title: A549, Butylparaben_1uM, 6h, rep1, D05

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.
SP0204_A549_cts.txt
R-BSW911B-T4_D3


title: acute study, mouse heart, doxo rep4

status: Public on Jan 11 2023

type: SRA

city: Nyon

first: Nicolas

last: Hulo

address: Avenue Reverdil 4

country: Switzerland

institute: Nuvamid SA

description:
Acute_Heart_Doxo_8
Heart_8

library_source: transcriptomic

data_processing:
Sequenced reads were mapped to mm10 genome using STAR (v2.7.3a) with default parameter. The bam output files were then passed to featureCounts (v2.0.0) with the mm10 gencode gtf file to generate the count table
Supplementary files format and content: Acute_Doxo_Heart.csv, csv files of count table for Acute experiment
Supplementary files format and content: Chronic_Doxo_Heart.csv, csv files of count table for Chronic experiment

molecule: total RNA

organism: Mus musculus

source_name: Heart

extract_protocol:
Frozen heart samples from the acute and chronic toxicity studies were submitted to Genewiz (Leipzig, Germany) or Azenta (former Genewiz, NJ, USA), respectively
Sequencing was performed on an Illumina NovaSeqTM 6000 platform after total RNA extraction, poly(A) selection and library generation.
Approximately 30 million single-end reads per sample were obtained

tag: tissue

value: Heart

tag: genotype

value: WT

tag: treatment

value: Doxo


title: Ahr_WT_CD8_LmOVA_R2

city: Gainesville

first: Liang

last: Zhou

state: FL

address: 2015 SW 16th Ave

department: IDI

country: USA

institute: University of Florida

data_processing:
FastQC was used to ensure high per-base sequence quality of reads.
[RNA-seq] Sequenced reads were mapped and raw count values quantified with STAR (v2.7.4a) to the Mus musculus genome (GRCm38/mm10 assembly) and filtered for uniquely mapped reads. Quantitated mRNA expression levels, FPKM aligned reads, were calculated based on exon regions using RSEM (v1.2.25)
[ChIP-seq] ChIP-seq reads were mapped to the mouse genome (mm10) with bowtie2 (Langmead and Salzberg, 2012). The mapped reads were filtered using samtools (Li et al., 2009), keeping only the uniquely aligned reads, and bedgraph files (scaled to 10 million reads) were made with bedtools (Quinlan and Hall, 2010).  CHIP-seq peak locations were identified using Homer (Heinz et al., 2010)
[scRNA-seq] Alignment, quantification, and quality control were performed using the Cell Ranger Software (v3.1.0) and default parameters. After quality control and removal of dead cells, doublets, and contaminating melanoma cells (Pmel mRNA count > 0) a total of 9726 cells remained for downstream analysis. Normalization, cell clustering (resolution = 2), dimensionality reduction, differential expression, visualization, and pseudotime analysis were performed using the R packages Seurat (Butler et al., 2018) and Monocle (Trapnell et al., 2014). The 3000 most variable features identified with the variance-stabilizing transformation (vst)-method were used for principal component analysis (PCA). Upon inspection of elbowplot and jackstraw plot, the first 20 principal components (PCs) were used for further analysis. Cell type annotation was performed manually by assessment of cluster marker genes.
Assembly: GRCm38/mm10
Supplementary files format and content: [RNA-seq] text file of raw counts for all samples, [ChIP-seq] bedgraph files for each sample, [scRNAseq] single cell barcodes, features, and matrix files for each sample

source_name: Small Intestine IEL CD8+ T cell

extract_protocol:
RNA was extracted using RNAeasy Micro Kit, followed by cDNA generation with SMART-Seq® HT Kit (TaKaRa).
cDNA generation was performed with SMART-Seq® HT Kit (Takara). Sequencing libraries were generated with Nextera® XT DNA Library Preparation Kit (Illumina).

value: Small Intestine IEL

tag: cell type

value: CD8+ T cell

tag: strain

value: Ahr+/+


title: Ahr_KO_CD8_LmOVA_R1

value: Ahr-/-


title: A549, Butylparaben_50uM, 6h, rep1, B04

city: Mason

first: Yuqing

last: Shan

state: Ohio

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.
SP0204_A549_cts.txt
R-BSW911B-T4_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

organism: Homo sapiens

source_name: Lung

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: Lung

value: epithelial cell

value: Carcinoma

tag: time

value: 6h exposure of chemical


title: HG-SOC endothelin-1 stimulated replicate 4

city: Torino

first: Ivan

last: Molineris

state: TO

address: Via Nizza 52

department: Life Science and System Biology

country: Italy

institute: University of Turin

data_processing:
Sequencing reads were aligned to human reference genome (version GRCh38.p10) using STAR v2.5.3a [PMID:23104886] (with parameters --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04) and providing a list of known splice sites extracted from GENCODE comprehensive annotation (version 27)
Read that align on ribosomal gene or ribosomal repeated sequences in the genome are removed
Gene expression levels were quantified with featureCounts v1.6.3 [PMID:24227677] (options: -t exon -g gene_name) using GENCODE gene annotation (version 27 basic). Multi-mapped reads were excluded from quantification.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: raw gene count

molecule: polyA RNA

source_name: Patient-derived HG-SOC primary cells

growth_protocol: Patient-derived high-grade serous ovarian cancer (HG-SOC) primary cells were isolated from the ascitic fluid of a HG-SOC patient through Ficoll-Histopaque 1077 (Sigma-Aldrich, St. Louis, Missouri,USA). Interface cells were washed in culture medium, and 5×106 viable cells were seeded in 75-cm2 culture flasks, in RPMI 1640 (Gibco, Grovemont Cir, Gaithersburg, USA) containing 1% penicillin streptomycin and 10% fetal bovine serum. All experiments were conducted between the first and second in vitro passage. The purity of primary cultures was assessed by immunophenotyping with a panel of monoclonal Abs (including WT1, keratin 7, calretinin and OCT-125) recognizing ovarian tumor-associated antigens by the alkaline phosphatase-peroxidase-antiperoxidase method. The early passage HG-SOC patient-derived cell line is named PMOV10 where PM stands for Preclinical Models, OV stands for ovarian serous cancer, and # is the order in which the cell line was established

extract_protocol:
Total RNA was isolated using the RNeasy Quick Start kit (Qiagen), according to the manufacturer’s protocol. Quantity and quality of the starting RNA were checked by NanoDrop (Thermo Scientific).
Before starting with library prep, RNA quality was determined running samples on Tapestation 4100 (Agilent). Only RNA samples with RIN above 7 were used in the next steps. To generate the NGS libraries, we exploited the TruSeq Stranded mRNA (Illumina) kit, starting from 100ng of total RNA. Libraries were barcoded, pooled, and sequenced on an Illumina NextSeq 500 sequencing system, in order to obtain for each sample ~ 20-30M single-end reads, 100 nt long.

treatment_protocol: Patient-derived HG-SOC cells (PMOV10) were seeded 1x106 cells/75-cm2 culture flask and incubated at 37°C for 24 hours, then were starved for 24 hours and stimulated with endothelin-1 (ET-1, 100 nM), or with macitentan (MAC, 1µM), alone or in combination with ET-1, or with acetic acid (1% in H20) as vehicle (CTR) for 24 hours.

tag: mac

value: N

value: Y


title: TXNIP WT RT input for BAT H3K27Ac ChIP

city: Grand Rapids

first: Ning

last: Wu

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Institute

library_source: genomic

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

molecule: genomic DNA

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: TXNIP WT

value: RT


title: A549, Butylparaben_500uM, 6h, rep1, 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.
SP0204_A549_cts.txt
R-BSW911B-T4_D1


title: HG-SOC endothelin-1 stimulated replicate 1


title: TXNIP WT H3J27Ac ChIP at RT, rep 2

value: Cell Signaling Tech 8173


title: Ahr_WT_CD8_LmOVA_R1


title: TXNIP WT H3J27Ac ChIP at RT, rep 1


title: HG-SOC endothelin-1 stimulated replicate 2


title: A549, theophylline_50uM, 6h, rep1, F04

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.
SP0204_A549_cts.txt
R-BSW911B-T27_D3


title: HG-SOC endothelin-1 stimulated replicate 3


title: acute study, mouse heart, control rep2

description:
Acute_Heart_CTRL_2
Heart_2

value: Heart

value: Vehicle


title: HG-SOC control 4


title: TXNIP WT cold input for BAT H3K27Ac ChIP

value: 4h cold stress


title: TXNIP WT H3J27Ac ChIP after 4h cold stress, rep 1


title: TXNIP KO RT input for BAT H3K27Ac ChIP

value: TXNIP KO


title: A549, theophylline_500uM, 6h, rep1, A07

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.
SP0204_A549_cts.txt
R-BSW911B-T27_D2


title: TXNIP WT H3J27Ac ChIP after 4h cold stress, rep 2


title: TXNIP KO H3J27Ac ChIP at RT, rep 2


title: HG-SOC macitentan treated replicate 1


title: HG-SOC control 3


title: A549, theophylline_1000uM, 6h, rep1, H02

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.
SP0204_A549_cts.txt
R-BSW911B-T27_D1


title: A549, 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.
SP0204_A549_cts.txt
R-BSW911B-T26_D3


title: HG-SOC control 2


title: TXNIP KO H3J27Ac ChIP after 4h cold stress, rep 2


title: cold input for BAT CEBPB ChIPseq

value: HA-CEBPB KI


title: HG-SOC control 1


title: TXNIP KO cold input for BAT H3K27Ac ChIP


title: A549, theobromine_500uM, 6h, rep1, F02

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.
SP0204_A549_cts.txt
R-BSW911B-T26_D2


