title: IDH1R132H immortalized human astrocytes, treatment, H3K27me3, replicate 3

description:
Library name: CT002-15
DEGup_promoters_K27me3_RPKM.txt


title: BPC_0-01_donor2_R2_P6

status: Public on Jan 06 2026

type: SRA

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description: Library name: s498

library_source: transcriptomic

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using  DRAGEN analysis v1.3.0 on the Illumina Basespace Sequence Hub (Illumina, Inc., San Diego, CA, USA). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the R-ODAF_Health_Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed December 2024), which manages workflows using snakemake v8.0 (Mölder et al., 2021) and relies on scripts in R (v.4.3.2). The preprocessing steps use fastp v0.23.2 for trimming (Chen et al., 2018), STAR v2.7.8a (Dobin et al., 2013) to perform alignment of raw reads to the reference sequence, and the qCount function of the QuasR R package (v1.30.0; Gaidatzis et al., 2015) to extract the feature counts from the aligned reads (BAM files) using features specified in a GTF file. A samples-by-probes count matrix was produced.
Assembly: Probe sequence set provided by biospyder based on Human Whole Transcriptome kit v2.1
Supplementary files format and content: Tab-delimited table containing read counts per TempO-Seq probe

molecule: total RNA

organism: Homo sapiens

source_name: Mammary

growth_protocol: HMECs from three biological donors were kept at low passage and not allowed to exceed 80% confluency to preserve epithelial subpopulations and maintained in complete media. Cells were cultured in T75 flasks supplemented Mammary Epithelial Cell Growth Medium containing phenol red at 37°C in a humidified atmosphere (5% CO2).

extract_protocol:
Cells were washed with phosphate-buffered saline and lysed in situ using 2x TempO-Seq lysis buffer diluted with an equal amount of PBS for TempO-Seq library building.
Gene expression was measured using the TempO-Seq Human Whole Transcriptome v2.0 and 2.1 kits (BioSpyder Technologies Inc, Carlsbad, California) as per the manufacturer’s instructions

treatment_protocol: For the experiment, cells (passage 7) were seeded at 20,000 cells per well in 96-well plates in supplemented MEGM without phenol red (Lonza Bioscience). After 48 h, the media were removed and replaced with supplement-free MEGM without phenol red containing chemicals of interest at eight concentrations (0.001, 0.01, 0.1, 0.5, 1, 5, 10, 50 µM) and E2 (0.1 and 1 nM). The experiment included at least six plate-matched solvent controls (0.1% DMSO) and four technical replicates from each donor were exposed for 48 h.

tag: tissue

value: Mammary

tag: cell line

value: Primary

tag: cell type

value: Epithelial

tag: genotype

value: WT

tag: treatment

value: chemical exposure

tag: chemical

value: bisphenol C

tag: dose

tag: donor

tag: batch


title: IDH1R132H immortalized human astrocytes, treatment, H3K4me3, replicate 2

city: Heidelberg

first: Sevin

last: Turcan

address: Im Neuenheimer Feld 420

country: Germany

institute: University Hospital Heidelberg

description:
Library name: CT002-23
DEGdn_promoters_K4me3_RPKM.txt

library_source: genomic

data_processing:
After alignment with bowtie2, peaks analysis was performed using SEACR, deeptools and bedtools.
Assembly: hg38
Supplementary files format and content: RPKM.txt files
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: astrocytes

extract_protocol:
CUT&Tag was performed with 60,000 cells per sample in triplicates. After bead-binding, cells were permeabilized and incubated with primary antibodies directed at H3K4me1 (Active Motif), H3K4me3 (Active Motif), H3K27me3 (Cell signaling) and H3K27ac (Active Motif), followed by secondary antibody incubation (guinea pig anti-rabbit, Antibodies online). For chromatin cleavage and adapter ligation, pAG-Tn-5 (Epicypher) was used.
Library preparation was conducted by PCR with barcoded primers. Samples underwent quality control utilizing D1000 Screen Tape on a Tapestation 4200 (Agilent).

value: astrocytes

value: immortalized IDH1R132H astrocytes

value: astrocyte


title: IDH1R132H immortalized human astrocytes, treatment, H3K27me3, replicate 1

description:
Library name: CT002-13
DEGdn_promoters_K27me3_RPKM.txt


title: BPC_0-001_donor2_R2_P6

description: Library name: s497


title: BPS_50_donor1_R2_P6

description: Library name: s496

value: 4,4'-bisphenol S


title: BPS_10_donor1_R2_P6

description: Library name: s495


title: IDH1R132H immortalized human astrocytes, control, H3K27me3, replicate 2

description:
Library name: CT002-2
DEGdn_promoters_K27me3_RPKM.txt


title: BPS_0-1_donor1_R2_P6

description: Library name: s491


title: VLX47

city: Geneva

first: Andrew

last: Biancolin

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

description: Library name: S114

data_processing:
Illumina bcl2fastq software (v.2.20.0) used for basecalling.
Assembly: UCSC hg38
Supplementary files format and content: csv, raw counts for each sample

source_name: Blood

extract_protocol:
Qiagen RNEasy
Illumina TruSeq HT stranded mRNA

value: Blood

value: No

value: Monocytes

tag: time

tag: treatment (light_condition)

value: Natural

tag: disease state

value: Type 2 Diabetes


title: BPC_1_donor2_R2_P6

description: Library name: s501


title: VLX48

description: Library name: S115


title: BPS_0-001_donor1_R2_P6

description: Library name: s489


title: BPS_0-5_donor1_R2_P6

description: Library name: s492


title: VLX45

description: Library name: S112

value: Artificial


title: BPS_0-01_donor1_R2_P6

description: Library name: s490


title: VLX44

description: Library name: S111


title: VLX46

description: Library name: S113


title: VLX42

description: Library name: S109


title: BPC_50_donor1_R2_P6

description: Library name: s488


title: VLX41

description: Library name: S108


title: BPC_10_donor1_R2_P6

description: Library name: s487


title: BPC_5_donor1_R2_P6

description: Library name: s486


title: IDH1R132H immortalized human astrocytes, control, H3K27me3, replicate 3

description:
Library name: CT002-3
DEGup_promoters_K27me3_RPKM.txt


title: BPC_0-5_donor1_R2_P6

description: Library name: s484


title: BPS_5_donor1_R2_P6

description: Library name: s494


title: VLX39

description: Library name: S105


title: VLX40

description: Library name: S107


title: BPC_0-01_donor1_R2_P6

description: Library name: s482


title: BPS_1_donor1_R2_P6

description: Library name: s493


title: VLX38

description: Library name: S104


title: BPC_0-1_donor1_R2_P6

description: Library name: s483


title: VLX36

description: Library name: S102


title: BPC_1_donor1_R2_P6

description: Library name: s485


title: BPC_0-001_donor1_R2_P6

description: Library name: s481


title: VLX35

description: Library name: S101


title: VLX43

description: Library name: S110


title: DMSO_0-1_donor3_R5_P5

description: Library name: s477

value: vehicle control

value: dimethyl sulfoxide


title: VLX37

description: Library name: S103


title: VLX34

description: Library name: S100


title: VLX33

description: Library name: S99


title: DMSO_0-1_donor3_R6_P5

description: Library name: s478

value: Mammary

value: Primary


title: VLX29

description: Library name: S94


title: DMSO_0-1_donor3_R4_P5

description: Library name: s476

value: Epithelial

value: WT


title: DMSO_0-1_donor3_R3_P5

description: Library name: s475


title: DMSO_0-1_donor3_R2_P5

description: Library name: s474


title: VLX31

description: Library name: S97


title: VLX30

description: Library name: S96


title: DMSO_0-1_donor3_R1_P5

description: Library name: s473


title: DMSO_0-1_donor2_R4_P5

description: Library name: s468


title: VLX25

description: Library name: S90


title: VLX27

description: Library name: S92


title: VLX26

description: Library name: S91


title: DMSO_0-1_donor2_R5_P5

description: Library name: s469


title: VLX24

description: Library name: S89


title: DMSO_0-1_donor2_R3_P5

description: Library name: s467


title: DMSO_0-1_donor2_R2_P5

description: Library name: s466


title: DMSO_0-1_donor1_R7_P5

description: Library name: s463


title: VLX21

description: Library name: S86


title: VLX23

description: Library name: S88


title: VLX22

description: Library name: S87


title: DMSO_0-1_donor1_R8_P5

description: Library name: s464


title: VLX20

description: Library name: S85


title: VLX32

description: Library name: S98


title: DMSO_0-1_donor1_R6_P5

description: Library name: s462


title: VLX17

description: Library name: S81


title: VLX19

description: Library name: S83


title: VLX28

description: Library name: S93


title: DMSO_0-1_donor1_R5_P5

description: Library name: s461


title: VLX18

description: Library name: S82


title: DMSO_0-1_donor2_R6_P5

description: Library name: s470


title: DMSO_0-1_donor1_R3_P5

description: Library name: s459


title: VLX15

description: Library name: S79


title: DMSO_0-1_donor1_R1_P5

description: Library name: s457


title: E2_10_donor1_R4_P5

description: Library name: s456

value: chemical exposure


title: E2_10_donor3_R1_P5

description: Library name: s454


title: E2_1_donor1_R4_P5

description: Library name: s455


title: DMSO_0-1_donor2_R1_P5

description: Library name: s465


title: VLX14

description: Library name: S78


title: VLX13

description: Library name: S77


title: VLX12

description: Library name: S76


title: VLX11

description: Library name: S75


title: E2_1_donor3_R1_P5

description: Library name: s453


title: VLX16

description: Library name: S80


title: E2_10_donor2_R1_P5

description: Library name: s452


title: VLX10

description: Library name: S74


title: E2_1_donor2_R1_P5

description: Library name: s451


title: VLX9

description: Library name: S120


title: E2_10_donor1_R1_P5

description: Library name: s450


title: DMSO_0-1_donor1_R4_P5

description: Library name: s460


title: VLX8

description: Library name: S119


title: E2_1_donor1_R1_P5

description: Library name: s449


title: BPS_50_donor1_R4_P5

description: Library name: s448


title: VLX7

description: Library name: S118


title: BPS_10_donor1_R4_P5

description: Library name: s447


city: Poznań

first: Paulina

last: Jackowiak

address: Zygmunta Noskowskiego str. 12/14

country: Poland

institute: Institute of Bioorganic Chemistry

description:
Library name: PacBio Iso-Seq (total RNA, amputated WT, 0 hpa)
genotype: CIW4 asexual; condition: WT ; tissue: whole-animal; time point: 0 hpa

data_processing:
Data were quality-checked with MultiQC and then trimmed using Trim-Galore to remove adapters and low-quality bases. Reads were aligned to the Schmidtea mediterranea genome using Minimap2 and quantified with Stringtie2.
Assembly: The reference genome SchMedS2. Genome annotation file (SchMed_Pn) can be downloaded from the foot in a GEO Series record

organism: Schmidtea mediterranea

source_name: whole-body sample

growth_protocol: Standard planarian culture conditions

extract_protocol:
Worms were flash-frozen in liquid nitrogen. Total RNA was isolated using the mirVana™ miRNA Isolation Kit  following the manufacturer’s protocol, and treated with TURBO™ DNase as per the provided instructions. The concentration of the purified RNA samples was quantified using a Qubit 4 Fluorometer and the Qubit™ RNA Broad Range (BR) Assay Kit. RNA quality was assessed using the Agilent TapeStation system with High Sensitivity RNA Assay. RNA with RIN >8 was used. Ribosomal RNA (rRNA) depletion was done with the riboPOOL kit. The sample was mixed with 1% spike-in, SIRV Set-4 (Iso Mix E0 / ERCC / Long SIRVs).
Library was prepared using Iso-Seq express 2.0 kit and Iso-Seq SMRTbell prep kit 3.0. Library quality and size distribution were assessed using a TapeStation High Sensitivity D5000 Assay, and library concentration was quantified using the Qubit 1x dsDNA HS Kit  to ensure optimal input for sequencing. Libraries were sequenced on a PacBio Sequel IIe.

