title: Control_FA-INPUT_48h TGFβ1_Replicate 2

city: West Lafayette

first: Emily

last: Dykhuizen

address: 201 S. University

department: medicinal chemistry and molecular pharmacology

institute: Purdue University

description: Library name: sgCt_FA_48h_INPUT_N2

data_processing:
Quality trimming (adapter removal, phred quality cutoff >=Q30, minimum read length 50 bp after quality filtering) of raw reads was performed using fastp  (version 0.19.5).
Trimmed reads were mapped to mouse mm10  genome build using bowtie2 (version 2.3.3) aligner.
BAMs were imported into Partek Flow and peak calling was performed with MACS3 (v3.0.0a7) within the Partek Flow suite (v11.0.24.0325) with – BROAD ON for SWI/SNF subunits
BAM to BigWig conversion was performed using deeptools(v3.5.1) with CPM normalization
Assembly: mm10
Supplementary files format and content: BigWig files for each sample and Peaks file (except for the input files)

source_name: NMuMG

growth_protocol: NMuMG cells were purchased from ATCC and grown in DMEM (Corning Mediatech) supplemented with 10% fetal bovine serum, 10 µg/mL Insulin (Sigma), 1% L-glutamine (Corning Mediatech), 1% antibiotics (100 units/ml penicillin and 100 g/ml streptomycin; Corning Mediatech), and 1% Sodium Pyruvate (Corning Mediatech) at 37 °C in a humidified atmosphere in a 5% CO2 incubator.

extract_protocol:
Cells were either cross-linked with 1% formaldehyde only (histone modifications, Fosb, Fosl2 ChIP-seq) for 10’, RT or sequentially dual crosslinked (Brg1, PHF10 and ATF3 ChIP-seq) with 2mM DSG, 45’, RT followed by 1% formaldehyde, 10’, RT . Crosslinking was quenched with 125mM Glycine, 10’, RT. The cells were washed by ice-cold 1X PBS, scraped and flash frozen to be stored at -80C until ready for processing. Cell pellets were thawed on ice, extracted with nuclear extraction buffer (50mM HEPES-KOH pH 8.0, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) for 10’ on ice and washed once with nuclear wash buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 0.5mM EGTA, 200mM NaCl). Nuclear pellets were resuspended in shearing buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 0.1% SDS) and sonicated using Branson SFX250 at 20% amplitude for 9 mins for dual cross-linked cells and 6 mins for single cross-linked cells at 0.5s ON and 1.5s OFF setting to obtain 200-800 bp fragment size. Sonicated chromatin was clarified by high-speed centrifugation and a 50ul aliquot was reverse cross-linked to check shearing efficiency. The chromatin was quantitated using absorbance at 260nm and further diluted with 2X ChIP dilution buffer (100mM HEPES-KOH pH 7.5, 600mM NaCl, 2mM EDTA, 2% Triton X-100, 0.2% Sodium Deoxycholate, 0.2% SDS) to obtain equal chromatin amounts in equal volume.
ChIP-seq library preparation was done using Ovation Ultralow System V2 UDI according to manufacturer’s directions and the final library was subjected to double sided size selection of 0.65x and 1x.

treatment_protocol: NMuMG cells were seeded in 15cm plates with or without 5ng/ml of TGFβ1 (R&D systems, Catalog # 7754-BH) for 0-48h to induce EMT such that they were ~80-90% confluent on the day of harvesting (30-40 million cells/15cm at harvest)

value: NMuMG

value: Epithelial cells

value: Control

value: 48h TGFβ1 treatment

value: No Ab


title: Control_FA-INPUT_Untreated_Replicate 2

status: Public on Jun 14 2026

type: SRA

state: IN

country: USA

description: Library name: sgCt_FA_0h_INPUT_N2

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: No treatment

tag: chip antibody


title: AS061_I

status: Public on Jun 15 2026

type: RNA

city: Lørenskog

first: Hilde

middle: Loge

last: Nilsen

address: Sykehusveien 25

country: Norway

institute: Akershus University Hospital

hyb_protocol: Amplification and labelling efficiency were controlled on the NanoDrop. The cRNA quality was assessed by measuring the RNA absorbance ratio 260nm/280nm. The specific activity of labeled cRNA (pmol Cy3 per ug cRNA) was defined to be 6 or above according to the Agilent recommendations.

scan_protocol: Standard Illumina Protocol

data_processing: Expression signals were normalized with the limma R package. Control probes were removed before processing. Background correction was done with the backgroundCorrect function, using the normexp method and offset 16. Hence the lowest possible normalized expression value is log2(16) = 4. Batch correction was done using the normalizeBetweenArrays function, using the quantile method.

molecule: total RNA

organism: Homo sapiens

source_name: Gut epithelium, NP, Ascendens

label_protocol: mRNA amplification, labelling, and hybridization were done following the manufacturer’s instructions (Agilent One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling). In short, 50 ng RNA was amplified and labelled with Cy3 using the Low Input Quick Amp Labeling Kit, one-color (product number 5190-2331), and the labelled cRNA was purified using the Qiagen RNeasy Mini Kit.

extract_protocol: Total RNA was isolated using AllPrep kit (Qiagen, Hilden, Germany). The tissue biopsies were homogenized in Buffer RLT using a 5 mm steal bead in the FastPrep-24 Classic Instrument (MP Biomedicals, Irvine, CA, USA) at 6 m/s for 40 sec. The samples were centrifuged and the lysate transferred to new tubes. Further processing was according to the manufacture’s protocol. RNA concentration was measured using the QiaCubeNanoDrop ND-1000 spectrophotometer (Qiagen). The RNA quality, indicated by the RNA integrity number (RIN), was assessed with an Agilent 2100 Bioanalyser, Agilent 2100 Expert software and Agilent RNA 6000 Nano Kit (Agilent Technologies Inc., Santa Clara, CA, USA). RNA samples with RIN number below 7.0 were excluded.

tag: tissue

value: gut epithelium

tag: status

value: Non-progressor

tag: segment

value: Ascendens

tag: inflammation

tag: neoplasia


title: Control-H3K14ac_ChIPseq_Untreated

description: Library name: sgCt_H3K14ac_0h

value: H3K14ac Ab (07-353 Millipore Sigma)


title: Control-H3K14ac_ChIPseq_48h TGFβ1

description: Library name: sgCt_H3K14ac_48h


title: Control-H3K27ac_ChIPseq_48h TGFβ1

description: Library name: sgCt_H3K27ac_48h

value: H3K27ac Ab (ab4729 Abcam)


title: Control-H3K18ac_ChIPseq_Untreated

description: Library name: sgCt_H3K18ac_0h

value: H3K18ac Ab (ab1191 Abcam)


title: Control-H3K18ac_ChIPseq_48h TGFβ1

description: Library name: sgCt_H3K18ac_48h


title: Control-H3K4me1_ChIPseq_48h TGFβ1

description: Library name: sgCt_H3K4me1_48h

value: H3K4me1 Ab (ab8895 Abcam)


title: Control-H3K27ac_ChIPseq_Untreated

description: Library name: sgCt_H3K27ac_0h


title: Control-H3K4me1_ChIPseq_Untreated

description: Library name: sgCt_H3K4me1_0h


title: Control-H3K4me3_ChIPseq_48h TGFβ1

description: Library name: sgCt_H3K4me3_48h

value: H3K4me3 Ab (ab8580 Abcam)


title: Control-H3K4me3_ChIPseq_Untreated

description: Library name: sgCt_H3K4me3_0h


title: Pbrm1 KO_FA-INPUT_48h TGFβ1_Replicate 1

description: Library name: sgPbrm1_FA_48h_INPUT_N1

value: Pbrm1 KO


title: Pbrm1 KO_FA-INPUT_Untreated_Replicate 1

description: Library name: sgPbrm1_FA_0h_INPUT_N1


title: Pbrm1 KO-Fosb_ChIPseq _48h TGFβ1

description: Library name: sgPbrm1_Fosb_48h

value: Fosb Ab (MA5-15056 Invitrogen)


title: Pbrm1 KO-Fosb_ChIPseq _Untreated

description: Library name: sgPbrm1_Fosb_0h


title: AS058_I


title: Pbrm1 KO-Fosl2_ChIPseq _48h TGFβ1

description: Library name: sgPbrm1_Fosl2_48h

value: Fosl2 Ab (sc-166102 Santa Cruz)


title: Control_FA-INPUT_Untreated_Replicate 1

description: Library name: sgCt_FA_0h_INPUT_N1

value: NMuMG


title: Control-Fosb_ChIPseq _48h TGFβ1

description: Library name: sgCt_Fosb_48h

value: Epithelial cells


title: Control-Fosb_ChIPseq _Untreated

description: Library name: sgCt_Fosb_0h

value: Control


title: Control_FA-INPUT_48h TGFβ1_Replicate 1

description: Library name: sgCt_FA_48h_INPUT_N1

value: 48h TGFβ1 treatment


title: Pbrm1 KO-Fosl2_ChIPseq _Untreated

description: Library name: sgPbrm1_Fosl2_0h


title: Control-Fosl2_ChIPseq _48h TGFβ1

description: Library name: sgCt_Fosl2_48h


title: Pbrm1 KO-Atf3_ChIPseq _48h TGFβ1

description: Library name: sgPbrm1_Atf3_48h

value: Atf3 Ab (ab207434 Abcam)


title: Pbrm1 KO-INPUT_24h TGFβ1_Replicate 3

description: Library name: sgPbrm1_24h_INPUT_N3

value: 24h TGFβ1 treatment

value: No Ab


title: Control-Fosl2_ChIPseq _Untreated

description: Library name: sgCt_Fosl2_0h

value: No treatment


title: Pbrm1 KO-Atf3_ChIPseq _24h TGFβ1

description: Library name: sgPbrm1_Atf3_24h


title: Pbrm1 KO-Atf3_ChIPseq _Untreated

description: Library name: sgPbrm1_Atf3_0h


title: Pbrm1 KO-INPUT_48h TGFβ1_Replicate 1

description: Library name: sgPbrm1_48h_INPUT_N1


title: Pbrm1 KO-INPUT_Untreated_Replicate 1

description: Library name: sgPbrm1_0h_INPUT_N1


title: Pbrm1 KO-Phf10_ChIPseq _48h TGFβ1_Replicate 1

description: Library name: sgPbrm1_Phf10_48h_N1

value: Phf10 Ab (PA5-30678 Invitrogen)