title: BAT CEBPB ChIPseq after 4h cold stress, rep 2

value: Cell Signaling tech 3724


title: A549, 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.
SP0204_A549_cts.txt
R-BSW911B-T24_D3


title: A549, theobromine_1000uM, 6h, rep1, G01

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.
SP0204_A549_cts.txt
R-BSW911B-T26_D1


title: BAT CEBPB ChIPseq after 4h cold stress, rep 1


title: BAT CEBPA ChIPseq at RT, rep 1

value: HA-CEBPA KI


title: 293FT_LIN28A_Zfm_CLIP_IP

city: Tokyo

first: Yutaro

last: Uchida

address: 1-5-45, Yushima, Bunkyo-Ku

country: Japan

institute: Tokyo Medical and Dental University

data_processing:
Library strategy: CLIP-Seq
Basecalls performed using bcl2fastq
Sequenced reads were aligned to human genome (GRCh38) with STAR
Mapped reads were peakcalled using Clipper (https://github.com/YeoLab/clipper)
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file of matrix table with raw gene counts for every gene and every sample

source_name: 293FT cells

extract_protocol:
Cells expressing WT or Zfm of LIN28A were performed CLIP-Seq using FLAG (FLA-1 MBL) antibody
CLIP-seq libraries were prepared with following protocols (Van Nostrand et al, Nat Methods 2016).

treatment_protocol: 293FT cells were transfected with lentivirus expressing control or wild type of LIN28A or zinc finger mutant of LIN28A

tag: expressed genes


title: BAT CEBPA ChIPseq at RT, rep 2


title: 293FT_LIN28A_WT_CLIP_Input


title: RT input for BAT CEBPA ChIPseq


title: A549, paraxanthine_500uM, 6h, rep1, H03

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.
SP0204_A549_cts.txt
R-BSW911B-T24_D2

value: Lung


title: BAT PGC1A ChIPseq after 4h cold stress, rep 3


title: 293FT_LIN28A_WT_CLIP_IP


title: BAT PGC1A ChIPseq after 4h cold stress, rep 2

value: PGC1A-HIsHA KI


title: TXNIP KO H3J27Ac ChIP at RT, rep 1


title: cold stress input for BAT PGC1A ChIPseq 2 & 3


title: 293FTcells_LIN28A_ZFm_rep2

data_processing:
Basecalls performed using bcl2fastq
Sequenced reads were aligned to human genome (GRCh38) with STAR
RSEM was used for read counting and generating count matrix.
Differentially expressed genes were analyzed by iDEP.91.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file of matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA from cells was isolated from treated 293FT cells with TRIZOL Reagent.
RNA-seq libraries were prepared with rRNA-depletion kit (E6310, New England Biolabs Japan, Tokyo, Japan) and a directional library synthesis kit (E6310, New Enagland Biolabs Japan).


title: TXNIP KO H3J27Ac ChIP after 4h cold stress, rep 1


title: BAT PGC1A ChIPseq after 4h cold stress, rep 1


title: A549, 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.
SP0204_A549_cts.txt
R-BSW911B-T17_D3

value: epithelial cell

value: Carcinoma


title: RT input for BAT PPARA ChIPseq

value: HA-PPARA KI


title: 293FTcells_LIN28A_ZFm_rep1


title: A549, 4-Hydroxybenzoic acid_50uM, 6h, rep1, C05

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.
SP0204_A549_cts.txt
R-BSW911B-T17_D2

value: 6h exposure of chemical


title: BAT PPARA ChIPseq at RT, rep 1

value: BAT


title: 293FTcells_LIN28A_WT_rep2


title: BAT PPARA ChIPseq at RT, rep 2


title: 293FT_LIN28A_Zfm_CLIP_Input


title: BAT CEBPA ChIPseq at RT, rep 3


title: A549, 4-Hydroxybenzoic acid_500uM, 6h, rep1, E09

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.
SP0204_A549_cts.txt
R-BSW911B-T17_D1


title: BAT PPARA ChIPseq after 4h cold stress, rep 3


title: BAT PPARA ChIPseq after 4h cold stress, rep 2


title: cold stress input for BAT PPARA ChIPseq


title: A549, Caffeine_50uM, 6h, rep1, C03

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.
SP0204_A549_cts.txt
R-BSW911B-T11_D3


title: 293FTcells_LIN28A_WT_rep1


title: 293FTcells_control_rep2

value: Control


title: A549, paraxanthine_1000uM, 6h, rep1, F06

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.
SP0204_A549_cts.txt
R-BSW911B-T24_D1


title: cold stress input for BAT PPARG ChIPseq, PGC1A ChIP 1

value: WT


title: A549, Caffeine_500uM, 6h, rep1, B12

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.
SP0204_A549_cts.txt
R-BSW911B-T11_D2


title: BAT PPARA ChIPseq after 4h cold stress, rep 1


title: BAT PPARG ChIPseq after 4h cold stress, rep 2

value: Cell Signaling Tech 2435


title: A549, Caffeine_1000uM, 6h, rep1, E08

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.
SP0204_A549_cts.txt
R-BSW911B-T11_D1


title: A549, Ethylparaben_500uM, 6h, rep1, G08

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.
SP0204_A549_cts.txt
R-BSW911B-T6_D1


title: 293FTcells_control_rep1


title: A549, DMSO, 6h, rep1, H08

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.
SP0204_A549_cts.txt
R-BSW911B-DMSO-H08

value: vehicle control


title: BAT PPARG ChIPseq after 4h cold stress, rep 3


title: BAT PPARG ChIPseq at RT, rep 3

value: RT


title: BAT PPARG ChIPseq after 4h cold stress, rep 1

value: 4h cold stress


title: BAT PPARG ChIPseq at RT, rep 1


title: A549, DMSO, 6h, rep1, F09

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.
SP0204_A549_cts.txt
R-BSW911B-DMSO-F09


title: nonEMTsal1

city: Zagreb

first: Marko

last: Marjanović

state: Zagreb

address: Bijenička c. 54

department: Division of Molecular Medicine

country: Croatia

institute: Ruđer Bošković Institute

description: HMLE_pBp_sal DESeq2 fpkm.txt

data_processing:
FASTQ Generation (ver 1.0.0) in Illumina BaseSpace Sequence Hub
RNA-Seq Alingment (ver 1.1.1) in Illumina BaseSpace sequence Hub
DESeq2 (ver 1.1.0) in Illumina BaseSpace Sequence Hub
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each biological replicate

source_name: breast

growth_protocol: Cells were grown in HMLE media (1:1 of HuMEC ready medium and DMEM complemented with 10%FBS, pen-strep, L-glutamine, insulin and hydrocortisone) at 37°C with 5%CO2

extract_protocol:
Total RNA was extracted with Zymo Research Quick-RNA Miniprep kit according to manufacturer protocol, DNase I was used to remove DNA contamination
Library was prepared with TrueSeq Stranded mRNA kit (Illumina) according to manufacturer guidlines

treatment_protocol: Cells were mock treated (DMSO) or treated with 0.2uM salinomycin for 24h

value: HMLE-pBp

value: breast

tag: phenotype

value: nonEMT

value: salinomycin


title: nonEMTsal3

description: HMLE_pBp_sal DESeq2 fpkm.txt


title: nonEMTsal2

description: HMLE_pBp_sal DESeq2 fpkm.txt


title: CEBPB WT BAT mRNAseq at RT, rep5

data_processing:
Reads were trimmed with TrimGalore! v0.6.0.
Using STAR v2.7.8a, trimmed reads were aligned to the GRCm38.p6 reference genome from GENCODE vM24 and gene counts were obtained.
Assembly: mm10
Supplementary files format and content: Tab delimited files containing gene counts.

extract_protocol:
Total RNA was extracted with PureLink RNA mini kit (Invitrogen)
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA Stranded mRNA-Seq Kit (v4.17) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA).