value: whole-body sample

value: No treatment; amputated and harvested immediately (0 hpa)


title: VLX6

description: Library name: S117


description:
Library name: PacBio Iso-Seq (rRNA-depleted composite, WT, multi-regeneration time points)
genotype: CIW4 asexual; condition: WT and cut worms; tissue: whole-animal; time point: 0, 1, 3, 6, 9, 12, 24, 48 hpa and 1 uncut worms

extract_protocol:
Worms were flash-frozen in liquid nitrogen. Total RNA was isolated using the mirVana™ miRNA Isolation Kit following the manufacturer’s protocol, and treated with TURBO™ DNase as per the provided instructions. The concentration of the purified RNA samples was quantified using a Qubit 4 Fluorometer and the Qubit™ RNA Broad Range (BR) Assay Kit. RNA quality was assessed using the Agilent TapeStation system with High Sensitivity RNA ScreenTapes. RNA with RIN >8 was used. 100 ng DNase-treated total RNA was then mixed with 1% spike-in, SIRV Set-4 (Iso Mix E0 / ERCC / Long SIRVs).
Library was prepared using Iso-Seq express 2.0 kit and Iso-Seq SMRTbell prep kit 3.0. Library quality and size distribution were assessed using a TapeStation High Sensitivity D5000 Assay, and library concentration was quantified using the Qubit 1x dsDNA HS Kit  to ensure optimal input for sequencing. Libraries were sequenced on a PacBio Sequel IIe.

value: No additional treatment; represents baseline and regenerating conditions


title: VLX5

description: Library name: S116


title: VLX4

description: Library name: S106


description:
Library name: PacBio Iso-Seq (rRNA-depleted RNA, amputated WT, 0 hpa)
genotype: CIW4 asexual; condition: WT ; tissue: whole-animal; time point: 0 hpa


title: BPS_0-5_donor1_R4_P5

description: Library name: s444

value: 4,4'-bisphenol S


title: BPS_0-1_donor1_R4_P5

description: Library name: s443


title: BPS_1_donor1_R4_P5

description: Library name: s445


title: BPS_0-01_donor1_R4_P5

description: Library name: s442


title: BPS_0-001_donor1_R4_P5

description: Library name: s441


title: VLX3

description: Library name: S95

value: Blood


title: SYAT_GFP_CR_1

city: Lausanne

first: David

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

institute: École polytechnique fédérale de Lausanne

description: Library name: SYAT_GFP_1_S8

data_processing:
Reads were aligned to the mouse reference genome mm10 and the Drosophila reference genome dm6 using STAR with settings ‘--alignMatesGapMax 2000 --alignIntronMax 1 --alignEndsType EndtoEnd -- outFilterMultimapNmax 1’. Duplicate reads were removed with Picard (Broad Institute) and reads not mapping to chromosomes 1–19, X, or Y were removed. Normalization factors were calculated on the number of non-duplicated reads uniquely mapped to Drosophila genome for each sample and applied to downsample the total number of reads mapped to mouse genome. For each sample, peaks were called with MACS2 with settings ‘-f BAMPE -g mm’.
Assembly: mm10
Supplementary files format and content: bigWig files include RPKM normalized reads
Supplementary files format and content: bed files with peaks obtained using MACS2
Library strategy: CUT&RUN

organism: Mus musculus

source_name: SYAT

growth_protocol: CGR8 mouse ES cells, SYAT mESC and ZHBTc4 mESC were routinely cultured at 37 °C and 5% CO2 on cell culture-treated dishes coated with 0.1% gelatin using the following culture medium: GMEM supplemented with 10% ES-cell qualified fetal bovine serum, 1% nonessential amino acids, 2mM L-glutamine,  2mM sodium pyruvate, 100μM 2-mercaptoethanol, 1% penicillin and streptomycin, in-house produced leukemia inhibitory factor (LIF), CHIR99021 at 3 μM and PD184352 at 0.8 μM. Cells were passaged by trypsinization every two to three days. Three days before all experiments, mESC medium was changed to Serum LIF medium: GMEM supplemented with 10% ES-cell qualified fetal bovine serum, nonessential amino acids, 2 mM L-glutamine, sodium pyruvate, 100 μM 2-mercaptoethanol, penicillin and streptomycin, in-house produced leukemia inhibitory factor (LIF). SYAT cells were cultured routinely with 200nM Auxinole (Control condition) to avoid basal degradation of SRCAP. For SRCAP degradation, SYAT cells were treated for 1, 2, 4, 6 or 8 h with 500µM Indole-3-Acetic Acid (IAA). For induction of Oct4 knock-down in ZHBTc4 cells, 1µg/mL Doxycycline was added for 9 or 12 h prior cell collection.

extract_protocol:
100000 SYAT cells were fixed with 0.1% formaldehyde for 5 minutes. Nuclei were then extracted and bound to Concanavalin A beads. Immunoprecipitation was performed with 1/50 antibody against GFP (ab290) or against SRCAP (ESL-103). After washes and elution, DNA was purifiied using Phenol-Chloroform extraction.
Libraries were prepared with NEBNext Ultra II DNA Library Prep Master Mix Set (NEB, #E7103) using insert size selection of 250 bp. Sequencing was performed using 75 nt paired end reads on an Element Biosciences Aviti sequencer.

value: SYAT

value: mESC

tag: chip antibody

value: Abcam #ab290


title: BPC_50_donor1_R4_P5

description: Library name: s440

value: bisphenol C


title: SYAT_SRCAP_CR_1

description: Library name: SYAT_SRCAP_1_S6

value: Kerafast #ESL-103


title: BPS_5_donor1_R4_P5

description: Library name: s446


title: BPC_1_donor1_R4_P5

description: Library name: s437


title: SYAT IAA500µM 2h Nanog  2

description: Library name: SYAT_IAA500uM_Nanog_2_S5

data_processing:
Reads were aligned to the mouse reference genome mm10 and the Drosophila reference genome dm6 using STAR with settings ‘--alignMatesGapMax 2000 --alignIntronMax 1 --alignEndsType EndtoEnd -- outFilterMultimapNmax 1’. Duplicate reads were removed with Picard (Broad Institute) and reads not mapping to chromosomes 1–19, X, or Y were removed. Normalization factors were calculated on the number of non-duplicated reads uniquely mapped to Drosophila genome for each sample and applied to downsample the total number of reads mapped to mouse genome. For each sample, peaks were called with MACS2 with settings ‘-f BAMPE -g mm’.
Assembly: mm10
Supplementary files format and content: bigWig files include RPKM normalized reads
Supplementary files format and content: bed files with peaks obtained using MACS2

extract_protocol:
5 million cells were fixed in 1% formaldehyde or formaldehyde+2mM DSG for TF for 10 min at room temperature, quenched with 250 mM Tris-HCl pH 8.0, washed with PBS, spun down, and stored at −80 °C. The cell pellet was resuspended in 1.5 ml LB1 (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% TritonX-100), incubated 10 min at 4 °C, spun down, and resuspended in 1.5 ml LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and incubated 10 min at 4 °C. The pellet was spun down and rinsed twice with SDS shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.15% SDS), and finally resuspended in 0.9 ml SDS shearing buffer. All buffers contain 1:100 diluted Protease Inhibitor Cocktail in DMSO (Sigma). The suspension was transferred to a milliTUBE 1 ml AFA fiber and sonicated on a E220 focused ultrasonicator (Covaris) using the following settings: 20 min, 200 cycles, 5% duty, 140W, and input sample aliquots were taken. 1.5-5μg of sonicated chromatin was incubated with suitable antibody and for normalization 10ng Drosophila chromatin (Active Motif) and 0.5μg anti-H2Av drosophila-specific antibody (Active Motif)/µg of mouse chromatin. ChIP was performed using ChIP-IT High Sensitivity kit (Active Motif) following manufacturer protocol.
Libraries were prepared with NEBNext Ultra II DNA Library Prep Master Mix Set (NEB, #E7103) using insert size selection of 250 bp. Sequencing was performed using 75 nt paired end reads on an Element Biosciences Aviti sequencer.

treatment_protocol: SRCAP degradation was induced by 2-hour treatment with different doses IAA.

value: Cell Signaling Technology #8822

value: IAA 500µM 2h


title: BPC_5_donor1_R4_P5

description: Library name: s438

value: Mammary


title: SYAT IAA5µM 2h Nanog  2

description: Library name: SYAT_IAA5uM_Nanog_2_S4

value: IAA 5µM 2h


title: VLX2

description: Library name: S84

value: No

value: Monocytes

value: Natural

value: Type 2 Diabetes


title: BPC_0-5_donor1_R4_P5

description: Library name: s436

value: Primary

value: Epithelial

value: WT

value: chemical exposure


title: BPC_0-1_donor1_R4_P5

description: Library name: s435


title: BPC_0-01_donor1_R4_P5

description: Library name: s434


title: VLX1

description: Library name: S73

value: Blood


title: BPS_50_donor3_R1_P5

description: Library name: s432

value: 4,4'-bisphenol S


title: SYAT IAA500nM 2h Nanog  2

description: Library name: SYAT_IAA500nM_Nanog_2_S3

value: SYAT

value: mESC

value: IAA 500nM 2h


title: BPC_0-001_donor1_R4_P5

description: Library name: s433

value: bisphenol C


title: BPS_10_donor3_R1_P5

description: Library name: s431


title: ISS-N1-targeting PMO ASO, replicate 3

city: Ames

first: Ravindra

middle: N

last: Singh

state: IA

address: 2034 Veterinary Medicine

department: Biomedical Sciences

country: USA

institute: Iowa State University

description: Library name: F20PMO_3

data_processing:
Reads from RNA-Seq were mapped to the human reference genome build GRCh38 using HISAT2
Mapped reads were assigned to genes according to the Gencode v33 human transcriptome annotation using the featureCounts script from the Subread software package
Assembly: hg38
Supplementary files format and content: Matrix of read count data by gene

source_name: Skin

growth_protocol: GM03813 cells were grown in MEM media (Gibco) supplemented with 15% FBS and 1X GlutaMAX in a 37˚C incubator in the presence of 5% CO2

extract_protocol:
Cells were collected in TRIzol reagent and RNA isolated following the manufacturer's protocol, then DNase treated with RQ1 RNase-free Dnase.
Libraries were generated from rRNA-depleted RNA using the NEBNext Ultra II directional RNA library prep kit for Illumina. Libraries were barcoded for multiplexing using NEBNext Dual Index oligos for Illumina.

