiviral vector

value: GFP


title: SampleL123


title: Biological replicate of X44 X48 (RNA-seq)

description: Biological replicate of X44


title: SampleL127


title: SampleL126


title: Exp6_GFP


title: Control BMDMs (M0) replicate 4

value: Control BMDMs (M0)


title: Exp5_GFP


title: BMDMs treated with NCI-H460 conditioned medium replicate 2


title: Control BMDMs (M0) replicate 2


title: Exp5_Pax5


title: MCF7, Theophylline_1000uM, 6h, rep1, H2

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-H2


title: SampleL122


title: Exp4_Pax5


title: Exp4_GFP


title: Biological replicate of X44 X46 (RNA-seq)

description: Biological replicate of X44

value: Bone healing callus


title: Exp7_GFP


title: Exp7_Pax5


title: Exp3_Pax5


title: Exp6_Pax5


title: Exp3_GFP


title: Day 14 callus  X44 (RNA-seq)

description: Day 14 callus

value: Day 14


title: MCF7, Caffeine_500uM, 6h, rep1, G4

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-G4

value: Breast; Mammary gland


title: SampleL120


title: MCF7, Ethylparaben_500uM, 6h, rep1, G8

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-G8

value: epithelial cell


title: SampleL119


title: MCF7, Propylparaben_1uM, 6h, rep1, G12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-G12

value: Adenocarcinoma


title: Exp2_Pax5


title: GV Oocytes, WT_Flox+_Cre-, rep5

first: Patrick

middle: S

last: Western

address: 27-31 Wright Street

department: Centre for Reproductive Health

institute: Hudson Institute of Medical Research

description:
Reference_gene_raw_count.txt
581

data_processing:
For oocyte dataset, adaptor and low quality sequences of raw sequencing reads were trimmed using AdaptorRemovel (v2.2.1) with following parameters: --trimns --trimqualities --minquality 20 --minlength 35. For bone growth plate and placenta datasets, adaptor and low quality sequences of raw reads were trimmed using trimmomatic (v0.39) with following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20.
Clean reads were mapped to mouse reference genome (GRCm38) using either STAR (v2.5.3a) for oocyte dataset with default settings, or STAR (v2.7.5c) for bone growth plate and placenta datasets with following settings: --outFilterMismatchNoverLmax 0.03 --alignIntronMax 10000.
For oocyte dataset, raw counts for mouse reference genes (ensembl-release-93) were calculated using featureCounts (v1.5.2) based on mapped bam files with following parameters: -Q 10 -s 2. For bone growth plate and placenta datasets, raw counts for mouse reference genes (ensembl-release-101) were calculated using STAR (v2.7.5c) with parameter "--quantMode GeneCounts" whening doing genome alignment.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text file including raw reads counts for mouse reference genes in all samples

source_name: GV Oocytes, WT Flox+ Cre-

growth_protocol: For oocyte sample collection, wild type and Eed deleted oocytes grown in vivo in C57bl6 mice. Eedfl/fl mice were crossed with ZP3Cre transgenic mice, facilitating oocyte specific deletion from the primary follicle oocyte stage. For production of placental and bone growth plate samples, females producing wild type (Eedfl/fl), heterozygous (Eedwt/del) of homozygous (Eeddel/del) oocytes were mated to isogenic wild type C57bl6 males to produce wild type or heterozygous offspring from oocytes that developed with wild type, heterozygous or homozygous null EED function. These offspring were produced from females producing Eed-wt, Eed-het or Eed-hom oocytes to generate wild type or heterozygous offspring as previously described by Prokopuk, L. et al. Clinical Epigenetics 10, 95 (2018). Heterozygous offspring generated from Eed heterozygous oocytes (HET-het offspring) or from Eed homozygous null oocytes (HET-hom offspring) are isogenic. However, the HET-hom offspring were generated from oocytes that completely lacked functional EED. In contrast, the HET-het offspring were generated from oocytes that had one functional copy of EED. As they are isogenic and heterozygous, comparison of HET-hom with HET-het offspring allowed the identification of differences that resulted from a loss of EED-dependent oocyte programming in the absence of confounding genetic differences. In addition, wild type offspring generated from Eed-het and Eed-wt oocytes allowing the comparison of WT-wt and WT-het offspring with HET-het and HET-hom offspring. This provided controls for differences generated as a result of Eed heterozygosity in offspring. The mouse lines used were obtained from the following sources: Zp3Cre mice (C57BL/6-Tg 93knw/J; Jackson Labs line 003651, constructed and shared by Prof Barabara Knowles), Eed floxed mice (Eedfl/fl) (B6; 129S1-Eedtm1Sho/J; Jackson Labs line 0022727; constructed and shared by Xie, H. et al. Cell Stem Cell 14, 68-80 (2014). The Eed line was backcrossed to a pure C57BL6/J and shared with us by Associate Professor Rhys Allen and Professor Marnie Blewitt, Walter and Eliza Hall Institute for Medical Research, Melbourne. All subsequent breeding and oocyte collection was performed by the authors at the Hudson Institute of Medical Research / Monash Medical Centre, Clayton, Victoria, Australia. Mice were housed at Monash Medical Centre Animal Facility using a 12-hour light-dark cycle as previously reported by Prokopuk, L. et al. Clinical Epigenetics 10, 95 (2018). Food and water were available ad libitum with room temperature maintained at 21-23°C with controlled humidity. All animal work was undertaken in accordance with Monash University Animal Ethics Committee (AEC) approvals.