value: CEBPB WT


title: BAT PPARG ChIPseq at RT, rep 2


title: A549, DMSO, 6h, rep1, E05

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.
SP0204_A549_cts.txt
R-BSW911B-DMSO-E05

value: Lung


title: CEBPB WT BAT mRNAseq at RT, rep3


title: CEBPB WT BAT mRNAseq at RT, rep4


title: A549, 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.
SP0204_A549_cts.txt
R-BSW911B-DMSO-D10

value: epithelial cell


title: nonEMTmock3

description: HMLE_pBp_mock DESeq2 fpkm.txt

value: mock


title: CEBPB WT BAT mRNAseq at RT, rep2


title: A549, DMSO, 6h, rep1, D02

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.
SP0204_A549_cts.txt
R-BSW911B-DMSO-D01

value: Carcinoma


title: nonEMTmock2

description: HMLE_pBp_mock DESeq2 fpkm.txt


title: CEBPB WT BAT mRNAseq at RT, rep1


title: nonEMTmock1

description: HMLE_pBp_mock DESeq2 fpkm.txt


title: CEBPB WT BAT mRNAseq after 4h cold stress, rep4


title: CEBPB WT BAT mRNAseq after 4h cold stress, rep3


title: EMTsal3

description: HMLE-Twist-sal DESeq2 fpkm.txt

value: HMLE-Twist

value: EMT


title: A549, DMSO, 6h, rep1, B06

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.
SP0204_A549_cts.txt
R-BSW911B-DMSO-B06


title: A549, DMSO, 6h, rep1, C07

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.
SP0204_A549_cts.txt
R-BSW911B-DMSO-C07


title: A549, 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.
SP0204_A549_cts.txt
R-BSW911B-DMSO-A11


title: CEBPB adipose specific KO BAT mRNAseq at RT, rep4

value: BAT

value: adipose specific CEBPB KO


title: EMTsal2

description: HMLE-Twist-sal DESeq2 fpkm.txt


title: CEBPB adipose specific KO BAT mRNAseq at RT, rep5


title: CEBPB adipose specific KO BAT mRNAseq at RT, rep3


title: CEBPB WT BAT mRNAseq after 4h cold stress, rep1


title: EMTmock3

description: HMLE-Twist-mock DESeq2 fpkm.txt


title: CEBPB adipose specific KO BAT mRNAseq at RT, rep1


title: HepG2, 4-Hydroxybenzoic acid_1uM, 6h, rep3, 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.
SP0178_HepG2_cts.txt
BSW913H_H12

source_name: Liver

value: Liver

value: epithelial-like

value: hepatocellular carcinoma

value: 6h exposure of chemical


title: EMTsal1

description: HMLE-Twist-sal DESeq2 fpkm.txt


title: CEBPB adipose specific KO BAT mRNAseq at RT, rep2

value: RT


title: HepG2, Ethylparaben_500uM, 6h, rep3, H09

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.
SP0178_HepG2_cts.txt
BSW913H_H09


title: CEBPB adipose specific KO BAT mRNAseq after 4h cold stress, rep4

value: 4h cold stress


title: EMTmock2

description: HMLE-Twist-mock DESeq2 fpkm.txt

value: breast


title: CEBPB adipose specific KO BAT mRNAseq after 4h cold stress, rep3


title: CEBPB WT BAT mRNAseq after 4h cold stress, rep5


title: CEBPB adipose specific KO BAT mRNAseq after 4h cold stress, rep1


title: CEBPB WT BAT mRNAseq after 4h cold stress, rep2


title: CEBPB adipose specific KO BAT mRNAseq after 4h cold stress, rep2


title: HepG2, DMSO, 6h, rep3, H08

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.
SP0178_HepG2_cts.txt
BSW913H_H08

value: vehicle control


title: HepG2, Propylparaben_1uM, 6h, rep3, H03

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.
SP0178_HepG2_cts.txt
BSW913H_H03


title: HG-SOC endothelin and macitentan treated replicate 4

value: Y


title: patient3, KTZ 10-9M

city: Solna

first: Tianyi

last: Li

address: Bioclinicum NKS J5:20, Solnavägen 30

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
bcl2fastq (v2.20.0.422) was used to demuliplex the fastq files.
umi_tools extract (v1.0) was then used to extract the barcodes/UMI and add them to the read names in the fastqs
Fastq files were aligned using STAR (v2.7.5b) to the human genome (GRCh38) obtained from Ensembl
The resulted bam files were then deduplicated using umi_tools dedup (v1.0)
Gene counting was then performed using featureCounts (v1.5.1) with Ensembl annotations (Homo_sapiens.GRCh38.101.gtf)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files for all Samples

source_name: ovary

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1 ng of total RNA was used for the construction of sequencing libraries.
Libraries was prepared using QIAseq UPX 3’Transcriptome kit (Qiagen) according to manufacturer's protocol

value: ovary

value: Primary ovarian cells

value: WT

value: Ketoconazole 10-9 M


title: HepG2, paraxanthine_500uM, 6h, rep3, G09

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.
SP0178_HepG2_cts.txt
BSW913H_G09


title: patient3, KTZ 10-5M

value: Ketoconazole 10-5 M


title: HepG2, Butylparaben_500uM, 6h, rep3, G07

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.
SP0178_HepG2_cts.txt
BSW913H_G07


title: CEBPB adipose specific KO BAT mRNAseq after 4h cold stress, rep5


title: patient3, DES 10-10M

value: Diethylstilbestrol 10-10 M


title: patient3, DMSO

value: DMSO


title: HepG2, paraxanthine_1000uM, 6h, rep3, G04

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.
SP0178_HepG2_cts.txt
BSW913H_G04


title: HepG2, 4-Hydroxybenzoic acid_500uM, 6h, rep3, G06

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.
SP0178_HepG2_cts.txt
BSW913H_G06


title: patient3, DES 10-6M

value: Diethylstilbestrol 10-6 M


title: EMTmock1

description: HMLE-Twist-mock DESeq2 fpkm.txt

value: HMLE-Twist

value: EMT

value: mock


title: patient2, KTZ 10-9M


title: mGR-D647V-tetra_Dex_3 GH4343

city: Bethesda

first: Gordon

last: Hager

state: MD

address: 41 Center Dr

department: NCI

institute: NIH

data_processing:
Raw sequencing data were demultiplexed by Bcl2fastq v2.17.
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment.
Trimmed sequence reads were aligned with mm10 and the annotated transcripts using STAR.
Read count extraction was performed using featureCounts and GENCODE_M21 GTF.
Assembly: mm10
Supplementary files format and content: tab-delimited raw tag counts obtained using featureCounts.

growth_protocol: GR WT and mutant cell lines were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 1% non-essential amino acids, 1% sodium pyruvate, and 5 µg/ml tetracycline (Sigma-Aldrich) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Each treatment condition was performed in triplicate. 5% Drosophila S2 cells were added to each harvested GR cell line to serve as spike-in control. RNA was extracted using the PureLink RNA Mini Kit (ThermoFisher Scientific) following the manufacturer’s protocol.
The quantity and quality of the RNA were assessed using the Agilent Bioanalyzer. Total RNAseq libraries were prepared using the Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit in the first batch, and TruSeq Stranded Total RNA Gold Kit with Ribo-Zero Plus was used in the second batch following the manufacturer’s protocol. Barcoded libraries were pooled together and subjected to paired-end sequencing on a NovaSeq 6000 S1 Sequencer to generate 100 bp paired-end reads

treatment_protocol:
Cells were cultured in DMEM supplemented with 10% charcoal/dextran-treated serum, 2 mM L-glutamine, 1% non-essential amino acids, 1% sodium pyruvate, and 5 µg/ml tetracycline (Sigma-Aldrich) in humidified atmosphere with 5% CO2 at 37C for at least 24h prior to dexamethasone activation
Cells were treated using either 100 nM dexamethasone or ethanol for 2h prior to total RNA isolation.

value: mammary adenocarcinoma

value: Dex


title: mGR-D647V-tetra_EtOH_3 GH4340

value: EtOH


title: mGR-D647V-tetra_EtOH_2 GH4339


title: mGR-D647V-tetra_EtOH_1 GH4338


title: mGR-D647V-tetra_Dex_2 GH4342


title: mGR-D647V-tetra_Dex_1 GH4341


title: mGR-D647V_EtOH_2 GH4333


title: mGR-D647V_EtOH_3 GH4334


title: mGR-D647V_EtOH_1 GH4332


title: mGRwt_Dex_2 GH4331

value: wt


title: mGR-D647V_Dex_1 GH4335


title: mGRwt_Dex_1 GH4330


title: patient2, KTZ 10-5M


title: HepG2, DMSO, 6h, rep3, F09

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.
SP0178_HepG2_cts.txt
BSW913H_F09

value: Liver

value: epithelial-like

value: hepatocellular carcinoma

value: vehicle control


title: HepG2, Butylparaben_50uM, 6h, rep3, F08

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.
SP0178_HepG2_cts.txt
BSW913H_F08

value: 6h exposure of chemical


title: mGR-D647V_Dex_2 GH4336


title: mGRwt_EtOH_2 GH4329


title: mGR-D647V_Dex_3 GH4337


title: mGRwt_EtOH_1 GH4328


title: HepG2, theobromine_500uM, 6h, rep3, F07

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.
SP0178_HepG2_cts.txt
BSW913H_F07


title: Y551A-Dim_EtOH_3 GH4297


title: patient2, DMSO

value: ovary

value: Primary ovarian cells

value: WT


title: patient2, DES 10-10M

value: Diethylstilbestrol 10-10 M


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW913H_F12


title: HepG2, Methylparaben_1uM, 6h, rep3, F04

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.
SP0178_HepG2_cts.txt
BSW913H_F04


title: patient2, DES 10-6M

value: Diethylstilbestrol 10-6 M


title: Y551A-Dim_EtOH_1 GH4295


title: Y551A-Dim_Dex_3 GH4294


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW913H_E12


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW913H_E10


title: patient1, KTZ 10-9M

value: Ketoconazole 10-9 M


title: patient1, KTZ 10-5M

value: Ketoconazole 10-5 M


title: Y551A_EtOH_3 GH4291


title: Y551A_EtOH_1 GH4289


title: Y551A_EtOH_2 GH4290


title: patient1, DMSO

value: DMSO


title: Y551A-Dim_Dex_2 GH4293

value: mammary adenocarcinoma


title: Y551A_Dex_3 GH4288

value: Dex


title: HepG2, Propylparaben_500uM, 6h, rep3, E09

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.
SP0178_HepG2_cts.txt
BSW913H_E09


title: Y551A_Dex_2 GH4287


title: HepG2, Caffeine_500uM, 6h, rep3, E07

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.
SP0178_HepG2_cts.txt
BSW913H_E07