treatment_protocol: Cells were treated with 6 µM ASO by nucleofection with a Lonza Amaxa 4D nucleofector using the primary cell P2 kit with the EN-150 electroporation protocol. Cells were collected 24 hours after nucleofection

value: Skin

value: Fibroblast

value: SMA


title: SYAT IAA250nM 2h Nanog  2

description: Library name: SYAT_IAA250nM_Nanog_2_S2

value: Cell Signaling Technology #8822

value: IAA 250nM 2h


title: BPS_1_donor3_R1_P5

description: Library name: s429

value: Mammary


title: BPS_0-01_donor3_R1_P5

description: Library name: s426


title: BPS_5_donor3_R1_P5

description: Library name: s430


title: ISS-N1-targeting OMe-modified ASO, replicate 3

description: Library name: F18OMe_3


title: SYAT IAA5µM 2h Nanog  1

description: Library name: SYAT_IAA5uM_Nanog_S7

value: IAA 5µM 2h


title: BPS_0-1_donor3_R1_P5

description: Library name: s427

value: Primary


title: Scrambled PMO ASO, replicate 3

description: Library name: ScrPMO_3


title: SYAT IAA500µM 2h Nanog  1

description: Library name: SYAT_IAA500uM_Nanog_S6

value: IAA 500µM 2h


title: SYAT NT 2h Nanog  2

description: Library name: SYAT_NT_Nanog_2_S1

value: Control


title: BPC_10_donor3_R1_P5

description: Library name: s423

value: Epithelial

value: WT

value: chemical exposure


title: SYAT IAA500nM 2h Nanog  1

description: Library name: SYAT_IAA500nM_Nanog_S8

value: SYAT


title: BPS_0-5_donor3_R1_P5

description: Library name: s428

value: 4,4'-bisphenol S


title: ISS-N1-targeting MOE-modified ASO, replicate 3

description: Library name: F18MOE_3


title: BPC_50_donor3_R1_P5

description: Library name: s424


title: Scrambled OMe-modified ASO, replicate 3

description: Library name: ScrOMe_3


title: SYAT IAA250nM 2h Nanog  1

description: Library name: SYAT_IAA250nM_Nanog_S9

value: mESC


title: Scrambled MOE-modified ASO, replicate 3

description: Library name: ScrMOE_3


title: Untreated sample, replicate 3

description: Library name: Untreated_3


title: BPC_1_donor3_R1_P5

description: Library name: s421

value: bisphenol C


title: ISS-N1-targeting PMO ASO, replicate 2

description: Library name: F20PMO_2

value: Skin


title: BPS_0-001_donor3_R1_P5

description: Library name: s425


title: BPC_0-1_donor3_R1_P5

description: Library name: s419


title: SYAT NT 2h Nanog  1

description: Library name: SYAT_NT_Nanog_S5


title: BPC_0-001_donor3_R1_P5

description: Library name: s417


title: BPC_0-01_donor3_R1_P5

description: Library name: s418


title: BPS_50_donor2_R1_P5

description: Library name: s416


title: E18 stroma, hgih adhesion, litter 3

city: Philadelphia

first: Alex

last: Hughes

state: PA

address: 390 Towne Building 220 S. 33rd Street

institute: University of Pennsylvania

description:
Library name: YLQF64_28
column name in YLQF64-E18-stroma_allsamples_expression-matrix.tsv: YLQF64_28_cpm, YLQF64_28_counts

data_processing:
Quality of the resulting fastq files was assessed using FastQC v0.12.1.
Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp.
Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1.
PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0.
Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32.
Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id.
Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.
Assembly: GRCm39
Supplementary files format and content: tab-separated value format file. Columns contain sample CPM and raw counts, and rows contain genes

molecule: polyA RNA

source_name: CD1 mouse fetal kidney

growth_protocol: Nephrogenic stroma were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicilin/streptomycin (P/S) in a humidified incubator set to 37oC and 5% CO2

extract_protocol:
Total RNA was isolated from cells using a Rneasy mini plus kit (Qiagen).
Libraries were prepared using a commercial service (Plasmidsaurus). In brief, 500-1000 ng total RNA per sample was subject to mRNA capture, reverse transcription, and second strand synthesis. This was followed by tagmentation and Illumina library indexing and amplification.

treatment_protocol: Nephrogenic zone cells (NZC) were isolated from pooled E18 wild-type CD1 kidneys following a 15 minute incubation at 37oC with a solution containing 0.25% pancreatin and 0.1% collagenase in DPBS. NZC isolation was quenched using FBS at 10% volume following digestion. NZCs were washed once in FACS media (DPBS with 2% FBS, 1% P/S, and 10 uM Y27632) prior to antibody incubation. NZCs were incubated in primary antibody on ice for 1 hour (1E6 cells per 200 ul; goat anti-PDGFRa-FITC (1:200 in FACS media)). NZCs were washed once with FACS media prior to secondary antibody incubation. NZCs were incubated in secondary antibody on ice for 1 hour (1E6 cells per 200 ul; rabbit anti-goat-AF647 (1:200 in FACS media)). NZCs were washed once with FACS media and passed through a 40 um cell strainer prior to FACS. The PDGFRa positive populaiton was isolated using a BD FACSAria Fusion as nephrogenic stroma. Isolated nephrogenic stroma were seeded onto PDMS coated coverslips prepared with low or high concenentration fibronectin solutions and cultured for 18 hours prior to RNA isolation. Glass coverslips were spincoated with PDMS and incubated in low (500 ng/mL in DPBS) or high (50,000 ng/mL in DPBS) concentration bovine fibronectin solutions for 4 hours in a humidified incubator set to 37oC and 5% CO2. Coverslips were washed once with DPBS prior to cell seeding.

value: CD1 mouse fetal kidney

value: nephrogenic stroma

value: wild-type

value: litter 3, PDMS substrated incubated in 50,000 ng/mL fibronectin in DPBS


title: E18 stroma, hgih adhesion, litter 2

description:
Library name: YLQF64_27
column name in YLQF64-E18-stroma_allsamples_expression-matrix.tsv: YLQF64_27_cpm, YLQF64_27_counts

value: litter 2, PDMS substrated incubated in 50,000 ng/mL fibronectin in DPBS


title: Scrambled PMO ASO, replicate 2

description: Library name: ScrPMO_2

value: Fibroblast

value: SMA


title: BPS_10_donor2_R1_P5

description: Library name: s415

value: Mammary

value: Primary


title: E18 stroma, hgih adhesion, litter 1

description:
Library name: YLQF64_26
column name in YLQF64-E18-stroma_allsamples_expression-matrix.tsv: YLQF64_26_cpm,YLQF64_26_counts

value: litter 1, PDMS substrated incubated in 50,000 ng/mL fibronectin in DPBS


title: BPC_5_donor3_R1_P5

description: Library name: s422

value: Epithelial

value: WT


title: BPS_5_donor2_R1_P5

description: Library name: s414

value: chemical exposure


title: Scrambled MOE-modified ASO, replicate 2

description: Library name: ScrMOE_2


title: ISS-N1-targeting MOE-modified ASO, replicate 2

description: Library name: F18MOE_2


title: BPS_0-1_donor2_R1_P5

description: Library name: s411

value: 4,4'-bisphenol S


title: BPS_0-5_donor2_R1_P5

description: Library name: s412


title: BPS_0-01_donor2_R1_P5

description: Library name: s410


title: BPS_1_donor2_R1_P5

description: Library name: s413


title: ISS-N1-targeting OMe-modified ASO, replicate 2

description: Library name: F18OMe_2


title: BPS_0-001_donor2_R1_P5

description: Library name: s409


title: E18 stroma, low adhesion, litter 3

description:
Library name: YLQF64_25
column names in YLQF64-E18-stroma_allsamples_expression-matrix.tsv: YLQF64_25_cpm,YLQF64_25_counts

value: litter 3, PDMS substrated incubated in 500 ng/mL fibronectin in DPBS


title: E18 stroma, low adhesion, litter 1

description:
Library name: YLQF64_23
column names in YLQF64-E18-stroma_allsamples_expression-matrix.tsv: YLQF64_23_cpm, YLQF64_23_counts

value: litter 1, PDMS substrated incubated in 500 ng/mL fibronectin in DPBS


title: BPC_50_donor2_R1_P5

description: Library name: s408

value: bisphenol C


title: E18 stroma, low adhesion, litter 2

description:
Library name: YLQF64_24
column names in YLQF64-E18-stroma_allsamples_expression-matrix.tsv: YLQF64_24_cpm, YLQF64_24_counts

value: CD1 mouse fetal kidney

value: litter 2, PDMS substrated incubated in 500 ng/mL fibronectin in DPBS


title: Scrambled OMe-modified ASO, replicate 2

description: Library name: ScrOMe_2

value: Skin


title: ISS-N1-targeting PMO ASO, replicate 1

description: Library name: F20PMO_1


title: BPC_10_donor2_R1_P5

description: Library name: s407


title: BPC_0-5_donor3_R1_P5

description: Library name: s420


title: BPC_0-5_donor2_R1_P5

description: Library name: s404


title: E14, 3D culture, mylk-shRNA, mCherry-negative, litter 3

description:
Library name: YLQF64_22
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_22_cpm, YLQF64_22_counts

growth_protocol: kidney explant cultures were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicilin/streptomycin (P/S) in a humidified incubator set to 37oC and 5% CO2

extract_protocol:
After 72 hours, kidney explant cultures were pooled per condition and digested using a solution composed of 1:1 (v/v) 0.25% trypsin-EDTA and 1% collagenase. Digests were carried out for 30 minutes in a humidified incubator set to 37oC and 5% CO2. Digests were quenched using FBS set to 10% volume and washed in FACS media (DPBS with 2% FBS and 1% P/S) prior to sorting. Cells within the top 25% of mCherry signal were collected as the positive fraction, and cells within the bottom 50% of mCherry signal were collected as the negative fraction. Cells were washed once with DPBS prior to total RNA isolation using a Rneasy mini plus kit (Qiagen).
Libraries were prepared and sequenced using a commercial service (Plasmidsaurus). In brief, 100-300 ng total RNA per sample was subject to mRNA capture, reverse transcription, and second strand synthesis. This was followed by tagmentation and Illumina library indexing and amplification.

treatment_protocol: E14 wild-type CD1 kidneys were isolated and transduced with AAV2 carrying cag driven mCherry transduction reporter upstream of two mir30 shRNA knockdown cassettes. Target sequences were designed against two regions of the Mylk gene (Mylk-shRNA), one region on the Rock1 gene and one region on the Rock2 gene (Rock1/2-shRNA), or randomly arranged Rock1 and Rock2 target sequences (scramble-shRNA). Kidneys were transduced in DMEM supplemented with 10% FBS and 1% P/S plus ~1012 GC/mL AAV2 for 4 hours in a humidified incubator set to 37oC and 5% CO2. Kidneys were washed once with media prior to embedding in a composite hydrogel composed of equivolume collagen I and matrigel. Cultures were maintained for 72 hours in DMEM supplemented with 10% FBS and 1% P/S.

value: embryonic kidney

value: wild-type

value: litter 3, mylk-shRNA, mCherry-negative


title: BPC_5_donor2_R1_P5

description: Library name: s406


title: BPC_0-01_donor2_R1_P5

description: Library name: s402


title: Scrambled PMO ASO, replicate 1

description: Library name: ScrPMO_1

value: Fibroblast

value: SMA


title: ISS-N1-targeting MOE-modified ASO, replicate 1

description: Library name: F18MOE_1


title: E14, 3D culture, mylk-shRNA, mCherry-negative, litter 1

description:
Library name: YLQF64_20
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_20_cpm, YLQF64_20_counts

value: litter 1, mylk-shRNA, mCherry-negative


title: BPC_0-001_donor2_R1_P5

description: Library name: s401

value: Mammary

value: Primary


title: E14, 3D culture, mylk-shRNA, mCherry-positive, litter 3

description:
Library name: YLQF64_19
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_19_cpm, YLQF64_19_counts

value: litter 3, mylk-shRNA, mCherry-positive


title: Scrambled MOE-modified ASO, replicate 1

description: Library name: ScrMOE_1


title: BPS_5_donor1_R1_P5

description: Library name: s398

value: Epithelial

value: WT

value: chemical exposure


title: BPS_50_donor1_R1_P5

description: Library name: s400

value: 4,4'-bisphenol S


title: E14, 3D culture, mylk-shRNA, mCherry-negative, litter 2

description:
Library name: YLQF64_21
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_21_cpm, YLQF64_21_counts

