title: E.G7 TIL Treg_rep2

data_processing:
Low quality reads and adaptor sequences were removed by Trim galore0.6.6
The clean reads were aligned to mouse genome mm10 by Hisat2 with default parameter
The uniquely mapping reads were summarized by featureCounts(from Subread package)
FPKM (Fragments Per Kilobase of exon model per Million mapped reads) were calculated using RSEM
Differentially expressed genes were identified by at least 2 fold change and fdr adjusted p-value 0.01 using DEseq2
Assembly: mm10
Supplementary files format and content: txt file including counts
Supplementary files format and content: txt file including FPKM value

source_name: Tumors

growth_protocol: Intra-tumoral Treg cells were sorted from E.G7 and Hepa1-6 tumor-bearing Foxp3YFP-cre mice on day 21 and day 23 post-inoculation, respectively. Treg cells sorted from lymph nodes of tumor-free mice were included as a control.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) according to manufacturer’s instructions.
RNA-seq library was constructed by BGI Genomics. BGISEQ-500 was used to obtain sequence reads.

treatment_protocol: E.G7 or Hepa1-6 tumor cells were subcutaneously injected into Foxp3YFP-cre mice. The E.G7 and Hepa1-6 tumor-bearing Foxp3YFP-cre mice were sacrificed on day 21 and day 23, respectively. Tumors were subjected to tumor-infiltrating lymphocytes (TIL) isolation. Intra-tumoral Treg cells were sorted from the isolated CD4+ T cells by using BD FACSAria Cell Sorter. Treg cells sorted from lymph nodes of tumor-free mice were included as a control.

value: Tumors

value: Treg cells

value: Foxp3YFP-cre mice

value: E.G7 tumor inoculation


title: E.G7 TIL Treg_rep1

status: Public on Feb 26 2024

type: SRA

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

country: China

institute: Tsinghua University

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: HepaPlate01_G08

city: College Station

first: Ivan

last: Rusyn

state: TX

address: 4458 TAMU

department: Department of Veterinary Integrative Biosciences

country: USA

institute: Texas A&M University

data_processing:
The libraries were sequenced (single-end, 50 bp in length) using HiSeq 2500 v.2 (Illumina, San Diego, CA).
This pipeline includes the use of STAR aligner (Dobin et al., 2013) and parameters used herein included a maximum number of mismatches of 3 and insertion and deletion open and extension penalties of 0.
Quality control steps with the following criteria were performed: 1) genes with fewer than 5 mean counts across the entire sample spacewere removed, 2) samples with mean expression across all genes lower than 25 were removed, 3) outliers in vehicle control samples were identified and removed using mean correlation at <0.85 as the criteria to ensure the stability of further transcriptomic dose-response and differential expression analyses, 4) in addition, principal component analysis (PCA) was conducted on vehicle control samples using raw counts to identify any remaining outliers.
Assembly: Whole transcriptome assay
Supplementary files format and content: iHep_normcounts.csv file with normalized count data using DESeq2 R package (Love et al., 2014)
Supplementary files format and content: iHep_hash.csv file with meta data of the QC samples

organism: Homo sapiens

source_name: Blank

extract_protocol:
The media and chemicals from the 384-well plates was fully aspirated and replaced with 10 μL/well of 2X lysis buffer. The plates were then shaken using an orbital plate shaker for 10 minutes. The plates were then checked to ensure that the cells were lysed, and if not placed back on the plate shaker for an additional five minutes. Once the cells were lysed, adhesive seals were placed on the plates and the lysates were frozen in the 384-well plates and stored at −80 °C until further processing.  The Templated Oligonucleotide Sequencing Assay (TempO-Seq™, BioSpyder Technologies, Carlsbad, CA) was used as an RNA sequencing technology of choice. Detailed protocols for TempO-seq are provided by the manufacturer and were previously reported  detailed elsewhere (Grimm et al., 2016; House et al., 2022).
TempO-seq libraries were prepared using the human whole transcriptome panel consisting of 22,537 protein-coding transcripts.

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: 6:2 Fluorotelomer sulfonic acid


title: Og2-3dpp-13

city: Guangzhou

first: Huayu

last: Qi

state: Guangdong

address: 190 Kaiyuan Boulevard, Science City, huangpu District

department: Center for Cell Lineage and Development

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description: Library 13

data_processing:
Over 100 million raw reads obtained were pre-processed with trim-galore for trimming Illumina adaptor sequences.  Processed reads were quantified using Kallisto in pseudoalignment mode to an index of transcripts from mouse genome build to generate count and TPM (Transcripts Per Million).  Differentially expressed genes were identified with the DESeq2 package using raw counts.
Assembly: mm10
Supplementary files format and content: Text file with TPM

source_name: Testis

extract_protocol:
OCT4-GFP positive spermatogonia were isolated from mice using FACS following enzyme digestion of testes.  Each sample contained about 1-2 X 10-4 cells.  Total RNAs were extracted from OCT4-GFP+ cells using ToTal RNA extraction kit (Tiangen, DP419).  RNA yield and purity were evaluated using a NanoDrop 1000 spectrophotometer (NanoDrop Technologies/Thermo Scientific, Waltham, MA).  Quality and integrity were determined by RBA 6000 Nano kit with a Bioanalyzer 2100 (Agilent Technology, Santa Clara, CA).
cDNA libraries were prepared using Vazyme VAHTS mRNA-seq V3 Library Prep kit for Illumina (Vazyme, NR611).

treatment_protocol: Testis digested with collagenase, DNaseI and Trypsin before FACS

value: Testis

value: Primary spermatogonia


title: Akt1s1-KO-2-3M-12

description: Library 12

value: Pou5f1-Gfp;Akt1s1 null


title: Akt1s1-KO-2-3M-11

description: Library 11


title: Hepa1-6 TIL Treg_rep4

value: Hepa1-6 tumor inoculation


title: Hepa1-6 TIL Treg_rep3


title: Akt1s1-KO-2-3M-10

description: Library 10


title: Ovarian cancer, NACT+P, Post (R210191)

city: Lyon

first: Olivia

last: Le Saux

address: 28 rue Laennec

country: France

institute: Cancer Research Center of Lyon

data_processing:
The primary base call files were converted into FASTQ sequence files using the bcl2fastq converter tool.
Raw sequencing reads were aligned on the human genome (GRCh38) with STAR (v2.7.3a)
Gene expression was quantified using Salmon (v1.0.0) and the annotation of known genes from gencode v29
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file included counts values for each Sample

source_name: Ovary

extract_protocol:
Total RNA from FFPE tissues was extracted using 2 to 5 10-μm FFPE sections from pre- and post-treatment samples with FormaPure RNA kit (Beckman Coulter). RNA concentration and absorbances were analyzed with NanoDrop spectrophotometer (Thermo Fisher Scientific), and quality profiles assessed on Tapestation (Agilent Technologies).
Libraries were prepared with the TruSeq RNA Exome kit (Illumina)

value: Ovary

value: Ovarian cancer

value: NACT+P, Post


title: HepaPlate01_G05

value: Perfluorotridecanoic acid


title: Ovarian cancer, NACT+P, Pre (R210190)

value: NACT+P, Pre


title: HepaPlate01_G06

value: Perfluoro-3-methoxypropanoic acid


title: Ovarian cancer, NACT, Pre (R210188)

value: NACT, Pre


title: Og2-2-3M-9

description: Library 9


title: Ovarian cancer, NACT, Post (R210189)

value: NACT, Post


title: Hepa1-6 TIL Treg_rep1

value: Tumors

value: Treg cells

value: Foxp3YFP-cre mice


title: Hepa1-6 TIL Treg_rep2


title: Og2-2-3M-7

description: Library 7


title: Tumor-free LN Treg_rep4

source_name: Lymph nodes

value: Lymph nodes

value: Not applicable


title: Ovarian cancer, NACT, Post (R210187)


title: Ovarian cancer, NACT, Pre (R210186)


title: Akt1s1-KO-7dpp-6

description: Library 6

value: Testis


title: HepaPlate01_G02

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluorooctanoic acid


title: Tumor-free LN Treg_rep3


title: Ovarian cancer, NACT, Post (R210185)

value: Ovary


title: HepaPlate01_G07

value: AFFF-7 (Tridol 6%)


title: HepaPlate01_F23

value: AFFF-3 (Phos-Check)


title: Tumor-free LN Treg_rep2


title: HepaPlate01_G04

value: Dodecafluoroheptanol


title: Akt1s1-KO-7dpp-4

description: Library 4

value: Primary spermatogonia

value: Pou5f1-Gfp;Akt1s1 null


title: Og2-7dpp-3

description: Library 3


title: HepaPlate01_G03

value: AFFF-4 (FireAde 6%)


title: Ovarian cancer, NACT+P, Post (R210183)

value: Ovarian cancer

value: NACT+P, Post


title: Tumor-free LN Treg_rep1

value: Treg cells


title: Ovarian cancer, NACT, Pre (R210184)

value: NACT, Pre


title: Ovarian cancer, NACT+P, Pre (R210182)

value: NACT+P, Pre


title: Akt1s1-KO-7dpp-5

description: Library 5


title: HepaPlate01_F20

value: AFFF-5 (Solberg 6%)


title: HepaPlate01_F21


title: Ovarian cancer, NACT+P, Post (R210181)


title: HepaPlate01_F22

value: 4:2 Fluorotelomer alcohol


title: RGCaxon

city: Shenzhen

first: Zhuoxuan

last: Yang

address: No. 1088 Xueyuan Avenue, Nanshan District

institute: Southern University of Science and Technology

data_processing:
The raw data was used fastp to filter low-quality reads.
The filtered reads were mapped to the mouse reference genome (mm10) using STAR v2.7.8a.
The resulting bam files were fed to featureCounts tool to count the number of RNA-seq reads.
The number of RNA-seq reads was further normalized to calculate TPM.
Specific genes were analyzed by comparing the gene expression of different samples.
Assembly: mm10

source_name: Retinal Ganglial Cell

growth_protocol: Dissociated dentate gyrus granule cells were cultured in Neurobasal A-medium with B27 supplement, GlutaMAX-1, and Penicillin-Streptomycin. Dissociated dorsal root ganglion cells were cultured in Neurobasal medium with B27 supplement, GlutaMAX-1, Penicillin-Streptomycin, 5FdU and NGF. Dissociated retinal ganglion cells were cultured in Neurobasal medium with GlutaMAX-1, cAMP, Froskolin, N2 and B27 supplement, Penicillin-Streptomycin and growth factors inclduing NT3, BDNF, EGF, FGF2.

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

treatment_protocol: Neurons are cultured in microfluidic chamber to separate axons from soma.

value: Retinal Ganglial Cell

tag: strain

tag: developmental stage

value: embryonic day 14.5


title: Ovarian cancer, NACT+P, Pre (R210180)


title: RBP-Jfl/fl Lyz2-Cre blood Ly6Clo monocyte

first: Tiantian

last: Kou

address: Haidian  District

institute: Tsinghua university

data_processing:
Basecal was performed on CASAVA 1.8
Tophat v2.1.0 was used for pair-end reads alignment with the parameters -i 70 -g 1–no-novelindels. Gene expression level were quantified by Cufflinks v2.2.1
Assembly: mm10
Supplementary files format and content: Tab-delimited file contains the gene expression (FPKM) and statistical analysis result (p-value).

source_name: blood

extract_protocol: RNA was harvested using   total RNA purification kit (GeneMarkbio). RNA was converted into RNA-seq quantification libraries, and RNA-seq libraries were sequenced with the pair-end option.

value: blood

value: Ly6Clo monocyte

value: RBP-Jfl/fl Lyz2-Cre


title: HepaPlate01_F19

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: 8:2 Fluorotelomer alcohol


title: HepaPlate01_F18

value: Sodium perfluorodecanesulfonate


title: SCR-sh-W4-26

city: Belmont

first: Joy

last: Otten

state: Massachusetts

address: 115 Mill Street

institute: McLean Hospital

data_processing:
The quality control (QC) of the raw reads was carried out to determine whether the sequencing data was suitable for subsequent analysis (Ewels et al., 2016). No reads were discarded. For additional QC and downstream analyses, the bcbioRNASeq R package was used (Steinbaugh et al., 2018).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: counts.csv: Comma-separated matrix table with raw gene counts for every gene and every sample.

source_name: hippocampus

growth_protocol: Mice were kept under standard laboratory conditions and were maintained on a 12 h light–dark cycle (lights on from 0700 to 1900 h), with food and water provided ad libitum.