title: patient1, DES 10-10M


title: Y551A_Dex_1 GH4286


title: mGRwt_EtOH_3 GH4285

value: EtOH


title: mGRwt_EtOH_2 GH4284

value: wt


title: Y551A-Dim_EtOH_2 GH4296


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW913H_D10

value: Liver


title: mGRwt_EtOH_1 GH4283


title: mGRwt_Dex_3 GH4282


title: patient1, DES 10-6M


title: HepG2, theobromine_1000uM, 6h, rep3, D09

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.
SP0178_HepG2_cts.txt
BSW913H_D09

value: epithelial-like


title: mGRwt_Dex_2 GH4281


title: Y551A-Dim_Dex_1 GH4292


title: mGRwt_Dex_1 GH4280


title: KGN, KTZ 10-5M, Passage 9 [KGN_P9_KTZ_5]

source_name: granulosa cancer cell line KGN

value: KGN

value: granulosa cancer


title: HepG2, Methylparaben_500uM, 6h, rep3, D08

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.
SP0178_HepG2_cts.txt
BSW913H_D08

value: hepatocellular carcinoma

value: 6h exposure of chemical


title: KGN, KTZ 10-9M, Passage 9 [KGN_P9_KTZ_9]

value: ovary


title: mPDAC_#6597_Mesenchymal_Yap

city: Washington

first: Chunling

last: Yi

state: DC

address: 3700 O St NW

department: Oncology

institute: Georgetown University

data_processing:
Cut&Tag reads were trimmed using TrimGalore (v 0.6.5)
Cut&Tag reads were aligned to the mm10 genome using Bowtie2 (v 2.4.5)
Duplicate reads were removed using Piccard (v 2.0.1)
Blacklist Regions, or genomic regions that frequently produce artifacts and noise, were removed using BEDtools (v 2.28.0)
Peaks were called using HOMER (v 4.11)
Normalized bigWig files were generated using the "makeUCSCfile" command, -bigwig option, from Homer (v 4.11), applying scaling factors calculated using the "csaw" package (v3.15) in RStudio
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: Cut&Tag

source_name: Pancreas

growth_protocol: Low Glucose DMEM, 10% FBS, 1% Pen/Strep

extract_protocol:
The Cut&Tag System operates by permeabilizing living cells with 0.05% Digitonin and the transposase operates to cleave DNA fragments of interest from the genome.
Libraries were prepared using NEBNext Hifi 2x PCR Master Mix for 13 cycles

value: Pancreas

value: Murine Primary PDAC Cells

value: KPF

tag: antibody

value: Yap

tag: morphology

value: Mesenchymal


title: mPDAC_#6597_Mesenchymal_H3K4me3


title: KGN, DMSO, Passage 9 [KGN_P9_DMSO]

value: WT

value: DMSO


title: KGN, DES 10-10M, Passage 9 [KGN_P9_DES_10]

value: Diethylstilbestrol 10-10 M


title: mPDAC_#6597_Mesenchymal_H3K27ac


title: mPDAC_#6394_Mesenchymal_Yap


title: HepG2, DMSO, 6h, rep3, E05

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.
SP0178_HepG2_cts.txt
BSW913H_E05

value: vehicle control


title: KGN, DES 10-6M, Passage 9 [KGN_P9_DES_6]

value: Diethylstilbestrol 10-6 M


title: mPDAC_#6394_Mesenchymal_H3K4me3


title: mPDAC_#6394_Mesenchymal_H3K27ac


title: mPDAC_#6394_Mesenchymal_BRD4


title: HepG2, DMSO, 6h, rep3, D02

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.
SP0178_HepG2_cts.txt
BSW913H_D02

value: Liver


title: KGN, KTZ 10-9M, Passage 8 [KGN_P8_KTZ_9]

value: Ketoconazole 10-9 M


title: mPDAC_#6134_Mesenchymal_Yap


title: mPDAC_#6134_Mesenchymal_H3K4me3


title: HepG2, DMSO, 6h, rep3, C07

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.
SP0178_HepG2_cts.txt
BSW913H_C07

value: epithelial-like


title: KGN, DMSO, Passage 8 [KGN_P8_DMSO]

value: KGN

value: granulosa cancer


title: HepG2, theophylline_500uM, 6h, rep3, D06

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.
SP0178_HepG2_cts.txt
BSW913H_D06

value: hepatocellular carcinoma

value: 6h exposure of chemical


title: K1, replicate 1, scRNAseq

city: Baltimore

first: Nan-ping

last: Weng

state: Maryland

address: 251 Bayview Blvd

institute: National Institute on Aging

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
Total RNA was extracted using Rnaeasy Kit on QIAcute (Qiagen) from resting and stimualted sorted naive CD8+ T cells (24 hours with anti-CD3/28 antibodies) from Kmt2d WT or Kmt2d KO mice. RNA samples were processed using the Illumina TruSeq Stranded mRNA Sample Preparation Kit. Poly (A) tailed RNA was purified from 1 ug of total RNA, fragmented, and reversed-transcribed into cDNAs. Double strand cDNAs were adenylated at the 3' ends and invidually indexed, followed by limited-cycle amplication.
Library was performed according to the manufacter’s instructions (single cell 5’ R2-only protocol, 10x Genomics).

value: Stimulated Naive CD8+ T cells (One day post anti-CD3/CD28)

value: Spleen

tag: age

value: ~4-5 weeks


title: HepG2, theobromine_50uM, 6h, rep3, C04

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.
SP0178_HepG2_cts.txt
BSW913H_C04


title: KGN, DES 10-10M, Passage 8 [KGN_P8_DES_10]

value: ovary


title: HepG2, paraxanthine_50uM, 6h, rep3, D04

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.
SP0178_HepG2_cts.txt
BSW913H_D04


title: K0, replicate 1, scRNAseq

description: 10x Genomics

value: Naive CD8+ T cells


title: mPDAC_#6597_Mesenchymal_BRD4

value: Pancreas

value: Murine Primary PDAC Cells

value: KPF

value: Mesenchymal


title: KGN, DES 10-6M, Passage 8 [KGN_P8_DES_6]

value: WT

value: Diethylstilbestrol 10-6 M


title: mPDAC_#6134_Mesenchymal_BRD4


title: mPDAC_#6055-2_Mesenchymal_Yap

value: Yap


title: W1, replicate 1, scRNAseq

description: 10x Genomics


title: HepG2, Ethylparaben_1uM, 6h, rep3, D03

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.
SP0178_HepG2_cts.txt
BSW913H_D03

value: Liver

value: epithelial-like


title: HepG2, DMSO, 6h, rep3, B06

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.
SP0178_HepG2_cts.txt
BSW913H_B06

value: vehicle control


title: mPDAC_#6055-2_Mesenchymal_H3K4me3


title: HepG2, Caffeine_50uM, 6h, rep3, 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.
SP0178_HepG2_cts.txt
BSW913H_B11

value: hepatocellular carcinoma


title: KGN, KTZ 10-9M, Passage 7 [KGN_P7_KTZ_9]

value: KGN

value: granulosa cancer

value: Ketoconazole 10-9 M


title: KGN, KTZ 10-5M, Passage 7 [KGN_P7_KTZ_5]

value: Ketoconazole 10-5 M


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW913H_A11


title: KGN, DMSO, Passage 7 [KGN_P7_DMSO]

value: ovary

value: DMSO


title: mPDAC_#6134_Mesenchymal_H3K27ac

value: Pancreas


title: mPDAC_#6055-2_Mesenchymal_BRD4

value: Murine Primary PDAC Cells


title: GB7741

first: Jinfag

last: Zhu

address: 10 Center Drive

department: Laboratory of Immune System Biology

institute: NIAID/NIH

data_processing:
PartekFlow was used for transcriptome comparison and expression analysis
Sequenced reads were trimmed for low-quality reads then mapped to mouse mm9 whole genome using STAR method.
The allined reads were quantified using "Quantify to annotated model(Partek E/M)
counts per million (CPM) method was used for data normalization. GSA method was used for differential gene expression analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with fold change and GS mean for every gene

extract_protocol:
Single cell suspension was prepared from erfused lungs digested with Collagenase (1 mg/ml) + Dnase (100 U/ml) for 30 min. Th2 cells (live CD4+ T1ST/2+) were isolated by FACS sorting.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

value: PBS

value: lung ILC2s (live lineage markers- CD127+ T1ST/2+)


title: KGN, KTZ 10-5M, Passage 8 [KGN_P8_KTZ_5]

value: WT


title: HepG2, theophylline_1000uM, 6h, rep3, C05

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.
SP0178_HepG2_cts.txt
BSW913H_C05

value: 6h exposure of chemical


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW913H_A10

value: Liver


title: mPDAC_#5462_Mesenchymal_Yap

value: KPF

value: Yap

value: Mesenchymal


title: KGN, DES 10-10M, Passage 7 [KGN_P7_DES_10]

value: KGN

value: Diethylstilbestrol 10-10 M


title: GB7739


title: mPDAC_#5462_Mesenchymal_Twist2


title: HepG2, 4-Hydroxybenzoic acid_50uM, 6h, rep3, A09

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.
SP0178_HepG2_cts.txt
BSW913H_A09

value: epithelial-like

value: hepatocellular carcinoma


title: GB7740


title: KGN, DES 10-6M, Passage 7 [KGN_P7_DES_6]

value: ovary

value: granulosa cancer

value: Diethylstilbestrol 10-6 M


title: mPDAC_#5462_Mesenchymal_Sox5

value: Pancreas

value: Murine Primary PDAC Cells


title: HepG2, Caffeine_1000uM, 6h, rep3, A02

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.
SP0178_HepG2_cts.txt
BSW913H_A02