title: Pbrm1 KO-Phf10_ChIPseq _Untreated_Replicate 1

description: Library name: sgPbrm1_Phf10_0h_N1


title: Control-INPUT_48h TGFβ1_Replicate 2

description: Library name: sgCt_48h_INPUT_N2


title: Control-Atf3_ChIPseq _Untreated

description: Library name: sgCt_Atf3_0h


title: Control-INPUT_Untreated_Replicate 2

description: Library name: sgCt_0h_INPUT_N2


title: Control-Phf10_ChIPseq _Untreated_Replicate 2

description: Library name: sgCt_Phf10_0h_N2


title: Control-Phf10_ChIPseq _48h TGFβ1_Replicate 2

description: Library name: sgCt_Phf10_48h_N2


title: Control-INPUT_24h TGFβ1_Replicate 1

description: Library name: sgCt_24h_INPUT_N1


title: Control-INPUT_48h TGFβ1_Replicate 1

description: Library name: sgCt_48h_INPUT_N1


title: Control-Phf10_ChIPseq _24h TGFβ1_Replicate 1

description: Library name: sgCt_Phf10_24h_N1


title: Control-INPUT_Untreated_Replicate 1

description: Library name: sgCt_0h_INPUT_N1


title: [ATAC-Seq] PBRM1 KO_72h_biol rep3

description:
Library name: sgPBRM1_72h_3
ATAC-seq libraries

data_processing:
Raw reads were trimmed using fastp with parameters quality_score > 30, read length > 50.
Quality trimmed reads were aligned to mouse (GRCm38) reference genome using bowtie2 with at most 1 mismatch.
Peak calling was performed with Genrich in ATAC-seq mode with parameters (-j -r  -e chrM  -m 30 -y  -v -k -q 0.05)
Assembly: GRCm38
Supplementary files format and content: Mapped reads in BigWig format

extract_protocol:
Cells were harvested at 0, 24, 48 and 72h post-treatment and processed according to the Omni-ATAC protocol (Corces et al. Nature Methods 2017)
Libraries were constructed as described in Omni-ATAC protocol (Corces et al. Nature Methods 2017). The final libraries were subjected to double size selection according to a published protocol (Library Preparation for ATAC-Sequencing of Mouse CD4+T Cells Isolated from the Lung and Lymph Nodes After Helminth Infection Laura D. Harmacek, Preeyam Patel, Rachel Woolaver, R. Lee Reinhardt, and Brian P. O’Connor) and quality checked using Qubit and Agilent Bioanalyzer by Purdue Genomics Core Facility.

treatment_protocol: NMuMG cells were seeded in 6-well plates with 5ng/ml of TGFβ1 (R&D systems, Catalog # 7754-BH) for 0-72h to induce EMT.

value: PBRM1 KO

value: 72h TGFbeta treatment


title: Control-Phf10_ChIPseq _Untreated_Replicate 1

description: Library name: sgCt_Phf10_0h_N1


title: [ATAC-Seq] PBRM1 KO_72h_biol rep2

description:
Library name: sgPBRM1_72h_2
ATAC-seq libraries


title: [ATAC-Seq] PBRM1 KO_48h_biol rep2

description:
Library name: sgPBRM1_48h_2
ATAC-seq libraries

value: 48h TGFbeta treatment


title: [ATAC-Seq] PBRM1 KO_48h_biol rep3

description:
Library name: sgPBRM1_48h_3
ATAC-seq libraries


title: [ATAC-Seq] PBRM1 KO_48h_biol rep1

description:
Library name: sgPBRM1_48h_1
ATAC-seq libraries


title: [ATAC-Seq] PBRM1 KO_24h_biol rep3

description:
Library name: sgPBRM1_24h_3
ATAC-seq libraries

value: 24h TGFbeta treatment


title: [ATAC-Seq] PBRM1 KO_0h_biol rep3

description:
Library name: sgPBRM1_0h_3
ATAC-seq libraries


title: [ATAC-Seq] PBRM1 KO_24h_biol rep1

description:
Library name: sgPBRM1_24h_1
ATAC-seq libraries


title: [ATAC-Seq] PBRM1 KO_0h_biol rep1

description:
Library name: sgPBRM1_0h_1
ATAC-seq libraries


title: [ATAC-Seq] Control_72h_biol rep3

description:
Library name: sgCT_72h_3
ATAC-seq libraries


title: [ATAC-Seq] Control_72h_biol rep1

description:
Library name: sgCT_72h_1
ATAC-seq libraries


title: [ATAC-Seq] Control_48h_biol rep3

description:
Library name: sgCT_48h_3
ATAC-seq libraries


title: [ATAC-Seq] Control_48h_biol rep2

description:
Library name: sgCT_48h_2
ATAC-seq libraries


title: [ATAC-Seq] Control_24h_biol rep3

description:
Library name: sgCT_24h_3
ATAC-seq libraries


title: [ATAC-Seq] Control_48h_biol rep1

description:
Library name: sgCT_48h_1
ATAC-seq libraries


title: [ATAC-Seq] Control_24h_biol rep2

description:
Library name: sgCT_24h_2
ATAC-seq libraries


title: [ATAC-Seq] Control_0h_biol rep3

description:
Library name: sgCT_0h_3
ATAC-seq libraries


title: [ATAC-Seq] Control_24h_biol rep1

description:
Library name: sgCT_24h_1
ATAC-seq libraries


title: [ATAC-Seq] Control_0h_biol rep1

description:
Library name: sgCT_0h_1
ATAC-seq libraries


title: 4T1_shPBRM1_D4__biol rep3

description:
counts_set3.xlsx
4T1_shPBRM1_D4_3

library_source: transcriptomic

data_processing:
For NMuMG cells,  by Novogene: Raw reads were trimmed for adapter, poly-N and low quality sequences and mapped to mouse mm10 genome build using STAR software (NMuMG sgPBRM1 datasets) or Hisat2 (NMuMG shATF3 datasets). Differential expression analysis was done using DESeq2 R package and the resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR).
For 4T1 shPBRM1 datasets, raw reads were trimmed for adapter sequences using trim-galore/0.6.7 and mapped to mouse mm10 genome build using STAR/2.7.10a software. Reads with MAPQ >10 were used for differential gene expression analysis using edgeR R package.
Assembly: mm10
Supplementary files format and content: Raw gene counts provided as tab-delimited excel files

growth_protocol: NMuMG cells were purchased from ATCC and grown in DMEM (Corning Mediatech) supplemented with 10% fetal bovine serum, 10 µg/mL Insulin (Sigma), 1% L-glutamine (Corning Mediatech), 1% antibiotics (100 units/ml penicillin and 100 g/ml streptomycin; Corning Mediatech), and 1% Sodium Pyruvate (Corning Mediatech) at 37 °C in a humidified atmosphere in a 5% CO2 incubator. 4T1 cells were grown in RPMI-1640 (Corning Mediatech) supplemented with 10% fetal bovine serum, 1% L-glutamine (Corning Mediatech), 1% antibiotics (100 units/ml penicillin and 100 g/ml streptomycin; Corning Mediatech), and 1% Sodium Pyruvate (Corning Mediatech) at 37 °C in a humidified atmosphere in a 5% CO2 incubator.

extract_protocol:
NMuMG cells were harvested at 0, 24, 48 and 72 h post-treatment in trizol and total RNA was isolated using the PureLink RNA isolation kit (Invitrogen, # 12183018A).  4T1 cells were seeded with or without TGFβ1 for 4 days and processed as above for total RNA isolation.
For NMuMG cells, downstream library construction, sequencing on Novaseq 6000 and data analysis was done by Novogene. For 4T1 cells, library construction was done using Illumina Stranded mRNA prep ligation kit (Illumina, #20040534) according to manufacturer’s instructions and checked for quality using Qubit and Agilent Bioanalyzer by Purdue Genomics Core Facility. Libraries were sequenced using 150bp PE sequencing on NovaSeq 6000 platform (Novogene, Sacramento, CA). All experiments were performed in three biological replicates.

treatment_protocol: NMuMG cells were seeded in 6-well plates with or without 5ng/ml of TGFβ1 (R&D systems, Catalog # 7754-BH) for 0-72h to induce EMT. 4T1 cells were seeded with or without 5ng/ml TGFβ1 for 4 days.