extract_protocol:
Total RNA was isolated using the Agilent absolutely RNA miniprep kit. Samples were processed by mRNA enrichment and rRNA removal.
The cDNA library was sequenced using the BGISEQ-500 platform by BGI (Hong Kong, China). Sequencing was done with a 100-bp paired-end sequencing and yielded on average 49.3 million raw reads of which on average 48.3 million (98%) is mapped to the M. musculus (GRC38/mm10) genome using STAR and Salmon was used to quantify the expression of the transcripts (Dobin et al., 2013; Patro et al., 2017).

treatment_protocol: Male mice (8 weeks of age) received bilateral viral infusions of pAAV9-U6-shRNA[Ska2#1]-PGK-mCherry (SKA2-knockdown-AAV) or pAAV9-U6-shRNA[SCR]-PGK-mCherry (Ctrl-AAV) into the dorsal hippocampus. Mice were sacrificed two or four weeks after viral-mediated knockdown of SKA2. Brains were removed, snap-frozen in isopentane at -40 °C, and stored at -80 °C until further processing. Tissue punches of hippocampus were collected.

tag: Sex

value: male

value: hippocampus

tag: condition

value: SCR-sh

tag: time point

value: 4 weeks


title: Ovarian cancer, NACT, Post (R210179)

value: Ovary

value: Ovarian cancer

value: NACT, Post


title: HepaPlate01_F17

value: Perfluoroundecanoic acid


title: WT blood Ly6Chi monocyte

value: Ly6Chi monocyte


title: WT blood Ly6Clo monocyte


title: HepaPlate01_F16

value: AFFF-2 (Chemguard 6%)


title: Ovarian cancer, NACT, Pre (R210178)

value: NACT, Pre


title: SKA2-sh1-W4-20


title: HepaPlate01_F15

value: AFFF-1 (Foamtec 3%)


title: RBP-Jfl/fl Lyz2-Cre blood Ly6Chi monocyte

value: blood

value: RBP-Jfl/fl Lyz2-Cre


title: Og2-7dpp-2

description: Library 2

value: Testis

value: Primary spermatogonia


title: SCR-sh-W4-18


title: Ovarian cancer, NACT, Post (R210177)


title: DGaxon

source_name: Dentate Gyrus

value: Dentate Gyrus

value: post natal day 8


title: HepaPlate01_F13

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: 8:2 Fluorotelomer sulfonic acid


title: Ovarian cancer, NACT, Pre (R210176)

value: Ovary


title: HCT-116 cells, DAC30_H3K27me3_2

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

description:
DAC30_IP_rep2
DAC30_conserved_peaks_Log2FC_all_regions.bed

library_source: genomic

data_processing:
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq (v1.9.0).
siQ-ChIP sequencing reads were 3’ trimmed and filtered for quality and adapter content using TrimGalore (v0.5.0) and quality was assessed by FastQC (v0.11.8). Reads were aligned to human assembly hg38 with bowtie2 (v2.3.5) and were deduplicated using removeDups from samblaster (v.0.1.24) (144). Aligned BAM files were used for quality control analysis with “deeptools” (v3.2.0) ‘plotFingerprint’ and ‘plotPCA’ functions. Aligned SAM files were then processed for pair-end reads with high mapping quality (MAQ >= 20), correct pair orientation (Sam Flags = 99, 163), and fragment length as described for siQ-ChIP (https://github.com/BradleyDickson/siQ-ChIP). Param.in files were prepared for each sample with all required parameters and measurements required for siQ-ChIP normalization. IP tracks (with H3K27me3 efficiency values) and comparative responses between drug treatments (relative to Vehicle) were generated with execution of getsiq.sh (version: February 2021) with the EXPlayout file
To determine the change in H3K27me3 distributions between inhibitor-treated samples and vehicle-treated samples, each inhibitor-treated biological replicate (e.g. DAC301) was individually compared to the two vehicle-treated biological replicates (e.g. DAC301vsVeh1, DAC301vsVeh2), and the average log2 fold-change in response (area of peak in inhibitor-treatment/area of peak in vehicle treatment) was calculated. Next, conserved peaks between inhibitor-treated biological duplicates were determined by calculating the proximity of replicate 1 peaks to replicate 2 peaks (e.g. DAC301, DAC302) using the ‘closest’ command from “bedtools” (v2.25.0). Peaks were considered conserved among biological replicates if the peaks overlapped or were within 200 bp of each other. Finally, the average log2 fold-change in response was calculated for the peaks conserved between the two inhibitor-treated biological replicates. Peaks were considered significant if the log2 fold-change in response was > 1.0 (increase in H3K27me3) or < -1.0 (decrease in H3K27me3).
Assembly: hg38
Supplementary files format and content: bigwig files for H3K27me3 efficiency values across genomic coordinates for each sample
Supplementary files format and content: tab delimited file of response calculations for each drug-treatment relative to Vehicle

molecule: genomic DNA

growth_protocol: HCT116 colon cancer cell lines was purchased from ATCC and maintained according to ATCC recommendations in McCoy's (Gibco 16600-082) media supplemented with 10% Fetal Bovine Serum (Millipore Sigma F0926) and 1% penicillin/streptomycin (Life Technologies, 15140-122) at 5% CO2 and 37C.

extract_protocol:
Cells exposed to drugs for 72 hours were fixed in buffer (1% formaldehyde, 50 mM HEPES-KOH pH 7.6, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0) for 10 min at room temp with shaking and then quenched with 125 mM glycine 5 min at room temp. Cells were scraped into cold PBS, washed 2X with cold PBS, flash frozen in liquid N2, and stored at -80°C until use. Thawed pellets were lysed in LB1 (50 mM HEPES-KOH pH 7.6, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100, Roche protease inhibitor cocktail) for 20 min with rotation at 4°C and cleared by centrifugation at 300 x g for 5 min at 4°C. Supernatant with intact nuclei was set aside. Cell pellets were lysed again in 4x LB1 (LB1 with 2% NP-40 and 1% Triton X-100) for 20 min. Intact nuclei from this and the saved supernatant were collected by centrifugation at 1,700 x g for 5 min at 4°C, resuspended and washed in LB2 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl, protease cocktail inhibitor) for 10 min with rotation at 4°C, and collected again by centrifugation at 1,700 x g for 5 min at 4°C. Nuclei were gently rinsed 2x with LB3 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 0.01% NP-40, protease cocktail inhibitor) without disturbing the pellet. Nuclei were resuspended in 1 mL LB3 and transferred to a 1 ml milliTUBE (Covaris). Chromatin was sheared to a range of 300-600 base-pair fragments using a Covaris E220 evolution Focused ultrasonicator with the following parameters: Peak power (140.0), Duty Factor (5.0), Cycles/Burst (200), Duration (600 seconds), Temperature (4°C). Sheared chromatin was quantified by Bradford Assay, and 450 µg of chromatin was brought to 500 µL in LB3 and 500 µL of ChIP Cocktail Mix (40 mM Tris-HCl pH 7.6, 150 mM NaCl, 1 mM EDTA pH 8.0, 1% Triton X-100, 0.5% NP-40, Protease inhibitor cocktail) was added. Prepared chromatin was pre-cleared by incubation with 20 µL of pre-washed Dynabeads Protein G magnetic beads (Invitrogen, 10004D) for 3 hours at 4°C with rotation. After bead removal, 10% input (100 µL) of pre-cleared chromatin was removed and set aside. Pre-cleared chromatin was immunoprecipitated with 5 µL of H3K27me3 antibody (Cell Signaling 9733) overnight at 4°C with constant rotation. Protein G magnetic beads (35 µL/IP) were blocked in buffer containing PBS, 0.5% BSA, and 20 µg Herring Sperm DNA (Sigma, D7290) with rotation at 4°C overnight. Blocked beads were washed 3X with PBS and 0.5% BSA and 2X with WB1 (50 mM Tris-HCl pH 7.6, 150 mM NaCl, 5 mM EDTA pH 8.0, 0.5% NP-40, 1% Triton X-100). Immuno-chromatin complexes were incubated with blocked beads for 3 hours with rotation at 4°C. Bead-immuno-chromatin complexes were then washed 3X for 5 min with rotation at 4°C with WB1, 3X with WB2 (50 mM Tris-HCl pH 7.6, 500 mM NaCl, 5 mM EDTA pH 8.0, 0.5% NP-40, 1% Triton X-100), 2X with WB1, and 1X with Low Salt TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 50 mM NaCl). Beads were incubated in 50 µl of Elution Buffer (10 mM Tris-HCl pH 8.0, 10 mM EDTA, 150 mM NaCl, 5 mM DTT, 1% SDS) at 65°C for 15 min in 50 µL volume to elute immuno-chromatin complexes. The elution step was repeated, and eluates combined. Eluents and input were incubated overnight at 65°C with constant shaking to reverse crosslinks, followed by incubation at 37°C for 1 hour with DNase-free RNase A, then at 37°C for 2 hours with 10 µL of Proteinase K (20 mg/mL stock). DNA was isolated with a 1.5x ratio of KAPA Pure Beads (KAPA Biosystems KK8000) to DNA volume.
Immunoprecipitated fragments and saved inputs were quantified with a Qubit dsDNA High Sensitivity Assay kit (Invitrogen Q32851), and 10 ng of purified DNA for each IP and input sample were used for library preparation with the KAPA Hyper Prep Kit (Kapa Biosystems KR0961). TAZ and Combo treatments required two IPs per biological replicate to attain enough material for library preparation, and this doubling has been accounted for in the parameters for siQ-ChIP (88,89) for these samples. Library preparation including fragment end-repair, A-tail extension, and adapter ligation was conducted per the manufacturer’s instructions (KAPA). Adapter-ligated fragments were amplified with 11 cycles following the recommended thermocycler program, and DNA was purified with two rounds of purification using KAPA Pure Beads (KK8000). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Individually indexed libraries were pooled and 75 bp, paired end sequencing was performed on an Illumina NextSeq 500 sequencer using a 150 bp HO sequencing kit (v2) (Illumina Inc., San Diego, CA, USA) or 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S2, 100 bp sequencing kit to a minimum read depth of 50M read pairs per IP library and 100M read pairs per Input library.

treatment_protocol: 5-aza-2’-deoxycytidine (DAC, Sigma A3656) was dissolved in DMSO:PBS at a ratio of 1:150 and stored at -80°C. Each drug or % vehicle equivalent was applied to attached cells for a period of 72 hours. Tazemetostat (TAZ or EPZ6438, Selleck Chemicals S7128 and Cayman Chemical 16174) was dissolved in DMSO and sotred at -20C. Cells were treated for 72 hours.

value: colorectal carcinoma

tag: passages

value: 4-5 passages

value: 5'aza-2'deoxycytidine (30 nM)

tag: time

value: 3 days

tag: chip antibody

value: Cell Signaling H3K27me3 (CST#9733, clone C36B11, lot 14)

tag: sequence length

value: 2 x 75bp


title: HCT-116 cells, DAC30_INPUT


title: HCT-116 cells, Veh_INPUT

value: DMSO


title: HepaPlate01_F14

value: AFFF-6 (FireStopper)


title: DRGaxon

source_name: Dorsal Root Ganglion

value: Dorsal Root Ganglion

value: embryonic day 13.5


title: HCT-116 cells, DAC30_H3K27me3_1

description:
DAC30_IP_rep1
DAC30_conserved_peaks_Log2FC_all_regions.bed


title: SCR-sh-W4-16

value: male

value: hippocampus

value: SCR-sh

value: 4 weeks


title: Ovarian cancer, NACT, Post (R210175)

value: Ovarian cancer

value: NACT, Post


title: SKA2-sh1-W4-13


title: SCR-sh-W4-19


title: Ovarian cancer, NACT+P, Pre (R210172)

value: Ovary

value: NACT+P, Pre


title: HepaPlate01_F12

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: AFFF-3 (Phos-Check)


title: HepaPlate01_F11

value: 4:2 Fluorotelomer alcohol


title: Ovarian cancer, NACT+P, Post (R210173)

value: NACT+P, Post


title: HCT-116 cells, Veh_H3K27me3_2

value: colorectal carcinoma

value: 4-5 passages

value: DMSO

value: 3 days

value: Cell Signaling H3K27me3 (CST#9733, clone C36B11, lot 14)

value: 2 x 75bp


title: SKA2-sh1-W4-11

value: male

value: hippocampus


title: HCT-116 cells, Veh_H3K27me3_1


title: HepaPlate01_F10


title: Ovarian cancer, NACT, Post (R210171)