title: mPDAC_#6055-2_Mesenchymal_H3K27ac


title: HepG2, Propylparaben_50uM, 6h, rep3, A08

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.
SP0178_HepG2_cts.txt
BSW913H_A08


title: mPDAC_#5462_Mesenchymal_Sox2


title: COV434, KTZ 10-9M, Passage 27 [COV_P27_KTZ_9]

source_name: granulosa cancer cell line COV434

value: Ketoconazole 10-9 M


title: W0, replicate 1, scRNAseq

description: 10x Genomics

value: Naive CD8+ T cells

value: Spleen

value: ~4-5 weeks


title: GB7734

value: Lung

value: Chronic papain

value: lung ILC2s (live lineage markers- CD127+ T1ST/2+)


title: GB7742

value: PBS

value: WT


title: GB7733


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW912H_H12

value: Liver

value: 6h exposure of chemical


title: COV434, DMSO, Passage 27 [COV_P27_DMSO]

value: DMSO


title: COV434, KTZ 10-5M, Passage 27 [COV_P27_KTZ_5]

value: ovary

value: Ketoconazole 10-5 M


title: GB7731


title: mPDAC_#5462_Mesenchymal_H3K4me3

value: KPF

value: Mesenchymal


title: GB7738


title: HepG2, DMSO, 6h, rep2, H08

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.
SP0178_HepG2_cts.txt
BSW912H_H08

value: epithelial-like

value: hepatocellular carcinoma

value: vehicle control


title: mPDAC_#5462_Mesenchymal_H3K27ac

value: Pancreas

value: Murine Primary PDAC Cells


title: COV434, DES 10-10M, Passage 27 [COV_P27_DES_10]

value: granulosa cancer

value: Diethylstilbestrol 10-10 M


title: HepG2, Propylparaben_50uM, 6h, rep2, H06

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.
SP0178_HepG2_cts.txt
BSW912H_H06


title: GB7737

value: Lung

value: Chronic papain

value: lung ILC2s (live lineage markers- CD127+ T1ST/2+)


title: HepG2, Caffeine_50uM, 6h, rep2, H04

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.
SP0178_HepG2_cts.txt
BSW912H_H04

value: Liver


title: COV434, DES 10-6M, Passage 27 [COV_P27_DES_6]

value: WT

value: Diethylstilbestrol 10-6 M


title: mPDAC_#5462_Mesenchymal_cJUN

value: cJun


title: GB7735


title: COV434, KTZ 10-9M, Passage 26 [COV_P26_KTZ_9]

value: ovary

value: Ketoconazole 10-9 M


title: mPDAC_#6749_Intermediate_Yap

value: KPF

value: Yap

value: Intermediate


title: COV434, KTZ 10-5M, Passage 26 [COV_P26_KTZ_5]

value: Ketoconazole 10-5 M


title: HepG2, Methylparaben_50uM, 6h, rep2, G03

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.
SP0178_HepG2_cts.txt
BSW912H_G03

value: epithelial-like

value: hepatocellular carcinoma

value: 6h exposure of chemical


title: HepG2, Butylparaben_1uM, 6h, rep2, H01

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.
SP0178_HepG2_cts.txt
BSW912H_H01


title: mPDAC_#5462_Mesenchymal_BRD4

value: Pancreas

value: Murine Primary PDAC Cells

value: Mesenchymal


title: mPDAC_#6749_Intermediate_H3K27ac


title: mPDAC_#6749_Intermediate_H3K4me3


title: COV434, DMSO, Passage 26 [COV_P26_DMSO]

value: granulosa cancer

value: DMSO


title: HepG2, theophylline_50uM, 6h, rep2, G02

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.
SP0178_HepG2_cts.txt
BSW912H_G02

value: Liver


title: HepG2, 4-Hydroxybenzoic acid_500uM, 6h, rep2, G01

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.
SP0178_HepG2_cts.txt
BSW912H_G01


title: COV434, DES 10-10M, Passage 26 [COV_P26_DES_10]

value: WT

value: Diethylstilbestrol 10-10 M


title: mPDAC_#6547-2_Intermediate_H3K4me3


title: COV434, KTZ 10-9M, Passage 24 [COV_P24_KTZ_9]

value: ovary


title: HepG2, DMSO, 6h, rep2, F09

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.
SP0178_HepG2_cts.txt
BSW912H_F09

value: vehicle control


title: COV434, KTZ 10-5M, Passage 24 [COV_P24_KTZ_5]


title: mPDAC_#6547-2_Intermediate_Yap

value: KPF


title: HepG2, Caffeine_1000uM, 6h, rep2, 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.
SP0178_HepG2_cts.txt
BSW912H_F10


title: HepG2, Propylparaben_500uM, 6h, rep2, F07

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.
SP0178_HepG2_cts.txt
BSW912H_F07


title: COV434, DMSO, Passage 24 [COV_P24_DMSO]


title: mPDAC_#6547-2_Intermediate_H3K27ac


title: HepG2, theophylline_500uM, 6h, rep2, F05

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.
SP0178_HepG2_cts.txt
BSW912H_F05


title: mPDAC_#6547-2_Intermediate_BRD4


title: COV434, DES 10-10M, Passage 24 [COV_P24_DES_10]


title: COV434, DES 10-6M, Passage 26 [COV_P26_DES_6]

value: Diethylstilbestrol 10-6 M


title: mPDAC_#6749_Intermediate_BRD4

value: Intermediate


title: HepG2, Methylparaben_1uM, 6h, rep2, F02

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.
SP0178_HepG2_cts.txt
BSW912H_F02


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW912H_E10


title: COV434, DES 10-6M, Passage 24 [COV_P24_DES_6]


title: MoDP5

city: Vienna

first: Martin

last: Knoefler

address: Waehringer Guertel 18-20

country: Austria

institute: Medical University of Vienna

description: monocytes isolated from Decidua Parietalis

data_processing:
alignement to human reference genome GRCh38 with Gencode 29 annotations using STAR aligner (version 2.6.1a) in 2-pass mode
reads per gene were counted by STAR
isoforms were quantified and compared using RSEM/EBSeq
genes with reads below 100 in 90% of samples were filtered out
differential gene expression was calculated using DESeq2 version 1.22.2
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv file of the count matrices for each batch; filtering step not applied

extract_protocol:
RNA was extracted using the SPLIT RNA extraction kit (Lexogen)
QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina

tag: gestational age

tag: tissue of origin

value: Decidua Parietalis

value: monocyte

tag: donor

tag: sequencing batch


title: HepG2, theobromine_50uM, 6h, rep2, E06

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.
SP0178_HepG2_cts.txt
BSW912H_E06

tag: genotype

value: epithelial-like

value: hepatocellular carcinoma


title: HepG2, 4-Hydroxybenzoic acid_50uM, 6h, rep2, E03

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.
SP0178_HepG2_cts.txt
BSW912H_E03

tag: treatment

value: 6h exposure of chemical


title: mPDAC_#6547-1_Intermediate_BRD4

tag: tissue

value: Pancreas

tag: cell type

value: Murine Primary PDAC Cells


title: mPDAC_#6547-1_Intermediate_H3K27ac

tag: cell line


title: mPDAC_#6547-1_Intermediate_H3K4me3


title: mPDAC_#6547-1_Intermediate_Yap

value: Yap


title: MoDP4


title: MoDB5

description: monocytes isolated from Decidua Basalis

value: Decidua Basalis


title: MoDB4

description: monocytes isolated from Decidua Basalis


title: mPDAC_#6484_Intermediate_Yap


title: HepG2, Propylparaben_1uM, 6h, rep2, E02

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.
SP0178_HepG2_cts.txt
BSW912H_E02

value: Liver

tag: time


title: mPDAC_#6484_Intermediate_H3K4me3


title: MoDP2


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW912H_D12


title: HepG2, DMSO, 6h, rep2, E05

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.
SP0178_HepG2_cts.txt
BSW912H_E05


title: BV_Ctrl_17

type: RNA

city: Beijing

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

country: China

institute: Beijing Zhiyun data technology co. LTD

hyb_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

data_processing: Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

organism: Rattus norvegicus

source_name: blood vessel_Ctrl

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions.