extract_protocol:
Oocytes: Cumulus-Oocyte Complexes (COCs) were collected from eight-twelve week old female mice and transferred to M2 media. Oocytes were denuded mechanically with a narrow-bore glass pipette and incubated with M2 media containing 5 μg/mL Hoechst 33342 for 10 minutes at 37°C. GV oocytes were then scored as either surrounded nucleolus (SN), or non-surrounded nucleolus (NSN) based on Hoechst staining. SN oocytes were then collected, frozen on dry ice and stored at -80°C until RNA extraction. Ten to fifteen oocytes isolated from each female were pooled and total RNA isolated using the Agencourt RNAdvance Cell V2 extraction kit. High quality RNA (RIN >7.5) was used for library preparation (>1.2ng total RNA) using the Nugen Trio Library protocol, MU01440V2; 2017. 75bp single end sequencing was carried out on 4-6 libraries / genotype using Illumina NextSeq500 High output mode and v2.5 chemistry (Illumina Protocol 15046563 v02, Mar 2016) to collect >25M reads per sample. Bone growth plate tissue was isolated at E17.5 and snap frozen as described in the associated manuscript (Jarred et al. In prep). Femoral growth plates were isolated from E17.5 offspring and growth plates were extracted from the distal end on both the left and right femurs, washed in PBS, digested in 3mg/ml collagenase for 15 min at 37°C in a 5% CO2 incubator. Growth plates were then washed in PBS, agitated in 0.5mg/ml collagenase in PBS to remove soft tissue, washed in PBS, frozen on dry ice and stored at -80°C. Placentas were isolated at E17.5, weighed and bisected. Half of the placenta was rinsed in PBS, snap-frozen on dry ice and stored at -80°C for RNA analysis. Growth plate and placental RNA was extracted from 4-5 samples / genotype using NucleoSpin RNA XS (bone growth plate) or NucleoSpin RNA Plus columns (Placenta). RNA quality was assessed on an Agilent Bioanalyzer and samples with RIN >7.5 used for library preparation and sequencing either on the Illumina NovaSeq 6000 S1 collecting >25M 150b PE reads (bone growth plates; Ramaciotti Centre for Genomics) or on the BGI Genomics platform (placentae, BGI Genomics, Hong Kong).
Oocyte libraries were constructed using Nugen Trio Library prep using protocol M01440v2; 2017 followed by 75bp SR sequencing using Illumina NextSeq500 High output mode and v2.5 chemistry. Illumina Protocol 15046563 v02, Mar 2016. Bone Growth Plate libraries were constructed using Illumina RNAseq chemistry followed by sequencing on an Illumina NovaSeq 6000 S1 2x150bp flowcell (Ramaciotti Centre for Genomics). Placental libraries were constructed using the BGI DNBseq protocol followed by 150bp PE sequencing on the BGI DNBSeq Eukaryotic Transcriptome Resequencing platform (Beijing Genomics)

treatment_protocol: Refer to growth protocol for mouse strain information. Mice were crossed to produce genotypes described for each sample.