value: Ovarian cancer


title: HepaPlate01_F09

value: AFFF-5 (Solberg 6%)


title: HUVEC, control, batch 2, rep 3

city: Detroit

first: Roger

last: Pique-Regi

state: Michigan

address: 540 E Canfield (Scott Hall 3309)

institute: Wayne State University

data_processing:
Aligned with HISAT2 to hg19
Removal of non-matching UMIs using UMItools
Samtools mpileup
Assembly: hg19
Supplementary files format and content: Samtools mpileup output in DP4 format (Reads for each allele and direction. Columns 1 and 2 are the chromosome and genomic location of the SNP, Colums 3 and 4 are the reference and alternate allele. Column 5 is the sample name. Columns 6, 7, 8, and 9 are the read counts for the reference forward, reference reverse, alternate forward, and alternate reverse configurations)

source_name: Lonza

extract_protocol:
QIAGEN RNeasy Plus Mini kit
Invitrogen Superscript III First-Strand Synthesis kit

treatment_protocol: Caffeine 1.16×10−3 M for 24 hours

value: Lonza

value: HUVEC

value: Water (vehicle control)


title: SKA2-sh1-W4-10

value: 4 weeks


title: Ovarian cancer, NACT, Pre (R210170)

value: Ovary

value: NACT, Pre


title: SCR-sh-W4-9

value: SCR-sh


title: HUVEC, control, batch 2, rep 2


title: HepaPlate01_F08

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: 8:2 Fluorotelomer alcohol


title: HepaPlate01_F07

value: Sodium perfluorodecanesulfonate


title: HUVEC, control, batch 2, rep 1


title: Ovarian cancer, NACT, Post (R210169)

value: NACT, Post


title: HepaPlate01_F06

value: Perfluoroundecanoic acid


title: SCR-sh-W4-21

value: male


title: HUVEC, control, batch 1, rep 3


title: Ovarian cancer, NACT, Pre (R210168)


title: SCR-sh-W4-6

value: hippocampus


title: SKA2-sh1-W4-8


title: Ovarian cancer, NACT+P, Post (R210167)

value: Ovarian cancer

value: NACT+P, Post


title: Ovarian cancer, NACT+P, Pre (R210166)

value: NACT+P, Pre


title: SKA2-sh1-W4-4


title: HUVEC, control, batch 1, rep 2

value: Lonza

value: HUVEC


title: HUVEC, control, batch 1, rep 1

value: Water (vehicle control)


title: HepaPlate01_F05

value: AFFF-2 (Chemguard 6%)


title: SKA2-sh1-W4-5

value: 4 weeks


title: Ovarian cancer, NACT, Post (R210165)

value: Ovary


title: SKA2-sh1-W4-2


title: HUVEC, caffieine, batch 2, rep 3

value: Caffeine


title: Ovarian cancer, NACT, Pre (R210164)

value: NACT, Pre


title: HepaPlate01_F03

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: AFFF-6 (FireStopper)


title: SCR-sh-W4-1

value: SCR-sh


title: HUVEC, caffieine, batch 2, rep 2


title: HepaPlate01_F02

value: 8:2 Fluorotelomer sulfonic acid


title: Ovarian cancer, NACT, Pre (R210162)


title: HUVEC, caffieine, batch 1, rep 3


title: SKA2-sh1-W2-20

value: male

value: hippocampus

value: 2 weeks


title: SCR-sh-W2-21


title: SCR-sh-W2-19


title: HepaPlate01_F04

value: AFFF-1 (Foamtec 3%)


title: Ovarian cancer, NACT+P, Pre (R210160)

value: Ovarian cancer

value: NACT+P, Pre


title: Ovarian cancer, NACT, Post (R210163)

value: NACT, Post


title: SKA2-sh1-W2-18


title: HepaPlate01_E20

value: AFFF-5 (Solberg 6%)


title: HUVEC, caffieine, batch 1, rep 2

value: Lonza

value: HUVEC


title: SKA2-sh1-W2-17


title: Ovarian cancer, NACT+P, Pre (R210158)

value: Ovary


title: HUVEC, caffieine, batch 1, rep 1

value: Caffeine


title: Ovarian cancer, NACT+P, Post (R210157)

value: NACT+P, Post


title: HepaPlate01_E23

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: AFFF-3 (Phos-Check)


title: HUVEC, caffieine, batch 2, rep 1


title: Ovarian cancer, NACT+P, Post (R210161)


title: HepaPlate01_E21


title: HepaPlate01_E22

value: 4:2 Fluorotelomer alcohol


title: HepaPlate01_E19

value: 8:2 Fluorotelomer alcohol


title: SCR-sh-W2-16

value: male

value: hippocampus

value: SCR-sh


title: wild type mixed embryos experiment 3rep4

city: Bethesda

first: Katherine

last: McJunkin

state: MD

address: 50 South Drive, Building 50 Room 3148

institute: National Institutes of Health

data_processing:
Small RNA libraries were trimmed using Cutadapt 3.4 (122), then mapped using bowtie2 2.4.4 with settings “--no-unal --end-to-end –sensitive” (123). BAM files were sorted and indexed using samtools 1.13, then assigned to miRNAs using htseq 0.13.5 (124, 125). For genome mapping and miRNA assignment, custom reference files were used which included the spiked in RNA oligos. Statistical analysis was performed using DESeq2 and GraphPad Prism (126). For spike-in normalization (Figure S3), size factors for DESeq2 analysis were calculated by dividing spike-in reads in each sample by the median number of spike-in reads per sample. For all other analyses, default DESeq2 normalization was performed using all endogenous miRNA-mapping reads (spike-in reads were excluded from analysis).
Assembly: genome_c_elegans.PRJNA13758.WS280.genomic_with_spike_mut_mir35.fa
Assembly: cel_mirGeneDB_spikeins_010622.gff
Supplementary files format and content: xlsx file containing counts of reads mapped to miRNA and spike in RNA annotations

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Nematode culture was performed on NGM plates seeded with OP50. Worms were maintained at 20°C except where otherwise noted. Embryo samples were harvested by hypochlorite treatment. For L4 and young adult samples, L1s were hatched overnight in M9 supplemented with cholesterol, then grown on NGM with OP50 for 48h at 20°C (for L4s) or for 44h at 25°C (for young adults).

extract_protocol:
Samples were snap frozen, then resuspended in Trizol and vortexed for 15 minutes at room temperature. Thereafter, total RNA was purified according to the Trizol manufacturer’s instructions (ThermoFisher).
Library preparation was performed using the NEBNext Small RNA Library Prep Set for Illumina with modifications. Size selection was performed only after reverse transcription, using 8% urea gels to purify ~65-75nt RT products. Prior to loading on the gel, each RT reaction was treated with 5000units of RNAse H (New England Biolabs) for 30 minutes at 37C.

tag: dev stage

value: mixed embryos

value: wild type

tag: alias in_text_and_figures

value: hermaphrodite

value: whole animal


title: Ovarian cancer, NACT+P, Pre (R210156)

value: Ovarian cancer

value: NACT+P, Pre


title: HepaPlate01_E18

value: Sodium perfluorodecanesulfonate


title: SCR-sh-W2-14

value: 2 weeks


title: alg-1(AEDH) mixed embryos experiment 3rep4

description: Library preparation was performed using the NEBNext Small RNA Library Prep Set for Illumina with modifications. Size selection was performed only after reverse transcription, using 8% urea gels to purify ~65-75nt RT products. Prior to loading on the gel, each RT reaction was treated with 5000units of RNAse H (New England Biolabs) for 30 minutes at 37C.

value: alg-1(cdb153) X


title: Ovarian cancer, NACT+P, Post (R210155)

value: Ovary

value: NACT+P, Post


title: HepaPlate01_E17

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluoroundecanoic acid


title: SCR-sh-W2-12

value: male


title: wild type mixed embryos experiment 3rep3


title: HepaPlate01_E16

value: AFFF-2 (Chemguard 6%)


title: Ovarian cancer, NACT+P, Pre (R210154)


title: Ovarian cancer, NACT, Post (R210153)

value: NACT, Post


title: SKA2-sh1-W2-9

value: hippocampus


title: SKA2-sh1-W2-11


title: alg-1(AEDH) mixed embryos experiment 3rep3

value: mixed embryos


title: SCR-sh-W2-8

value: SCR-sh


title: alg-2(AEDH)  mixed embryos experiment 3rep3

value: alg-2(cdb155) II

value: hermaphrodite

value: whole animal


title: SCR-sh-W2-7


title: alg-2(AEDH)  mixed embryos experiment 3rep2


title: alg-2(AEDH)  mixed embryos experiment 3rep4


title: HepaPlate01_E14

value: AFFF-6 (FireStopper)


title: Ovarian cancer, NACT, Pre (R200633)

value: Ovarian cancer

value: NACT, Pre


title: Ovarian cancer, NACT+P, Pre (R200632)

value: Ovary

value: NACT+P, Pre


title: HepaPlate01_E15

value: Blank

value: AFFF-1 (Foamtec 3%)


title: Ovarian cancer, NACT+P, Post (R200671)

value: NACT+P, Post


title: HepaPlate01_E13

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: 8:2 Fluorotelomer sulfonic acid


title: HepaPlate01_E12

value: AFFF-3 (Phos-Check)


title: HepaPlate01_E11

value: 4:2 Fluorotelomer alcohol


title: SCR-sh-W2-5

value: male

value: hippocampus

value: 2 weeks


title: wild type mixed embryos experiment 3rep2

value: mixed embryos

value: wild type

value: hermaphrodite


title: SKA2-sh1-W2-4


title: alg-2(AEDH)  mixed embryos experiment 3rep1

value: alg-2(cdb155) II

value: whole animal


title: Ovarian cancer, NACT, Pre (R200629)

value: Ovary

value: Ovarian cancer

value: NACT, Pre


title: HepaPlate01_E10

value: Blank


title: SKA2-sh1-W2-3


title: alg-1(AEDH) mixed embryos experiment 3rep1

value: alg-1(cdb153) X


title: Ovarian cancer, NACT, Pre (R200627)


title: HepaPlate01_E09

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: AFFF-5 (Solberg 6%)


title: alg-1(AEDH) mixed embryos experiment 3rep2


title: Ovarian cancer, NACT+P, Pre (R200631)

value: NACT+P, Pre


title: wild type mixed embryos experiment 3rep1


title: Ovarian cancer, NACT, Pre (R200626)


title: HepaPlate01_E08

value: 8:2 Fluorotelomer alcohol


title: Ovarian cancer, NACT+P, Pre (R200624)


title: HepaPlate01_E07

value: Sodium perfluorodecanesulfonate


title: HepaPlate01_E05

value: AFFF-2 (Chemguard 6%)


title: Ovarian cancer, NACT+P, Pre (R200625)


title: Ovarian cancer, NACT+P, Pre (R200620)


title: HepaPlate01_E06

value: Perfluoroundecanoic acid


title: HepaPlate01_E04

value: AFFF-1 (Foamtec 3%)


title: Ovarian cancer, NACT+P, Pre (R200619)


title: HepaPlate01_E03

value: AFFF-6 (FireStopper)


title: female mouse 78, ELS, FKBP51 lox/lox wild-type mouse, hippocampus

city: Munich

first: Mathias

middle: V.

last: Schmidt

state: Bayern

address: Kraepelinstrasse 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Allignment to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2Rpackage (1.20.0). DESeq2. Resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.
Genes with an adjusted P-value <=0.2 found by DESeq2 were assigned as differentially expressed
Assembly: Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Supplementary files format and content: vanDoeselaar_2024_GEO_all_compare_readcounts.txt
Supplementary files format and content: txt file: table with ENSEMBL gene id, read counts for each of the samples, gene name and description of the gene

source_name: Brain

growth_protocol: Brains were extracted, snap-frozen in methyl butane on dry-ice and stored at -80 degrees

extract_protocol:
RNA isolation was achieved with help of the miRNeasy Mini Kit (cat. no. 1038703, QIAGEN) RNA extraction kit, according to the manufacturer’s protocol.
libraries were prepared by the company Novogene UK, according to their standardized protocols

treatment_protocol: Knockout and wildtype mice underwent a limited-bedding and nesting material early life stress or control condition. No further treatment of tissues

value: Brain

value: Hippocampus

value: Wild-type

value: ELS


title: female mouse 72, ELS, FKBP51 lox/lox wild-type mouse, hippocampus


title: female mouse 56, ELS, FKBP51 lox/lox wild-type mouse, hippocampus


title: female mouse 8, ELS, FKBP51 lox/lox wild-type mouse, hippocampus


title: female mouse 4, ELS, FKBP51 lox/lox wild-type mouse, hippocampus


title: Ovarian cancer, NACT+P, Pre (R200618)

value: Ovary

value: Ovarian cancer


title: Crispr Mouse with ReDeeM, Batch1, Cell Hash Site, sample 14

city: Boston

last: Weng

state: OH

address: 415 Main St, Cambridge

department: Genetics

institute: Broad Institute and Whitehead Institute

description: Cell Hash library (Cell barcodes are matchable with ATAC, mtDNA, mRNA, TargetSite lib in sample 14): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains Hashing barcode.