value: litter 2, mylk-shRNA, mCherry-negative


title: BPC_1_donor2_R1_P5

description: Library name: s405

value: bisphenol C


title: ISS-N1-targeting OMe-modified ASO, replicate 1

description: Library name: F18OMe_1


title: BPS_1_donor1_R1_P5

description: Library name: s397


title: BPS_0-001_donor1_R1_P5

description: Library name: s393


title: Untreated sample, replicate 1

description: Library name: Untreated_1


title: Scrambled OMe-modified ASO, replicate 1

description: Library name: ScrOMe_1


title: BPS_0-5_donor1_R1_P5

description: Library name: s396


title: BPC_50_donor1_R1_P5

description: Library name: s392


title: E14, 3D culture, rock1/2-shRNA, mCherry-negative, litter 3

description:
Library name: YLQF64_15
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_15_cpm, YLQF64_15_counts

value: CD1 mouse fetal kidney

value: litter 3, rock1/2-shRNA, mCherry-negative


title: E14, 3D culture, mylk-shRNA, mCherry-positive, litter 1

description:
Library name: YLQF64_17
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_17_cpm, YLQF64_17_counts

value: embryonic kidney

value: litter 1, mylk-shRNA, mCherry-positive


title: E14, 3D culture, rock1/2-shRNA, mCherry-negative, litter 1

description:
Library name: YLQF64_13
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_13_cpm, YLQF64_13_counts

value: wild-type

value: litter 1, rock1/2-shRNA, mCherry-negative


title: BPC_10_donor1_R1_P5

description: Library name: s391


title: BPC_0-1_donor2_R1_P5

description: Library name: s403


title: 46_GFP-ChIP-seq_BRD2-AID_GFP-BRD4_2hH2O

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Library name: S46

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Illumina output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the hg38 and dm6 (spike-in) genomes using Bowtie2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments,  normalized using spike-in reads and reformatted in the bigWig file format. GFP ChIP was not spike-in normalized since different construct has different expression level except for JQ1 treatment. Spikein normalization was not used for some BRD2 and histone acetylation samples, as indicated in Methods.
Assembly: hg38, dm6 for spike-in reads
Supplementary files format and content: bigWig

source_name: colon

growth_protocol: All cell lines were cultured in DMEM (Corning, #10013CV), supplemented with 10% FBS (Sigma-Aldrich, #F2442), 1% Glutmax (Gibco, #35050061), and 1% PS (Gibco, #15140122), in 37°C incubator with 5% CO2.

extract_protocol:
DNA was purified with either QIAquick PCR purification kit (Qiagen, #28106) or ChIP DNA Clean & Concentrator kit (Zymo Research, #D5205).
Libraries were prepared by using the KAPA HTP library preparation kit (Roche, #07961901001) and sequenced on the Illumina NovaSeq 6000 or NextSeq 2000.

treatment_protocol: Auxin (#ab146403) was purchased from abcam. Doxycycline (#72742) was obtained from Stem Cell Technologies. dEBT6 (#S8762) was purchased from Selleckchem. JQ1 (#4499) was purchased from Tocris.BET and mutant expression were achieved by adding 50nM Dox into the medium and incubating for 36 or 48h.

value: colon

value: DLD-1 BRD2-AID

value: epithelial

tag: antibody

value: GFP

tag: construct

tag: treatment 2


title: BPC_5_donor1_R1_P5

description: Library name: s390

value: Mammary

value: Primary


title: BPC_0-5_donor1_R1_P5

description: Library name: s388

value: Epithelial

value: WT


title: E14, 3D culture, rock1/2-shRNA, mCherry-negative, litter 2

description:
Library name: YLQF64_14
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_14_cpm, YLQF64_14_counts

value: litter 2, rock1/2-shRNA, mCherry-negative


title: BPS_10_donor1_R1_P5

description: Library name: s399

value: chemical exposure

value: 4,4'-bisphenol S


title: E14, 3D culture, mylk-shRNA, mCherry-positive, litter 2

description:
Library name: YLQF64_18
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_18_cpm, YLQF64_18_counts

value: CD1 mouse fetal kidney

value: litter 2, mylk-shRNA, mCherry-positive


title: BPS_0-1_donor1_R1_P5

description: Library name: s395


title: E14, 3D culture, rock1/2-shRNA, mCherry-positive, litter 3

description:
Library name: YLQF64_11
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_11_cpm, YLQF64_11_counts

value: embryonic kidney

value: litter 3, rock1/2-shRNA, mCherry-positive


title: BPC_0-1_donor1_R1_P5

description: Library name: s387

value: bisphenol C


title: BPC_0-01_donor1_R1_P5

description: Library name: s386


title: BPC_0-001_donor1_R1_P5

description: Library name: s385


title: 45_Pol2-ChIP-seq_BRD4-IAA7_48hDox_GFP-BRD4∆BD_3hAux

description: Library name: S45

value: DLD-1 BRD4-AID

value: RPB1 NTD

tag: treatment 1


title: 10_Pol2-ChIP-seq_BRD2-AID_48hDox_GFP-BRD2_3hAux

description: Library name: S10

tag: tissue

value: colon

value: DLD-1 BRD2-AID


title: E14, 3D culture, rock1/2-shRNA, mCherry-positive, litter 2

description:
Library name: YLQF64_10
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_10_cpm, YLQF64_10_counts

value: wild-type

value: litter 2, rock1/2-shRNA, mCherry-positive


title: DMSO_0-1_donor3_R23_P4

description: Library name: s381

value: Mammary

tag: cell line

value: Primary

value: vehicle control

value: dimethyl sulfoxide


title: BPC_1_donor1_R1_P5

description: Library name: s389

tag: cell type

value: Epithelial

value: WT

value: chemical exposure


title: DMSO_0-1_donor3_R24_P4

description: Library name: s382

tag: genotype


title: 9_Pol2-ChIP-seq_BRD2-AID_48hDox_GFP_3hAux

description: Library name: S09

value: epithelial

value: GFP


title: 47_GFP-ChIP-seq_BRD2-AID_GFP-BRD4_2hAux

description: Library name: S47


title: DMSO_0-1_donor2_R24_P4

description: Library name: s380

tag: treatment


title: DMSO_0-1_donor1_R24_P4

description: Library name: s378

tag: chemical


title: E14, 3D culture, rock1/2-shRNA, mCherry-positive, litter 1

description:
Library name: YLQF64_9
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_9_cpm, YLQF64_9_counts

value: CD1 mouse fetal kidney

value: embryonic kidney

value: litter 1, rock1/2-shRNA, mCherry-positive


title: E14, 3D culture, scramble-shRNA, mCherry-negative, litter 3

description:
Library name: YLQF64_7
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_7_cpm, YLQF64_7_counts

value: litter 3, scramble-shRNA, mCherry-negative


title: DMSO_0-1_donor1_R23_P4

description: Library name: s377

tag: dose


title: DMSO_0-1_donor3_R21_P4

description: Library name: s373

tag: donor


title: E14, 3D culture, scramble-shRNA, mCherry-negative, litter 2

description:
Library name: YLQF64_6
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_6_cpm, YLQF64_6_counts

value: litter 2, scramble-shRNA, mCherry-negative


title: E14, 3D culture, scramble-shRNA, mCherry-negative, litter 1

description:
Library name: YLQF64_5
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_5_cpm, YLQF64_5_counts

value: litter 1, scramble-shRNA, mCherry-negative


title: 8_Pol2-ChIP-seq_BRD2-AID_48hDox_GFP_3hH2O

description: Library name: S08

value: colon

value: DLD-1 BRD2-AID

value: RPB1 NTD


title: 7_GFP-ChIP-seq_BRD4-IAA7_18hDox_GFP-BRD4_3hJQ1

description: Library name: S07

value: DLD-1 BRD4-AID


title: DMSO_0-1_donor3_R22_P4

description: Library name: s374

value: Mammary

value: Primary

value: vehicle control

tag: batch


title: DMSO_0-1_donor1_R22_P4

description: Library name: s370

value: Epithelial

value: WT

value: dimethyl sulfoxide


title: DMSO_0-1_donor2_R23_P4

description: Library name: s379


title: E14, 3D culture, scramble-shRNA, mCherry-positive, litter 3

description:
Library name: YLQF64_3
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_3_cpm, YLQF64_3_counts

value: wild-type

value: litter 3, scramble-shRNA, mCherry-positive


title: 6_GFP-ChIP-seq_BRD4-IAA7_18hDox_GFP-BRD4_3hDMSO

description: Library name: S06

value: epithelial

value: GFP


title: 5_GFP-ChIP-seq_DLD-1_18hDox_GFP-BRD2_3hJQ1

description: Library name: S05


title: 11_Pol2-ChIP-seq_BRD2-AID_48hDox_GFP-BRD2∆BD_3hAux

description: Library name: S11


title: E14, 3D culture, scramble-shRNA, mCherry-positive, litter 2

description:
Library name: YLQF64_2
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_2_cpm, YLQF64_2_counts

value: CD1 mouse fetal kidney

value: embryonic kidney

value: litter 2, scramble-shRNA, mCherry-positive


title: E2_1_donor3_R4_P4

description: Library name: s365

value: chemical exposure


title: E2_10_donor3_R4_P4

description: Library name: s366


title: DMSO_0-1_donor2_R22_P4

description: Library name: s372


title: DMSO_0-1_donor1_R21_P4

description: Library name: s369


title: 4_GFP-ChIP-seq_DLD-1_18hDox_GFP-BRD2_3hDMSO

description: Library name: S04

value: colon


title: E14, 3D culture, scramble-shRNA, mCherry-positive, litter 1

description:
Library name: YLQF64_1
column name in YLQF64-E14-shRNA_allsamples_expression-matrix.tsv: YLQF64_1_cpm,YLQF64_1_counts

value: litter 1, scramble-shRNA, mCherry-positive


title: 25_IP_SN10_rep1_H3K27me3

city: Seattle

first: Shivani

last: Srivastava

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description:
Library name: 25_IP_SN10_rep1_H3K27me3
25_IP_SN10_rep1_H3K27me3

data_processing:
Trim Galore was used to examine read quality and trim adapters. Reads were aligned to mm10 reference genome using Bowtie2. Genome coverage profiles were generated using bedtools genomecov.
Assembly: mm10
Supplementary files format and content: bigwig file, containing genome coverage normalized to count per million.
Library strategy: CUT&Tag

source_name: T cells

growth_protocol: Retrovirus was produced by transient transfection of Plat-E cells with MP71 vectors encoding ROR1 CAR, cJun.ROR1 CAR, or BATF.ROR1 CAR. Viral supernatant was harvested 48 hr after transfection, filtered through a 0.45 μm pore filter, and snap-frozen in liquid nitrogen for long-term storage. Cell suspensions were prepared from spleen and peripheral lymph nodes of donor mice by tissue disruption with glass slides and filtered through a 40 μm filter. Murine CD8+  T cells were enriched from spleens and peripheral lymph nodes of donor mice using untouched negative isolation kits (Stem Cell) and stimulated with anti-CD3/28 Mouse T-Activator Dynabeads (ThermoFisher) at a bead to cell ratio of 1:1 for 24 hr in a 37°C, 5% CO2 incubator in complete RPMI (RPM1 1640, 10% heat inactivated FBS, 1 mM sodium pyruvate, 1 mM HEPES, 100 U/ml penicillin/streptomycin, 50 μM b-mercaptoethanol) supplemented with 50 U/ml recombinant human IL-2 (Peprotech). Non-tissue culture plates were coated with 12.5 μg/ml RetroNectin (TaKaRa) according to the manufacturer’s protocol, and plates were loaded with pre-titered virus per well and centrifuged for 2 hr at 3000xg at 32°C. Murine T cells were harvested and resuspended at 1x10^6 cells/ml in fresh complete RPMI supplemented with 50 U/ml IL-2. Viral supernatant was aspirated from RetroNectin-coated plates, plates were rinsed with PBS, and T cells were added to each virus-coated well. Plates were then centrifuged at 800g for 30 min at 32°C and returned to 37°C, 5% CO2 incubators. After 24 hours, T cells were harvested and resuspended in complete RPMI with 50 U/ml IL-2. T cells were subsequently harvested, counted, and maintained at 1x106 cells/ml in complete RPMI with 50 ng/ml human IL-15 every 1-2 days after. Four days after transduction, magnetic beads were removed. Transduced cells were enriched using the EasySep CD19 Positive Selection Kit II (Stem Cell) and cryopreserved in complete RPMI supplemented with 10% FBS and 10% DMSO.