value: GV Oocytes

value: Eed.fl.Zp3Cre on C57BL/6 background

value: Eedfl/fl


title: SampleL118

value: M

value: Sprague Dawley

value: feces


title: MCF7, Theobromine_50uM, 6h, rep1, G11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-G11

extract_protocol:
6h after treatment, 100uL of TempoSeq lysis buffer used to lyse cells per 96-well, which were then frozen and 2ul used for TempO-Seq library building
In TempO-Seq, each Detector Oligo (DO) consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

value: 6h exposure of chemical


title: GV Oocytes, WT_Flox+_Cre-, rep4

description:
Reference_gene_raw_count.txt
501


title: Exp2_GFP


title: GV Oocytes, WT_Flox+_Cre-, rep3

description:
Reference_gene_raw_count.txt
503


title: SampleL117

value: IUGR-RC

value: 16S rDNA


title: MCF7, Theobromine_1000uM, 6h, rep1, G1

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-G1


title: SampleL116

value: F

value: PM


title: SampleL115


title: A7_Hyp WT 4

value: lung

value: Hyperoxia

tag: disease state

value: BPD


title: GV Oocytes, WT_Flox+_Cre-, rep1

description:
Reference_gene_raw_count.txt
471


title: MCF7, Methylparaben_1uM, 6h, rep1, F8

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-F8

value: Breast; Mammary gland


title: GV Oocytes, WT_Flox+_Cre-, rep2

description:
Reference_gene_raw_count.txt
492


title: MCF7, DMSO, 6h, rep1, F9

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-F9

value: epithelial cell

value: vehicle control


title: MCF7, Paraxanthine_1000uM, 6h, rep1, F6

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-F6

value: Adenocarcinoma


title: SampleL114


title: MCF7, Theophylline_50uM, 6h, rep1, F4

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-F4


title: GV Oocytes, WT_Flox-_Cre+, rep1

description:
Reference_gene_raw_count.txt
569

source_name: GV Oocytes, WT Flox- Cre+

value: GV Oocytes

value: Eed.fl.Zp3Cre on C57BL/6 background


title: GV Oocytes, WT_Flox-_Cre+, rep2

description:
Reference_gene_raw_count.txt
653


title: SampleL112


title: Exp1_GFP

value: GFP


title: MCF7, Theobromine_500uM, 6h, rep1, F2

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-F2


title: SampleL111

value: Sprague Dawley


title: MCF7, Ethylparaben_1uM, 6h, rep1, F10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-F10


title: GV Oocytes, Homozygous_KO, rep5

description:
Reference_gene_raw_count.txt
510

source_name: GV Oocytes, Homozygous KO


title: SampleL110

value: feces


title: GV Oocytes, Homozygous_KO, rep4

description:
Reference_gene_raw_count.txt
494


title: SampleL113


title: MCF7, Caffeine_1000uM, 6h, rep1, E8

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-E8

value: 6h exposure of chemical


title: MCF7, DMSO, 6h, rep1, E5

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-E5


title: GV Oocytes, Homozygous_KO, rep2

description:
Reference_gene_raw_count.txt
466


title: MCF7, Paraxanthine_50uM, 6h, rep1, E12

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-E12


title: SampleL109

value: IUGR-RC


title: MCF7, Propylparaben_50uM, 6h, rep1, E10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-E10


title: GV Oocytes, Homozygous_KO, rep1

description:
Reference_gene_raw_count.txt
464


title: MCF7, 4-Hydroxybenzoic acid_500uM, 6h, rep1, E9

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-E9


title: GV Oocytes, Heterozygous_KO, rep4

description:
Reference_gene_raw_count.txt
512

source_name: GV Oocytes, Heterozygous KO


title: MCF7, Butylparaben_1uM, 6h, rep1, D5

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-D5


title: GV Oocytes, Heterozygous_KO, rep5

description:
Reference_gene_raw_count.txt
559


title: GV Oocytes, Homozygous_KO, rep3

description:
Reference_gene_raw_count.txt
474


title: SampleL108

value: AM

value: 16S rDNA


title: SampleL106

value: F


title: SampleL104


title: SampleL107


title: MCF7, Butylparaben_50uM, 6h, rep2, B2

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW912A-B2


title: MCF7, Methylparaben_500uM, 6h, rep1, D3

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-D3


title: SampleL103


title: SampleL105


title: AKI

city: Beijing

first: Shuang

state: Beijing

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

description: AKI

data_processing:
fastp was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases
sequence quality was also verified using fastp We used Bowtie2 and Tophat2 to map reads to the genome of Homo sapiens GRCh38
CIRCExplorer was used to de novo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion and CIRCExplorer. All samples were generated unique circular RNAs.
Circular RNA expressions from different samples or groups were calculated by SRPBM = (number of back-spliced junction reads)/(number of mapped reads) × 1,000,000,000. Only the comparisons with p value<0.05 were regarded as showing differential expression by R package edgeR
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: peripheral blood

growth_protocol: asphyxia-induced AKI neewborns and relatively healthy controls

extract_protocol:
Total RNA was isolated from the above two tubes and purified by Trizol reagent (Invitrogen, Carlsbad, CA, US) following the manufacturer's instruction.
Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used Bowtie2 and Tophat2 to map reads to the genome of species. Remaining reads (unmapped reads) were still mapped to genome using tophat-fusion. CIRCExplorer2 and CIR was used to denovo assemble the mapped reads to circular RNAs at first. Then, back splicing reads were identified in unmapped reads by tophat-fusion.