value: Triple Negative Breast Cancer

value: PBRM1 KD

value: 4 days TGFbeta treatment


title: 4T1_shPBRM1_D4__biol rep1

description:
counts_set3.xlsx
4T1_shPBRM1_D4_1


title: 4T1_shPBRM1_D4__biol rep2

description:
counts_set3.xlsx
4T1_shPBRM1_D4_2


title: 4T1_shPBRM1_0h_biol rep3

description:
counts_set3.xlsx
4T1_shPBRM1_0h_3


title: 4T1_shPBRM1_0h_biol rep2

description:
counts_set3.xlsx
4T1_shPBRM1_0h_2


title: 4T1_shPBRM1_0h_biol rep1

description:
counts_set3.xlsx
4T1_shPBRM1_0h_1


title: 4T1_pLKO_D4__biol rep3

description:
counts_set3.xlsx
4T1_pLKO_D4_3


title: 4T1_pLKO_D4__biol rep2

description:
counts_set3.xlsx
4T1_pLKO_D4_2


title: 4T1_pLKO_D4__biol rep1

description:
counts_set3.xlsx
4T1_pLKO_D4_1


title: 4T1_pLKO_0h_biol rep3

description:
counts_set3.xlsx
4T1_pLKO_0h_3


title: 4T1_pLKO_0h_biol rep2

description:
counts_set3.xlsx
4T1_pLKO_0h_2


title: shATF3_72h_biol rep3

description:
counts_set2.xlsx
shATF3_72h_3

value: ATF3 KD


title: 4T1_pLKO_0h_biol rep1

description:
counts_set3.xlsx
4T1_pLKO_0h_1


title: shATF3_72h_biol rep2

description:
counts_set2.xlsx
shATF3_72h_2

value: NMuMG


title: shATF3_48h_biol rep3

description:
counts_set2.xlsx
shATF3_48h_3

value: Epithelial cells


title: shATF3_48h_biol rep2

description:
counts_set2.xlsx
shATF3_48h_2


title: shATF3_48h_biol rep1

description:
counts_set2.xlsx
shATF3_48h_1


title: shATF3_24h_biol rep2

description:
counts_set2.xlsx
shATF3_24h_2


title: shATF3_24h_biol rep3

description:
counts_set2.xlsx
shATF3_24h_3


title: shATF3_24h_biol rep1

description:
counts_set2.xlsx
shATF3_24h_1


title: shATF3_0h_biol rep3

description:
counts_set2.xlsx
shATF3_0h_3


title: shATF3_0h_biol rep1

description:
counts_set2.xlsx
shATF3_0h_1


title: shATF3_0h_biol rep2

description:
counts_set2.xlsx
shATF3_0h_2


title: pLKO_72h_biol rep2

description:
counts_set2.xlsx
pLKO_72h_2

value: Control


title: pLKO_72h_biol rep3

description:
counts_set2.xlsx
pLKO_72h_3


title: pLKO_72h_biol rep1

description:
counts_set2.xlsx
pLKO_72h_1


title: pLKO_48h_biol rep3

description:
counts_set2.xlsx
pLKO_48h_3


title: pLKO_48h_biol rep2

description:
counts_set2.xlsx
pLKO_48h_2


title: pLKO_48h_biol rep1

description:
counts_set2.xlsx
pLKO_48h_1


title: pLKO_24h_biol rep2

description:
counts_set2.xlsx
pLKO_24h_2


title: pLKO_24h_biol rep3

description:
counts_set2.xlsx
pLKO_24h_3


title: pLKO_24h_biol rep1

description:
counts_set2.xlsx
pLKO_24h_1


title: pLKO_0h_biol rep3

description:
counts_set2.xlsx
pLKO_0h_3


title: pLKO_0h_biol rep2

description:
counts_set2.xlsx
pLKO_0h_2


title: pLKO_0h_biol rep1

description:
counts_set2.xlsx
pLKO_0h_1


title: PBRM1 KO_72h_biol rep2

description:
counts_set1.xlsx
sgPBRM1_72h_2


title: PBRM1 KO_72h_biol rep1

description:
counts_set1.xlsx
sgPBRM1_72h_1


title: PBRM1 KO_48h_biol rep3

description:
counts_set1.xlsx
sgPBRM1_48h_3


title: PBRM1 KO_48h_biol rep2

description:
counts_set1.xlsx
sgPBRM1_48h_2


title: PBRM1 KO_48h_biol rep1

description:
counts_set1.xlsx
sgPBRM1_48h_1


title: PBRM1 KO_24h_biol rep3

description:
counts_set1.xlsx
sgPBRM1_24h_3


title: PBRM1 KO_24h_biol rep2

description:
counts_set1.xlsx
sgPBRM1_24h_2


title: PBRM1 KO_24h_biol rep1

description:
counts_set1.xlsx
sgPBRM1_24h_1


title: shATF3_72h_biol rep1

description:
counts_set2.xlsx
shATF3_72h_1


title: PBRM1 KO_0h_biol rep3

description:
counts_set1.xlsx
sgPBRM1_0h_3


title: PBRM1 KO_0h_biol rep2

description:
counts_set1.xlsx
sgPBRM1_0h_2


title: PBRM1 KO_0h_biol rep1

description:
counts_set1.xlsx
sgPBRM1_0h_1


title: Control_72h_biol rep3

description:
counts_set1.xlsx
sgCT_72h_3


title: Control_72h_biol rep2

description:
counts_set1.xlsx
sgCT_72h_2


title: Control_72h_biol rep1

description:
counts_set1.xlsx
sgCT_72h_1


title: Control_48h_biol rep2

description:
counts_set1.xlsx
sgCT_48h_2


title: Control_48h_biol rep3

description:
counts_set1.xlsx
sgCT_48h_3


title: Control_48h_biol rep1

description:
counts_set1.xlsx
sgCT_48h_1


title: Control_24h_biol rep2

description:
counts_set1.xlsx
sgCT_24h_2


title: Control_24h_biol rep3

description:
counts_set1.xlsx
sgCT_24h_3


title: Control_24h_biol rep1

description:
counts_set1.xlsx
sgCT_24h_1


title: Control_0h_biol rep3

description:
counts_set1.xlsx
sgCT_0h_3


title: Control_0h_biol rep2

description:
counts_set1.xlsx
sgCT_0h_2


title: Control_0h_biol rep1

description:
counts_set1.xlsx
sgCT_0h_1


title: II3

city: Madrid

first: Aitor

last: Arrogante

state: Madrid

address: Ctra. De La Coruña, Km 7,5

department: Animal Biotechnology

country: Spain

institute: INIA-CSIC

description: Library name: Sample 15

data_processing:
low-quality bases at the 3’ ends of reads were trimmed using a Phred quality threshold of Q20.
Assembly: USDA_OmykA1_1
Supplementary files format and content: txt file with raw counts of genes of all samples

organism: Oncorhynchus mykiss

source_name: Gill

growth_protocol: single Lactococcus petauri colonies were cultured into 200 mL of Tryptic Soy Broth (TSB) (Pronadisa, Spain) and incubated at 30°C for 18 h, with gentle agitation (100 rpm) under aerobic conditions

extract_protocol:
total RNA was extracted from the gills using TRIzol Reagent (Fisher Scientific) and then quantified using a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific)
MGIEasy Fast RNA Library kit with polyA capture on the MGISP-100 platform (CE-IVD)

treatment_protocol: The infection with L. petauri were performed by bath. In two aerated 15L basins with a concentration of 1 x 1012 CFU/mL or tryptic soy broth (TBS) alone for non infected samples. After 30 days, a secondary challenge with the same bacterial strain was conducted using the same protocol.

value: Gill

value: Infected with Lactococcus petauri in the two rounds (II)


title: II4

description: Library name: Sample 16


title: II2

description: Library name: Sample 14


title: II1

description: Library name: Sample 13


title: PBRM1 KO_72h_biol rep3

description:
counts_set1.xlsx
sgPBRM1_72h_3


title: CI4

description: Library name: Sample 12

value: Infected with Lactococcus petauri only in the second round (CI)


title: CI3

description: Library name: Sample 11


title: CI1

description: Library name: Sample 9


title: IC4

description: Library name: Sample 8

value: Infected with Lactococcus petauri only in the first round (IC)


title: CI2

description: Library name: Sample 10


title: IC3

description: Library name: Sample 7


title: IC2

description: Library name: Sample 6


title: CC4

description: Library name: Sample 4

value: Non infected in any of the two rounds (CC)


title: Control-Atf3_ChIPseq _48h TGFβ1

description: Library name: sgCt_Atf3_48h

value: 48h TGFβ1 treatment

value: Atf3 Ab (ab207434 Abcam)


title: IC1

description: Library name: Sample 5


title: Control-Atf3_ChIPseq _24h TGFβ1

description: Library name: sgCt_Atf3_24h

value: 24h TGFβ1 treatment


title: Control-INPUT_24h TGFβ1_Replicate 3

description: Library name: sgCt_24h_INPUT_N3

value: No Ab


title: Control-Phf10_ChIPseq _48h TGFβ1_Replicate 1

description: Library name: sgCt_Phf10_48h_N1

value: Phf10 Ab (PA5-30678 Invitrogen)


title: CC3

description: Library name: Sample 3


title: CC2

description: Library name: Sample 2


title: CC1

description: Library name: Sample 1


title: HeLa NXF1-dTAG, dTAG-13, 3' end-seq, biological replicate 2

city: Beijing

first: Cheng

last: Peng

address: 1 Beichen West Road, Chaoyang District, Beijing, China

country: China

institute: China National Center for Bioinformation, Chinese Academy of Sciences

description:
Library name: 3endseq_dTAG13_rep2
3' end sequencing (QuantSeq 3' mRNA-Seq Library Prep Kit V2, Lexogen) from HeLa NXF1-dTAG cells treated with 500 nM dTAG-13 for 6 h to induce NXF1 degradation. Biological replicate 2.

data_processing:
Raw reads were trimmed using Trim Galore (v0.6.7) to remove adaptor sequences, poly(A) artifacts, and low-quality bases.
Trimmed reads were aligned to the human reference genome (hg38) using STAR (v2.7.10a) with default parameters.
PAS identification and APA quantification were performed using APAcatcher with default parameters. bedGraph files were generated for each sample using BEDTools genomeCoverageBed.
Differential APA analysis between dTAG-13 and DMSO conditions was performed using APAcatcher (FDR < 0.05, |ΔPDUI| > 0.1).
Assembly: hg38 (GRCh38)
Supplementary files format and content: bedGraph files: genome-wide coverage tracks of 3' end sequencing reads, one file per sample. Format: chromosome, start, end, coverage (score).

molecule: polyA RNA

source_name: cervix

growth_protocol: HeLa-NXF1-dTAG stable cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in a humidified incubator at 37°C under 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. RNA quality and concentration were assessed prior to library preparation.
3' end sequencing libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit V2 (Lexogen) following the manufacturer's protocol. Briefly, first-strand cDNA synthesis was initiated from the poly(A) tail using an oligo(dT) primer containing the sequencing adaptor sequence. After second-strand synthesis and library amplification, libraries were purified and quality controlled. Libraries were sequenced on the DNBSEQ-T7 platform to generate 150 bp paired-end reads.

treatment_protocol: Cells were treated with 500 nM dTAG-13 to induce NXF1 degradation, or an equivalent volume of DMSO as vehicle control, for 6 hours. Following treatment, total RNA was extracted using TRIzol reagent according to the manufacturer's instructions.

value: cervix

value: HeLa

value: epithelial cell

value: NXF1-dTAG knock-in


title: Control-Brg1_ChIPseq _Untreated

description: Library name: sgCt_Brg1_0h

value: NMuMG

value: No treatment

value: Brg1 Ab (ab110641 Abcam


title: HeLa NXF1-dTAG, dTAG-13, 3' end-seq, biological replicate 1

description:
Library name: 3endseq_dTAG13_rep1
3' end sequencing (QuantSeq 3' mRNA-Seq Library Prep Kit V2, Lexogen) from HeLa NXF1-dTAG cells treated with 500 nM dTAG-13 for 6 h to induce NXF1 degradation. Biological replicate 1.


title: HeLa NXF1-dTAG, DMSO, 3' end-seq, biological replicate 2

description:
Library name: 3endseq_Ctrl_rep2
3' end sequencing (QuantSeq 3' mRNA-Seq Library Prep Kit V2, Lexogen) from HeLa NXF1-dTAG cells treated with DMSO for 6 h. Biological replicate 2.

value: DMSO, 500 nM equivalent, 6 h


title: HeLa NXF1-dTAG, dTAG-13 treatment, RNA-seq, biological replicate 1

description:
Library name: RNA-seq_dTAG13_rep1
Poly(A)+ RNA-seq from HeLa NXF1-dTAG cells treated with 500 nM dTAG-13 for 6 h to induce NXF1 degradation. Biological replicate 1.

data_processing:
RNA-seq: Raw reads were trimmed using Trim Galore (v0.6.7) to remove adaptors and low-quality bases. Trimmed reads were aligned to the human reference genome (hg38) using STAR (v2.7.10a) with default parameters. Gene-level counts were quantified using featureCounts (Subread v2.0.3) with GENCODE v38 annotation.
3' end-seq: Raw reads were processed using the QuantSeq analysis pipeline. Reads were trimmed for adaptor sequences and poly(A) artifacts using Trim Galore. Trimmed reads were aligned to hg38 using STAR. PAS identification and APA quantification were performed using APAcatcher with default parameters.
Assembly: hg38 (GRCh38)
Supplementary files format and content: gene_counts_matrix.txt: tab-delimited text file containing raw read counts per gene for all RNA-seq samples, generated by featureCounts.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. RNA quality and concentration were assessed prior to library preparation.
RNA-seq: 500 ng of total RNA was used for library preparation. Poly(A)+ RNA was enriched using oligo(dT) magnetic beads and fragmented under controlled conditions. First-strand cDNA was synthesized using random primers, followed by second-strand synthesis. Libraries were prepared using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology) with insert sizes of approximately 300-350 bp, purified using AMPure XP beads, and sequenced on the DNBSEQ-T7 platform (150 bp paired-end). 3' end-seq: Libraries were prepared from the same total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit V2 (Lexogen). First-strand cDNA synthesis was initiated from the poly(A) tail using an oligo(dT) primer containing the sequencing adaptor sequence, followed by second-strand synthesis, amplification, and purification. Libraries were sequenced on the DNBSEQ-T7 platform (150 bp paired-end).