treatment_protocol: Cryopreserved CAR-T cell infusion products were thawed, washed, and stained with Live/Dead Fixable Aqua Dye (Invitrogen) and surface markers in FACS Buffer. Up to 5,000 live CD8+GFP+ CAR-T cells were sorted and incubated overnight with concanavalin A beads (Bangs Laboratories Inc.) and antibodies recognizing H3K4me3 (Abcam #ab213224), H3K27me3 (Cell Signaling Technology #9733S), or IgG control (Cell Signaling Technology #3900S).

value: T cells

value: CD8+ T cells

value: BATF.ROR1 CAR-T

value: H3K27me3 antibody


title: E2_10_donor2_R4_P4

description: Library name: s364

value: Mammary

value: Primary

value: Epithelial


title: 3_GFP-ChIP-seq_DLD-1_18hDox_GFP-BRD2∆BD

description: Library name: S03


title: E2_10_donor1_R4_P4

description: Library name: s362

value: WT


title: 2_GFP-ChIP-seq_DLD-1_18hDox_GFP-BRD2

description: Library name: S02


title: TMBPF_50_donor3_R4_P4

description: Library name: s359

value: tetramethyl bisphenol F


title: TMBPF_10_donor3_R4_P4

description: Library name: s358


title: 23_IP_SS95_rep1_H3K27me3

description:
Library name: 23_IP_SS95_rep1_H3K27me3
23_IP_SS95_rep1_H3K27me3

value: cJun.ROR1 CAR-T


title: DMSO_0-1_donor3_R20_P4

description: Library name: s360

value: vehicle control

value: dimethyl sulfoxide


title: 24_IP_SS95_rep2_H3K27me3

description:
Library name: 24_IP_SS95_rep2_H3K27me3
24_IP_SS95_rep2_H3K27me3


title: E2_1_donor1_R4_P4

description: Library name: s361


title: E2_1_donor2_R4_P4

description: Library name: s363


title: 1_GFP-ChIP-seq_DLD-1_18hDox_GFP

description: Library name: S01

value: epithelial

value: GFP


title: PRO-seq_04_DLD-1_2hdBET6

description: Library name: S04

library_source: other

data_processing:
Low-quality bases and adapters from 3’ ends were removed using cutadapt requiring a read length of 16–36 bp. Ribosomal RNA reads were also removed.
The remaining reads were aligned using bowtie 2.2.6 with --very-sensitive option91 to a concatenated genome comprised of human hg38 and fly dm6 assemblies. 5’ ends of aligned reads with MAPQ ≥ 30 were retained and assigned to the opposite strand.
Read counts were normalized to total reads aligned to the spike-in genome for the output of bigwig files.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: PRO-Seq

molecule: other

extract_protocol:
Briefly, DLD-1 cell nuclei (10 million for BRD4 depletion and 1 million for dBET6 treatment) were mixed with Drosophila S2 spike-in nuclei, which were then used for the nuclear run-on assay.
Libraries were synthesized using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760L). Libraries were sequenced on Illumina NextSeq 500 or NovaSeq 6000.


title: PRO-seq_03_DLD-1_0hdBET6

description: Library name: S03

value: NT


title: TMBPF_0-5_donor3_R4_P4

description: Library name: s355

value: chemical exposure


title: 22_IP_SS78_rep2_H3K27me3

description:
Library name: 22_IP_SS78_rep2_H3K27me3
22_IP_SS78_rep2_H3K27me3

value: ROR1 CAR-T


title: TMBPF_5_donor3_R4_P4

description: Library name: s357


title: TMBPF_0-1_donor3_R4_P4

description: Library name: s354


title: TMBPF_0-01_donor3_R4_P4

description: Library name: s353


title: 14_IP_SN10_rep2_H3K4me3

description:
Library name: 14_IP_SN10_rep2_H3K4me3
14_IP_SN10_rep2_H3K4me3

value: T cells

value: H3K4me3 antibody


title: TMBPF_1_donor3_R4_P4

description: Library name: s356


title: DMSO_0-1_donor3_R19_P4

description: Library name: s352


title: BPAF_10_donor3_R4_P4

description: Library name: s351

value: bisphenol AF


title: Donor 3 mRNA after CTL co-culture

city: New York

first: Alberto

last: Herrera

state: New York

department: Medicine

institute: Weill Cornell Medicine

description:
Library name: dNEFNPIM2_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
FASTQ files from the 10x gene expression, surface protein, and TCR α/β libraries were processed using Cell Ranger v7.0.1 (10x Genomics), using either the count or the multi pipeline (when TCR libraries were available) with default parameters.
RNA transcripts from ECCITE-seq were mapped to a modified version of Cell Ranger’s GRCh38-2020-A reference package (GRCh38 / GENCODE v32 annotations), with the addition of the HIV-1 HXB2 reference sequence. TCR α/β libraries were mapped to Cell Ranger’s cellranger-vdj-GRCh38-alts-ensembl-7.1.0 reference package.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: *.h5 (feature barcode matrices in HDF5 format)
Supplementary files format and content: CellRanger output files: *.filtered_contig_annotations.csv (high-level annotations of each high-confidence contigs from cell-associated barcodes)
Supplementary files format and content: CellRanger output files: *.feature_reference.csv
Library strategy: CITE-seq

source_name: peripheral blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from leukapheresis samples from HIV negative donors obtained from Stemcell technologies. Naïve CD4+ T cells were magnetically isolated from thawed PBMCs using the EasySep™ Human Naïve CD4+ T Cell Isolation Kit (Stemcell) according to the manufacturer’s instructions. Purified naïve CD4+ T cells were then activated using human anti-CD3/CD28-coated magnetic beads (one bead for two cells, Gibco Cat. #11131D) in the presence of human anti-IL-4 (1µg/106 cells Peprotech 500-P24), human anti-IL-12 (2µg/106 cells Peprotech 500-P154G), and Tumor Growth Factor (TGF)-b1 (10ng/106 Peprotech 100-21) to prevent cell polarization. After 3 days, cells were maintained at a concentration of 106 cells /mL in media containing 50 IU of human recombinant IL-2. At day 7, the cultured TCM were infected with either WT HIVJRCSF or HIVJRCSF TW10escape. One quarter of the cells were infected by the addition of 200 units of virus (see virus production details below for unit description) per 1x107 cells in 1mL and centrifugation at 1500xg for 2h at 37°C. Following this 'spinoculation', the infected cell cultures were mixed in flasks containing the remaining three quarters of the cells at 2x106 cells/mL in media containing 50 IU of human recombinant IL-2. At day 10, the cells were crowded in 96-well round bottom plates at a density of 2x105 cells/200uL/well to enhance cell-to-cell transmission of HIV. On day 13, cells were cryopreserved in FBS with 10% DMSO and stored in liquid nitrogen for future experiments.

extract_protocol:
Cryopreserved infected CD4+ T-cells were thawed for 1-2 minutes in a 37o C water bath, washed twice RPMI 1640 supplemented with 10% FBS. Infected cells were then rested for 2 days at 2 x 106 cells per mL in media containing 50 IU of human IL-2.  Prior to co-culture with CTL, cells expressing high levels of CD4 were depleted by magnetic selection using the EasySep™ Human CD4 Positive Selection Kit II (Stemcell); this step enriches for CD4- infected cells (since HIV-infected cells downregulate CD4). Cells infected with WT HIVJRCSF were labeled with CFSE (dilution 1:5,000) and cells infected with HIVJRCSF TW10escape were labeled with CTV (dilution 1:10,000). These were then mixed together before adding a TW10-specific CTL that had been labeled with CellTrace™ Blue CTB (dilution 1:10,000). No CTL control conditions were cultured in parallel. Post-killing, cells were harvested for staining with anti-CD4 BV785 (1:100), Live/Dead fixable Aqua (1:200), bNAbs PGT121 conjugated with Zenon Kit PE (1µg per 1 x 106 cells) and bNAbs N6/PGDM1400x10E8 conjugated with Zenon Kit AF647 (1µg per 1 x 106 cells) at 37C for 1h. Live cells productively infected CFSE-labeled WT HIVJRCSF and CTV-labeled HIVJRCSF TW10escape were sorted by gating on the double positive population for PGT121 and N6/PGDM1400x10E8.
All experiments were performed using the 10x genomics V(D)J solution which incorporates scRNA-seq with additional profiling of protein surface markers . Antibody oligo counts are listed in the ADT and HTO tables. Stained cells from each sample were pooled and loaded into the 10X Chromium Single Cell Immune Profiling workflow according to the manufacturer’s instructions (CG000330, revision G)

treatment_protocol: Infection  with WT HIVJRCSF (WT) or HIVJRCSF TW10escape (TW10esc) virus strains.

value: peripheral blood

value: CD4+ T-cells

value: mixed sample ((Survivors, Bystanders) after CTL co-culture


title: 13_IP_SN10_rep1_H3K4me3

description:
Library name: 13_IP_SN10_rep1_H3K4me3
13_IP_SN10_rep1_H3K4me3

value: CD8+ T cells

value: BATF.ROR1 CAR-T


title: Donor 3 ADT and HTO after CTL co-culture

description:
Library name: dNEFNPIM2_ADT/HTO
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads; HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

molecule: protein

tag: adt

value: TotalSeq-C Human Universal Cocktail, V1.0 (BioLegend Cat. No. 399905)

tag: hto

value: TotalSeq-C0301 anti-mouse Hashtag 1 (WT, Survivors), TotalSeq-C0303 anti-mouse Hashtag 3 (TW10esc, Bystanders)


title: BPAF_5_donor3_R4_P4

description: Library name: s350

value: Mammary

value: Primary

value: Epithelial

value: WT


title: 12_IP_SS95_rep2_H3K4me3

description:
Library name: 12_IP_SS95_rep2_H3K4me3
12_IP_SS95_rep2_H3K4me3

value: cJun.ROR1 CAR-T


title: BPAF_1_donor3_R4_P4

description: Library name: s349

value: chemical exposure


title: DMSO_0-1_donor2_R21_P4

description: Library name: s371

value: vehicle control

value: dimethyl sulfoxide


title: BPAF_0-1_donor3_R4_P4

description: Library name: s347


title: BPAF_0-5_donor3_R4_P4

description: Library name: s348


title: BPAF_0-01_donor3_R4_P4

description: Library name: s346


title: 11_IP_SS95_rep1_H3K4me3

description:
Library name: 11_IP_SS95_rep1_H3K4me3
11_IP_SS95_rep1_H3K4me3

value: T cells

value: H3K4me3 antibody


title: BPAF_0-001_donor3_R4_P4

description: Library name: s345

value: bisphenol AF


title: BPA_50_donor3_R4_P4

description: Library name: s344

value: bisphenol A


title: Donor 2 survivor mRNA after CTL co-culture

description:
Library name: WT_3_29_22_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: peripheral blood

value: CD4+ T-cells

value: WT HIV infected survivors after CTL co-culture


title: 10_IP_SS78_rep2_H3K4me3

description:
Library name: 10_IP_SS78_rep2_H3K4me3
10_IP_SS78_rep2_H3K4me3

value: CD8+ T cells

value: ROR1 CAR-T


title: BPA_5_donor3_R4_P4

description: Library name: s342

value: Mammary


title: 3_IP_SN10_rep1_IgG

description:
Library name: 3_IP_SN10_rep1_IgG
3_IP_SN10_rep1_IgG

value: BATF.ROR1 CAR-T

value: IgG antibody


title: BPA_10_donor3_R4_P4

description: Library name: s343

value: Primary

value: Epithelial

value: WT


title: 4_IP_SN10_rep2_IgG

description:
Library name: 4_IP_SN10_rep2_IgG
4_IP_SN10_rep2_IgG


title: PBS_7837 [NGS3341]