treatment_protocol: Peripheral blood samples were collected from asphyxial AKI newborns and controls. Samples were mixed with TRIzol and then frozen in liquid nitrogen until they were tested for circRNA sequencing or quantification.

value: peripheral blood

tag: diagnosis

value: acute kidney injury


title: MCF7, DMSO, 6h, rep1, D2

first: Yuqing

address: 8700 mason montgomery road

institute: Procter & Gamble

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-D2

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R.
The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample.
Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user.
The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Assembly: hWTv2
Supplementary files format and content: txt file


title: GV Oocytes, Heterozygous_KO, rep1

description:
Reference_gene_raw_count.txt
465


title: GV Oocytes, Heterozygous_KO, rep3

description:
Reference_gene_raw_count.txt
493


title: RNAseq-WT-testis-30dpp

source_name: testis

extract_protocol:
Total RNA from frozen testis samples and from sorted germ cells was extracted using mirVana miRNA isolation kit (Thermo Fisher, AM1560).
Library construction for strand-specific RNA libraries was performed as previously described (Zhang, Z., Theurkauf, W.E., Weng, Z., and Zamore, P.D. (2012). Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence 3, 9.)

tag: antibody

tag: Stage

value: 30 days postpartum


title: MCF7, 4-Hydroxybenzoic acid_1uM, 6h, rep1, D11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-D11

value: Breast; Mammary gland

tag: cell type


title: GV Oocytes, Heterozygous_KO, rep2

description:
Reference_gene_raw_count.txt
491

tag: strain


title: Exp1_Pax5


title: Sample95

value: PM

value: HFhf


title: SampleL101


title: MCF7, DMSO, 6h, rep1, D10

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-D10

tag: cell line

value: epithelial cell

tag: treatment

value: Adenocarcinoma

value: vehicle control


title: RNAseq-WT-testis-27dpp

value: 27 days postpartum


title: RNAseq-WT-testis-21dpp

value: 21 days postpartum


title: SampleL102

value: Sprague Dawley

value: feces


title: MCF7, DMSO, 6h, rep1, C7

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-C7

tag: genotype

tag: time


title: Sample94

tag: age (day)


title: Control

description: Control

tag: tissue

value: control


title: pR_HPC_RNAseq

city: Napoli

first: Maria

middle: Rosaria

last: Matarazzo

address: Via Pietro Castellino 111

institute: Institute of Genetics and Biophysics "ABT"

data_processing:
The quality of the PE reads were assessed using FastQC. Low-quality read filtering and adapter-trimming were performed using the fastp tool by setting the following parameters: -f 10 -q 25 -l 35 -w 4. The PE reads were aligned to the hg38 reference assembly using STAR aligner with following settings:  --outSAMtype BAM SortedByCoordinate –alignEndsProtrude 50 ConcordantPair  --chimOutType WithinBAM --chimSegmentMin 10.
Gene expression was quantified as read counts using the FeatureCounts function from Rsubread package  (useMetaFeatures=TRUE, allowMultiOverlap=FALSE, strandSpecific=2, CountMultiMappingReads=FALSE).  The raw count matrix were pre-processed to filter out low  counts and TMM normalised using HTSFilter R package. A stringent threshold of posterior probability (pp) > 0.95 and log2FC ± 1.2 was applied to call deregulated genes in both ICF1 HPCs vs WT1 HPCs.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: HPCs; Day 14

growth_protocol: Hematopoietic progenitor cells (HPCs) were obtained from WT and ICF iPSCs through a feeder-free differentiation protocol (StemDiff Hematopoietic Kit, 05310, Stem Cell Technologies). The cell population expressing the pan hematopoietic marker CD43 (eBio84-3C1, PE, eBioscience) was analyzed for CD45 (HI30, FITC, eBioscience) and CD34 (4H11, APC, eBioscience) expression, and sorted by FACS (BD FACS ARIAIII cell sorter) for bulk RNA-Seq experiments.