tag: strain background

value: Wistar

tag: strain/model

value: control rat

value: 8 week

tag: Sex

value: male

value: blood vessel


title: MoDB2

description: monocytes isolated from Decidua Basalis


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW912H_D10

value: vehicle control


title: MoDP6


title: mPDAC_#6484_Intermediate_BRD4

value: KPF

value: Intermediate


title: mPDAC_#6032-3_Intermediate_Yap


title: MoDB6

description: monocytes isolated from Decidua Basalis

value: monocyte


title: mPDAC_#6484_Intermediate_H3K27ac


title: HepG2, Ethylparaben_50uM, 6h, rep2, D08

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.
SP0178_HepG2_cts.txt
BSW912H_D08

value: epithelial-like


title: P5

description: macrophages isolated from Decidua Placenta

source_name: PAMM

value: Placenta

value: macrophage


title: HepG2, DMSO, 6h, rep2, D02

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.
SP0178_HepG2_cts.txt
BSW912H_D02

value: hepatocellular carcinoma


title: mPDAC_#6032-3_Intermediate_H3K4me3

value: Pancreas

value: Murine Primary PDAC Cells


title: BV_LPS_6

source_name: blood vessel_LPS

value: LPS rat


title: BV_Ctrl_18


title: BV_Ctrl_16


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW912H_C11

value: Liver

value: 6h exposure of chemical


title: mPDAC_#6032-3_Intermediate_H3K27ac


title: HepG2, paraxanthine_500uM, 6h, rep2, C08

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.
SP0178_HepG2_cts.txt
BSW912H_C08


title: BV_Ctrl_20

value: Wistar

value: control rat


title: P4


title: BV_LPS_3

value: 8 week

value: male


title: P2


title: mPDAC_#6032-2_Intermediate_Yap

value: Yap


title: P6


title: BV_LPS_7

value: blood vessel


title: BV_Ctrl_15


title: HepG2, DMSO, 6h, rep2, C07

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.
SP0178_HepG2_cts.txt
BSW912H_C07

value: vehicle control


title: HepG2, theobromine_1000uM, 6h, rep2, C03

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.
SP0178_HepG2_cts.txt
BSW912H_C03


title: BV_LPS_5


title: DP5

description: macrophages isolated from Decidua Parietalis

source_name: decPAM

value: Decidua Parietalis


title: mPDAC_#6032-2_Intermediate_H3K4me3

value: KPF

value: Intermediate


title: mPDAC_#6032-2_Intermediate_H3K27ac


title: mPDAC_#6032-3_Intermediate_BRD4


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW912H_B10

value: epithelial-like


title: DP4

value: macrophage


title: HepG2, DMSO, 6h, rep2, B06

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.
SP0178_HepG2_cts.txt
BSW912H_B06

value: hepatocellular carcinoma


title: DP2


title: mPDAC_#6032-2_Intermediate_BRD4

value: Pancreas

value: Murine Primary PDAC Cells


title: mPDAC_#6032-1_Intermediate_Yap


title: HepG2, theobromine_500uM, 6h, rep2, B04

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.
SP0178_HepG2_cts.txt
BSW912H_B04

value: Liver


title: HepG2, paraxanthine_50uM, 6h, rep2, B03

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.
SP0178_HepG2_cts.txt
BSW912H_B03

value: 6h exposure of chemical


title: mPDAC_#6032-1_Intermediate_H3K4me3


title: DB4

description: macrophages isolated from Decidua Basalis

source_name: decBAM

value: Decidua Basalis


title: mPDAC_#6032-1_Intermediate_H3K27ac


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW912H_A11


title: DB2


title: DB5


title: BV_LPS_1

value: Wistar

value: LPS rat


title: HepG2, Caffeine_500uM, 6h, rep2, A08

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.
SP0178_HepG2_cts.txt
BSW912H_A08


title: mPDAC_#5520_Intermediate_Yap


title: FP24

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalized using quantile normalization with GenomeStudio software

label: biotin

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Illumina Gene Expression Profiling Assay Guide).

growth_protocol: NCI-H460 cells (2.5x106 cells/mouse) were injected subcutaneously on the mice right flank of 8- to 9-week-old female athymic nude mice

extract_protocol: RNA was extracted with QIAGEN FFPE RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: Mice were peritumorally (p.t.) treated with 200g of monoclonal antibody anti mouse PD-1 (clone RMP1-14) starting 3 days after tumor injection

value: untreated


title: FP22


title: FP23

value: Anti-PD-1 antibody


title: HepG2, Butylparaben_500uM, 6h, rep2, A04

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.
SP0178_HepG2_cts.txt
BSW912H_A04


title: mPDAC_#5520_Intermediate_H3K4me3


title: mPDAC_#6032-1_Intermediate_BRD4


title: DP7


title: FP14


title: FP21


title: FP16


title: HepG2, Butylparaben_50uM, 6h, rep2, B02

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.
SP0178_HepG2_cts.txt
BSW912H_B02


title: FP20


title: HepG2, theophylline_1000uM, 6h, rep2, A03

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.
SP0178_HepG2_cts.txt
BSW912H_A03


title: DB7


title: mPDAC_#5520_Intermediate_BRD4


title: FP18


title: G_A7964

first: Timothy

middle: G

last: Myers

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

hyb_protocol: Illumina BeadChip standard protocol

scan_protocol: HiScan-SQ

data_processing: Signal data were extracted from the image files with the Gene Expression module (v. 1.9.0) of the GenomeStudio software (v. 2011.1) from Illumina, Inc. Signal intensities were converted to log2 scale. Calculation of detection p-values is described in the GenomeStudio Gene Expression Module User Guide. Data for array probes with insufficient signal (probes not having at least two arrays with detection P value < 0.1) were removed from the dataset. After dropping nonperforming probes, quantile normalization was applied across all arrays

source_name: cultured monocytes

label_protocol: Ambion® Illumina® TotalPrep™ RNA Amplification Kit (Ambion, Inc, Austin, TX) was used similarly to manufacturer instructions and as previously described here (PMID: 1689846) to prepare biotinylated cRNA from isolated total RNA. Input was normalized to 300 ng to 500 ng per sample and yields ranged from 10 µg to 70 µg

growth_protocol: Monocytes from human donors will be seeded in T-25 tissue culture flasks at a concentration of 1 x 10^6 cells/ml in 10 mls for a total of 1 x 10^7 cells per flask.

extract_protocol: Rneasy

treatment_protocol: IFN Treatment Conditions: IFN-alpha (200 ng/ml), IFN-gamma (200 ng/ml), IFN-alpha (100 ng/ml) + IFN-gamma (100 ng/ml); All treatment times: 24 hours

tag: stimulation

value: Interferon gamma

tag: exp replicate


title: HepG2, Ethylparaben_50uM, 6h, rep1, H07

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.
SP0178_HepG2_cts.txt
BSW911H_H07


title: AG_A7965

value: IFNa + IFNg


title: AG_A7967


title: A_A7961

value: Interferon alpha


title: FP15


title: mPDAC_#5346_Intermediate_Yap

value: KPF

tag: antibody

value: Yap

tag: morphology


title: G_A7963


title: DB8

tag: gestational age


title: G_A7962


title: DB6

tag: tissue of origin


title: HepG2, Propylparaben_500uM, 6h, rep1, H04

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.
SP0178_HepG2_cts.txt
BSW911H_H04

value: epithelial-like


title: mPDAC_#5520_Intermediate_H3K27ac

value: Intermediate


title: A_A7960

tag: donor


title: DP8

value: Decidua Parietalis

value: macrophage

tag: sequencing batch


title: HepG2, DMSO, 6h, rep1, H08

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.
SP0178_HepG2_cts.txt
BSW911H_H08

tag: genotype

value: hepatocellular carcinoma

value: vehicle control


title: DP3


title: HepG2, paraxanthine_500uM, 6h, rep1, H03

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.
SP0178_HepG2_cts.txt
BSW911H_H03

value: Liver

tag: treatment

value: 6h exposure of chemical


title: AG_A7966


title: FP17


title: A_A7959


title: mPDAC_#5346_Intermediate_H3K27ac

tag: tissue

value: Pancreas

value: Murine Primary PDAC Cells


title: mPDAC_#5346_Intermediate_H3K4me3

tag: cell type


title: DP6


title: DB3

value: Decidua Basalis


title: FP13

value: untreated


title: FP19

value: Anti-PD-1 antibody


title: mPDAC_#5346_Intermediate_BRD4

tag: cell line


title: DP1


title: HepG2, theophylline_1000uM, 6h, rep1, H02

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.
SP0178_HepG2_cts.txt
BSW911H_H02

tag: time


title: DB1


title: mPDAC_#6516_Epithelial_H3K4me3

value: Epithelial


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW911H_G12


title: mPDAC_#6516_Epithelial_Yap


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW911H_G11


title: MM-seq_T7E1_Cre

city: Guangzhou

first: Zhang

last: Zhang

state: Guangdong

address: Xingangxi Roda 135#

institute: Sun Yat-sen University

data_processing:
library strategy: MM-seq (Modification-induced Mismatch Sequencing)
Raw reads were firsly removed sequencing adaptors by cutadapt (v. 1.15). Clean reads were mapped to reference genome using bowtie2 (v 2.3.3) with default parameters except one mismatch. The sorted bam file was generated using samtools (v1.6; ref). Integrative Genomics Viewer (IGV) was used for data visualization. Picard (v1.129) MarkDuplicates was used to mark and remove duplicates.
For MM-seq data using T7E1/MBN endonuclease, we discarded single-end mapping results and counted both 5’ and 3’ terminals of each fragment as potential T7E1 digest sites. For MM-seq data using lambda exonuclease, only 5’ terminal of sequenced fragments were calculated. A binominal distribution model was assumed that each fragment could be randomly sheared or cleavage by structure-sensitive enzymes. The P-values were further corrected by Bonferroni correction, and FDR≤0.01 was set as the cutoff.
Genome_build: human (hg19), mouse (mm10), Chlamydomonas reinhardtii (v5.5), Escherichia coli (ensembl release-45)
Supplementary_files_format_and_content: genomic positions of 6mA

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas reinhardtii

growth_protocol: Chlamydomonas reinhardtii was cultured in Tris Acetate Phosphate (TAP) medium with modified trace element solution (pH 7.5) at 110 rpm at 22 ℃. Human cell lines were cultured in 10% (v/v)  FBS (Gibco) containing DMEM (Corning) at 37 °C under 5 % CO2 and passed mycoplasma contamination test.