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

state: CA

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie against the mouse genome assembly GRCm38.
Assembly: GRCm38
Supplementary files format and content: TSV count matrices

source_name: lung

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

value: lung

value: PBS


title: Donor 2 bystander ADT after CTL co-culture

description:
Library name: TW10_3_29_22_ADT
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: TW10esc HIV infected bystanders after CTL co-culture

value: TotalSeq-C Human Universal Cocktail, V1.0 (BioLegend Cat. No. 399905)


title: Donor 2 survivor ADT after CTL co-culture

description:
Library name: WT_3_29_22_ADT
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads


title: Donor 2 bystander mRNA after CTL co-culture

description:
Library name: TW10_3_29_22_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: PBS_7836 [NGS3341]


title: 9_IP_SS78_rep1_H3K4me3

description:
Library name: 9_IP_SS78_rep1_H3K4me3
9_IP_SS78_rep1_H3K4me3

value: T cells

value: H3K4me3 antibody


title: BPA_0-5_donor3_R4_P4

description: Library name: s340

value: chemical exposure

value: bisphenol A


title: 2_IP_SS95_rep2_IgG

description:
Library name: 2_IP_SS95_rep2_IgG
2_IP_SS95_rep2_IgG

value: cJun.ROR1 CAR-T


title: Donor 1 survivor TCRab after CTL co-culture

description:
Library name: 888_JRCSF_WT_TCR
VDJ library: read1 file contains cell barcode and UMI; read2 file contains VDJ fragment

value: peripheral blood

value: CD4+ T-cells

value: WT HIV infected survivors after CTL co-culture


title: Donor 1 survivor ADT after CTL co-culture

description:
Library name: 888_JRCSF_WT_ADT
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads


title: PBS_7834 [NGS3341]


title: BPA_0-1_donor3_R4_P4

description: Library name: s339

value: Mammary


title: 21_IP_SS78_rep1_H3K27me3

description:
Library name: 21_IP_SS78_rep1_H3K27me3
21_IP_SS78_rep1_H3K27me3

value: CD8+ T cells

value: ROR1 CAR-T

value: H3K27me3 antibody


title: 1_IP_SS95_rep1_IgG

description:
Library name: 1_IP_SS95_rep1_IgG
1_IP_SS95_rep1_IgG

value: IgG antibody


title: BPA_0-01_donor3_R4_P4

description: Library name: s338

value: Primary

value: Epithelial

value: WT


title: PBS_7835 [NGS3341]

value: lung

value: PBS


title: BPA_1_donor3_R4_P4

description: Library name: s341


title: Donor 1 survivor mRNA after CTL co-culture

description:
Library name: 888_JRCSF_WT_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Donor 2 bystander TCRab after CTL co-culture

description:
Library name: TW10_3_29_22_TCR
VDJ library: read1 file contains cell barcode and UMI; read2 file contains VDJ fragment

value: TW10esc HIV infected bystanders after CTL co-culture


title: Donor 1 survivor TCRab No CTL added

description:
Library name: 888_JRCSF_WT_CTL_TCR
VDJ library: read1 file contains cell barcode and UMI; read2 file contains VDJ fragment

value: WT HIV infected no CTL added


title: BLM_aOSM_7852 [NGS3341]

value: bleomycin + anti-OSM


title: DMSO_0-1_donor2_R20_P4

description: Library name: s336

value: vehicle control

value: dimethyl sulfoxide


title: Primary mouse cardiac fibroblasts treated with TGF-β (10 ng/mL, 48 h), replicate 3

city: Nanjing

first: Zhenyang

last: Su

address: No.300 GuangZhou Road

country: China

institute: the First Affiliated Hospital of Nanjing Medical University

description: Library name: M3

data_processing:
Sequencing fragment image data captured by high-throughput sequencers is converted into sequence data (reads) through base recognition by CASAVA. The resulting files are in fastq format, primarily containing the sequence information of the sequencing fragments along with their corresponding sequencing quality metrics.
Raw sequencing data contains a small number of reads with sequencing adapters or low sequencing quality. To ensure the quality and reliability of data analysis, raw data must undergo filtering, which includes the following steps: Remove reads containing adapters; Remove reads containing Ns (where N indicates an unidentified base); Remove low-quality reads (reads where bases with Qphred ≤ 5 constitute over 50% of the total read length).
Sequencing fragments are randomly sheared from mRNA. To determine which genes transcribed these fragments, quality-controlled clean reads must be aligned against a reference genome. HISAT2 software is used to perform fast and accurate alignment of clean reads against the reference genome, thereby obtaining read positioning information on the reference genome.
Based on the positional information of gene alignments on the reference genome, the number of reads covering each gene (including newly predicted genes) from start to end is counted. Reads are filtered out based on the following criteria: reads with alignment quality scores below 10, reads on non-consensus sequences, and reads mapped to multiple genomic regions. This analysis utilizes the featureCounts tool within the subread software package.
Due to the effects of sequencing depth and gene length, gene expression values in RNA-seq are typically represented not by read counts but by FPKM, which has been adjusted for both sequencing depth and gene length. After calculating the expression values (FPKM) for all genes across each sample, we used box plots to visualize the distribution of gene expression levels among different samples.
Assembly: GRCm38/mm10
Supplementary files format and content: gene_count.txt includes raw counts for each Sample
Supplementary files format and content: gene_fpkm.txt includes FPKM value for each Sample

source_name: whole heart

growth_protocol: Neonatal mouse cardiac fibroblasts were isolated from 1-day-old C57BL/6J mice as previously described.[28] Briefly, hearts were harvested and minced into small fragments, followed by enzymatic digestion with 15 mg/mL collagenase II (2275GR001, BioFroxx) at 37℃ with continuous shaking (120rpm) for 30 min. The resulting cell suspension was plated in DMEM(C11995500, Gibco) containing 10% fetal bovine serum. After incubation at 37°C with 5% CO₂ for 40 min, adherent fibroblasts were retained, whereas cardiomyocytes, red blood cells, and other non-adherent cells were removed. Fibroblasts were further cultured in DMEM  supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin at 37°C under 5% CO₂.

extract_protocol:
RNA was extracted from cardiac fibroblasts using Trizol (R411, Vazyme).
Enrich mRNA from total RNA using Oligo dT magnetic beads. Following fragmentation, synthesize the first strand of cDNA using random hexamer primers, followed by second-strand cDNA synthesis. After end repair, A-tailing, adapter ligation, fragment selection, amplification, and purification, the library is ready.

treatment_protocol: Cardiac fibroblasts were treated with TGF-β1 (HY-P7117, MedChemExpress) at 10 ng/mL to establish an in vitro fibrotic model. To inhibit MRN complex activity, Mirin (HY-117693, MedChemExpress) was added directly to the culture medium at 10 μM.

value: whole heart

value: primary cell

value: mouse cardiac fibroblasts

value: TGF-β (10 ng/mL) for 48 hours


title: Primary mouse cardiac fibroblasts treated with TGF-β (10 ng/mL, 48 h), replicate 2

description: Library name: M2


title: Donor 1 survivor ADT No CTL added

description:
Library name: 888_JRCSF_WT_CTL_ADT
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: peripheral blood

value: CD4+ T-cells

value: TotalSeq-C Human Universal Cocktail, V1.0 (BioLegend Cat. No. 399905)


title: Primary mouse cardiac fibroblasts treated with TGF-β (10 ng/mL, 48 h), replicate 1

description: Library name: M1


title: BLM_aOSM_7851 [NGS3341]


title: TMBPF_10_donor2_R4_P4

description: Library name: s334

value: Mammary

value: Primary

value: chemical exposure

value: tetramethyl bisphenol F


title: BLM_aOSM_7850 [NGS3341]

value: lung


title: TMBPF_50_donor2_R4_P4

description: Library name: s335

value: Epithelial

value: WT


title: Donor 1 survivor mRNA No CTL added

description:
Library name: 888_JRCSF_WT_CTL_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: WT HIV infected no CTL added


title: Donor 1 bystander TCRab after CTL co-culture

description:
Library name: 888_JRCSF_TW10_TCR
VDJ library: read1 file contains cell barcode and UMI; read2 file contains VDJ fragment

value: TW10esc HIV infected bystanders after CTL co-culture


title: PBS_7833 [NGS3341]

value: PBS


title: Donor 1 bystander mRNA after CTL co-culture

description:
Library name: 888_JRCSF_TW10_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: TMBPF_5_donor2_R4_P4

description: Library name: s333


title: BLM_aOSM_7849 [NGS3341]

value: bleomycin + anti-OSM


title: Primary mouse cardiac fibroblasts, untreated, replicate 4

description: Library name: N4

value: whole heart

value: primary cell


title: Primary mouse cardiac fibroblasts, untreated, replicate 2

description: Library name: N2

value: mouse cardiac fibroblasts


title: Primary mouse cardiac fibroblasts treated with TGF-β (10 ng/mL, 48 h), replicate 4

description: Library name: M4

value: TGF-β (10 ng/mL) for 48 hours


title: BLM_aOSM_7848 [NGS3341]


title: Primary mouse cardiac fibroblasts, untreated, replicate 3

description: Library name: N3


title: TMBPF_0-5_donor2_R4_P4

description: Library name: s331


title: Donor 1 bystander TCRab No CTL added

description:
Library name: 888_JRCSF_TW10_CTL_TCR
VDJ library: read1 file contains cell barcode and UMI; read2 file contains VDJ fragment

value: peripheral blood

value: CD4+ T-cells

value: TW10esc HIV infected no CTL added


title: Donor 1 bystander ADT after CTL co-culture

description:
Library name: 888_JRCSF_TW10_ADT
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

value: TotalSeq-C Human Universal Cocktail, V1.0 (BioLegend Cat. No. 399905)


title: TMBPF_1_donor2_R4_P4

description: Library name: s332

value: Mammary

value: Primary

value: chemical exposure


title: BLM_aIL6_aOSM_7856 [NGS3341]

value: lung

value: bleomycin + anti-IL6 + anti-OSM


title: Primary mouse cardiac fibroblasts, untreated, replicate 1

description: Library name: N1

value: WT


title: BPA_0-001_donor3_R4_P4

description: Library name: s337

value: Epithelial

value: bisphenol A


title: BLM_aIL6_aOSM_7857 [NGS3341]


title: TMBPF_0-1_donor2_R4_P4

description: Library name: s330

value: tetramethyl bisphenol F


title: Donor 1 bystander ADT No CTL added

description:
Library name: 888_JRCSF_TW10_CTL_ADT
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads


title: Donor 1 bystander mRNA No CTL added

description:
Library name: 888_JRCSF_TW10_CTL_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: TMBPF_0-01_donor2_R4_P4

description: Library name: s329


title: Donor 4 mRNA after CTL co-culture

description:
Library name: RG138_mRNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mixed sample ((Survivors, Bystanders) after CTL co-culture


title: HA_8

city: Shanghai

first: Jiren

last: Yan

state: Shanghai

address: 600 Yishan Road, Xuhui District, Shanghai

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: RAW_L4

data_processing:
Raw reads were filtered using fastp for quality control and adapter removal. Clean reads were aligned to the mouse reference genome (GRCm38) using STAR.
Differential gene expression analysis was performed with DESeq2, applying a threshold of fold change >2 and adjusted p < 0.05.
Heatmaps were generated to visualize global transcriptomic shifts.
Gene set enrichment analysis (GSEA) was conducted using the MSigDB database to identify significantly enriched pathways.
Assembly: GRCm38
Supplementary files format and content: csv files include FPKM values for each Sample

extract_protocol:
Raw264.7 cells were cultured with HA/Mg scaffolds or TABS for 3 days under standard conditions, with four replicates per group. Total RNA was extracted using TRIzol, and RNA integrity was assessed with an Agilent 2100 Bioanalyzer (RIN > 7).
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit and sequenced on an Illumina NovaSeq platform to generate 150-bp paired-end reads.