extract_protocol:
RNA-seq Total RNA from ICF1 and WT HPCs was extracted with RNAeasy plus mini kit (74134, Qiagen) according to the manufacturer protocol including a gDNA elimination step.
Strand-specific TruSeq paired-end (PE) libraries were prepared according to Illumina's instructions and the libraries were sequenced using the Illumina NovaSeq6000 platform.

value: HPCs; Day 14


title: pG_HPC_RNAseq


title: WT1_HPC_RNAseq


title: RNAseq-WT-testis-14dpp

value: 14 days postpartum


title: Sample91

value: F

tag: collection time

tag: specimen

value: IUGR-HFhf

value: 16S rDNA


title: RNAseq-WT-testis-17dpp

value: 17 days postpartum


title: RNAseq-WT-testis-11dpp

value: 11 days postpartum


title: Sample89

value: PM

tag: group

tag: molecule


title: RNAseq-WT-testis-4dpp

value: 4 days postpartum


title: MCF7, Butylparaben_500uM, 6h, rep1, C11

city: Mason

last: Shan

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-C11

value: Breast; Mammary gland

value: epithelial cell

value: 6h exposure of chemical


title: MCF7, 4-Hydroxybenzoic acid_50uM, 6h, rep1, C5

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-C5

value: Adenocarcinoma


title: true naive B3

city: Szczecin

first: Tomasz

middle: K

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

description: DNA extracted from sorted B cell population from healthy donor

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Data were processed in R, normalized using BMIQ normalization.

source_name: Healthy donor blood

extract_protocol: DNA was extracted from each sorted B cell population using the AllPrep® DNA/RNA Micro Kit (Qiagen) following the manufacturer's instructions

tag: cell population

value: true naive B

tag: real concentration


title: MCF7, Caffeine_50uM, 6h, rep1, C3

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-C3

source_name: Breast; Mammary gland


title: Sample86

tag: Sex

value: Sprague Dawley

value: CON


title: Sample90

value: feces


title: RNAseq-WT-testis-2dpp

tag: antibody

value: 2 days postpartum


title: MCF7, Butylparaben_50uM, 6h, rep1, B4

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-B4


title: true naive B4


title: Sample83

value: AM

value: HFhf


title: Sample85

value: F


title: true naive B2


title: MCF7, Methylparaben_50uM, 6h, rep1, B11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-B11


title: MCF7, DMSO, 6h, rep1, A11

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-A11

value: vehicle control


title: unswitched memo B3

value: unswitched memo B


title: CUTRUN-AMYB-pachyteneCell-rep2

source_name: pachytene spermatocytes

extract_protocol:
In brief, FACS-sorted germ cells were lysed using nuclear extraction buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 0.5mM Spermidine, 0.1% Triton X-100, 20% Glycerol) and centrifuged at 600g for 3 min at 4°C to isolate nuclei. Next, isolated nuclei were immobilized on BioMag Plus Concanavilin A coated magnetic beads (Bangs Laboratories, BP531) at room temperature for 20 min. After immobilizing nuclei to magnetics beads, nuclei were blocked using blocking buffer (20mM HEPES-KOH pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.1% BSA, 2mM EDTA) at room temperature for 5 min. Thereafter, 2.5 µg anti-AMYB antibody (Sigma, HPA008791, lot # C105987) was added to the beads and incubated at 4°C for 4 h using end-over-end tumbler. Of note, as negative control, we performed CUT and RUN reaction without antibody. After antibody incubation, beads were washed twice in wash buffer (20mM HEPES-KOH pH 7.5, 150mM NaCl, 0.5mM Spermidine, 0.1% BSA) and incubated with 1.5 µl protein A-MNase (pA-MN; 140 µg/ml) at 4°C for 2 h using end-over-end tumbler. To remove unbound pA-MN, beads were washed twice in wash buffer. To cleave DNA beneath TCFL5 or A-MYB, 3 µl CaCl2 was directly added to the beads and incubated at 0°C for 7 min. The cleavage reaction was then stopped by chelation in 2× STOP buffer (200mM NaCl, 20mM EDTA, 4mM EGTA, 50 µg/ml RNase A, 40 µg/ml glycogen). To release the CUT and RUN fragments from insoluble nuclear chromatin, beads were incubated in 2× STOP buffer including RNase A at 37°C for 20 min and centrifuged at 16,000 g at 4°C. The supernatant containing CUT and RUN fragments were transferred to fresh 1.7 ml tube. Finally, we extracted DNA by phenol:chloroform:isoamyl alcohol (25:24:1) (pH 8)
Library construction for anti-AMYB DNA was performed after DNA extraction as previously described (Zhang, Z., Theurkauf, W.E., Weng, Z., and Zamore, P.D. (2012). Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence 3, 9.).