extract_protocol:
Chlamydomonas reinhardtii: cells were treated with lysis buffer (50mM Tris-HCl(pH8.0), 200mM NaCl, 20mM EDTA, 2% SDS, 1mg/ml Proteinase K) and CTAB buffer (50mM Tris-HCl (pH8.0), 20mM EDTA, 1.4M NaCl, 2% CTAB, 1% PVP4000) at 65℃ for 30 min. Total RNA was digested using 100 µg/ml RNase A for 20 min at room temperature. Genomic DNA was isolated by phenol-chloroform extraction and ethanol precipitation. E. coli: Genomic DNA was extracted using FastPure Bacteria DNA Isolation Mini Kit (Vazyme, DC103). Cell lines: Cells were collected and then lysed by lysis buffer (0.1% TritonX-100, 0.1% Tween-20 diluted in 1× PBS) supplemented with 5 μg Proteinase K (Sangon) and 2 μl RNase A (Takara) under the condition of shaking (~1000 rpm) at 37 ℃ for 30 min. E. coli: MinElute PCR Purification Kit (QIAGEN, 28006) was used to isolate genomic DNA.
During MM-seq with endonuclease digestion, 6mA immunoprecipitation reaction was conducted in total volume of 500μL with 4μg fragmented gDNA, 5μL (0.5mg/mL) anti-m6A monoclonal antibody (CST), 100μL 5×IP Buffer, 30μL pre-block protein-A magnetic beads. The mixture was transferred to head-over-tail rotating wheel to incubate at 4 °C overnight and placed on a magnetic rack until beads are captured. The supernatant was discarded and the beads was washed with 500 μL ice-cold 1×IP Buffer by gentle vortex. The beads were re-suspended in the T7E1 or MBN digestion system (M0302S or M0250S, NEB) and incubated for 30 min at 37 °C. After washed with 500 μL ice-cold 1×IP Buffer, 5μL Proteinase K was added to the beads and incubated for 2h at 65 °C with 1,000 rpm. The products were purified by Zymo Research oligo Clean & Concentrator and eluted in 12 μL ddH2O. NGS libraries were constructed for products from genomic DNA using NEBNext Ultra II DNA Library Prep Kit (E7645S). Same procedure about 6mA immunoprecipitation reaction was applied when using exonuclease cleavage in MM-seq. The beads with IP products were conducted primer extension, end-repair, adaptor ligation and primer extension steps using T4 DNA polymerase (M0203S, NEB), T4PNK (T4 Polynucleotide Kinase, M0201S, NEB), T4 DNA ligase (M0202S, NEB) and Phi29 DNA polymerase (M0264S, NEB), respectively. The beads were washed by 500 μL ice-cold 1×IP Buffer after each treatment. The beads were resuspended in the lambda exonuclease (M0262S, NEB) digestion system incubating for 30 min at 37 °C. After washed by 1×IP Buffer, the beads were treated by 5μL Proteinase K to digest antibody. The mixture were incubated for 2h at 65 °C with 1,000 rpm speed. Then the beads were spin down briefly and placed the tube on magnetic rack for 30s until beads were captured and transferred the supernatant in a new tube. The products were purified by Zymo Research oligo Clean & Concentrator and elute in 12 μL ddH2O. After primer extension by Phi29 DNA polymerase, the products were added into R2 Adapter ligation reaction. Then, the products were clean up by using 52 μL well-mixed AMPure beads and eluted dsDNA fragment in 30 μL ddH2O. After the PCR amplification, the library was purified using 50 μL well mixed AMPure beads or agarose gel size selection.

tag: cell line or tissue

tag: sequence type

value: MM-seq by T7E1 endonucIeases

value: wide type


title: HepG2, Ethylparaben_500uM, 6h, rep1, G08

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.
SP0178_HepG2_cts.txt
BSW911H_G08

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

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.


title: mPDAC_#6516_Epithelial_H3K27ac

value: KPF


title: MM-seq_MBN_Cre

value: MM-seq by MBN endonucIeases


title: HepG2, theobromine_1000uM, 6h, rep1, G01

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.
SP0178_HepG2_cts.txt
BSW911H_G01

value: epithelial-like


title: HepG2, DMSO, 6h, rep1, F09

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.
SP0178_HepG2_cts.txt
BSW911H_F09


title: HepG2, Methylparaben_1uM, 6h, rep1, F08

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.
SP0178_HepG2_cts.txt
BSW911H_F08


title: MM-seq_lambda_Cre_rep2

value: MM-seq by lambda exonucleases


title: MM-seq_lambda_Cre_rep1


title: mPDAC_#6389_Epithelial_H3K4me3


title: U_A7956

value: Unstimulated


title: HepG2, paraxanthine_1000uM, 6h, rep1, F06

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.
SP0178_HepG2_cts.txt
BSW911H_F06

value: hepatocellular carcinoma


title: mPDAC_#6389_Epithelial_Yap

value: Yap


title: mPDAC_#6389_Epithelial_H3K27ac


title: HepG2, theophylline_50uM, 6h, rep1, F04

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.
SP0178_HepG2_cts.txt
BSW911H_F04

value: Liver


title: anti-PD1 + SN-38 (rep2)

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Trimming adaptor sequences and removing reads of low quality were performed by cutadapt (v2.4).
Quantified reads were aligned to the mouse genome (GRCm38) by STAR (v2.7.2a) and then gene-level read counts were generated based on the annotations of Gencode (vM19)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: Head and neck squamous cell carcinoma

growth_protocol: A total of 6x10^6 Sq-1979 cells were suspended in 0.1 mL of saline, mixed with 0.1 mL Matrigel (BD Biosciences) homogeneously, and the subcutaneously injected into the back area of 6-week-old male C3H/HeN mice.

extract_protocol:
Total RNA was isolated using the AllPrep DNA/RNA mini kit (Qiagen)
Libraries were prepared using a TruSeq Stranded mRNA Preparation Kit (Illumina)

treatment_protocol: The vehicle control, rat anti-PD1 antibody, and SN-38 drug were treated, respectivley

value: Head and neck squamous cell carcinoma

tag: strain

value: C3H/HeN mice

value: anti-PD1 and SN-38


title: anti-PD1 + SN-38 (rep1)


title: HepG2, theobromine_500uM, 6h, rep1, F02

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.
SP0178_HepG2_cts.txt
BSW911H_F02

value: 6h exposure of chemical


title: mPDAC_#6516_Epithelial_BRD4

value: Pancreas

value: Murine Primary PDAC Cells


title: G_A7705

tag: stimulation

value: Interferon gamma


title: G_A7706

tag: exp replicate


title: U_A7957


title: AG_A7708

value: IFNa + IFNg


title: anti-PD1 + SN-38 (rep3)


title: mPDAC_#6055-1_Epithelial_Yap

tag: antibody

value: Epithelial


title: U_A7958


title: G_A7704


title: A_A7703

value: Interferon alpha


title: A_A7702


title: A_A7701


title: AG_A7709


title: mPDAC_#6389_Epithelial_BRD4

value: KPF

tag: morphology


title: SN-38 (rep2)


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW911H_E12

value: epithelial-like


title: mPDAC_#6055-1_Epithelial_H3K4me3


title: mPDAC_#6055-1_Epithelial_H3K27ac


title: U_A7700


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW911H_E10


title: AG_A7707


title: SN-38 (rep1)


title: HepG2, 4-Hydroxybenzoic acid_500uM, 6h, rep1, E09

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.
SP0178_HepG2_cts.txt
BSW911H_E09


title: mPDAC_#6055-1_Epithelial_BRD4


title: anti-PD1 (rep3)


title: HepG2, DMSO, 6h, rep1, E05

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.
SP0178_HepG2_cts.txt
BSW911H_E05

value: vehicle control


title: U_A7699

value: Unstimulated


title: mPDAC_#5601_Epithelial_H3K4me3


title: HepG2, Caffeine_1000uM, 6h, rep1, E08

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.
SP0178_HepG2_cts.txt
BSW911H_E08

value: hepatocellular carcinoma


title: anti-PD1 (rep1)


title: anti-PD1 (rep2


title: mPDAC_#5601_Epithelial_Yap

value: Yap


title: AG_A7696


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW911H_D11

value: Liver


title: Vehicle (rep3)

value: Head and neck squamous cell carcinoma

value: Vehicle control


title: mPDAC_#5601_Epithelial_H3K27ac


title: SN-38 (rep3)

value: C3H/HeN mice


title: Vehicle (rep2)


title: mPDAC_#5601_Epithelial_BRD4


title: Vehicle (rep1)


title: mPDAC_#5596_Epithelial_H3K4me3


title: mPDAC_#5596_Epithelial_Yap


title: Beta cells IFNγ 5ng.mL #3

city: Paris

first: Masaya

last: OSHIMA

address: 123 boulevard de Port Royal

country: France

institute: INSERM U1016

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

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.

value: Beta cells

value: IFNγ 5ng.mL, 20h


title: HepG2, DMSO, 6h, rep1, D10

first: Yuqing

last: Shan

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.
SP0178_HepG2_cts.txt
BSW911H_D10


title: HepG2, Butylparaben_1uM, 6h, rep1, D05

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.
SP0178_HepG2_cts.txt
BSW911H_D05

value: 6h exposure of chemical


title: HepG2, DMSO, 6h, rep1, D02

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.
SP0178_HepG2_cts.txt
BSW911H_D02


title: HepG2, Methylparaben_500uM, 6h, rep1, D03

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.
SP0178_HepG2_cts.txt
BSW911H_D03


title: Beta cells IFNγ 5ng.mL #2

value: Pancreas


title: mPDAC_#5596_Epithelial_H3K27ac

value: Murine Primary PDAC Cells


title: AG_A7697

value: IFNa + IFNg


title: Beta cells IFNγ 5ng.mL #1


title: HepG2, DMSO, 6h, rep1, C07

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.
SP0178_HepG2_cts.txt
BSW911H_C07


title: HepG2, Butylparaben_500uM, 6h, rep1, 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.
SP0178_HepG2_cts.txt
BSW911H_C11


title: mPDAC_#5596_Epithelial_BRD4

value: Epithelial


title: AG_A7695


title: G_A7693

value: Interferon gamma


title: F-N-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)