treatment_protocol: Cells were treated with 500 nM dTAG-13 (to induce NXF1 degradation) or an equivalent volume of DMSO (vehicle control) for 6 hours. Following treatment, total RNA was extracted using TRIzol reagent according to the manufacturer's instructions.


title: HeLa NXF1-dTAG, dTAG-13 treatment, RNA-seq, biological replicate 2

description:
Library name: RNA-seq_dTAG13_rep2
Poly(A)+ RNA-seq from HeLa NXF1-dTAG cells treated with 500 nM dTAG-13 for 6 h to induce NXF1 degradation. Biological replicate 2.


title: HeLa NXF1-dTAG, DMSO, 3' end-seq, biological replicate 1

description:
Library name: 3endseq_Ctrl_rep1
3' end sequencing (QuantSeq 3' mRNA-Seq Library Prep Kit V2, Lexogen) from HeLa NXF1-dTAG cells treated with DMSO for 6 h. Biological replicate 1.


title: HeLa NXF1-dTAG, DMSO treatment, RNA-seq, biological replicate 2

description:
Library name: RNA-seq_DMSO_rep2
Poly(A)+ RNA-seq from HeLa NXF1-dTAG cells treated with DMSO (vehicle control) for 6 h. Biological replicate 2.


title: [ATAC-Seq] PBRM1 KO_24h_biol rep2

description:
Library name: sgPBRM1_24h_2
ATAC-seq libraries

value: Epithelial cells

value: PBRM1 KO

value: 24h TGFbeta treatment


title: [ATAC-Seq] PBRM1 KO_72h_biol rep1

description:
Library name: sgPBRM1_72h_1
ATAC-seq libraries

value: 72h TGFbeta treatment


title: HeLa NXF1-dTAG, DMSO treatment, RNA-seq, biological replicate 1

description:
Library name: RNA-seq_DMSO_rep1
Poly(A)+ RNA-seq from HeLa NXF1-dTAG cells treated with DMSO (vehicle control) for 6 h. Biological replicate 1.


title: 4T1_CUT&RUN_PBRM1-sgCT-TGF-biol rep2

description:
Library name: 4T1_CnR_PBRM1-sgCT-TGF-N2
CUT&RUN libraries

data_processing:
Raw paired-end reads were aligned using a dual-mapping strategy to separately quantify reads from the target genome and the exogenous E. coli spike-in. Alignment to the mouse mm10 target genome was performed with Bowtie2 using local alignment parameters appropriate for the short, size-selected CUT&RUN fragments (--local –very-sensitive-local –no-unal –no-mixed –no-discordant –phred33 -I 10 -X 700), which permit minor adapter read-through common in short fragments while maintaining alignment stringency. Alignment to the E. coli K12 MG1655 spike-in genome was performed in a separate run using end-to-end parameters (--end-to-end –very-sensitive –no-overlap –no-dovetail –no-unal –no-mixed –no-discordant –phred33 -I 10 -X 700) to avoid soft-clipping artifacts on the small bacterial reference.
Resulting BAM files were filtered with SAMtools to retain only properly paired, uniquely mapped reads (-f 2 -q 10). PCR duplicates were flagged using SAMtools markdup to assess library complexity and amplification efficiency but were not removed from downstream analysis. Reads overlapping ENCODE mm10 blacklisted regions (v2) were excluded using BEDTools intersect (-v).
A spike-in scaling factor was calculated for each sample as 100,000 divided by the number of high-quality, properly paired E. coli read pairs, providing cross-sample normalization that is independent of sequencing depth. Spike-in normalized bigwig tracks were generated using bamCoverage from deepTools (--normalizeUsing None --scaleFactor [sample-specific value] --extendReads --exactScaling --binSize 10) for genome browser visualization.
Chromatin occupancy peaks were called using MACS2 in paired-end mode (-f BAMPE -q 0.05 --keep-dup all) against two independent IgG negative controls, one derived from sgPbrm1 cells and one from sgCt cells, to stringently account for background signal in both experimental backgrounds. Peak annotation was performed using the R package ChIPseeker (v3.15).
Assembly: mm10
Supplementary files format and content: Bigwig files
Supplementary files format and content: Peak files
Library strategy: CUT&Run

growth_protocol: 4T1 cells were grown in RPMI-1640 (Corning Mediatech) supplemented with 10% fetal bovine serum, 1% L-glutamine (Corning Mediatech), 1% antibiotics (100 units/ml penicillin and 100 g/ml streptomycin; Corning Mediatech), and 1% Sodium Pyruvate (Corning Mediatech) at 37 °C in a humidified atmosphere in a 5% CO2 incubator.

extract_protocol:
Cut&Run was done according to the protocol available from EpiCypher (v2.2) with minor modifications- in-house prepared pAG-MNase was used and incubation of cells with pAG-MNase in section IV was done at 4C for 1h. Amount of pAG-MNase used was 37ng/reaction. Antibodies used were PHF10 (Invitrogen #PA5-30678), H3K4me3 (EpiCypher 13-0060), Pbrm1 (Bethyl # A301-591A), and Rabbit control IgG (EpiCypher # 13-0042)
Libraries were prepared using the CUTANA™ CUT&RUN Library Prep Kit according to the manufacturer’s instructions, and quality checked using Qubit and Agilent TapeStation by Purdue Genomics Core Facility. Libraries were sequenced using 150bp PE sequencing on Aviti platform (Element Biosciences) by the Purdue Genomics Core Facility. All experiments were performed with two biological replicates.

treatment_protocol: 4T1 cells were seeded in 6-well plates with or without 5ng/ml TGFβ1 (R&D systems, Catalog # 7754-BH) for 4 days.

value: Triple Negative Breast Cancer

value: sgControl

value: 4 days TGFb

value: Pbrm1 (Bethyl # A301-591A)


title: [ATAC-Seq] PBRM1 KO_0h_biol rep2

description:
Library name: sgPBRM1_0h_2
ATAC-seq libraries


title: 4T1_CUT&RUN_PBRM1-sgCT-biol rep2

description:
Library name: 4T1_CnR_PBRM1-sgCT-N2
CUT&RUN libraries

value: No TGFb


title: 4T1_CUT&RUN_PBRM1-sgCT-TGF-biol rep1

description:
Library name: 4T1_CnR_PBRM1-sgCT-TGF-N1
CUT&RUN libraries


title: 4T1_CUT&RUN_PBRM1-sgCT-biol rep1

description:
Library name: 4T1_CnR_PBRM1-sgCT-N1
CUT&RUN libraries


title: 4T1_CUT&RUN_PHF10-sgPB-TGF-biol rep1

description:
Library name: 4T1_CnR_PHF10-sgPB-TGF-N1
CUT&RUN libraries

value: PHF10 (Invitrogen #PA5-30678)


title: 4T1_CUT&RUN_PHF10-sgPB-biol rep1

description:
Library name: 4T1_CnR_PHF10-sgPB-N1
CUT&RUN libraries


title: 4T1_CUT&RUN_PHF10-sgCT-biol rep1

description:
Library name: 4T1_CnR_PHF10-sgCT-N1
CUT&RUN libraries


title: 4T1_CUT&RUN_PHF10-sgCT-TGF-biol rep1

description:
Library name: 4T1_CnR_PHF10-sgCT-TGF-N1
CUT&RUN libraries


title: 4T1_CUT&RUN_IgG_Control-sgCT

description:
Library name: 4T1_CnR_Control-IgG-sgCT
CUT&RUN libraries

value: Rabbit control IgG (EpiCypher # 13-0042)


title: 4T1_CUT&RUN_H3K4me3-sgCt-TGF

description:
Library name: 4T1_CnR_H3K4me3-sgCt-TGF
CUT&RUN libraries

value: H3K4me3 (EpiCypher 13-0060


title: 4T1_CUT&RUN_H3K4me3-sgCt

description:
Library name: 4T1_CnR_H3K4me3-sgCt
CUT&RUN libraries


title: [ATAC-Seq] Control_72h_biol rep2

description:
Library name: sgCT_72h_2
ATAC-seq libraries

value: Control


title: 4T1_CUT&RUN_PHF10-sgPB-TGF-biol rep2

description:
Library name: 4T1_CnR_PHF10-sgPB-TGF-N2
CUT&RUN libraries


title: 4T1_CUT&RUN_PHF10-sgPB-biol rep2

description:
Library name: 4T1_CnR_PHF10-sgPB-N2
CUT&RUN libraries


title: 4T1_CUT&RUN_PHF10-sgCT-TGF-biol rep2

description:
Library name: 4T1_CnR_PHF10-sgCT-TGF-N2
CUT&RUN libraries


title: 4T1_CUT&RUN_PHF10-sgCT-biol rep2

description:
Library name: 4T1_CnR_PHF10-sgCT-N2
CUT&RUN libraries


title: 4T1_PBRM1_KO_TGF_ATAC-seq_biol rep3

description:
Library name: 4T1_sgPB_TGF_N3
ATAC-seq libraries

data_processing:
Paired-end reads were aligned to the mouse mm10 reference genome using Bowtie2 (v2.4.5) with ENCODE ATAC-seq standard parameters (--very-sensitive -X 2000 --no-mixed --no-discordant). Aligned reads were filtered with SAMtools to remove unmapped, non-primary, supplementary, and improperly paired alignments, as well as reads failing quality filters (SAMtools flags -F 1804 -f 2), and reads with mapping quality below MAPQ 30 (-q 30); mitochondrial reads were also excluded. Reads overlapping ENCODE mm10 blacklisted regions (v2) were subsequently removed using BEDTools intersect (-v). PCR duplicates were identified and removed using the SAMtools fixmate and markdup pipeline.
To correct for the 9 bp staggered insertion introduced by Tn5 transposase nick repair, reads were shifted +4 bp on the forward strand and −5 bp on the reverse strand using the alignmentSieve –ATACshift function from deepTools. Chromatin accessibility peaks were called on the deduplicated BAM files using MACS2 (v2.2.7.1) in paired-end mode (-f BAMPE -g mm -q 0.01 –call-summits –keep-dup all); the –keep-dup all flag was used because duplicates had already been removed in the preceding step.
CPM-normalized bigwig files for genome browser visualization were generated from Tn5-shifted BAM files using bamCoverage from deepTools (--normalizeUsing CPM –effectiveGenomeSize 2308125349 –binSize 10 –extendReads –blackListFileName mm10-blacklist.v2.bed). Differential accessibility analysis was done using MACS2 and PCA was performed using DiffBind (v3.8.4), and peak annotation was performed using the R package ChIPseeker (v3.15).
Assembly: mm10
Supplementary files format and content: Mapped reads in BigWig format

extract_protocol:
Cells were harvested at 4 days with or without treatment and processed according to the Omni-ATAC protocol (Corces et al. Nature Methods 2017)
Libraries were constructed as described in Omni-ATAC protocol (Corces et al. Nature Methods 2017). The final libraries were subjected to double size selection according to a published protocol (Library Preparation for ATAC-Sequencing of Mouse CD4+T Cells Isolated from the Lung and Lymph Nodes After Helminth Infection Laura D. Harmacek, Preeyam Patel, Rachel Woolaver, R. Lee Reinhardt, and Brian P. O’Connor) and quality checked using Qubit and Agilent TapeStation by Purdue Genomics Core Facility.