value: rabbit anti AMYB antibody; Sigma, HPA008791

tag: Stage

value: adult


title: CUTRUN-AMYB-pachyteneCell-rep1


title: true naive B1

tag: cell type


title: Sample74

tag: strain

value: 16S rDNA


title: sRNAseq-WT-testis-rep2

data_processing:
For small RNA-seq data, after removing 3′ adaptor sequence from the reads, we filtered reads whose PHRED score was <5. Those reads that passed the quality check were then mapped to mouse genome (mm10) using piPipes that uses bowtie 2.2.5 allowing one mismatch.  For RNA-seq data, we first removed rRNA reads using bowtie 2.2.5 with default parameters and then the unaligned reads were further mapped to mouse genome (mm10) using STAR. Mapped results were generated as SAM format that was further transformed into duplication removed sorted BAM format using SAMtools 1.8 and Umitools. For ChIP-seq data, raw reads were mapped to mapped to mouse genome (mm10) using Bowtie 2.2.5 with parameter —very-sensitive —no-unal —no-mixed —no-discordant. We then removed duplicate reads using SAMtools. Normalized genome coverage files in bigWig format were generated using homemade script. For CUT&RUN data, Raw reads were mapped to mapped to mouse genome (mm10) using Bowtie 2.2.5 with parameter —very-sensitive —no-unal —no-mixed —no-discordant. We presented the data in bigWig file that was reported as unique mapping reads as read depth per million reads (rpm).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol: none provided by the submitter


title: sRNAseq-WT-testis-rep1


title: cG50_CTCF_input_rep1

data_processing:
The quality of the sequenced single-end (SE) reads from IP and input were assessed using FastQC. The low quality SE reads were filtered out and the Illumina adapters were trimmed using Cutadapt with the following settings: -q > 30; -m > 40. The reads were aligned to the hg38 reference genome using Bowtie2 with default parameters. Aligned SE reads with MAPQ score < 20 were filtered out and  the duplicates were removed using samtools markdup command.
Assembly: hg38
Supplementary files format and content: N/A

source_name: iPSCs

growth_protocol: The iPSC lines were cultured on Geltrex™ LDEV-Free Reduced Growth Factor Basement Membrane Matrix (A1413302, Gibco™) coated plates and maintained in StemMACS™ iPS-Brew XF, human medium (130-104-368, Miltenyi Biotec).

extract_protocol:
Decrosslinking from beads was performed in a 1% SDS solution containing Tris-HCl pH8 and 10 mM EDTA for 2 hours at 69°C with agitation. Decrosslinking of the DNA-protein complex was performed by adding Proteinase K (20 ng/mL) for 2 hours at 62°C with agitation. DNA was then purified using ExpinTM PCR SV (103-102, GeneAll®).
ChIP-Seq libraries were generated according to Illumina's instructions and single-end (SE) sequencing was performed on the Illumina Hi-Seq 2500 system at the Technion Genome Center (Haifa, Israel)

value: iPSCs

tag: condition

tag: chip antibody


title: switched memo B1

value: switched memo B


title: cG50_CTCF_input_rep2


title: ChIPseq-Input-for-AMYB-testis-rep1

data_processing:
For small RNA-seq data, after removing 3′ adaptor sequence from the reads, we filtered reads whose PHRED score was <5. Those reads that passed the quality check were then mapped to mouse genome (mm10) using piPipes that uses bowtie 2.2.5 allowing one mismatch.  For RNA-seq data, we first removed rRNA reads using bowtie 2.2.5 with default parameters and then the unaligned reads were further mapped to mouse genome (mm10) using STAR. Mapped results were generated as SAM format that was further transformed into duplication removed sorted BAM format using SAMtools 1.8 and Umitools. For ChIP-seq data, raw reads were mapped to mapped to mouse genome (mm10) using Bowtie 2.2.5 with parameter —very-sensitive —no-unal —no-mixed —no-discordant. We then removed duplicate reads using SAMtools. Normalized genome coverage files in bigWig format were generated using homemade script. For CUT&RUN data, Raw reads were mapped to mapped to mouse genome (mm10) using Bowtie 2.2.5 with parameter —very-sensitive —no-unal —no-mixed —no-discordant. We presented the data in bigWig file that was reported as unique mapping reads as read depth per million reads (rpm).
Genome_build: mm10; rheMac8
Supplementary_files_format_and_content: bigWig