title: BPAF_10_donor2_R4_P4

description: Library name: s327

value: bisphenol AF


title: DMSO_0-1_donor2_R19_P4

description: Library name: s328

value: vehicle control

value: dimethyl sulfoxide


title: Donor 4 ADT and HTO after CTL co-culture

description:
Library name: RG138_ADT/HTO
ADT library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads; HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: peripheral blood

value: TotalSeq-C0301 anti-mouse Hashtag 1 (WT, survivors), TotalSeq-C0303 anti-mouse Hashtag 3 (TW10esc, bystanders)


title: IDH1R132H immortalized human astrocytes, MM-102, replicate 3

first: Marilin

last: Koch

description: Library name: MM-102 3

data_processing:
BAM files were produced with the following configurations: RNA paired bulk,  Reference genome: 1KGRef_PhiX, Alignment program: STAR Version 2.5.3a, Merging/duplication marking program: Sambamba Version 0.6.5
Assembly: hg38
Supplementary files format and content: all samples_normCPM_table.txt

source_name: immortalized IDH1R132H astrocytes

extract_protocol:
For RNA-Seq, samples were seeded in triplicates and harvested 48 days after the last treatment with Doxycycline and MM-102 as described above. RNA was isolated with the Rneasy Mini Kit (Qiagen).
UltraLowRNAv4, NEBNext Multiplex Oligos for Illumina UDI

value: immortalized IDH1R132H astrocytes


title: BPAF_5_donor2_R4_P4

description: Library name: s326

extract_protocol:
Cells were washed with phosphate-buffered saline and lysed in situ using 2x TempO-Seq lysis buffer diluted with an equal amount of PBS for TempO-Seq library building.
Gene expression was measured using the TempO-Seq Human Whole Transcriptome v2.0 and 2.1 kits (BioSpyder Technologies Inc, Carlsbad, California) as per the manufacturer’s instructions


title: TABS_7

description: Library name: RAW_H3


title: BLM_aIL6_7847 [NGS3341]

value: bleomycin + anti-IL6


title: BLM_aIL6_aOSM_7854 [NGS3341]


title: BLM_aIL6_7844 [NGS3341]


title: IDH1R132H immortalized human astrocytes, MM-102, replicate 2

description: Library name: MM-102 2


title: Donor 2 survivor TCRab after CTL co-culture

description:
Library name: WT_3_29_22_TCR
VDJ library: read1 file contains cell barcode and UMI; read2 file contains VDJ fragment

value: CD4+ T-cells

value: WT HIV infected survivors after CTL co-culture


title: TABS_6

description: Library name: RAW_H2


title: IDH1R132H immortalized human astrocytes, MM-102, replicate 1

description: Library name: MM-102 1


title: BPAF_1_donor2_R4_P4

description: Library name: s325

value: Mammary

value: Primary

value: chemical exposure


title: BLM_aIL6_7846 [NGS3341]

value: lung


title: HA_5

description: Library name: RAW_L1


title: BLM_aIL6_7845 [NGS3341]


title: BPAF_0-01_donor2_R4_P4

description: Library name: s322

value: Epithelial

value: WT


title: IDH1R132H immortalized human astrocytes, control, replicate 3

description: Library name: control 3


title: BLM_aIL6_7843 [NGS3341]


title: BLM_aIL6_aOSM_7853 [NGS3341]

value: bleomycin + anti-IL6 + anti-OSM


title: BPAF_0-5_donor2_R4_P4

description: Library name: s324


title: HA_6

description: Library name: RAW_L2


title: BLM_aIL6_aOSM_7855 [NGS3341]


title: HA_7

description: Library name: RAW_L3


title: TABS_5

description: Library name: RAW_H1


title: IDH1R132H immortalized human astrocytes, control, replicate 2

description: Library name: control 2


title: BPA_50_donor2_R4_P4

description: Library name: s320

value: bisphenol A


title: HA_4

description: Library name: S3T3_L4

extract_protocol:
MC3T3-E1 cells were cultured with HA/Mg scaffolds or TABS for 3 days under standard conditions, with four replicates per group. Total RNA was extracted using TRIzol, and RNA integrity was assessed with an Agilent 2100 Bioanalyzer (RIN > 7).
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit and sequenced on an Illumina NovaSeq platform to generate 150-bp paired-end reads.


title: BLM_7841 [NGS3341]

value: bleomycin


title: IDH1R132H immortalized human astrocytes, control, replicate 1

description: Library name: control 1


title: Ovary, KO_4

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

country: Japan

institute: Yamaguchi university

data_processing:
Reads with >2 ambiguous nucleotides and reads with quality scores of <20 as calculated by the Phred program were removed using CLC Genomics Work Bench (version 8.01, Qiagen)
In addition, long reads with >1000 nucleotides and short reads with <20 nucleotides were discarded.
Trimmed reads were mapped to the mouse reference genome GRCm38/mm10 in default settings.
Read count normalization were performed using CLC Genomics Work Bench.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each sample.

source_name: Ovary

extract_protocol:
Total RNA was extracted from the ovaries using the RNeasy Mini Kit (Qiagen), and mRNA was purified with Oligo dT beads (NEBNext Poly (A) mRNA magnet Isolation Module, New England Biolabs).
NEBNext Ultra II RNA library Prep kit (NEB) and NEBNext Multiplex Oligos (Illumina) were used to generate cDNA libraries.

treatment_protocol: Mice were intraperitoneal administered pregnant mare serum gonadotropin (PMSG, 5 IU) and human Chorionic Gonadotropin (hCG, 5 IU) at 48-hour intervals. Ovaries clollected at indicated time point were stored in RNAlater.

value: Ovary

tag: time

value: 24h after hCG i.p.

tag: age

tag: strain

value: ICR (Crl:CD1)


title: BPA_0-01_donor2_R4_P4

description: Library name: s314

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using  DRAGEN analysis v1.3.0 on the Illumina Basespace Sequence Hub (Illumina, Inc., San Diego, CA, USA). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the R-ODAF_Health_Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed December 2024), which manages workflows using snakemake v8.0 (Mölder et al., 2021) and relies on scripts in R (v.4.3.2). The preprocessing steps use fastp v0.23.2 for trimming (Chen et al., 2018), STAR v2.7.8a (Dobin et al., 2013) to perform alignment of raw reads to the reference sequence, and the qCount function of the QuasR R package (v1.30.0; Gaidatzis et al., 2015) to extract the feature counts from the aligned reads (BAM files) using features specified in a GTF file. A samples-by-probes count matrix was produced.
Assembly: Probe sequence set provided by biospyder based on Human Whole Transcriptome kit v2.1
Supplementary files format and content: Tab-delimited table containing read counts per TempO-Seq probe


title: SFSN-TC_1

first: Rong

last: Bao

state: shanghai

address: 600 YISHAN ROAD

institute: Department of Orthopaedics Shanghai Jiao Tong University Affiliated Sixth People

description: Library name: SCX1_1

data_processing:
Data filtering
The sequencing data was filtered with SOAPnuke [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Structure variation detection
The clean reads were mapped to the reference genome using HISAT2 [2]. After that, Ericscript (v0.5.5) [3] and rMATS (V4.1.2) [4] were used to detect fusion genes and differential splicing genes (DSGs), respectively
RNA identification
Bowtie2[5] was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis
Expression level of gene was calculated by RSEM (v1.3.1) [6]. The heatmap was drawn by pheatmap (v1.0.12) [7] according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.34.0) [8] (or DEGseq （v1.48.0）[9] or PoissonDis[10])with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) [11].
For more details, see the data_processing_readme.txt
Assembly: NCBI_GCF_000001895.5_Rnor_6.0
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

organism: Rattus norvegicus

source_name: rat bone marrow mesenchymal stem cells

extract_protocol:
1. Introduction This protocol allows to extract both high-quality genomic DNA and total RNA from the same sample. The purified DNA and RNA can be used directly for library preparation. 2.Experimental Procedures 2.1 Sample Lysis 2.1.1 Transfer 30mg of tissue into a 2mL tube with beads. 2.2.1 Add 600µL Buffer RLT Plus. If using snap-frozen cells (no more than 1 × 10⁷ cells), simply add 600µL Buffer RLT Plus directly into the same tube. Homogenize at 65Hz for 60s, then stay at room temperature for 5min. 2.2.3 Centrifuge at 12,000g for 3min. Transfer the supernatant to an AllPrep DNA spin column in a collection tube. Centrifuge at 10,000g for 30s in room temperature. 2.2.4 Collect the flow-through for RNA purification. 2.2 RNA Purification 2.2.1 Add one volume of 70% ethanol to the flow-through. Mix by pipetting at least 5 times. 2.2.2 Transfer 700µL of the mixture into an RNeasy spin column in a collection tube. Centrifuge at 10,000g for 30s; discard the flow-through. Repeat until all mixture has passed through the column. 2.2.3 Add 700μL Buffer RW1 to RNeasy spin column, centrifuge at 10,000×g for 30s in room temperature and discard the filtrate. 2.2.4 Add 500μL Buffer RPE to RNeasy spin column, centrifuge at 10,000×g for 30s in room temperature and discard the filtrate. 2.2.5 Add 500μL Buffer RPE to RNeasy spin column, centrifuge at 10,000×g for 30s in room temperature and discard the filtrate. 2.2.6 Centrifuge at 16,000g for 2min to dry the purification column. Transfer the RNeasy spin column to a 1.5mL tube. 2.2.7 Add 30µL RNase-free water to the RNeasy spin column. Stay at room temperature for 1min, then centrifuge at 16,000g for 2min to elute RNA. 2.2.8 Check RNA quality as required. 2.3 DNA Purification 2.3.1 Add 500μL Buffer AW1 to AlIPrep DNA spin column, centrifuge at 10,000×g for 30s in room temperature and discard the filtrate. 2.3.2 Add 500μL Buffer AW2 to AlIPrep DNA spin column, centrifuge at 10,000×g for 30s in room temperature and discard the filtrate. 2.3.3 Centrifuge at 16,000g for 2min to dry the purification column. Transfer the AllPrep DNA spin column to a 1.5mL tube. 2.3.4 Add 30µL Buffer EB to theAllPrep DNA spin column. Stay at room temperature for 1min, then centrifuge at 16,000g for 2min to elute DNA. 2.3.5 Check DNA quality as required.
1. Introduction RNA-Seq (Quantification) uses a new generation of high-throughput sequencing technology to study the gene expression pattern of eukaryotic cells and provide accurate digital expression profile detection by sequencing and comparing transcripts. Transcriptome research is the basis and starting point of gene function and structure research. Through the new generation of high-throughput sequencing, almost all transcripts of a specific tissue or organ of a species can be obtained comprehensively and quickly. 2.Experimental Procedure 2.1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2.2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 2.3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 2.4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 2.5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 2.6 PCR The PCR reaction system and program are configured and set up to amplify the product. 2.7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 2.8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 2.9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: rat bone marrow mesenchymal stem cells

value: SFSN

tag: sample group

value: SFSN-TC


title: BLM_7840 [NGS3341]


title: HA_2

description: Library name: S3T3_L2


title: BPA_5_donor2_R4_P4

description: Library name: s318


title: HA_1

description: Library name: S3T3_L1


title: SFSN-TC_3

description: Library name: SCX1_3


title: SFSN-TC_2

description: Library name: SCX1_2


title: TABS_2

description: Library name: S3T3_H2


title: BPA_10_donor2_R4_P4

description: Library name: s319


title: BPA_1_donor2_R4_P4

description: Library name: s317


title: SFSN-Ot_3

description: Library name: RUNX21_3

value: SFSN-Ot


title: BPA_0-1_donor2_R4_P4

description: Library name: s315


title: Ovary, WT_6


title: TABS_3

description: Library name: S3T3_H3


title: Saline_D5_CD64_0224 [NGS2117]