data_processing:
Standard ReDeeM pipeline was used for pre-processing mtDNA data as described above. The Target Site data was pre-processed using Python package Cassiopeia. Briefly, reads with identical cellBC and UMI were collapsed into a single, error-corrected consensus sequence representing a single-expressed transcript. Consensus sequences were identified within a cell based on a maximum of 10 high-quality mismatches (PHRED score greater than 30) and an edit distance less than 2 (default pipeline parameters). UMIs within a cell reporting more than one consensus sequence were resolved by selecting the consensus sequence with more reads. Each consensus sequence was aligned to the wild-type reference Target Site sequence using a local alignment strategy, and the intBC and indel alleles were called from the alignment. Cells with fewer than 2 reads per UMI on average or fewer than 10 UMIs overall were filtered out. These data were summarized in a molecule table which records the cellBC, UMI, intBC, indel allele, read depth, and other relevant information. Then, character matrices were formed summarizing indel information across the N cells in a population and their M cut-sites. Characters (i.e., cut-sites) with more than 80% missing information or containing a mutation that was reported in greater than 98% of cells were filtered out for downstream analysis
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: mtDNA mutation raw genotype and depth: mtDNA.RawGenotypes.Total.StrandBalance, mtDNA.depth
Supplementary files format and content: Analyzed Indels per cell by Cassiopeia:  indel_alleles.tar.gz
Supplementary files format and content: TotalSeq-A Cell hash analyzed: Hash_calls.tsv, Hash_annotation.tsv
Library strategy: Hash DNA

source_name: Lung cancer

extract_protocol:
Mouse experiments were approved by the Massachusetts Institute of Technology Institutional Animal Care and Use Committee (IACUC) (institutional animal welfare assurance no. A-3125-01). A male mouse embryonic stem cell (mESC) line harbouring the conditional alleles KrasLSL-G12D/+ and Trp53fl/fl (KP) was engineered with the lineage tracer cassettes. The detailed engineering process, including vector information, tumour harvest and single-cell suspension were prepared as described in Yang et al.  Two independent mESC lines were used for batch-1 and batch-2 experiments.
The single cells of batch-1 from multiple tumors were labelled with Cell Hash and were profiled using ReDeeM except the following modification. Additional Target Site libraries were needed. The amplified cDNA libraries were further amplified with Target Site-specific primers containing Illumina-compatible adapters and sample indices (oDYT023-oDYT038, forward:5′CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGAATCCAGCTAGCTGTGCAGC; reverse:5′-AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCTTTCCCTACACGACGCTCTTCCGATCT; “N” denotes sample indices) using Kapa HiFi ReadyMix (Roche), as described.
For sequencing scRNA, scATAC, mtDNA libraries, the same strategy as described for ReDeeM were used, except that four sets of mouse specific probes were designed to enrich mitochondrial fragments. For sequencing Target Site libraries, 15,000 total reads per cell were expected, and the following read lengths were used: Read1: 26 cycles, i7: 8 cycles, Read2: 290 cycles).

value: Lung cancer

tag: library type

value: Hash


title: HepaPlate01_E02

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: 8:2 Fluorotelomer sulfonic acid


title: SKA2-sh1-W2-2

value: male

tag: tissue

value: hippocampus

value: 2 weeks


title: Crispr Mouse with ReDeeM, Batch1, RNA, sample 14

description: 3' mRNA library (Cell barcodes are matchable with ATAC and mtDNA TargetSite and CellHash lib in sample 14): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains transcript.

library_source: transcriptomic single cell

data_processing:
Standard ReDeeM pipeline was used for pre-processing mtDNA data as described above. The Target Site data was pre-processed using Python package Cassiopeia. Briefly, reads with identical cellBC and UMI were collapsed into a single, error-corrected consensus sequence representing a single-expressed transcript. Consensus sequences were identified within a cell based on a maximum of 10 high-quality mismatches (PHRED score greater than 30) and an edit distance less than 2 (default pipeline parameters). UMIs within a cell reporting more than one consensus sequence were resolved by selecting the consensus sequence with more reads. Each consensus sequence was aligned to the wild-type reference Target Site sequence using a local alignment strategy, and the intBC and indel alleles were called from the alignment. Cells with fewer than 2 reads per UMI on average or fewer than 10 UMIs overall were filtered out. These data were summarized in a molecule table which records the cellBC, UMI, intBC, indel allele, read depth, and other relevant information. Then, character matrices were formed summarizing indel information across the N cells in a population and their M cut-sites. Characters (i.e., cut-sites) with more than 80% missing information or containing a mutation that was reported in greater than 98% of cells were filtered out for downstream analysis
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: mtDNA mutation raw genotype and depth: mtDNA.RawGenotypes.Total.StrandBalance, mtDNA.depth
Supplementary files format and content: Analyzed Indels per cell by Cassiopeia:  indel_alleles.tar.gz
Supplementary files format and content: TotalSeq-A Cell hash analyzed: Hash_calls.tsv, Hash_annotation.tsv

molecule: polyA RNA

value: mRNA


title: female mouse 66, ELS, FKBP51-Nex knockout mouse, hippocampus

tag: cell line

value: Knockout


title: Ovarian cancer, NACT+P, Pre (R200617)

value: NACT+P, Pre


title: HepaPlate01_D23

tag: cell type

value: AFFF-3 (Phos-Check)


title: Ovarian cancer, NACT, Pre (R200621)

value: NACT, Pre


title: female mouse 68, ELS, FKBP51 lox/lox wild-type mouse, hippocampus

value: Brain

value: Hippocampus

tag: genotype

value: Wild-type


title: female mouse 62, ELS, FKBP51-Nex knockout mouse, hippocampus

tag: treatment

value: ELS


title: HepaPlate01_D22

value: 4:2 Fluorotelomer alcohol


title: Ovarian cancer, NACT+P, Pre (R200616)

value: Ovary

value: Ovarian cancer


title: female mouse 60, ELS, FKBP51-Nex knockout mouse, hippocampus


title: HepaPlate01_D20

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: AFFF-5 (Solberg 6%)


title: Crispr Mouse with ReDeeM, Batch1, Target Site, sample 14

description: Target Site library (Cell barcodes are matchable with ATAC and mtDNA and CellHash lib in sample 14): read1 (1-28nt) file contains cell barcode and UMI; read2 file contains the indels generated by CRISPR Cas9 for lineage tracing. Use software Cassiopeia for analysis

data_processing:
Standard ReDeeM pipeline was used for pre-processing mtDNA data as described above. The Target Site data was pre-processed using Python package Cassiopeia. Briefly, reads with identical cellBC and UMI were collapsed into a single, error-corrected consensus sequence representing a single-expressed transcript. Consensus sequences were identified within a cell based on a maximum of 10 high-quality mismatches (PHRED score greater than 30) and an edit distance less than 2 (default pipeline parameters). UMIs within a cell reporting more than one consensus sequence were resolved by selecting the consensus sequence with more reads. Each consensus sequence was aligned to the wild-type reference Target Site sequence using a local alignment strategy, and the intBC and indel alleles were called from the alignment. Cells with fewer than 2 reads per UMI on average or fewer than 10 UMIs overall were filtered out. These data were summarized in a molecule table which records the cellBC, UMI, intBC, indel allele, read depth, and other relevant information. Then, character matrices were formed summarizing indel information across the N cells in a population and their M cut-sites. Characters (i.e., cut-sites) with more than 80% missing information or containing a mutation that was reported in greater than 98% of cells were filtered out for downstream analysis
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz
Supplementary files format and content: mtDNA mutation raw genotype and depth: mtDNA.RawGenotypes.Total.StrandBalance, mtDNA.depth
Supplementary files format and content: Analyzed Indels per cell by Cassiopeia:  indel_alleles.tar.gz
Supplementary files format and content: TotalSeq-A Cell hash analyzed: Hash_calls.tsv, Hash_annotation.tsv
Library strategy: mtDNA

value: Lung cancer

value: Target Site


title: Ovarian cancer, NACT+P, Pre (R200615)


title: ob/ob mice, AAV8-FH, HFD 2

city: Hangzhou

first: Sike

last: Yu

address: No.1 Xiangshan Branch Lane, Xihu District

institute: Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences

data_processing:
The sequence alignment, and counts were made using the STAR software v2.7.11a (https://github.com/alexdobin/STAR)
The sequence alignment, and counts were made using the STAR software v2.7.11a (https://github.com/alexdobin/STAR)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Liver

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.
RNA libraries was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA.

value: Liver

value: Primary hepatocytes

value: Hepatocyte


title: ob/ob mice, AAV8-FH, HFD 3


title: HepaPlate01_D21


title: Ovarian cancer, NACT, Pre (R200613)


title: Ovarian cancer, NACT, Pre (R200614)


title: ob/ob mice, AAV8-FH, HFD 1


title: female mouse 10, ELS, FKBP51-Nex knockout mouse, hippocampus

value: Knockout


title: C57BL/6 mice, AAV8-FH, 24h-fasted 3


title: HepaPlate01_D19

value: 8:2 Fluorotelomer alcohol


title: Ovarian cancer, NACT, Pre (R200612)

value: NACT, Pre


title: HepaPlate01_D18

value: Sodium perfluorodecanesulfonate


title: C57BL/6 mice, AAV8-FH, 24h-fasted 2


title: female mouse 74, control, FKBP51 lox/lox wild-type mouse, hippocampus

value: Brain

value: Hippocampus

value: Wild-type

value: Control


title: HepaPlate01_D17

value: Perfluoroundecanoic acid


title: Ovarian cancer, NACT, Pre (R200611)

value: Ovary

value: Ovarian cancer


title: female mouse 50, control, FKBP51 lox/lox wild-type mouse, hippocampus


title: C57BL/6 mice, AAV8-FH, 24h-fasted 1


title: Ovarian cancer, NACT+P, Pre (R200610)

value: NACT+P, Pre


title: female mouse 44,  control, FKBP51 lox/lox wild-type mouse, hippocampus


title: female mouse 58, ELS, FKBP51-Nex knockout mouse, hippocampus

value: ELS


title: ob/ob mice, AAV8-vector, HFD 3


title: Ovarian cancer, NACT+P, Post (R200677)

value: NACT+P, Post


title: HepaPlate01_D15

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: AFFF-1 (Foamtec 3%)


title: HepaPlate01_D16

value: AFFF-2 (Chemguard 6%)


title: female mouse 38, ELS, FKBP51-Nex knockout mouse, hippocampus

value: Knockout


title: ob/ob mice, AAV8-vector, HFD 2

value: Liver

value: Primary hepatocytes

value: Hepatocyte


title: Ovarian cancer, NACT+P, Post (R200676)


title: female mouse 34, control, FKBP51 lox/lox wild-type mouse, hippocampus

value: Brain

value: Hippocampus


title: ob/ob mice, AAV8-vector, HFD 1


title: HepaPlate01_D14

value: AFFF-6 (FireStopper)


title: Ovarian cancer, NACT+P, Post (R200675)


title: Ovarian cancer, NACT, Post (R200674)

value: NACT, Post


title: HepaPlate01_D13

value: 8:2 Fluorotelomer sulfonic acid


title: HepaPlate01_D12

value: AFFF-3 (Phos-Check)


title: C57BL/6 mice, AAV8-vector, 24h-fasted 2


title: female mouse 28, control, FKBP51 lox/lox wild-type mouse, hippocampus

value: Wild-type

value: Control


title: C57BL/6 mice, AAV8-vector, 24h-fasted 1


title: Ovarian cancer, NACT+P, Post (R200673)

value: Ovary

value: Ovarian cancer

value: NACT+P, Post


title: female mouse 54, control, FKBP51-Nex knockout mouse, hippocampus


title: Ovarian cancer, NACT+P, Post (R200672)


title: HepaPlate01_D10

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes


title: tumor_mix_rep2_cp

city: Montreal

first: Christian

last: Beauséjour

state: QC

address: 3175, chemin de la Côte-Sainte-Catherine, 6.17.315.6

country: Canada

institute: CHUSJ

description:
CMO304,CMO305,CMO306
CellPlex (CP)