extract_protocol:
In brief, testis frozen tissues were cut into small pieces on dry ice and collected to 1.7 ml tubes containing cold PBS in which samples were cross-linked with 2% (w/v) formaldehyde at room temperature for 30 min using end-over-end tumbler. We then crushed fixed tissues in the presence of ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) by 40 strokes with a Dounce homogenizer pestle “B” (Kimble-Chase, Vineland, USA). To shear the chromatin into 150 to 200 bp, lysed samples were sonicated using Covaris ultrasonicator (Covaris, E220). Sonicated lysate was then diluted 1:10 with ChIP dilution buffer (0.01% SDS, 1.1% Triton X-1001.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl) and we performed immunoprecipitation using 5 µg anti-TCFL5 antibody (Sigma, HPA055223, lot # 000000907). Following the immunoprecipitation of the chromatin, we extracted DNA by phenol:chloroform:isoamyl alcohol (25:24:1) (pH 8).
Library construction for input DNA was performed after DNA extraction as previously described (Zhang, Z., Theurkauf, W.E., Weng, Z., and Zamore, P.D. (2012). Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence 3, 9.).

value: Input

value: adult, three month


title: MCF7, DMSO, 6h, rep1, B6

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-B6

tag: cell line

value: Breast; Mammary gland

tag: genotype

value: epithelial cell

tag: treatment

value: Adenocarcinoma


title: unswitched memo B4


title: switched memo B2


title: Sample82

tag: age (day)

value: Sprague Dawley

value: feces


title: sRNAseq-TCFL5Mut-testis-rep2


title: pG_CTCF_input_rep1


title: cR7_CTCF_input_rep2


title: sRNAseq-TCFL5Mut-testis-rep1


title: Sample71

tag: collection time

value: PM


title: unswitched memo B1


title: cR7_CTCF_input_rep1


title: Sample72

tag: specimen

value: HFhf


title: A549 Rec

city: Sapporo

first: Fumihito

last: Hikage

state: Hokkaido

address: S1 W16, Chuo-ku

country: Japan

institute: Sapporo Medical University School of Medicine

description: A549, Recoverin over expression, rep.3

data_processing:
FastQC v 0.11.7
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v 0.38 (parameter- Quality limit: 0.01)
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2 v 2.1.0 (parameters- ILLUMINACLIP 2:30:10, LEADING = 20, TRAILING = 20, SLIDINGWINDOW = 4:15, MINLEN = 36)
Read count extraction and normalization were performed using featureCounts v 1.6.3
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: text files include FPKM values for each Sample in each column

source_name: Lung

growth_protocol: Both cell lines were cultured in HG-DMEM culture medium supplemented with 8 mg/L d-biotin, 4 mg/L calcium pantothenate, 100 U/mL penicillin, 100 μg/mL streptomycin (b.p. HG-DMEM), 10 % CS and methylcellulose (Methocel A4M) at 37°C and 5% CO2 for 6 days.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTMII Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: We compared the transcriptional signatures of recoverin (Rec) negative lung adenocarcinoma A549 cells which had been transfected with a plasmid containing human recoverin cDNA (A549 Rec) or an empty plasmid as a mock control (A549 MOCK).

tag: tissue

value: Lung

value: adenocarcinoma

value: Recoverin over expression


title: Sample78

value: F

value: AM

tag: group

value: IUGR-HFhf

tag: molecule


title: RNAseq-WT-testis-rep6

value: adult


title: A549 Rec2

description: A549, Recoverin over expression, rep.2

value: transfected with a plasmid containing human recoverin cDNA


title: pR_CTCF_input_rep2

value: iPSCs


title: unswitched memo B2

tag: cell population

value: unswitched memo B

tag: real concentration


title: A549 Rec1

description: A549, Recoverin over expression, rep.1


title: RNAseq-WT-testis-rep5

tag: antibody


title: Sample70

tag: Sex

value: 16S rDNA


title: Sample69


title: WT1_CTCF_input_rep2

tag: cell type


title: A549 Mock

description: A549, Mock, rep.3

value: Mock

value: transfected with a plasmid containing an empty plasmid


title: MCF7, Theophylline_500uM, 6h, rep1, A7

description:
4 cell lines were used and experiment were performed in 96-well plates . Each 96-well plate included 8 DMSO controls. Each chemical were tested at 3 doses and 3 reps.
SP0183_MCF7_cts.txt
RBSW911A-A7