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.

tag: gender

value: female

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

tag: diet

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

tag: disease state

value: Non-alcoholic steatohepatitis


title: A_A7689

value: Interferon alpha

tag: donor


title: G_A7694


title: Beta cells control #3

value: Control


title: Beta cells control #2


title: G_A7692


title: F-N-KO-2

value: Liver

tag: genotype


title: F-N-KO-3


title: HepG2, 4-Hydroxybenzoic acid_50uM, 6h, rep1, C05

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.
SP0178_HepG2_cts.txt
BSW911H_C05

value: epithelial-like

tag: treatment

value: hepatocellular carcinoma


title: HepG2, Caffeine_50uM, 6h, rep1, C03

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.
SP0178_HepG2_cts.txt
BSW911H_C03


title: A_A7690


title: A_A7691


title: MM-seq_lambda_Ecoli_SYSY_dcm_minus

data_processing:
Raw reads were firsly removed sequencing adaptors by cutadapt (v. 1.15). Clean reads were mapped to reference genome using bowtie2 (v 2.3.3) with default parameters except one mismatch. The sorted bam file was generated using samtools (v1.6; ref). Integrative Genomics Viewer (IGV) was used for data visualization. Picard (v1.129) MarkDuplicates was used to mark and remove duplicates.
For MM-seq data using T7E1/MBN endonuclease, we discarded single-end mapping results and counted both 5’ and 3’ terminals of each fragment as potential T7E1 digest sites. For MM-seq data using lambda exonuclease, only 5’ terminal of sequenced fragments were calculated. A binominal distribution model was assumed that each fragment could be randomly sheared or cleavage by structure-sensitive enzymes. The P-values were further corrected by Bonferroni correction, and FDR≤0.01 was set as the cutoff.
Assembly: human (hg19), mouse (mm10), Chlamydomonas reinhardtii (v5.5), Escherichia coli (ensembl release-45)
Supplementary files format and content: genomic positions of 6mA
Library strategy: MM-seq (Modification-induced Mismatch Sequencing)

organism: Escherichia coli

source_name: Ecoli DH5α

extract_protocol:
Chlamydomonas reinhardtii: cells were treated with lysis buffer (50mM Tris-HCl(pH8.0), 200mM NaCl, 20mM EDTA, 2% SDS, 1mg/ml Proteinase K) and CTAB buffer (50mM Tris-HCl (pH8.0), 20mM EDTA, 1.4M NaCl, 2% CTAB, 1% PVP4000) at 65℃ for 30 min. Total RNA was digested using 100 µg/ml RNase A for 20 min at room temperature. Genomic DNA was isolated by phenol-chloroform extraction and ethanol precipitation. E. coli: Genomic DNA was extracted using FastPure Bacteria DNA Isolation Mini Kit (Vazyme, DC103). Cell lines: Cells were collected and then lysed by lysis buffer (0.1% TritonX-100, 0.1% Tween-20 diluted in 1× PBS) supplemented with 5 μg Proteinase K (Sangon) and 2 μl RNase A (Takara) under the condition of shaking (~1000 rpm) at 37 ℃ for 30 min. E. coli: MinElute PCR Purification Kit (QIAGEN, 28006) was used to isolate genomic DNA.
During MM-seq with endonuclease digestion, 6mA immunoprecipitation reaction was conducted in total volume of 500μL with 4μg fragmented gDNA, 5μL (0.5mg/mL) anti-m6A monoclonal antibody (CST), 100μL 5×IP Buffer, 30μL pre-block protein-A magnetic beads. The mixture was transferred to head-over-tail rotating wheel to incubate at 4 °C overnight and placed on a magnetic rack until beads are captured. The supernatant was discarded and the beads was washed with 500 μL ice-cold 1×IP Buffer by gentle vortex. The beads were re-suspended in the T7E1 or MBN digestion system (M0302S or M0250S, NEB) and incubated for 30 min at 37 °C. After washed with 500 μL ice-cold 1×IP Buffer, 5μL Proteinase K was added to the beads and incubated for 2h at 65 °C with 1,000 rpm. The products were purified by Zymo Research oligo Clean & Concentrator and eluted in 12 μL ddH2O. NGS libraries were constructed for products from genomic DNA using NEBNext Ultra II DNA Library Prep Kit (E7645S).  Same procedure about 6mA immunoprecipitation reaction was applied when using exonuclease cleavage in MM-seq. The beads with IP products were conducted primer extension, end-repair, adaptor ligation and primer extension steps using T4 DNA polymerase (M0203S, NEB), T4PNK (T4 Polynucleotide Kinase, M0201S, NEB), T4 DNA ligase (M0202S, NEB) and Phi29 DNA polymerase (M0264S, NEB), respectively. The beads were washed by 500 μL ice-cold 1×IP Buffer after each treatment. The beads were resuspended in the lambda exonuclease (M0262S, NEB) digestion system incubating for 30 min at 37 °C. After washed by 1×IP Buffer, the beads were treated by 5μL Proteinase K to digest antibody. The mixture were incubated for 2h at 65 °C with 1,000 rpm speed. Then the beads were spin down briefly and placed the tube on magnetic rack for 30s until beads were captured and transferred the supernatant in a new tube. The products were purified by Zymo Research oligo Clean & Concentrator and elute in 12 μL ddH2O. After primer extension by Phi29 DNA polymerase, the products were added into R2 Adapter ligation reaction. Then, the products were clean up by using 52 μL well-mixed AMPure beads and eluted dsDNA fragment in 30 μL ddH2O. After the PCR amplification, the library was purified using 50 μL well mixed AMPure beads or agarose gel size selection.

value: MM-seq by lambda exonucleases

value: dam+/dcm-


title: U_A7686

value: Unstimulated


title: Alpha cells IFNγ 5ng.mL #3

tag: tissue

value: Pancreas

value: Alpha cells

value: IFNγ 5ng.mL, 20h


title: F-N-KO-1


title: MM-seq_T7E1_Ecoli

value: MM-seq by T7E1 endonucIeases

value: wide type


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW911H_B11

tag: cell type

value: 6h exposure of chemical


title: Alpha cells IFNγ 5ng.mL #2


title: U_A7688


title: U_A7687


title: F-N-C-3

value: female

value: Control mouse


title: F-N-C-5

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

value: Non-alcoholic steatohepatitis


title: HepG2, DMSO, 6h, rep1, B06

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.
SP0178_HepG2_cts.txt
BSW911H_B06

tag: cell line

value: vehicle control


title: Alpha cells IFNγ 5ng.mL #1


title: F-N-C-2

value: Liver


title: HepG2, 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.
SP0178_HepG2_cts.txt
BSW911H_A11

value: epithelial-like

tag: time


title: MM-seq_lambda_Ecoli

tag: cell line or tissue


title: Alpha cells control #3

value: Control


title: F-N-C-1


title: HepG2, theophylline_500uM, 6h, rep1, A07

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.
SP0178_HepG2_cts.txt
BSW911H_A07

value: hepatocellular carcinoma


title: Alpha cells control #2


title: HepG2, Caffeine_500uM, 6h, rep1, B12

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.
SP0178_HepG2_cts.txt
BSW911H_B12


title: MM-seq_lambda_Ecoli_CST

tag: sequence type

value: MM-seq by lambda exonucleases

value: wild type


title: Beta cells control #1

value: Pancreas

tag: strain

value: Beta cells


title: F-HF-KO-4

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: Alpha cells control #1

value: Alpha cells


title: F-HF-KO-3

value: female


title: HepG2, Ethylparaben_1uM, 6h, rep1, A03

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.
SP0178_HepG2_cts.txt
BSW911H_A03

value: 6h exposure of chemical


title: Delta cells IFNγ 5ng.mL #3

value: Delta cells

value: IFNγ 5ng.mL, 20h


title: Delta cells IFNγ 5ng.mL #2


title: F-HF-KO-2


title: MCF7, DMSO, 6h, rep3, 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
RBSW913A-H8

source_name: Breast; Mammary gland

value: Breast; Mammary gland

value: epithelial cell

value: Adenocarcinoma

value: vehicle control


title: Delta cells IFNγ 5ng.mL #1


title: F-HF-KO-1

value: Liver


title: F-HF-C-4

value: Control mouse


title: MCF7, Propylparaben_1uM, 6h, rep3, 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
RBSW913A-H3


title: HepG2, Butylparaben_50uM, 6h, rep1, A06

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.
SP0178_HepG2_cts.txt
BSW911H_A06

value: epithelial-like

value: hepatocellular carcinoma


title: Delta cells control #3

value: Pancreas

value: Control


title: MCF7, 4-Hydroxybenzoic acid_1uM, 6h, rep3, 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
RBSW913A-H12


title: Delta cells control #2


title: MCF7, Ethylparaben_500uM, 6h, rep3, H9

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-H9