treatment_protocol: 4T1 cells were seeded in 6-well plates with or without 5ng/ml TGFβ1 (R&D systems, Catalog # 7754-BH)  for 4 days.

value: 4 days TGFb treated


title: 4T1_PBRM1_KO_TGF_ATAC-seq_biol rep2

description:
Library name: 4T1_sgPB_TGF_N2
ATAC-seq libraries


title: 4T1_PBRM1_KO_TGF_ATAC-seq_biol rep1

description:
Library name: 4T1_sgPB_TGF_N1
ATAC-seq libraries


title: 4T1_PBRM1_KO_0h_ATAC-seq_biol rep3

description:
Library name: 4T1_sgPB_0h_N3
ATAC-seq libraries

value: No treatment


title: Huh7_sgKEAP1_3

city: Shanghai

first: Wei

last: Wang

address: No. 25, Lane 2200, Xietu Road, Xuhui District

institute: Shanghai Cancer Institute

description: Library name: Sample 24

data_processing:
Illumina Casava 1.8.2 software used for basecalling. The quality score encoding is in +Phred 33.
Raw sequencing reads were mapped to the human genome (GRCh38) using STAR (version 2.4.2g1).
Gene-level read counts were generated using featureCounts from the subRead package with default settings.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver

growth_protocol: Cell lines were cultured in DMEM medium

extract_protocol:
Total RNA was extracted and purified using the Trizol reagent (Invitrogen)
The library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina).

treatment_protocol: We treated liver cancer cells with control vehicle,KPT-330 or siRNAcontrol and siRNA of NCOR1. Then, RNA sequencing was conducted to quantify the mRNA expression level. These treatment induced expression changes were obtained based on the resultant data.

value: liver

value: liver cancer cell line

value: cell line

tag: batch


title: 4T1_PBRM1_KO_0h_ATAC-seq_biol rep2

description:
Library name: 4T1_sgPB_0h_N2
ATAC-seq libraries

value: PBRM1 KO


title: Huh7_sgKEAP1_2

description: Library name: Sample 23


title: 4T1_CUT&RUN_IgG_Control-sgPB

description:
Library name: 4T1_CnR_Control-IgG-sgPB
CUT&RUN libraries


title: 4T1_PBRM1_KO_0h_ATAC-seq_biol rep1

description:
Library name: 4T1_sgPB_0h_N1
ATAC-seq libraries


title: [ATAC-Seq] Control_0h_biol rep2

description:
Library name: sgCT_0h_2
ATAC-seq libraries

value: NMuMG

value: Epithelial cells


title: Huh7_sgKEAP1_1

description: Library name: Sample 22


title: 4T1_control_TGF_ATAC-seq_biol rep3

description:
Library name: 4T1_sgCt_TGF_N3
ATAC-seq libraries

value: Triple Negative Breast Cancer


title: 4T1_control_TGF_ATAC-seq_biol rep2

description:
Library name: 4T1_sgCt_TGF_N2
ATAC-seq libraries


title: Huh7_WT_3

description: Library name: Sample 21


title: Huh7_WT_2

description: Library name: Sample 20


title: 4T1_control_TGF_ATAC-seq_biol rep1

description:
Library name: 4T1_sgCt_TGF_N1
ATAC-seq libraries


title: Huh7_WT_1

description: Library name: Sample 19


title: 4T1_control_0h_ATAC-seq_biol rep3

description:
Library name: 4T1_sgCt_0h_N3
ATAC-seq libraries


title: Hep3B_sgKEAP1_3

description: Library name: Sample 18


title: 4T1_control_0h_ATAC-seq_biol rep2

description:
Library name: 4T1_sgCt_0h_N2
ATAC-seq libraries


title: Hep3B_sgKEAP1_2

description: Library name: Sample 17


title: AS053_V

source_name: Gut epithelium, P, Rectum

value: gut epithelium

value: Progressor

value: Rectum

value: Chronic active

value: LGD


title: 4T1_control_0h_ATAC-seq_biol rep1

description:
Library name: 4T1_sgCt_0h_N1
ATAC-seq libraries


title: Hep3B_WT_3

description: Library name: Sample 15


title: 4T1_PBRM1_KO_TGF_biol rep3

description:
Library name: 4T1_sgPB_TGF_N3
3Z9XSS_12_Sg_TGFb_n3

data_processing:
Data analysis till raw counts generation was done by Plasmidosaurus. Raw reads were filtered using fastp (v0.24.0): poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Alignment was done to the mouse genome build mm39 using STAR (v2.7.11) with non-canonical splice junction removal and output of unmapped reads. Coordinate sorting of BAM files was done using samtools (v1.22.1). Gene-level read counts were quantified with featureCounts subread package (v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file. Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation.
Differential expression analysis was performed using edgeR (v3.38.4). Read counts were normalized using TMM method after removing lowly expressed genes with the filterByExpr function at default settings. A group-level model was fit to enable testing of all pairwise contrasts between the four conditions, including the interaction term between Pbrm1 genotype and TGFβ1 treatment status. Genes with FDR-adjusted p-values < 0.05 were considered differentially expressed. Volcano plots, heatmaps, MA plots, and summary tables were generated in R.
Assembly: mm39
Supplementary files format and content: Raw gene counts provided as tab-delimited excel files

extract_protocol:
4T1 cells were treated with or without TGFβ1 for 4 days, then trypsinzed and the cell pellets were lysed in Zymo 1X DNA/RNA Shield™ (Zymo Research #R1100-50)
RNA isolation, library construction and sequencing was done by Plasmidosaurus (Briefly, mRNA is converted into cDNA via reverse transcription using a poly(dT)VN primer, followed by second-strand synthesis, and then tagmentation, library indexing, and amplification. This approach uses 3’ end counting to capture differential gene expression. The single end sequencing is stranded and sequences towards the 3' end. Unique molecular identifiers (UMIs) are used to deduplicate, and unique dual indices (UDIs) to prevent index hopping). All experiments were performed in three biological replicates.


title: 4T1_PBRM1_KO_TGF_biol rep2

description:
Library name: 4T1_sgPB_TGF_N2
3Z9XSS_11_Sg_TGFb_n2


title: Hep3B_WT_2

description: Library name: Sample 14


title: Hep3B_sgKEAP1_1

description: Library name: Sample 16


title: 4T1_PBRM1_KO_TGF_biol rep1

description:
Library name: 4T1_sgPB_TGF_N1
3Z9XSS_10_Sg_TGFb_n1


title: Hep3B_WT_1

description: Library name: Sample 13


title: Huh7_KPT_3

description: Library name: Sample 12


title: 4T1_PBRM1_KO_0h_biol rep3

description:
Library name: 4T1_sgPB_0h_N3
3Z9XSS_9_Sg_n3


title: Amygdala, SMRT-KO, P21, rep3

city: Maebashi

first: Izuki

last: Amano

state: Gunma

address: 3-9-22 Showa-machi

department: Department of Integrative Physiology, Graduate School of Medicine

country: Japan

institute: Gunma University

description: Library name: SMRT-KO A03

data_processing:
BCL (base call) binaries were converted to FASTQ using the illumina package bcl2fastq. Removal of adapters and low-quality reads was performed using fastp (version 0.21.0). Reads after trimming were used for mapping to the mm10 reference genome and for read counting in the STAR (version 2.5.3a)-RSEM (version 1.3.3) pipeline.
Assembly: mm10
Supplementary files format and content: text file includes raw counts for each Sample

source_name: Amygdala

extract_protocol:
Total RNA was extracted following the instruction for RNeasy Lipid Tissue Mini Kit (QIAGEN).
Library preparation was performed using the TruSeq stranded mRNA kit (Illumina).

value: Amygdala

value: SMRT-KO


title: Amygdala, SMRT-KO, P21, rep2

description: Library name: SMRT-KO A02


title: Amygdala, SMRT-KO, P21, rep1

description: Library name: SMRT-KO A01


title: 4T1_PBRM1_KO_0h_biol rep2

description:
Library name: 4T1_sgPB_0h_N2
3Z9XSS_8_Sg_n2


title: Huh7_KPT_2

description: Library name: Sample 11


title: 4T1_PBRM1_KO_0h_biol rep1

description:
Library name: 4T1_sgPB_0h_N1
3Z9XSS_7_Sg_n1


title: Amygdala, NCoR1-KO, P21, rep3

description: Library name: NCoR1-KO A03


title: Huh7_KPT_1

description: Library name: Sample 10


title: cortical NSPCs, sh3F, Day5, replicate 2

city: Shinjuku-ku

first: Takuya

last: Shimazaki

state: Tokyo

address: 35 Shinanomachi

department: Physiology

institute: Keio University School of Medicine

description:
Library name: sh3F_2
Colum name in raw_counts_KD_samples_csv: _sh3F_2

data_processing:
Base calling, quality scoring, FASTQ file generation and de-multiplexing were performed by MGI Sequencer basecall software. Removed reads containing adapters, N > 10% (N represents the base cannot be determined), and low quality (Qscore<= 5) base which is over 50% of the total base.
Reads were aligned to the mouse reference genome (GRCm38) and quantified with Salmon on RaNA-Seq platform (Prieto and Barrios, 2020).
Assembly: mm10
Supplementary files format and content: csv files include raw counts for each sample

growth_protocol: Neural stem and progenitor cells (NSPCs) were derived from E11.5 dorsal telencephalon and cultured as free-floating neurospheres as described (Naka et al., 2008). Tissues were mechanically dissociated into single cells and plated at a density of 2 × 105 cells/mL and infected with lentivirus vectors in neurosphere medium [DMEM/F12 (Gibco, 1210004/21700075), 5 mM HEPES (Sigma, H-4034), 13.4 mM NaHCO3 (Sigma, G-7021), 25 ug/ml Insulin (human, recombinant) (Wako, 093-06476), 60 uM putrescine dihydrochloride (Sigma, P-5780), 100 ug/ml apo-transferrin from human (Nacalai Tesque, 34401-55), 30 nM selenium sodium salt (Sigma S-9133), 20 nM progesterone (Sigma, P-6149), 0.2% BSA (Sigma, A-3311), 20 ng/ml bFGF (PeproTech, 100-18B)] at 37℃ and 5% CO2 for 5 days.

extract_protocol:
Total RNA was purified with NucleoSpin® RNA Plus XS kit. 100ng of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were prepared with NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manufacturer's instruction.

treatment_protocol: Tissue dissociates were transduced with CS-EG-shControl (MOI: 30) or pCS-EG-shPhf21b, pLV-EG-shZfp7 and pLV-EG-shZfp57 (MOI: 10 each) simultaneously.