value: Breast; Mammary gland

value: epithelial cell

value: Adenocarcinoma

tag: time

value: 6h exposure of chemical


title: Sample67

value: PM

tag: strain

value: Sprague Dawley

value: feces


title: Sample66

value: F


title: WT1_CTCF_input_rep1

tag: condition

tag: chip antibody


title: pR_CTCF_input_rep1


title: RNAseq-WT-testis-rep4

tag: Stage


title: RNAseq-WT-testis-rep3


title: RNAseq-WT-testis-rep2


title: A549 Mock1

description: A549, Mock, rep.1

value: Lung

tag: cell line

value: adenocarcinoma

tag: genotype

tag: treatment


title: cG50_CTCF_IP_rep2

value: CTCF, Abcam


title: Sample73

tag: age (day)

tag: collection time

value: AM

tag: specimen

value: CON


title: cG50_CTCF_IP_rep1

value: iPSCs


title: pG_CTCF_IP_rep1


title: Sample81

tag: group

value: HFhf

tag: molecule

value: 16S rDNA


title: RNAseq-TCFL5Het-testis-rep6

value: adult


title: RNAseq-WT-testis-rep1


title: Sample64


title: cR7_CTCF_IP_rep2


title: Sample65

value: IUGR-HFhf


title: A549 Mock2

description: A549, Mock, rep.2

tag: tissue

value: Mock

value: transfected with a plasmid containing an empty plasmid


title: RNAseq-TCFL5Het-testis-rep5

tag: antibody


title: CTR33n1

city: Irvine

first: Leslie

middle: M.

last: Thompson

address: 845 Health Sciences Road

institute: University of California, Irvine

description: CTR33n1 day69 GLAST iPSC-derived astrocyte single-nuclei RNA-seq

library_source: transcriptomic single cell

data_processing:
Illumina CASAVA 1.8 bcl2fastq2-v2.20.0.422-centos-7 was used for basecalling.
Sequenced reads were aligned to hg19 whole transcriptome using cellranger v3.1.0:  cellranger count  --transcriptome=refdata-cellranger-hg19-3.0.0
Cell ranger counts were input into Seurat using SeuratObject(…, min.cells = 3, min.features = 200)
Cells were subset based on QC measures in Seurat using subset = nFeature_RNA > 200 & nFeature_RNA < 6000 & percent.mt < 5
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for all cells that pass QC in every sample

molecule: polyA RNA

extract_protocol:
Single-cell suspensions were strained using a 70 µm strainer, washed using cold 0.08% BSA (Gibco) in PBS, and counted using TC20 Automated Cell Counter (BioRad) with trypan blue exclusion as described in the 10x Genomics® Demonstrated Protocol: Single Cell Suspensions from Cultured Cell Lines for Single Cell RNA Sequencing (Document CG00054). To obtain a single-nuclei suspension, cells were lysed using Nuclei EZ Lysis Buffer (Sigma Aldrich, NUC101-1KT) for 5 min on ice. Lysed cells were centrifuged 500 rcf for 5 min at 4°C, then washed by twice resuspending in 1% BSA (Gibco), 0.2 U/µL of Human Placenta RNase Inhibitor (NEB), in PBS and centrifuged again. After two washes, the nuclei were strained using a 40µm cell strainer, counted using the TC20 Automated Cell counter (Bio-Rad), resuspended at 1000 nuclei/µL in 0.08% BSA (Gibco) in PBS, then proceeded immediately with the 10x Genomics® Chromium Single cell 3’ gene expression v3 platform.
RNA libraries were prepared for sequencing using 10x Genomics single cell v3 and standard Illumina protocols

value: iPSC-derived astrocyte

value: control


title: HD46n10

description: CTR46n10 day69 GLAST iPSC-derived astrocyte single-nuclei RNA-seq

value: HD


title: HD53n3

description: CTR53n3 day69 GLAST iPSC-derived astrocyte single-nuclei RNA-seq


title: Sample63

tag: Sex

value: PM

value: Sprague Dawley

value: feces


title: CTR18n6

description: CTR18n6 day69 GLAST iPSC-derived astrocyte single-nuclei RNA-seq

tag: cell type


title: Sample62

value: F


title: cR7_CTCF_IP_rep1

value: CTCF, Abcam


title: RNAseq-TCFL5Het-testis-rep2

first: Tianxiong

address: 364 Plantation St

institute: Umass Med


title: Sample60

value: AM


title: Sample61

value: CON


title: pR_CTCF_IP_rep1

value: iPSCs