library_source: other

data_processing:
Data processing was done using CellRanger V6 using the "multi" approach.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: protein

source_name: Tumor infiltrating cells

extract_protocol:
Cells from the BM were obtained after flushing with a needle the soft center of tibias and femurs. Tumor infiltrating cells were obtained upon dissociation of the tumor.  Splenic cells were obtained by dissociating the spleen at the single clell level.
Libraries were generated according to the manufacturer's instruction (single cell 3' V3.1 10X Genomics) with the addition of CellPlex lipids for cell multiplexing

treatment_protocol: 6weeks old mice are subjected to a sublethal dose of total body irradion of 6,5Gy. Mice were used 12 weeks after TBI. 50mg/kg/body of ABT263 was given to mice for two cycles of 5 consecutive days, with a week of rest between cycles

value: Tumor infiltrating cells

value: Female

tag: strain

value: CP


title: Ovarian cancer, NACT+P, Post (R200670)


title: HepaPlate01_D09

value: AFFF-5 (Solberg 6%)


title: tumor_mix_rep2_mRNA

description: polyA RNA

value: mRNA


title: tumor_mix_rep1_cp

description:
CMO301,CMO302,CMO303
CellPlex (CP)


title: Ovarian cancer, NACT+P, Post (R200669)


title: female mouse 42, control, FKBP51-Nex knockout mouse, hippocampus

value: Brain

value: Hippocampus

value: Knockout


title: female mouse 32, control, FKBP51-Nex knockout mouse, hippocampus


title: C57BL/6 mice, AAV8-vector, 24h-fasted 3

value: Liver

value: Primary hepatocytes

value: Hepatocyte


title: female mouse 30, control, FKBP51 lox/lox wild-type mouse, hippocampus

value: Wild-type

value: Control


title: female control, FKBP51-Nex knockout mouse, hippocampus


title: HepaPlate01_D07

value: Sodium perfluorodecanesulfonate


title: HepaPlate01_D11

value: 4:2 Fluorotelomer alcohol


title: Ovarian cancer, NACT, Post (R200667)

value: Ovary

value: Ovarian cancer

value: NACT, Post


title: HepaPlate01_D06

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: Perfluoroundecanoic acid


title: Ovarian cancer, NACT+P, Post (R200666)

value: NACT+P, Post


title: BM_mix_cp

description:
CMO307, CMO308, CMO309
CellPlex (CP)

source_name: Bone Marrow

value: Bone Marrow

value: Female

value: CP


title: cochlea-Sox2+ve cells at E16.5

city: Seattle

last: Bermingham-McDonogh

state: WA

address: 1959  NE Pacific St box 357420

department: Biological Structure

institute: University of Washington

data_processing:
Read demutliplexing and intensity to fastq conversion done using cellranger mkfastq,
Gene by cell matricies were created using cellranger count
Downstream processing was performed in R using Seurat
Assembly: mm10
Supplementary files format and content: CellRanger outputs: filtered feature bc matrices in h5 format

source_name: cochlea

growth_protocol: embryonic dissection and FACS for Sox2+ve cells to enrich for Sensory precursors

extract_protocol:
10x genomics protocol
10x Chromium Single Cell 3' V3.1 (scRNA-seq)

value: cochlea

value: C57Bl6 strain

tag: developmental stage

value: WT


title: Ovarian cancer, NACT, Post (R200668)


title: female mous 12, control, FKBP51-Nex knockout mouse, hippocampus

value: Brain

value: Hippocampus

value: Knockout


title: tumor_mix_rep1_mRNA

description: polyA RNA

value: Tumor infiltrating cells

tag: Sex

value: mRNA


title: HepaPlate01_D05

source_name: Blank

value: AFFF-2 (Chemguard 6%)


title: Ovarian cancer, NACT+P, Post (R200665)

value: Ovary

value: Ovarian cancer


title: cochlea-Sox2+ve cells at E14.5


title: female mouse 52, control, FKBP51-Nex knockout mouse, hippocampus

value: Control


title: Spleen_mix_cp

description:
CMO310, CMO311,CMO312
CellPlex (CP)

source_name: Splenocytes

value: Splenocytes


title: cochlea-Sox2+ve cells at E12.5


title: Ovarian cancer, NACT+P, Post (R200664)

source_name: Ovary

value: NACT+P, Post


title: HepaPlate01_D08

value: Blank

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

value: 8:2 Fluorotelomer alcohol


title: Small Intestine Apc Eif3h Rep4

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Cancer Research UK Scotland Institute

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts

source_name: Small Intestine

extract_protocol:
RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq RNA sample kit, then run on an Illumina NextSeq 500 (2x36 cycles, paired end, single index).

treatment_protocol: Induction of genetic recombination was performed by 2 x 80mg/kg intraperitoneal injection of Tamoxifen 24 hrs apart. Tissues  were harvested after 7 days.

value: Small Intestine

value: Male

value: Day 4

value: VilCreER Apc fl/fl Eif3h fl/fl


title: Spleen_mix_mRNA

description: polyA RNA

value: Female


title: Ovarian cancer, NACT+P, Post (R200662)


title: HepaPlate01_D02

data_processing:
The libraries were sequenced (single-end, 50 bp in length) using HiSeq 2500 v.2 (Illumina, San Diego, CA).
This pipeline includes the use of STAR aligner (Dobin et al., 2013) and parameters used herein included a maximum number of mismatches of 3 and insertion and deletion open and extension penalties of 0.
Quality control steps with the following criteria were performed: 1) genes with fewer than 5 mean counts across the entire sample spacewere removed, 2) samples with mean expression across all genes lower than 25 were removed, 3) outliers in vehicle control samples were identified and removed using mean correlation at <0.85 as the criteria to ensure the stability of further transcriptomic dose-response and differential expression analyses, 4) in addition, principal component analysis (PCA) was conducted on vehicle control samples using raw counts to identify any remaining outliers.
Assembly: Whole transcriptome assay
Supplementary files format and content: iHep_normcounts.csv file with normalized count data using DESeq2 R package (Love et al., 2014)
Supplementary files format and content: iHep_hash.csv file with meta data of the QC samples

value: 8:2 Fluorotelomer sulfonic acid


title: Ovarian cancer, NACT, Post (R200663)

value: NACT, Post


title: Small Intestine Apc Eif3h Rep3


title: Caco2, intact, rep2

city: Kaunas

first: Jurgita

last: Skiecevičienė

address: Eiveniu str. 4

department: Institute for Digestive Research

country: Lithuania

institute: Lithuanian University of Health Sciences

data_processing:
Adapter were trimmed-of and quality trimming was done using Trim Galore v 0.6.10 with these non default  flags “-fastqc --small_rna --length 17   --max_length 40“
miRNAs/isomiRs in the fastq sequences were annotated using miraligner from seqbuster v3.5 with these   flags: "-sub 1 -trim 3 -add 3 -s hsa -freq" . As a reference  - dataset tagged as “CURRENT” were used from miRBase (https://www.mirbase.org/ftp/CURRENT, downloaded at June2023)
Assembly: hg38
Supplementary files format and content: tab-delimited text file, includes miraligner assignments
Supplementary files format and content: comma-delimited text file, includes raw  counts per a miRNA variant (a t3 and t5 values combination is considered a variant of a miRNA)  per library.

source_name: Colon

extract_protocol:
Total RNA from colorectal adenocarcinoma cells Caco-2 (n = 2) was extracted using miRNeasy Mini Kit (Qiagen, MD, USA), according to manufacturer recommendations.
Sequencing libraries were constructed using the TruSeq Small RNA Sample Preparation Kit (Illumina, USA).

value: Colon

value: Epithelial


title: Caco2, intact, rep1


title: Liver, Mir483Pat-KO, rep7 (miRNA-seq)

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

description: Liver, Mir483Pat-KO, rep7 miR483_489 miRNA

data_processing:
Data was aliigned to GRCm38 and miRNA abundance were determined using miRge3.0
Assembly: GRCm38
Supplementary files format and content: miR.Counts.csv contains raw miRNA counts in CSV format

molecule: cytoplasmic RNA

extract_protocol:
Total RNA was extracted using a miRNeasy Mini Kit (Qiagen – 217004), according to manufacturer's protocol. Quantity and quality of RNA were assessed using an Agilent 2100 Bioanalyzer and RNA 6000 Nano Kits (Agilent – 5067-1511)
1 µg total RNA per sample was used to prepare libraries using Illumina's TruSeq Small RNA Library kit, according to manufacturer's protocol.

value: Liver

value: female

tag: library


title: HepaPlate01_D04

last: Rusyn

address: 4458 TAMU

institute: Texas A&M University

extract_protocol:
The media and chemicals from the 384-well plates was fully aspirated and replaced with 10 μL/well of 2X lysis buffer. The plates were then shaken using an orbital plate shaker for 10 minutes. The plates were then checked to ensure that the cells were lysed, and if not placed back on the plate shaker for an additional five minutes. Once the cells were lysed, adhesive seals were placed on the plates and the lysates were frozen in the 384-well plates and stored at −80 °C until further processing.  The Templated Oligonucleotide Sequencing Assay (TempO-Seq™, BioSpyder Technologies, Carlsbad, CA) was used as an RNA sequencing technology of choice. Detailed protocols for TempO-seq are provided by the manufacturer and were previously reported  detailed elsewhere (Grimm et al., 2016; House et al., 2022).
TempO-seq libraries were prepared using the human whole transcriptome panel consisting of 22,537 protein-coding transcripts.

value: AFFF-1 (Foamtec 3%)


title: Small Intestine Apc Eif3h Rep1

tag: time point


title: Liver, Mir483Pat-KO, rep6 (miRNA-seq)

description: Liver, Mir483Pat-KO, rep6 miR483_487 miRNA


title: Ovarian cancer, NACT, Post (R200660)

data_processing:
The primary base call files were converted into FASTQ sequence files using the bcl2fastq converter tool.
Raw sequencing reads were aligned on the human genome (GRCh38) with STAR (v2.7.3a)
Gene expression was quantified using Salmon (v1.0.0) and the annotation of known genes from gencode v29
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file included counts values for each Sample

value: Ovary

value: Ovarian cancer


title: Liver, Mir483Pat-KO, rep4 (miRNA-seq)

description: Liver, Mir483Pat-KO, rep4 miR483_428 miRNA


title: Small Intestine Apc Eif3h Rep2


title: Small Intestine Apc Rep3

value: VilCreER Apcfl/fl


title: BM_mix_mRNA

description: polyA RNA

value: Bone Marrow

value: mRNA


title: Ovarian cancer, NACT, Post (R200661)


title: 847

city: Philadelphia

first: Megha

last: Lal

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

description: 2x150bp configuration

data_processing:
Data quality of sequencing reads was assessed using FastQC 0.14.1 and MultiQC 1.10.
Trimmomatic 0.39 was used to trim low-quality reads as well as to remove adapters.
Reads were pseudo-aligned and quantified using kallisto 0.46.0 against GRCh38.p13 reference genome.
Reads were converted to counts per million (CPM) and log2 transformed to filter low abundance genes.
Reads were further normalized using TMM (weighted trimmed mean of M-values) as implemented in the R package, edgeR 3.38.4
Assembly: hg38 (GRCh38.p13)
Supplementary files format and content: tab-delimited text file that includes raw counts for each sample
Supplementary files format and content: tab-delimited text file that includes log2 normalized for each sample

source_name: Esophageal epithelium

extract_protocol:
Esophageal biopsies were dissociated, and CD45+ cells were removed using positive isolation beads (STEMCELL TECHNOLOGIES). The untouched epithelial enriched cell fraction was washed with PBS before Tri Reagent (Sigma-Aldrich) lysis. Total RNA was extracted directly from the epithelial enriched cell fraction without expansion in culture by column purification using PicoPure™ RNA Isolation Kit (Thermo Fisher Scientific) and stored at -80°C until further use.
RNA sequencing libraries of esophageal epithelial organoids were prepared using the SMART-Seq HT Ultra Low Input RNA kit (Clontech).