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie against the human genome assembly GRCm38.
Assembly: GRCm38
Supplementary files format and content: TSV count matrices.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit.
Libraries were prepared using the Illumina TruSeq RNA Library Prep Kit.

value: CD64+ macrophage

value: day 5

value: saline


title: BPA_0-5_donor2_R4_P4

description: Library name: s316

value: Mammary

value: Primary

value: chemical exposure


title: BLM_7838 [NGS3341]

value: lung


title: TABS_4

description: Library name: S3T3_H4


title: TABS_1

description: Library name: S3T3_H1


title: BPAF_0-001_donor2_R4_P4

description: Library name: s321

value: Epithelial

value: WT

value: bisphenol AF


title: BLM_7839 [NGS3341]

value: bleomycin


title: Saline_D5_CD64_0222 [NGS2117]


title: BPA_0-001_donor2_R4_P4

description: Library name: s313

value: bisphenol A


title: Ovary, WT_5

value: Ovary

value: 24h after hCG i.p.

value: ICR (Crl:CD1)


title: Saline_D5_Alveolar_0218 [NGS2117]

value: alveolar macrophage


title: CD8+ T cell 9-pahsa treated rep4

city: Hangzhou

first: xiaozhen

last: zhang

state: province

address: 79 Qingchun Road

institute: The first affiliated hospital, zhejiang university school of medicine

description: Library name: P9_4

data_processing:
Adapter sequences and low-quality bases were trimmed from the paired-end raw reads using fastp (v0.23.2) or Trimmomatic (v0.39) with standard parameters.
The trimmed reads were aligned to the specified reference genome assembly using Bowtie2 (v2.4.5) in --very-sensitive mode. Mitochondrial reads were excluded during or after alignment. Resulting SAM files were converted to sorted, indexed BAM files using samtools (v1.15).
Aligned reads were filtered to remove unmapped, non-primary, and low-quality (MAPQ < 30) alignments. Duplicate reads, originating from PCR amplification, were removed using picard MarkDuplicates (v2.27.4)
Nucleosome-free regions (peaks of open chromatin) were identified from the filtered, deduplicated BAM files using MACS2 (v2.2.7.1) callpeak in BAMPE mode with parameters optimized for ATAC-seq (--nomodel --shift -100 --extsize 200). A matched input sample is typically not used; peaks are called against the background model inherent in MACS2.
Normalized chromatin accessibility tracks (bigWig files) for visualization were generated using deeptools bamCoverage (v3.5.2) with normalization to CPM or BPM. Fragment size distribution plots were generated to assess data quality. Downstream analyses included differential accessibility analysis (using DESeq2 or diffBind), motif enrichment analysis with HOMER (v4.11), and annotation of peaks to genomic features.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: Mouse CD8+ T cell

extract_protocol:
The assay for transposase-accessible chromatin (ATAC) was performed based on the Omni-ATAC protocol for optimal signal-to-noise ratio in immune cells. Briefly, fresh or cryopreserved CD8+ T cells were counted and washed in cold PBS. A total of 50,000 to 100,000 viable cells were lysed in cold ATAC Lysis Buffer to isolate nuclei. The nuclei were then immediately subjected to tagmentation reaction using the Illumina Nextera Tn5 Transposase, which simultaneously fragments accessible genomic DNA and inserts sequencing adapters. The reaction was performed at 37°C for 30 minutes in a buffer containing Mg2+. Tagmentation was stopped by adding SDS and EDTA. The tagmented DNA was then purified using a MinElute PCR Purification Kit , eluting in a small volume of Elution Buffer or nuclease-free water. The purified DNA constituted the pre-amplified library.
The library construction was initiated directly from the purified tagmentation product, as the Tn5 transposase had already inserted the core adapter sequences. The DNA was first subjected to a limited-cycle, dual-indexing PCR amplification (typically 8-12 cycles) using a high-fidelity DNA polymerase and Nextera-compatible i5 and i7 indexing primers. The PCR program included an initial extension step (72°C for 5 minutes) for full adapter repair, followed by standard cycling conditions (98°C denaturation, 60-63°C annealing/extension). The amplified libraries were size-selected using a double-SPRI bead cleanup to remove excessive primer dimers and large fragments, enriching for nucleosome-free (< 200 bp) and mononucleosome (~200-600 bp) fragments. Final library quality and size distribution were assessed using an Agilent Bioanalyzer (High Sensitivity DNA chip) or TapeStation, and concentration was quantified via qPCR . Libraries were normalized and pooled for paired-end sequencing on an Illumina platform

value: Mouse CD8+ T cell

value: 9-pahsa treated


title: Saline_D5_Alveolar_0217 [NGS2117]

value: day 5


title: CD8+ T cell 9-pahsa treated rep3

description: Library name: P9_3


title: DMSO_0-1_donor1_R20_P4

first: Matthew

last: Meier

description: Library name: s312

value: vehicle control

value: dimethyl sulfoxide


title: TMBPF_50_donor1_R4_P4

description: Library name: s311

value: Mammary

value: Primary

value: tetramethyl bisphenol F


title: CD8+ T cell 9-pahsa treated rep2

description: Library name: P9_2


title: Saline_D14_CD64_0236 [NGS2117]

value: lung

value: CD64+ macrophage

value: day 14

value: saline


title: Saline_D5_Alveolar_0216 [NGS2117]


title: TMBPF_10_donor1_R4_P4

description: Library name: s310

value: Epithelial

value: WT

value: chemical exposure


title: TMBPF_5_donor1_R4_P4

description: Library name: s309


title: TL3-3

city: Lan zhou

first: Pan

middle: Yu

last: Cai

state: Gansu

address: Yin Tan Road Street, An Ning District

department: College of Animal Science and Technology

institute: Gansu Agricultural University

description: Library name: Sample 12

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads  without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss USDA_OmykA_1.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Oncorhynchus mykiss

source_name: liver tissues

growth_protocol: Rainbow trout (85 ± 0.5 g) for laboratory evaluation were obtained from a commercial aquaculture farm in Gansu (China) and checked free of pathogenic infections after an autopsy. The fish were raised in 1000 L tanks at water temperatures of 12 ± 1℃. During the experiments, the pH ranged from 7.6 to 7.8, and the dissolved oxygen was about 8.5 mg/L. Feeding with commercial dry feed pellets (Shandong Hanye Biotechnology Co., Ltd, China) was performed twice daily, a rate of 2% of their body weight. Animal care and use protocols were approved by Animal Welfare Committee of Gansu Agricultural University (GSAU-Eth-AST-2021-004), and carried out in accordance with the recommendations of the National Institutes of Health Guide for the Care and Use of Laboratory Animals (No. 2020001).

extract_protocol:
The total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the formal experiment, rainbow trout in control group were intraperitoneally injected with PBS, and two experimental groups were intraperitoneally injected with 150 μL inactivated IHNV vaccine (vaccine group) and 150 μL APS combined inactivated IHNV vaccine (APS+vaccine group), respectively. Each experimental group had 200 fish, 100 of which were used for mortality measurements and the remaining 100 for sampling. At 14 days (D 14) after vaccination, 200 fish per group were injected intraperitoneally with 50 µl IHNV (107 TCID50 ml-1) and monitored for mortality for two weeks. The relative percentage of survival (RPS) was calculated using the formula: 1-(vaccinated group mortality/control group mortality) × 100%. For sampling, the anesthetics and its doses were the same as in the vaccine safety tests. Liver and blood were collected from four fish from each group at D1, D3, D7, D14, D15, D21, D30, D60 and D90 to assay for immune-related gene expression and non-specific enzyme activities. Liver samples from D21 were also used for transcriptomic and metabolomic analyses. In addition, the spleens of three fish for each group were collected at D7, D14, D15, D21, D30, D60 and D90 for histopathological examination.

value: liver tissues

value: vaccine group_IHNV challenged


title: TMBPF_1_donor1_R4_P4

institute: Government of Canada

description: Library name: s308

source_name: Mammary


title: TL3-2

description: Library name: Sample 11


title: CD8+ T cell 9-pahsa treated rep1

description: Library name: P9_1

value: Mouse CD8+ T cell


title: CD8+ T cell control rep4

description: Library name: Control_4


title: Saline_D14_CD64_0235 [NGS2117]


title: TL2-3

description: Library name: Sample 9

value: arc+vaccine group_IHNV challenged


title: BLM_7842 [NGS3341]

value: bleomycin


title: Saline_D14_CD64_0234 [NGS2117]


title: TL3-1

description: Library name: Sample 10


title: CD8+ T cell control rep3

description: Library name: Control_3


title: Ovary, WT_4

value: Ovary

value: 24h after hCG i.p.

value: ICR (Crl:CD1)


title: TMBPF_0-5_donor1_R4_P4

description: Library name: s307

value: Mammary

value: Primary


title: Saline_D14_Alveolar_0230 [NGS2117]

value: lung

value: alveolar macrophage


title: TMBPF_0-1_donor1_R4_P4

description: Library name: s306

value: tetramethyl bisphenol F


title: CD8+ T cell control rep2

description: Library name: Control_2


title: HA_3

description: Library name: S3T3_L3


title: TL2-2

description: Library name: Sample 8


title: Saline_D14_Alveolar_0229 [NGS2117]

value: day 14

value: saline


description:
Library name: Illumina RNA-seq (rRNA-depleted composite, WT, multi-regeneration time points)
genotype: CIW4 asexual; condition: WT and cut worms; tissue: whole-animal; time point: 0, 1, 3, 6, 9, 12, 24, 48 hpa and 1 uncut worms
Barcodes were not incorporated during the library preparation to annotate the time points, the pooling strategy was designed solely to enrich for a broad set of transcripts for transcriptome assembly. It isnot feasible to perform demultiplexing to segregate the reads by individual time points.

data_processing:
Data were quality-checked with MultiQC and then trimmed using Trim-Galore to remove adapters and low-quality bases. Reads were aligned to the Schmidtea mediterranea genome using STAR and quantified with Stringtie2.
Assembly: The reference genome SchMedS2. Genome annotation file (SchMed_Pn) can be downloaded from the foot in a GEO Series record

extract_protocol:
Worms were flash-frozen in liquid nitrogen. Total RNA was isolated using the mirVana™ miRNA Isolation Kit  following the manufacturer’s protocol, and treated with TURBO™ DNase as per the provided instructions. The concentration of the purified RNA samples was quantified using a Qubit 4 Fluorometer and the Qubit™ RNA Broad Range (BR) Assay Kit. RNA quality was assessed using the Agilent TapeStation system with High Sensitivity RNA Assay. RNA with RIN >8 was used. Ribosomal RNA (rRNA) depletion was done with the riboPOOL kit. The sample was mixed with 1% spike-in, SIRV Set-4 (Iso Mix E0 / ERCC / Long SIRVs).
Library was prepared and sequenced at Macrogen, Inc., South Korea.

value: whole-body sample

value: WT

value: No additional treatment; represents baseline and regenerating conditions


title: CD8+ T cell control rep1

description: Library name: Control_1


title: TMBPF_0-01_donor1_R4_P4

description: Library name: s305

value: Epithelial

value: chemical exposure


title: Saline_D14_Alveolar_0228 [NGS2117]


title: DMSO_0-1_donor1_R19_P4

description: Library name: s304

value: vehicle control

value: dimethyl sulfoxide