value: neural progenitor cells

value: primary

value: Phf21, Sfp7, Zfp57 knockdown

value: transduced with lentivirus vectors expressing shPhf21b, shZfp7, and shZfp57


title: Huh7 siNCOR1_KPT_3

description: Library name: Sample 9

value: liver

value: liver cancer cell line


title: cortical NSPCs, sh3F, Day5, replicate 1

description:
Library name: sh3F_1
Colum name in raw_counts_KD_samples_csv: _sh3F_1


title: Amygdala, NCoR1-KO, P21, rep2

description: Library name: NCoR1-KO A02


title: 4T1_control_TGF_biol rep2

description:
Library name: 4T1_sgCt_TGF_N2
3Z9XSS_5_Ct_TGFb_n2

value: Control

value: 4 days TGFb treated


title: 4T1_control_TGF_biol rep3

description:
Library name: 4T1_sgCt_TGF_N3
3Z9XSS_6_Ct_TGFb_n3


title: Amygdala, NCoR1-KO, P21, rep1

description: Library name: NCoR1-KO A01


title: Huh7 siNCOR1_KPT_2

description: Library name: Sample 8

value: cell line


title: 4T1_control_TGF_biol rep1

description:
Library name: 4T1_sgCt_TGF_N1
3Z9XSS_4_Ct_TGFb_n1

value: Triple Negative Breast Cancer


title: cortical NSPCs, shControl, Day5, replicate 2

description:
Library name: shCont_2
Colum name in raw_counts_KD_samples_csv: shCont_2

value: WT

value: transduced with lentivirus vector expressing shControl


title: Amygdala, control, P21, rep4

description: Library name: control A04

value: control


title: Huh7 siNCOR1_KPT_1

description: Library name: Sample 7


title: SH DNA replicate 1

city: Indianapolis

first: Yunlong

last: Liu

address: 410 W 10th Street, HS5000

department: Center for Computational Biology and Bioinformatics

institute: Indiana School of Medicine

description: SH_DNA_rep1_REF, SH_DNA_rep1_ALT

data_processing:
Reads were demultiplexed using cutadapt (v2.7)
UMIs were appended to each read name with umi_tools (v1.0.0)
Primer sequences were trimmed using cutadapt
Resulting reads were mapped to the MPRA oligo library using bowtie2
Reads containing mismatches were filtered out using samtools (v1.10)
The number of unique reads for each oligo sequence were counted using umi_tools count.
Assembly: hg38
Supplementary files format and content: unique_counts.txt contains tab-delimited unique reads for the REF and ALT oligo of each variant evaluated by MPRA

growth_protocol:
SH: 1:1 mixture of EMEM (American Type Culture Collection; ATCC) and F12K medium (10025-CV, Thermo Fisher Scientific) with 10% (vol/vol) fetal bovine serum (ATCC) and 1% penicillin and streptomycin
MG: Prigrow III medium with 10% (vol/vol) fetal bovine serum (16000-044, Thermo Fisher Scientific) and 1% penicillin-streptomycin in type I collagen-coated (1:30; Sigma-Aldrich, C3867) six 6-well plates

extract_protocol:
AllPrep DNA/RNA mini kit (Qiagen). Poly-A RNA was isolated using Dynabeads oligo(dT)25 (Thermo Fisher Scientific) and mRNA treated with gDNA wipeout buffer (Qiagen) before preparing sequencing libraries
Poly(A)RNA (500 ng) from each independent transfection was reverse transcribed to cDNA using QuantiTech Reverse Transcription kit (Qiagen) using a reporter-specific first strand primer that contains the R1 Illumina adapter sequence, a 9-12 nt barcode (with staggered starts) and a 10 nt unique molecular index (UMI). The resulting cDNA was then PCR-amplified with a primer containing the R2 Illumina adapter sequence and one of 6 barcodes, one for each independent transfection (HJ7214-HJ7219).
DNA was PCR-amplified with another first strand primer and one of 6 barcodes for replicate

treatment_protocol: Lipofectamine 3000 used for transfection

value: neuroblastoma


title: cortical NSPCs, shControl, Day5, replicate 1

description:
Library name: shCont_1
Colum name in raw_counts_KD_samples_csv: shCont_1


title: 4T1_control_0h_biol rep3

description:
Library name: 4T1_sgCt_0h_N3
3Z9XSS_3_Ct_n3

value: No treatment


title: Amygdala, control, P21, rep3

description: Library name: control A03

value: Amygdala


title: Huh7 siNCOR1_3

description: Library name: Sample 6


title: 4T1_control_0h_biol rep2

description:
Library name: 4T1_sgCt_0h_N2
3Z9XSS_2_Ct_n2


title: Ulcerative colitis, replicate 6, RNA_seq

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

description: Library name: UC26

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: colon

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon


title: Amygdala, control, P21, rep2

description: Library name: control A02


title: Huh7 siNCOR1_2

description: Library name: Sample 5


title: 4T1_control_0h_biol rep1

description:
Library name: 4T1_sgCt_0h_N1
3Z9XSS_1_Ct_n1


title: Ulcerative colitis, replicate 5, RNA_seq

description: Library name: UC23


title: Huh7 siNCOR1_1

description: Library name: Sample 4


title: Ulcerative colitis, replicate 4, RNA_seq

description: Library name: UC19


title: Amygdala, control, P21, rep1

description: Library name: control A01


title: ILC3_Igf1_Rep3

first: Qiang

state: Shanghai

address: 533 Puchi Road

department: Shanghai Immune Therapy Institute

institute: Renji Hospital, Shanghai Jiao Tong University School of Medicine

description: Library name: Sample 6

data_processing:
fastp v0.23.2, HISAT2 v2.2.1, samtools v1.15.1, featureCounts v1.5.3
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw gene-level read counts for each sample

source_name: small intestine

extract_protocol:
Cells were lysed using the 10X Lysis Buffer provided in the SMART-Seq HT Kit (Takara Bio) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using SMART-Seq HT Kit (Takara Bio) following manufacturer's protocols

value: small intestine

value: Group 3 innate lymphoid cells (ILC3)

value: wild-type


title: Hippocampus, SMRT-KO, P21, rep3

description: Library name: SMRT-KO H03

source_name: Hippocampus

value: Hippocampus

value: SMRT-KO


title: Huh7 Ctrl_3

description: Library name: Sample 3

value: liver

value: liver cancer cell line


title: ILC3_Ctrl_Rep3

description: Library name: Sample 5


title: Ulcerative colitis, replicate 2, RNA_seq

description: Library name: UC10


title: Huh7 Ctrl_2

description: Library name: Sample 2

value: Control


title: ILC3_Igf1_Rep2

description: Library name: Sample 4


title: Hippocampus, SMRT-KO, P21, rep1

description: Library name: SMRT-KO H01


title: Hippocampus, SMRT-KO, P21, rep2

description: Library name: SMRT-KO H02


title: Ulcerative colitis, replicate 3, RNA_seq

description: Library name: UC16


title: Huh7 Ctrl_1

description: Library name: Sample 1

value: cell line


title: Ulcerative colitis, replicate 1, RNA_seq

description: Library name: UC6


title: ILC3_Ctrl_Rep2

description: Library name: Sample 3


title: Hippocampus, NCoR1-KO, P21, rep3

description: Library name: NCoR1-KO H03


title: WT,rep3

city: Weifang

first: ronglan

last: zhao

address: No.7166 Bao Tong West Street

institute: Shandong Second Medical University

description: Library name: WT3

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . StringTie was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts and RPKM values for each Sample

source_name: A549 cell line

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

value: A549 cell line

tag: transfection

value: negative control plasmid


title: Hippocampus, NCoR1-KO, P21, rep2

description: Library name: NCoR1-KO H02


title: WT,rep2

description: Library name: WT2


title: ILC3_Igf1_Rep1

description: Library name: Sample 2


title: Healthy control, replicate 5, RNA_seq

description: Library name: HC36


title: Healthy control, replicate 6, RNA_seq

description: Library name: HC37


title: ILC3_Ctrl_Rep1

description: Library name: Sample 1


title: Hippocampus, NCoR1-KO, P21, rep1

description: Library name: NCoR1-KO H01


title: WT,rep1

description: Library name: WT1


title: Healthy control, replicate 4, RNA_seq

description: Library name: HC29


title: SBM, OPT, mouse2

city: Chongqing

first: Yiguo

last: Qiu

state: Chongqing

address: 13 Tianchi Road, Banan District

institute: Chongqing International Institute for Immunology

description: Library name: SBM_OPT

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skull bone marrow

extract_protocol:
Mice were anesthetized, intracardially perfused with buffer (± inhibitors), and tissues (brain or calvaria) were dissected. Brain tissue was minced, digested with papain buffer (± inhibitors: Actinomycin D, Triptolide, Anisomycin), triturated, and purified via Percoll gradient centrifugation to remove myelin. SBM was minced in ice-cold buffer, digested post-mincing with inhibitors, lysed with ACK buffer, and filtered through a 40 µm strainer. Both tissues underwent inhibitor-matched dead cell removal (Miltenyi kit), followed by centrifugation and resuspension in PBS/0.2% BSA for library preparation. Inhibitor-treated (OPT) and untreated (CTL) groups were processed identically except for inhibitor inclusion during dissociation and purification steps.
Single-cell suspensions were loaded onto a 10X Chromium Controller (10X Genomics) at a concentration of 1,000 cells/uL, targeting a capture of 10,000 cells per well. Gel Beads-in-Emulsion (GEMs) droplets were generated and scRNA-seq libraries were constructed using Chromium Next GEM Chip K Single Cell Kit (10X Genomics) and Chromium Next GEM Single Cell 5’ V2 GEM, Library & Gel Bead Kit (10X Genomics). Each GEM underwent a reverse transcription reaction to generate single-cell cDNA, when each encapsulated cell was labeled with a unique 12-nt cell barcode, and each transcript was labeled with a unique molecular identifier (UMI). Amplified cDNA was used for library preparation, consisting of fragmentation, end repair, A-tailing, adaptor ligation and sample index PCR according to the manufacturer’s instructions. Final libraries were sequenced on a NovaSeq X Plus Sequencing System (Illumina).