value: Esophageal epithelium

tag: disease status

value: ACTIVE

tag: age

value: 1  years

tag: gender

tag: eos/hpf

tag: swallowed steroids

value: N

tag: ppi

tag: diet

value: Unrestricted

tag: race

value: White

tag: ethinicity

value: Not Hispanic or Latino


title: 834

description: 2x150bp configuration

tag: tissue

value: 11  years

value: Female

value: Y

value: Restricted

value: Hispanic or Latino


title: Ovarian cancer, NACT+P, Post (R200658)

last: Le Saux

address: 28 rue Laennec

institute: Cancer Research Center of Lyon

extract_protocol:
Total RNA from FFPE tissues was extracted using 2 to 5 10-μm FFPE sections from pre- and post-treatment samples with FormaPure RNA kit (Beckman Coulter). RNA concentration and absorbances were analyzed with NanoDrop spectrophotometer (Thermo Fisher Scientific), and quality profiles assessed on Tapestation (Agilent Technologies).
Libraries were prepared with the TruSeq RNA Exome kit (Illumina)

value: Ovary

tag: cell line

value: NACT+P, Post


title: Liver, Mir483Pat-KO, rep2 (miRNA-seq)

description: Liver, Mir483Pat-KO, rep2 miR483_423 miRNA

value: Liver

value: female

tag: genotype


title: Small Intestine Apc Rep4

value: Small Intestine

value: Male

value: Day 4

value: VilCreER Apcfl/fl


title: F379

description: 2x150bp configuration

value: Esophageal epithelium

value: ACTIVE

value: 16  years

value: N


title: HepaPlate01_D03

city: College Station

value: Blank

tag: cell type

value: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes

tag: treatment

value: AFFF-6 (FireStopper)


title: Ovarian cancer, NACT, Post (R200657)

value: Ovarian cancer

value: NACT, Post


title: Liver, Mir483Pat-KO, rep1 (miRNA-seq)

description: Liver, Mir483Pat-KO, rep1 miR483_418 miRNA

tag: Sex

tag: developmental stage


title: Small Intestine Apc Rep1

value: Female

tag: time point


title: 844

description: 2x150bp configuration

tag: disease status

value: 4  years

value: Restricted

value: Black or African American

value: Not Hispanic or Latino


title: Liver, Mir483Pat-KO, rep5 (miRNA-seq)

description: Liver, Mir483Pat-KO, rep5 miR483_485 miRNA

value: Liver

value: female

tag: library


title: F388

description: 2x150bp configuration

tag: age

value: 12  years

tag: gender

value: Male

value: Y

value: White


title: Ovarian cancer, NACT+P, Post (R200656)

value: Ovary

value: NACT+P, Post


title: Liver, wild-type, rep5 (miRNA-seq)

description: Liver, wild-type, rep5 miR483_474 miRNA

value: Wild-type


title: Small Intestine WT Rep4

value: Small Intestine

value: Day 7

value: Wild Type


title: Liver, Mir483Pat-KO, rep3 (miRNA-seq)

description: Liver, Mir483Pat-KO, rep3 miR483_426 miRNA


title: Ovarian cancer, NACT+P, Post (R200659)

value: Ovarian cancer


title: 602-3

description: 2x150bp configuration

value: Esophageal epithelium

value: ACTIVE

value: 6  years

tag: eos/hpf

tag: swallowed steroids

value: N


title: Small Intestine WT Rep3


title: Liver, wild-type, rep3 (miRNA-seq)

description: Liver, wild-type, rep3 miR483_412 miRNA

value: Liver


title: Ovarian cancer, NACT+P, Post (R200654)


title: Small Intestine Apc Rep2

value: Day 4

value: VilCreER Apcfl/fl


title: Liver, wild-type, rep4 (miRNA-seq)

description: Liver, wild-type, rep4 miR483_421 miRNA

value: female


title: Small Intestine WT Rep2

value: Male


title: Liver, wild-type, rep1 (miRNA-seq)

description: Liver, wild-type, rep1 miR483_408 miRNA


title: 838

description: 2x150bp configuration

value: 1  years

tag: ppi

tag: diet

value: Restricted

value: Black or African American

value: Not Hispanic or Latino


title: Ovarian cancer, NACT, Post (R200655)

value: Ovary

value: NACT, Post


title: Ovarian cancer, NACT+P, Post (R200651)

value: NACT+P, Post


title: [Liver] [Alcohol] [Replicate 7]

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Sequencing was performed on an NextSeq 500 (Illumina)
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the GRCm38 reference assembly using Tophat2 (v2.0.13).
Read counts for gene regions were obtained with HTSeq v.0.10.0 using GRCm38.84.gtf.
Assembly: GRCm38
Supplementary files format and content: htseq raw counts

extract_protocol:
Total RNA from mouse liver tissue was isolated using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA).  mRNA was enriched with magnetic beads containing oligo(dT). Following fragmentation, RNA samples were used as templates to synthesize cDNA followed by PCR.
Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit- Set A (Cat# RS-122-2101) and Set B (Cat# RS-122-2102) with poly-A enrichment.

value: isocaloric high-fat liquid diet plus alcohol 27 g/kg/day and weekly alcohol binge (5g/Kg)

value: male

tag: strain

value: 8 week treatment high-fat liquid diet plus alcohol 27 g/kg/day and weekly alcohol binge (5g/Kg)


title: Small Intestine WT Rep1

tag: tissue

value: Small Intestine

value: Day 7

value: Wild Type


title: Ovarian cancer, NACT+P, Post (R200652)

city: Lyon

tag: cell line

value: Ovarian cancer


title: 849

description: 2x150bp configuration

value: Esophageal epithelium

value: ACTIVE

value: 9  years

value: N

tag: race

tag: ethinicity


title: F416

description: 2x150bp configuration

value: 18  years

value: Male

value: Unrestricted

value: Other

value: Hispanic or Latino


title: Liver, wild-type, rep2 (miRNA-seq)

description: Liver, wild-type, rep2 miR483_411 miRNA

value: Liver

value: female

tag: genotype

value: Wild-type


title: F376

description: 2x150bp configuration

value: 12  years

value: Y

value: Restricted

value: Unknown

value: Not Hispanic or Latino


title: Liver, iTgMir483, rep6

description: Liver, iTgMir483, rep6 CMVxmiR #29

data_processing:
STAR 2.5.0A was used to perform the alignment and gene level count with GRCm38/Ensembl 100
Assembly: GRCm38
Supplementary files format and content: raw gene level count in tab-delimited format

source_name: liver

extract_protocol:
Total RNA was extracted using a miRNeasy Mini Kit (Qiagen – 217004), according to manufacturer's protocol. Quantity and quality of RNA were assessed using an Agilent 2100 Bioanalyzer and RNA 6000 Nano Kits (Agilent – 5067-1511)
500 ng total RNA per sample was used to prepare libraries using Illumina's TruSeq RNA Library kit, according to manufacturer's protocol.

value: liver

tag: Sex

value: 15 weeks postnatal

value: over-expressor


title: [Liver] [Alcohol] [Replicate 6]

value: isocaloric high-fat liquid diet plus alcohol 27 g/kg/day and weekly alcohol binge (5g/Kg)

value: male

tag: treatment

value: 8 week treatment high-fat liquid diet plus alcohol 27 g/kg/day and weekly alcohol binge (5g/Kg)


title: F382

description: 2x150bp configuration

value: Esophageal epithelium

value: CONTROL

value: 14  years

value: Male

value: N

value: White


title: Liver, iTgMir483, rep5

description: Liver, iTgMir483, rep5 CMVxmiR #28

value: female


title: Ovarian cancer, NACT+P, Post (R200649)

value: Ovary

value: Ovarian cancer

value: NACT+P, Post


title: Ovarian cancer, NACT+P, Post (R200650)


title: 828

description: 2x150bp configuration

value: 9 years

value: Y

value: Restricted

value: Not Hispanic or Latino


title: Liver, iTgMir483, rep4

description: Liver, iTgMir483, rep4 CMVxmiR #27

value: liver

value: 15 weeks postnatal

value: over-expressor


title: Ovarian cancer, NACT+P, Post (R200653)


title: [Liver] [Alcohol] [Replicate 4]

value: Liver

value: isocaloric high-fat liquid diet plus alcohol 27 g/kg/day and weekly alcohol binge (5g/Kg)

value: male

value: 8 week treatment high-fat liquid diet plus alcohol 27 g/kg/day and weekly alcohol binge (5g/Kg)


title: Ovarian cancer, NACT, Post (R200648)

value: NACT, Post


title: 782

description: 2x150bp configuration

value: Esophageal epithelium

value: CONTROL

value: 17  years

value: Male

value: N

value: White


title: Ovarian cancer, NACT, Post (R200647)

value: Ovary

value: Ovarian cancer


title: [Liver] [Alcohol] [Replicate 2]


title: [Liver] [Alcohol] [Replicate 3]


title: F384

description: 2x150bp configuration

value: 1 year

value: Female

value: Y

value: Restricted

value: Not Hispanic or Latino


title: 842

description: 2x150bp configuration

value: Unrestricted


title: [Liver] [Alcohol] [Replicate1]

value: Liver

value: isocaloric high-fat liquid diet plus alcohol 27 g/kg/day and weekly alcohol binge (5g/Kg)

value: male


title: Ovarian cancer, NACT, Post (R200645)

value: NACT, Post


title: 823

description: 2x150bp configuration

value: Esophageal epithelium

value: CONTROL


title: Liver, iTgMir483, rep2

description: Liver, iTgMir483, rep2 CMVxmiR #16

value: liver

value: female

value: 15 weeks postnatal

value: over-expressor


title: Ovarian cancer, NACT+P, Post (R200644)

value: Ovary

value: Ovarian cancer

value: NACT+P, Post


title: Liver, Control, rep6

description: Liver, Control, rep6 CMVxmiR #36

value: control


title: Liver, iTgMir483, rep1

description: Liver, iTgMir483, rep1 CMVxmiR #6


title: Liver, Control, rep5

description: Liver, Control, rep5 CMVxmiR #30


title: [Liver] [Control] [Replicate 5]

value: isocaloric high-fat liquid diet

value: 8 week treatment isocaloric high-fat liquid diet


title: 812

description: 2x150bp configuration

value: 17  years

value: Male

value: N

value: Y

value: Unrestricted

value: White

value: Not Hispanic or Latino


title: [Liver] [Control] [Replicate 4]

value: Liver

value: male


title: [Liver] [Alcohol] [Replicate 5]

value: isocaloric high-fat liquid diet plus alcohol 27 g/kg/day and weekly alcohol binge (5g/Kg)

value: 8 week treatment high-fat liquid diet plus alcohol 27 g/kg/day and weekly alcohol binge (5g/Kg)


title: Ovarian cancer, NACT+P, Pre (R200643)

value: Ovary

value: NACT+P, Pre


title: 821

description: 2x150bp configuration

value: Esophageal epithelium

value: CONTROL

value: Female


title: Liver, Control, rep4

description: Liver, Control, rep4 CMVxmiR #26

value: liver

value: female

value: 15 weeks postnatal

value: control


title: [Liver] [Control] [Replicate 3]

value: isocaloric high-fat liquid diet

value: 8 week treatment isocaloric high-fat liquid diet


title: 822

description: 2x150bp configuration

value: 15  years

value: N

value: Y

value: Unrestricted

value: White


title: Liver, iTgMir483, rep3

description: Liver, iTgMir483, rep3 CMVxmiR #17

value: over-expressor


title: Liver, Control, rep3

description: Liver, Control, rep3 CMVxmiR #25


title: Ovarian cancer, NACT+P, Pre (R200642)

value: Ovary

value: Ovarian cancer


title: [Liver] [Control] [Replicate 1]

value: Liver

value: male


title: Ovarian cancer, NACT, Post (R200646)

value: NACT, Post


title: Ovarian cancer, NACT+P, Pre (R200641)

value: NACT+P, Pre


title: F383

description: 2x150bp configuration

value: Esophageal epithelium

value: CONTROL

value: 13  years

value: Female

value: Not Hispanic or Latino


title: [Liver] [Control] [Replicate 2]

value: isocaloric high-fat liquid diet

value: 8 week treatment isocaloric high-fat liquid diet


title: Ovarian cancer, NACT, Pre (R200640)

value: NACT, Pre


title: 835

description: 2x150bp configuration

value: 11  years

value: N

value: Y

value: Unrestricted


title: Liver, Control, rep1

description: Liver, Control, rep1 CMVxmiR #5

value: liver

value: female

value: 15 weeks postnatal

value: control


title: Ovarian cancer, NACT+P, Pre (R200638)

value: Ovary

value: Ovarian cancer

value: NACT+P, Pre


title: Liver, Mir483Pat-KO, rep5 (RNA-seq)

description: Liver, Mir483Pat-KO, rep5 miR483_489

data_processing:
STAR 2.5.0A was used to perform the alignment and gene level count with GRCm38/Ensembl 100
Assembly: GRCm38
Supplementary files format and content: Gene level count in tab-delimited format