value: skull bone marrow

value: WT


title: Hippocampus, control, P21, rep4

description: Library name: control H04

value: control


title: KD,rep3

description: Library name: KD3

value: GV102‐P2X7R‐scrambled shRNA


title: Healthy control, replicate 3, RNA_seq

description: Library name: HC27


title: SBM, CTL, mouse1

description: Library name: SBM_CTL


title: Hippocampus, control, P21, rep3

description: Library name: control H03


title: brain, OPT, mouse2

description: Library name: brain_OPT

source_name: brain

value: brain


title: KD,rep2

description: Library name: KD2


title: Hippocampus, control, P21, rep2

description: Library name: control H02


title: KD,rep1

description: Library name: KD1


title: brain, CTL, mouse1

description: Library name: brain_CTL


title: Healthy control, replicate 1, RNA_seq

description: Library name: HC24

value: colon


title: in situ Hi-C of DSMZ’s U-937 cell line with no stimulation

city: Mitaka-shi

first: Tetsuko

last: Kobayashi

institute: Kyorin University

description: Library name: Sample 1

data_processing:
FASTQ files were processed through the Juicer software package.
Reads were aligned to the genome using BWA, and only reads with a MAPQ score >=30 were used for the subsequent analyses.
Compartments were identified at a 1 Mb resolution using Juicer Tool’s eigenvector program.
Topologically associating domains (TADs) were identified using Juicer’s Arrowhead software and chromatin loops were called using Juicer’s HiCCUPS software, both were run with default parameters.
Juicer’s output files were processed through Active Motif’s proprietary analysis program which generate Excel tables containing detailed information on gene annotations and the location of compartments, TADs, and loops.
Assembly: GRCh38/hg38
Supplementary files format and content: .fastq.gz, .hic, .bedpe, .bed.gz, .bed.gz.tbi, .txt.gz, .txt.gz.tbi

source_name: bone marrow

growth_protocol: 90 % RPMI 1640 + 10 % h.i. FBS. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Sample was processed using Arima-HiC Kit, Library Preparation using Swift Biosciences® Accel-NGS® 2S Plus DNA Library Kit [Arima A510008] .
Sample was lysed and crosslinked followed by restriction enzyme digestion and ligation. Ligated DNA was purified, sheared, and used for library generation using Active Motif Next Gen DNA Library Kit [Active Motif 53216].

value: bone marrow

value: acute monocytic leukemia

value: no treatment


title: patient-3

status: Public on Jun 13 2026

city: 北京-Beijing

first: QING

state: 北京市

address: Department of Neurology, Peking Union Medical College Hospital (PUMCH), Peking Union Medical College (PUMC) & Chinese Academy of Medical Science (CAMS), Beijing, China

description: Library name: sample6

data_processing:
Data analysis included quality control of sequencing reads, filtering of low-quality reads, and alignment of sequences using HISAT2. Gene expression levels were quantified with featureCounts, and differential expression analysis was performed using DESeq2. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted with clusterProfiler.
Assembly: GRCh38
Supplementary files format and content: gene_count -1.xls

extract_protocol:
During sample collection and preparation, RNA was extracted and assessed for integrity and quantity using the Agilent 2100 Bioanalyzer.
For library construction, polyA-tailed mRNA was enriched using Oligo(dT) magnetic beads, followed by cDNA synthesis and purification. After end repair, A-tailing, and adapter ligation, cDNA fragments of 370–420 bp were selected using AMPure XP beads, followed by PCR amplification and additional purification to obtain the final library. The completed library was quantified using the Qubit 2.0 Fluorometer to ensure an effective concentration above 2 nM. Qualified libraries were pooled and subjected to sequencing using the Sequencing by Synthesis method.

value: motor neuron


title: patient-2

institute: Peking Union Medical College Hospital (PUMCH), Peking Union Medical College (PUMC) & Chinese Academy of Medical Science (CAMS)

description: Library name: sample5


title: patient-1

description: Library name: sample4


title: control-3

description: Library name: sample3


title: control-2

description: Library name: sample2


title: patient with HCM,Peripheral blood,sample13

city: Shijiazhuang City

first: Xiqin

state: Hebei Province

address: Yuhua District

department: Department of Internal Medicine

institute: Yuhua Yunfang Integrated Traditional Chinese and Western Medicine Clinic

data_processing:
Raw reads were quality controlled with FastQC and SeqPrep. Detailed methods were as follows: (1) adapter sequences in reads were removed; (2) Bases (quality values < 20) were trimmed; (3) reads with an N ratio of more than 10% were removed; (4) Sequences (< 20 bp in length) were discarded.
Repeated fragments (the main source for PCR amplification) that have a great impact on the discovery of genomic mutations were removed. Picard was used to remove marked repeats.
We used the BaseRecalibrator module and RealignerTargetCreator module in GATK for local indel-realignment and base recalibration.Strelka software was selected to determine the single-nucleotide variations (SNVs) and indels.
ExomeCopy software is used to detect copy number variation(CNV) and filter copy.count and nranges. The standard is copy.count ! = 2, nranges > 5.
Assembly: hg38
Supplementary files format and content: Provides CNV results, csv format.
Supplementary files format and content: Provides SNV results, include annotation results;snv.raw.txt , and site analysis: snv.txt.
Library strategy: Whole Exome Sequencing (WES)

source_name: Whole blood

extract_protocol:
Genomic DNA from peripheral blood was extracted for the whole exome sequencing (WES).  AxyPrep Mag PCR Kit was used for library construction. Finally, qualified libraries were paired-end using the Agilent v6 chip platform 150 PE sequencing modes for sequencing.
Then the DNA fragments were broken up for PCR. AxyPrep Mag PCR Kit was used for library construction
Finally, qualified libraries were paired-end using the Agilent v6 chip platform 150 PE sequencing modes for sequencing.

value: Whole blood

tag: Sex

value: Male

tag: diagnosis

value: hypertrophic cardiomyopathy (HCM)

tag: clinical phenotype

value: Hypertrophic cardiomyopathy has been diagnosed


title: patient with HCM,Peripheral blood,sample14


title: control-1

description: Library name: sample1


title: patient with HCM,Peripheral blood,sample11

value: Female

value: 1 :Left anterior descending branch and Hui branch proximal calcium spots, lumen mild stenosis

value: 2 :Multiple hepatic cysts

value: 3 :Left renal cyst

value: 4 :Right renal small adenoma

value: 5 :ECG showed :complete right bundle branch block left ventricular high voltage, partial lead ST-T abnormalities ( V2 ~ V5 lead T wave inversion ), QTc prolongation.


title: patient with HCM,Peripheral blood,sample9

value: 1 left atrial enlargement of the main atherosclerosis.

value: 2 :Left ventricular diastolic function decreased, three heart valves are not closed.

value: 3 :I degree atrioventricular block, ST-T segment abnormalities


title: patient with HCM,Peripheral blood,sample10

value: Hypertrophic cardiomyopathy has been diagnosed ; cardiac ultrasound myocardial hypertrophy


title: patient with HCM,Peripheral blood,sample7

value: hypertension


title: patient with HCM,Peripheral blood,sample6

value: Chest pain, early repolarization type 3 electric storm high risk


title: ATAC_FOP2

city: Philadelphia

first: Ellen

last: Zhang

state: PA

address: 36th Street and Hamilton Walk

department: Orthopaedic Surgery

institute: University of Pennsylvania

description: Library name: ATAC_FOP2

data_processing:
Raw reads were trimmed using Trimmomatic.
Trimmed reads were aligned to mm10 using Bowtie2 and filtered using SAMtools.
Peaks were called using MACS2, merged across samples using bedtools, and quantified using featureCounts.
Differential accessibility analysis was performed using DESeq2 (adjusted p-value < 0.01, |log2FoldChange| > 0).
Assembly: mm10 (GRCm38)
Supplementary files format and content: bed files for regions closed in mutant group (FOP_down.bed) and regions opened in mutant group (FOP_up.bed) included

source_name: mouse embryonic fibroblasts

growth_protocol: Wild-type (Acvr1+/+) and mutant (Acvr1R206H/+) mouse embryonic fibroblasts (MEFs) were isolated from E13.5 embryos. Cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C with 5% CO2.

extract_protocol:
Nuclei from 1x10^5 MEFs were isolated using ATAC Lysis Buffer and tagmented using the Active Motif ATAC-Seq Kit at 37°C for 30 minutes. Purified DNA was PCR-amplified using Q5 High-Fidelity Polymerase (NEB) with 10 cycles of indexing, followed by SPRI bead size selection. Library quality was verified by Bioanalyzer (Agilent) and quantified using NEBNext Library Quant Kit.
Libraries were sequenced as 150 bp paired-end reads on an Illumina platform (Genewiz).

value: mouse embryonic fibroblasts

value: Acvr1R206H/+ (FOP mutant)


title: ATAC_FOP1

description: Library name: ATAC_FOP1


title: ATAC_WT3

description: Library name: ATAC_WT3

value: Acvr1+/+ (wild-type)


title: patient with HCM,Peripheral blood,sample4

value: Whole blood

value: hypertrophic cardiomyopathy (HCM)

value: 1 :Heart failure

value: 2 :Right ventricular dilatation

value: 3 :ARVC in right ventricular cardiomyopathy

value: 4 :Pulmonary hypertension, with tricuspid regurgitation, pericardial effusion

value: 5 :ECG T wave changes


title: patient with HCM,Peripheral blood,sample3

value: Female

value: 1:Early cirrhosis

value: 2:Liver fibroplastic nodules

value: 3:Large spleen

value: 4:Congenital heart disease.


title: ATAC_WT1

description: Library name: ATAC_WT1


title: patient with HCM,Peripheral blood,sample2

value: Male

value: 1:Infective endocarditis with aortic valve perforation and heart failure.

value: 4:Postoperative varicose veins in both lower limbs.


title: patient with HCM,Peripheral blood,sample1

value: Hypertrophic cardiomyopathy has been diagnosed


title: Sample 2: mouse C57BL/6J, Male, 14 weeks

city: Cambridge

first: Limor

last: Cohen

state: MA

address: 38 Oxford Street

institute: Harvard University

description: Library name: Sample 2

data_processing:
Salmon
Assembly: mm10

extract_protocol:
Total RNA was extracted from a mouse brain tissue sample, with position along the anterior-posterior axis matched to the posterior slices imaged by MERFISH, using TRIzol Reagent (Thermo Fisher) followed by column-based purification with in-column DNase treatment. Briefly, 1 mL of TRIzol was added to the tissue sample and incubated for 5 minutes at room temperature to ensure complete dissociation of nucleoprotein complexes. Phase separation was initiated by adding 0.2 mL of chloroform per 1 mL of TRIzol, followed by vigorous shaking and a 2-3-minute incubation. Samples were centrifuged at 12,000 × g for 15 minutes at 4 oC, and the resulting aqueous phase was carefully transferred to a new tube. An equal volume of 100% ethanol was added to the aqueous phase (1:1), mixed thoroughly, and the solution was applied to a Zymo-Spin™ IC Column (Zymo Research). After centrifugation, the flow-through was discarded. Columns were then washed with 400 µL RNA Wash Buffer. For genomic DNA removal, DNase I treatment was performed in-column by applying 40 µL of freshly prepared DNase I reaction mix (5 µL DNase I enzyme and 35 µL DNA Digestion Buffer) directly onto the column matrix, followed by a 15-minute incubation at room temperature. After DNase treatment, RNA purification continued according to the manufacturer’s RNA Clean-up protocol. Columns were washed sequentially with 400 µL RNA Prep Buffer, 700 µL RNA Wash Buffer, and a final wash with 400 µL RNA Wash Buffer. To elute the RNA, 15 µL of nuclease-free water was applied directly to the column matrix and centrifuged. Eluted RNA was stored at -80 oC until further use.
Library preparation, quality control, and RNA sequencing were performed by Novogene. Total RNA samples were assessed for integrity and used to construct sequencing libraries following standard Illumina protocols. Libraries were sequenced on an Illumina platform to generate 150 bp paired-end reads. Paired-end FASTQ files were quantified using Salmon against the GENCODE mouse vM25 transcriptome reference. A Salmon index was generated from gencode.vM25.transcripts.fa using k-mer size 31. Transcript-level abundances were estimated using Salmon quasi-mapping with automatic library type detection (-l A), selective-alignment validation (--validateMappings), GC-bias correction (--gcBias), and sequence-specific bias correction (--seqBias). Salmon output files include transcript-level TPM values, estimated counts, and effective transcript lengths.