value: Liver

tag: developmental stage

tag: index


title: Liver, Mir483Pat-KO, rep4 (RNA-seq)

description: Liver, Mir483Pat-KO, rep4 miR483_487


title: 814

description: 2x150bp configuration

value: Esophageal epithelium

tag: disease status

value: CONTROL

value: 13 years

value: Female

value: White


title: 48h-4_H3K4me3_Cut&Run

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

data_processing:
Libraries were analyzed with Partek Flow software v10.
unaligned reads were filtered out of contaminants using default parameter in the Filter contaminants (Bowtie 2) -2.2.5 Partek task then aligned with the Bowtie algorithm
Peaks calling was carried out using MACS3 using the input datasets as background peaks and a Cutoff q-value of 0.01 and the mm10 mouse genome version, additionally, scale was adjusted to the larger dataset in the Partek parameters for the MACS3 algorithm.
Genomic regions were quantified with the defaults parameter in Partek flow and normalized to transcripts per million counts in each library to explore the samples with PCA analysis accounting by feature variability.
Differential region enrichment was analyzed with Partek Flow’s version of the GSA algorithm.
Motif enrichment was studied within the positively enriched regions of the GSA analysis at 10 and 2 days against the JASPAR vertebrate database of binding motifs with a following manual curation of transcript factor motifs present in mouse.
The enriched genesets between 48 hours and 10 days Sox9 CUT&RUN datasets were used for pathway analysis against the Gene Ontology (GO) database on Partek.
Assembly: mm10
Supplementary files format and content: BigWig, narrowPeaks (Except for Input files)
Library strategy: Cut&Run

source_name: Kidney

extract_protocol:
Briefly cortices and outer medulla regions of the kidney were dissected and thoroughly minced in 1mlcold DMEM/F12 media using sterile fine forceps. The minced tissue  resuspended in fresh 1ml DMEM/F12 media supplemented with 7.5mg/ml of B. Licheniformis Cold Active Protease, 125U/ml DNase1  and 0.1mg/ml Liberase TL  and continuously kept on ice for 1 hour with frequent pipetting using 1ml pipette every 10 min. After complete dissociation of tissues into single cells (an aliquot of cell suspension was taken every 20 min to check dissociation of the tissue under the microscope), the enzymatic reaction was stopped using cold DMEMF12 media + 10% FBS. The cell suspension was filtered through a 40μm cell strainer. The filtrate was then centrifuged at 300g for 5 min and transferred to FACS tubes (BD Biosciences). Cells were washed in PBS and resuspended in 1.5ml of FACS sorting buffer containing 1mg/ml DAPI (1:1000, Life Technologies). Cell sorting was performed using the FACSAria III cell sorter (BD Biosciences). Cell populations were gated to exclude debris and doublets using FACSDiva software (BD Biosciences). Cells were collected from relevant gated cell populations in 1.5mL collection tubes (Eppendorf) containing collection buffer.
Cells pellets of around 100.000 cells from 2 or 10 days post injury were lighly fixed in 0.2% PFA and freeze at –80 for storage until all samples were collected. Each sample was split in 3 aliquots for subsequent processing with  Sox9 antibody (#AB5535, Millipore), as a positive control with H3K4me3 (#9751, Cell signaling) or as an input control. CUT&RUN assays were carried out with the Cell Signalling assay kit and protocol (Catalog number #86652, Cell Signaling) and next-generation sequencing libraries were generated from the immuno-enriched DNA samples using the DNA Library Prep Kit for Illumina with the Multiplex Oligos for Illumina Systems (Dual Index Primers) kits (#56795 and #47538, Cell Signaling, respectively). The final libraries quality was assessed by fragment size in a TapeStation before sequencing.

treatment_protocol: Age- (9 – 12 weeks old) and weight –matched (25 – 30 gm) male mice were subjected to bilateral renal ischemia reperfusion injury (IRI) surgery. .To obtain Sox9 lineage cells, tamoxifen was administered at induction of kidney IRI to Sox9IRES-CreERT2/+:R26RtdT/+ animals and the cells were isolated at 48h and day10 post-IRI as stated in the below stated extract protocol.

value: Kidney

tag: cell type

value: Sox9-lineage cells (tdTomato positive) at d10 post-IRI, Tamoxifen at IRI, FACS-enriched, biol rep 4

tag: cut&run antibody

value: H3K4me3 (#9751, Cell signaling)


title: Ovarian cancer, NACT+P, Pre (R200637)


title: 48h-4_Sox9_Cut&Run

value: Sox9 (#AB5535, Millipore)


title: IFN-γ treated EPC2-hTERT organoids

description: 2x150bp configuration

growth_protocol: 2 x 103 EPC2-hTERT cells were mixed in 50µl of Matrigel (Corning®) and seeded into a well of a 24-well plate. Once Matrigel solidified, 500µl of high Ca2+ KSFM was added to each well. 3D organoids derived from EPC2-hTERT were  grown in high Ca2+ (1.8mM Ca2+) KSFM (Gibco) , 1ng/ml recombinant epidermal growth factor (rEGF), 1ng/ml bovine pituitary extract (BPE)and 10,000 U/mL Penicillin-Streptomycin (Thermo Fisher Scientific) for 11 days at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
For RNA extraction, Day 11 organoids were isolated from the Matrigel matrix, washed with PBS, lysed using Tri Reagent (Sigma-Aldrich) and stored at -80°C until further use. RNA was extracted for traditional RNA sequencing using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol
RNA sequencing libraries of esophageal epithelial organoids were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina.

treatment_protocol: 3D organoids derived from EPC2-hTERT were treated with varying concentrations of IFN-α (Fisher Scientific) and IFN-γ (Sigma-Aldrich) on Day 7 and Day  9 to assess the effect of varying interferon concentrations on epithelial behavior.

value: Esophageal keratinocyte cell line

value: WT

value: IFN-gamma 5ng/ml


title: Liver, Mir483Pat-KO, rep3 (RNA-seq)

description: Liver, Mir483Pat-KO, rep3 miR483_485

value: female


title: 48h-4_Input_Cut&Run


title: 48h-3_Sox9_Cut&Run

value: Sox9-lineage cells (tdTomato positive) at d10 post-IRI, Tamoxifen at IRI, FACS-enriched, biol rep 3


title: Ovarian cancer, NACT+P, Pre (R200636)

value: Ovary

value: Ovarian cancer


title: IFN-α treated EPC2-hTERT organoids

description: 2x150bp configuration

value: IFN-alpha 200U/ml


title: 48h-3_Input_Cut&Run


title: Liver, Mir483Pat-KO, rep2 (RNA-seq)

description: Liver, Mir483Pat-KO, rep2 miR483_428

value: Liver


title: Control EPC2-hTERT organoids

description: 2x150bp configuration

value: Control


title: Ovarian cancer, NACT+P, Pre (R200635)

value: NACT+P, Pre


title: 48h-3_H3K4me3_Cut&Run


title: Liver, Mir483Pat-KO, rep1 (RNA-seq)

description: Liver, Mir483Pat-KO, rep1 miR483_426


title: Ovarian cancer, NACT, Pre (R200634)

value: NACT, Pre


title: Liver, wild-type, rep5 (RNA-seq)

description: Liver, wild-type, rep5 miR483_474

value: Wild-type


title: Liver, Control, rep2

description: Liver, Control, rep2 CMVxmiR #12

value: liver

tag: age

value: 15 weeks postnatal

value: control

tag: library


title: HeLa cells, SRSF1 P89S

city: NEW HAVEN

first: MANOJ

last: PILLAI

state: CT

address: 300 GEORGE STREET #786

institute: YALE UNIVERSITY

description:
Sample_B5
WT-P89S.rMATS.tar.gz

data_processing:
Sequence reads were trimmed for adaptors with Cutadapt
Trimmed sequence reads were mapped to hg38 using STAR aligner
Aligned bam files were used to determine alternative splicing using
Cuffdiff was used to generate differential expression files (gene and isoform ending in _exp.diff files) using default parameters for Cuffdiff version 2.2.0
rMATS was used to generate differential expression files (rMATS.tar.gz files) using default parameters of rMATS version 4.0.2
Assembly: hg38
Supplementary files format and content: Cuffdiff and rMATS files

source_name: HeLa

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1  ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using strand-speecific  Illumina-compatible cDNA libraries  (dUTP protocol)

value: HeLa

value: epithelial cells

value: SRSF1 P89S


title: Ovarian cancer, NACT+P, Pre (R200639)

first: Olivia


title: 839

description: 2x150bp configuration

value: Esophageal epithelium

value: CONTROL

value: 9  years

tag: gender

value: Male

tag: eos/hpf

tag: swallowed steroids

value: N

tag: ppi

value: Restricted

value: White

value: Not Hispanic or Latino


title: 48h-2_Sox9_Cut&Run

tag: tissue

value: Kidney

value: Sox9-lineage cells (tdTomato positive) at d10 post-IRI, Tamoxifen at IRI, FACS-enriched, biol rep 2

value: Sox9 (#AB5535, Millipore)


title: Liver, wild-type, rep4 (RNA-seq)

description: Liver, wild-type, rep4 miR483_421

value: Liver

value: female

value: Wild-type


title: 48h-2_Input_Cut&Run


title: Ovarian cancer, NACT+P, Pre (R200630)

value: Ovary

tag: cell line

value: Ovarian cancer

value: NACT+P, Pre


title: HeLa cells, SRSF1 wild type

description:
Sample_B3
WT-E60D.rMATS.tar.gz
WT-P89S.rMATS.tar.gz

value: HeLa

value: epithelial cells

value: SRSF1 wild type


title: HeLa cells, SRSF1 E60D

description:
Sample_B4
WT-E60D.rMATS.tar.gz

value: SRSF1 E60D


title: Liver, wild-type, rep3 (RNA-seq)

description: Liver, wild-type, rep3 miR483_412


title: Caco-2,Mimic WT-miR-1246, repl5

data_processing:
Quality trimming and adapter sequences removal using DDBuk program from BBmap v38.87.
Trimmed reads were aligned to human reference genome GRCh38.p13 using STAR v2.7.9 Gencode v34 annotations
Counts per gene were detected using Verse v0.1.5.
ComBat-seq was applied for batch effect.
Further analysis was performed using DESeq2 v1.32.0
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include gene id,  gene  name, gene  type along with  gene count  values for each sample

extract_protocol:
RNA from tansfected cells was extracted using miRNeasy Mini Kit (Qiagen, MD, USA) 48h post-transfection, according to manufacturer recommendations.
Polyadenylated RNA sequencing libraries were generated with 1 µg of total RNA input per sample applying a standard Illumina TrueSeq Stranded mRNA protocol.

treatment_protocol: Reverse transfection with miRNA mimic of ISO-miR-1246_G, ISO-miR-1246_a and  WT-miR-1246  as well  as negative control  was performed using Lipofectamine 3000 reagent.

tag: passage index

value: Mimic WT-miR-1246


title: Liver, wild-type, rep2 (RNA-seq)

description: Liver, wild-type, rep2 miR483_411

tag: genotype


title: 48h-1_Sox9_Cut&Run

value: Sox9-lineage cells (tdTomato positive) at d10 post-IRI, Tamoxifen at IRI, FACS-enriched, biol rep 1


title: Ovarian cancer, NACT+P, Pre (R200622)


title: Caco-2,Mimic WT-miR-1246, repl4


title: 48h-2_H3K4me3_Cut&Run

value: H3K4me3 (#9751, Cell signaling)


title: FA-D2 cells

description:
Sample_A1
FAD2_FAD2+FANCD2.rMATS.tar.gz

value: fibroblasts

value: FANCD2 deficient cells


title: FA-D2+FANCD2 cells

description:
Sample_A2
FAD2_FAD2+FANCD2.rMATS.tar.gz

value: FANCD2 corrected cells


title: Liver, wild-type, rep1 (RNA-seq)

description: Liver, wild-type, rep1 miR483_408

tag: Sex


title: 48h-1_Input_Cut&Run

value: Kidney


title: Caco-2,Mimic WT-miR-1246, repl3

tag: treatment


title: HeLa cells, siSRSF1-2

description:
Sample_B2
si_CTRL-siSRSF1.gene_exp.diff
si_CTRL-siSRSF1.isoform_exp.diff

value: SRSF1 knockdown


title: Pos121322 - snATACseq

library_source: genomic single cell

data_processing:
TdT+ filtered peak matrices were generated at the Genomic Core at Cedars-Sinai with Cell Ranger
Datasets were analyzed with ArchR and plots were postprocessed with ggplot2
datasets quality check and basic filters were applied filtering doublets and cells considered of bad quality (low TSS enrichment and or number of fragments based on a combined bidimensional threshold function)
For dimensional reduction and bach corrections iterative LSI and Harmony algorithms were applied with UMAP embedding generated over the harmony-derived matrix
Preliminary clustering was generated by graph-based clustering and cluster marker gene tested with Wilcoxon statistic approach
Chromatin accessibility enrichment was denoised by weight imputation based on Markov affinity-based graph imputation of cells diffusion matrix
Low quality clusters were filtered, and remaining cells reprocessed
Integration with scRNAseq datasets was used to define a preliminary cell type clustering which was refined based in the internal clustering of the scATACseq dataset
MACS2 was used for calling peaks and motif enrichment was defined using the CisBP motif set and chromVAR package
Supervised trajectory analysis (defined by the unsupervised trajectory determined in the scRNAseq datasets) was calculated and integrative pseudo-time analyses were carried out with the default parameters in ArchR in a subset of the snATACseq dataset corresponding to the SoxOn-On population lineage
Assembly: mm10
Supplementary files format and content: chromatin accessibility enrichment was denoised by weight imputation based on Markov affinity-based graph imputation of cells diffusion matrix

extract_protocol:
Briefly cortices and outer medulla regions of the kidney were dissected and thoroughly minced in 1mlcold DMEM/F12 media using sterile fine forceps. The minced tissue  resuspended in fresh 1ml DMEM/F12 media supplemented with 7.5mg/ml of B. Licheniformis Cold Active Protease, 125U/ml DNase1  and 0.1mg/ml Liberase TL  and continuously kept on ice for 1 hour with frequent pipetting using 1ml pipette every 10 min. After complete dissociation of tissues into single cells (an aliquot of cell suspension was taken every 20 min to check dissociation of the tissue under the microscope), the enzymatic reaction was stopped using cold DMEMF12 media + 10% FBS. The cell suspension was filtered through a 40μm cell strainer. The filtrate was then centrifuged at 300g for 5 min and transferred to FACS tubes (BD Biosciences). Cells were washed in PBS and resuspended in 1.5ml of FACS sorting buffer containing 1mg/ml DAPI (1:1000, Life Technologies). Cell sorting was performed using the FACSAria III cell sorter (BD Biosciences). Cell populations were gated to exclude debris and doublets using FACSDiva software (BD Biosciences). Cells were collected from relevant gated cell populations in 1.5mL collection tubes (Eppendorf) containing collection buffer.
TdTomato positive enriched sorted cells were processed following the manufacture instruction. Sorted cells nuclei were isolated as described in 10xGenomics protocol (CG000169 Nuclei Isolation for Single Cell ATAC Sequencing), following the low input version and with a 1:5 diluted Lysis Buffer in Nuclease-free water. Isolated cell samples were immediately processed with a Chromium Next GEM Single Cell ATAC Kit v2 (10xGenomics)
snATAC-seq

treatment_protocol: Age- (9 – 12 weeks old) and weight –matched (25 – 30 gm) male mice were subjected to bilateral renal ischemia reperfusion injury (IRI) surgery. To obtain Sox9-lineage cells at day10 post-IRI,  tamoxifen was administered at induction of kidney IRI to Sox9IRES-CreERT2/+:R26RtdT/+ animals and the lineage-cells (tdTomato positive cells) were isolated as stated in the below stated extract protocol.

value: day10 Sox9 lineage cells, Lineage of cells that activated Sox9 after IRI, Tamoxifen at IRI, FACS-enriched, biol rep 2

value: 9-12 weeks


title: 48h-1_H3K4me3_Cut&Run


title: Caco-2,Mimic WT-miR-1246, repl2


title: HeLa cells, siSRSF1 -1

description:
Sample_A5
si_CTRL-siSRSF1.gene_exp.diff
si_CTRL-siSRSF1.isoform_exp.diff


title: Pos121222 - snATACseq

value: day10 Sox9 lineage cells, Lineage of cells that activated Sox9 after IRI, Tamoxifen at IRI, FACS-enriched, biol rep 1


title: Caco-2,Mimic WT-miR-1246, repl1


title: HeLa cells, siRNA Control-2

description:
Sample_B1
si_CTRL-siSRSF1.gene_exp.diff
si_CTRL-siSRSF1.isoform_exp.diff

value: WT


title: HeLa cells, siRNA Control-1

description:
Sample_A3
si_CTRL-siSRSF1.gene_exp.diff
si_CTRL-siSRSF1.isoform_exp.diff


title: Caco-2,Mimic negative control, repl5

value: Mimic negative control


title: cells expressing Sox9 at d14 post-IRI, Tamoxifen d10, d12 post-IRI, FACS-enriched, biol rep 2

data_processing:
Raw sequencing data was demultiplexed and converted to fastq format by using bcl2fastq v2.20(Illumina, San Diego, California). Then reads were aligned to the transcriptome using STAR(version 2.6.1) (Dobin A et al., 2013) / RSEM (version 1.2.28) (Li B and Dewey CN, 2011) withdefault parameters, using a custom MOUSE GRCh38 transcriptome reference downloaded fromhttp://www.gencodegenes.org, containing all protein coding and long non-coding RNA genesbased on MOUSE GENCODE version 33 annotation. Expression counts for each gene in allsamples were normalized by a modified trimmed mean of the M-values normalization method andthe unsupervised PC analysis (PCA) was performed with DESeq2 Bioconductor package version1.26.0 in R version 3.6.3. Each gene was fitted into a negative binomial generalized linear model,and the Wald test was applied to assess the differential expressions between two sample groups byDESeq2. Benjamini and Hochberg procedure was applied to adjust for multiple hypothesis testing,and differential expression gene candidates were selected with a false discovery rate less than 0.05.
Further filtering of candidate differentially expressed genes to false discovery rate less than 0.01and an absolute log 2 fold-change greater than 1 was applied to the studies comparing normaluninjured PTEC vs. Sox9:48h IRI vs. Sox9: day14 post IRI. GO term enrichment was conductedwith DAVID retaining only terms with a p-value for enrichment less than 0.01. After manuallymerging redundant biological process GO terms, relevant terms among the top 20 were plottedusing custom scripts in R and the ggplot2 (version 3.3.3) package. For visualization of coordinatedgene expression in samples, a two-way hierarchical clustering with Pearson correlation distancematrix was performed with samples and DEG candidates using the Bioconductor g-plots package(version 3.0.3) in R. MA plots, and PCA plots were created using custom R scripts and theBioconductor FactoMineR package (version 2.4).
Assembly: mm10
Supplementary files format and content: tab-deliminited text files include raw files for each sample

extract_protocol:
Briefly cortices and outer medulla regions of the kidney were dissected and thoroughly minced in 1mlcold DMEM/F12 media using sterile fine forceps. The minced tissue  resuspended in fresh 1ml DMEM/F12 media supplemented with 7.5mg/ml of B. Licheniformis Cold Active Protease, 125U/ml DNase1  and 0.1mg/ml Liberase TL  and continuously kept on ice for 1 hour with frequent pipetting using 1ml pipette every 10 min. After complete dissociation of tissues into single cells (an aliquot of cell suspension was taken every 20 min to check dissociation of the tissue under the microscope), the enzymatic reaction was stopped using cold DMEMF12 media + 10% FBS. The cell suspension was filtered through a 40μm cell strainer. The filtrate was then centrifuged at 300g for 5 min and transferred to FACS tubes (BD Biosciences). Cells were washed in PBS and resuspended in 1.5ml of FACS sorting buffer containing 1mg/ml DAPI (1:1000, Life Technologies). Cell sorting was performed using the FACSAria III cell sorter (BD Biosciences). Cell populations were gated to exclude debris and doublets using FACSDiva software (BD Biosciences). Cells were collected from relevant gated cell populations in 1.5mL collection tubes (Eppendorf) containing collection buffer. RNA was extracted from TdTomato positive enriched sorted cells were processed following the manufacture instruction mRNA easy, Qiagen). Briefly, total RNA samples were assessed for concentration using a Nanodrop (Nanodrop 504 ND8000, Thermo Fisher Scientific, Carlsbad, CA) and quality using the TapeStation 505 (4200 TapeStation, Agilent Technologies, Santa Clara, CA). Up to 30 ng of total RNA per sample was used for poly-A mRNA selection.
Libraries for RNA-Seq were prepared with Nugen Universal plus mRNA-Seq Kit (part number: 0508) to generate strand-specific RNA-seq libraries. The workflow consists of poly(A) RNA selection, RNA fragmentation and double-stranded cDNA generation using a mixture of random and oligo(dT) priming, followed by end repair to generate blunt ends, adaptor ligation, strand selection, and PCR amplification to produce the final library. Different index adaptors were used for multiplexing samples in one sequencing lane. The concentration of the amplified library was measured with a Qubit fluorometer and an aliquot of the library was resolved on a Bioanalyzer.

treatment_protocol: Age- (9 – 12 weeks old) and weight –matched (25 – 30 gm) male mice were subjected to bilateral renal ischemia reperfusion injury (IRI) surgery. To obtain control uninjured PTECs, tamoxifen was administered to Slc34a1IRES-CreERT2/+:R26RtdT/+ animals and the cells were isolated as stated in the below stated extract protocol.To obtain cells that activated Sox9 at 48h after kidney IRI, tamoxifen was administered at induction of kidney IRI to Sox9IRES-CreERT2/+:R26RtdT/+ animals and the cells were isolated as stated in the below stated extract protocol.To obtain cells that continued to express Sox9 at d14 post-kidney IRI, tamoxifen was administered at d10 and d12 after IRI to Sox9IRES-CreERT2/+:R26RtdT/+ animals and the cells were isolated as stated in the below stated extract protocol.

value: d14 IRI:Cre induced TdT+ cells


title: 10d-4_Sox9_Cut&Run

value: Sox9-lineage cells (tdTomato positive) at d10 post-IRI, Tamoxifen at IRI, FACS-enriched, biol rep 4

value: Sox9 (#AB5535, Millipore)


title: 10d-4_H3K4me3_Cut&Run


title: cells expressing Sox9 at d14 post-IRI, Tamoxifen d10, d12 post-IRI, FACS-enriched, biol rep 3


title: Caco-2,Mimic negative control, repl4


title: 10d-3_Sox9_Cut&Run

value: Sox9-lineage cells (tdTomato positive) at d10 post-IRI, Tamoxifen at IRI, FACS-enriched, biol rep 3


title: Caco-2,Mimic negative control, repl3


title: cells expressing Sox9 at d14 post-IRI, Tamoxifen d10, d12 post-IRI, FACS-enriched, biol rep 1


title: 10d-4_Input_Cut&Run


title: B59

city: Guangzhou

first: Peng

last: Deng

address: Panyu

institute: SYSUCC

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by STAR instruction
RSEM were used for counting
R scripts were used for visualization
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

source_name: locally advanced rectal cancer

growth_protocol: 13 locally advanced rectal cancer (LARC) patients with neoadjuvant chemotherapy were harvested for RNA-seq.

extract_protocol:
Total RNA of patient samples were harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared using standard Illumina protocols.

value: locally advanced rectal cancer


title: 10d-3_Input_Cut&Run


title: cells activating Sox9 at 48h post-IRI, Tamoxifen at IRI, FACS-enriched, biol rep 3

value: 48 IRI:Cre induced TdT+ cells


title: B93

treatment_protocol: 13 locally advanced rectal cancer (LARC) patients with neoadjuvant chemotherapy were harvested for RNA-seq.


title: cells activating Sox9 at 48h post-IRI, Tamoxifen at IRI, FACS-enriched, biol rep 2


title: 10d-3_H3K4me3_Cut&Run

value: H3K4me3 (#9751, Cell signaling)


title: Caco-2,Mimic negative control, repl2


title: Caco-2,Mimic negative control, repl1


title: B101


title: 10d-2_Sox9_Cut&Run

value: Sox9-lineage cells (tdTomato positive) at d10 post-IRI, Tamoxifen at IRI, FACS-enriched, biol rep 2


title: cells activating Sox9 at 48h post-IRI, Tamoxifen at IRI, FACS-enriched, biol rep 1


title: B83


title: 10d-2_Input_Cut&Run


title: uninjured Slc34a1 expressing PTECs, Tamoxifen-labeled, FACS-enriched, biol rep 3

value: Cre induced TdT+ cells