value: brain

value: WT


title: Day21 Proximal, replicate 3, RNA_seq

description: Library name: D21_CP3

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

value: colon

tag: strain


title: Day21 Proximal, replicate 2, RNA_seq

description: Library name: D21_CP2


title: RNA_FOP2

description: Library name: RNA_FOP2

data_processing:
Raw reads were trimmed using Trimmomatic.
Trimmed reads were aligned to mm10 using STAR.
Gene counts were generated using featureCounts (Subread).
Differential expression analysis was performed using DESeq2 (adjusted p-value < 0.05, |log2FoldChange| > 1.0).
Assembly: mm10 (GRCm38)
Supplementary files format and content: csv file including TPM values for each sample

extract_protocol:
RNA was extracted from passage 0 MEFs cultured for 2 days in six-well plates using TRIzol Reagent (Invitrogen) and purified with the Direct-zol RNA Microprep Kit (Zymo Research).
Libraries were prepared via rRNA depletion and sequenced as 150 bp paired-end reads on an Illumina platform (Genewiz).

value: mouse embryonic fibroblasts

value: Acvr1R206H/+ (FOP mutant)


title: RNA_FOP1

description: Library name: RNA_FOP1


title: Day21 Proximal, replicate 1, RNA_seq

description: Library name: D21_CP1


title: RNA_WT3

description: Library name: RNA_WT3

value: Acvr1+/+ (wild-type)


title: Day7 Proximal, replicate 3, RNA_seq

description: Library name: D7_CP3


title: RNA_WT2

description: Library name: RNA_WT2


title: Day7 Proximal, replicate 1, RNA_seq

description: Library name: D7_CP1


title: RNA_WT1

description: Library name: RNA_WT1


title: Day1 Proximal, replicate 3, RNA_seq

description: Library name: D1_CP3


title: Sample 1: mouse C57BL/6J, Male, 14 weeks

description: Library name: Sample 1

data_processing:
Reads were aligned to the reference genome using HISAT2 v2.0.5, and gene expression levels were quantified for downstream analysis by Novogene using their in-house pipeline.
Assembly: mm10
Supplementary files format and content: bam files

extract_protocol:
Total RNA was extracted from a third mouse brain tissue sample, with position along the anterior-posterior axis matched to the anterior slices imaged by MERFISH, using TRIzol Reagent (Thermo Fisher) followed by column-based purification with in-column DNase treatment. Briefly, 1 mL of TRIzol was added to the tissue sample and incubated for 5 minutes at room temperature to ensure complete dissociation of nucleoprotein complexes. Phase separation was initiated by adding 0.2 mL of chloroform per 1 mL of TRIzol, followed by vigorous shaking and a 2-3-minute incubation. Samples were centrifuged at 12,000 × g for 15 minutes at 4 oC, and the resulting aqueous phase was carefully transferred to a new tube. An equal volume of 100% ethanol was added to the aqueous phase (1:1), mixed thoroughly, and the solution was applied to a Zymo-Spin™ IC Column (Zymo Research). After centrifugation, the flow-through was discarded. Columns were then washed with 400 µL RNA Wash Buffer. For genomic DNA removal, DNase I treatment was performed in-column by applying 40 µL of freshly prepared DNase I reaction mix (5 µL DNase I enzyme and 35 µL DNA Digestion Buffer) directly onto the column matrix, followed by a 15-minute incubation at room temperature. After DNase treatment, RNA purification continued according to the manufacturer’s RNA Clean-up protocol. Columns were washed sequentially with 400 µL RNA Prep Buffer, 700 µL RNA Wash Buffer, and a final wash with 400 µL RNA Wash Buffer. To elute the RNA, 15 µL of nuclease-free water was applied directly to the column matrix and centrifuged. Eluted RNA was stored at -80 oC until further use.
Library preparation, quality control, and RNA sequencing were performed by Novogene. Total RNA samples were assessed for integrity and used to construct sequencing libraries following standard Illumina protocols. Libraries were sequenced on an Illumina platform to generate 150 bp paired-end reads.

tag: age

value: 14 weeks


title: Day1 Proximal, replicate 2, RNA_seq

description: Library name: D1_CP2


title: Eed KO rep2

city: Bronx

first: Deyou

last: Zheng

state: NY

address: 1301 Morris Park Avenue

department: Department of Genetics

institute: Albert Einstein College of Medicine

description: Library name: Epidermis_Eed KO3 (KO3)

data_processing:
Paired-end reads from RNA sequencing were aligned using the STAR aligner (v2.7.9a) to the mouse reference genome (mm39).
The alignment data were then used by the RSEM (v1.3.3) to quantify individual gene expression in the Ensembl annotation (v105), yielding estimated read counts and transcripts per million (TPMs).
Genes with a TPM >= 1 in at least one of the samples were used for differential expression analysis by DEseq2 (v1.38.3).
Assembly: mm39
Supplementary files format and content: csv-format text file includes raw counts and TPMs for each sample

source_name: Skin epidermis

extract_protocol:
Adult back skins were collected and subjected to 0.25% trypsin digestion for 60 minutes at 37ºC with 80 rpm shaking. 1:200 Sca1-PerCP-Cy5.5, 1:200 α6-integrin-FITC , and 1:100 EpCAM-APC  for 30 minutes on ice and washed twice with 1x DPBS before cell sorting. Interfollicular epidermis, enriched for epidermal progenitors, was sorted as EpCAM(+), Sca1(+), and α6-integrin(high). FACS-purified cells were collected directly into RLT Plus buffer  and total RNA was isolated with the RNeasy Plus Micro Kit .
Libraries were constructed from 50ng of total RNA using the Universal Plus mRNA-Seq with NuQuant®. Following the manufacturer’s instructions of mRNA elution, mRNA was subjected to fragmentation at 94°C for 8 minutes. RNA-seq library preparation was carried out by following the manufacturer’s instructions. The concentration and quality of the libraries were determined using Qubit (Invitrogen) and Bioanalyzer (Agilent). Constructed RNA-seq libraries were sequenced at GENEWIZ (Azenta) on the Illumina Nova-seq platform, obtaining 150 nucleotide paired-end reads.

treatment_protocol: For hydroxyl-tamoxifen (4OH-Tam) (Sigma-Aldrich) topical treatment, 4OH-Tam was dissolved in absolute ethanol (Sigma-Aldrich) to a final concentration of 20 mg/ml. To induce recombination, 100ul of 4OT-Tam topically applies on shaved back skin of P50 mice once per day for 4 days. mice are collected after 5-month-old.

value: Skin epidermis

value: Epidermal cells

value: Eed -/-

value: hydroxyl-tamoxifen treated


title: Eed KO rep3

description: Library name: Epidermis_Eed KO4 (KO4)


title: Day1 Proximal, replicate 1, RNA_seq

description: Library name: D1_CP1


title: Eed KO rep1

description: Library name: Epidermis_Eed KO1 (KO1)


title: Control rep3

description: Library name: Epidermis_Control10 (C10)

value: wild-type


title: DSS Proximal, replicate 4, RNA_seq

description: Library name: DP4


title: Control rep2

description: Library name: Epidermis_Control6 (C6)


title: Control rep1

description: Library name: Epidermis_Control1 (C1)


title: DSS Proximal, replicate 2, RNA_seq

description: Library name: DP2


title: DSS Proximal, replicate 3, RNA_seq

description: Library name: DP3


title: SCC-Eed-2

description: Library name: SCC-Eed-B2

data_processing:
Reads were trimmed with Trim Galore (v0.6.7) and aligned to the mouse reference genome (mm10) using Bowtie2 (v.2.2.5). Deduplicated reads were removed using samtools (v.1.14). Peaks were identified using a sliding window method to determine genomic regions with >1.5 mapping read enrichment over IgG control and adjusted p < 0.05. The BAM file for each replicate was converted to a TDF file for Integrative Genomics Viewer (IGV) software.
Assembly: mm10
Supplementary files format and content: TDF, tag density file
Library strategy: CUT&RUN

source_name: skin cancer

extract_protocol:
The basal layer epidermal cells were isolated from adult back skin. Back skins were collected and washed with 1x DPBS and incubated for 0.25% Trypsin/EDTA at 37℃ for 1 hour.  The cells were stained with 1:200 PerCP-Cy5.5-Sca1 (Thermo Fisher Scientific), 1:200 FITC-α6-integrin (Thermo Fisher Scientific), and 1:100 APC-EpCAM (Biolegend) in staining buffer (2% FBS in HBSS (Corning)) for 30 minutes on ice and then washed twice with DPBS before cell sorting. Epidermal basal cells were sorted as EpCAM(+), Sca1(+), and α6-integrin (high). Tumors were collected from the mice and cut into small pieces (< 1mm3) with razor blades in 10cm plate. Chopped tumors were incubated with 0.25% collagenase (Millipore Sigma) in HBSS for 45 minutes. After collagenase incubation, chopped tumors were treated with 1 unit DNase (Millipore Sigma) for 10 minutes. Collect the tumors and medium filtered through 100μm filters and transfer the tumors from filters into 10cm plate. Tumors were incubated 0.25% Trypsin/EDTA (Corning) at 37C for 30 minutes.  The cancer cells were stained with 1:200 Alexa fluor 700-β1-integrin (Biolegend), 1:200 APC-Cy7-α6-integrin (Biolegend), and 1:300 APC-CD11b, APC-CD31 and APC-CD45 (Biolegend) in staining buffer for 30 minutes on ice and then washed twice with DPBS before cell sorting. Cancer cells were sorted as CD11b, CD31, CD45 (-), β1-integrin (high), and α6-integrin (high).
CUT&RUN was conducted using the CUTANA™ ChIC/CUT&RUN Kit (Epicypher) for FACS-isolated epidermal keratinocytes or SCC cells. Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, NEB) and NEBNext Multiplex Oligos (NEB) for Illumina following the manufacturer’s instructions. PCR-amplified libraries were purified using 1X ratio of Agencourt AMPure-XP Beads (Beckman) and eluted in 15μl TE buffer.

value: skin cancer

value: Epidermal  SCC cells


title: DSS Proximal, replicate 1, RNA_seq

description: Library name: DP1


title: SCC-Eed-1

description: Library name: SCC-Eed-B1


title: Healthy control, replicate 2, RNA_seq

description: Library name: HC26


title: DSS Distal, replicate 5, RNA_seq

description: Library name: DD5


title: DSS Distal, replicate 4, RNA_seq

description: Library name: DD4


title: Hippocampus, control, P21, rep1

description: Library name: control H01

data_processing:
BCL (base call) binaries were converted to FASTQ using the illumina package bcl2fastq. Removal of adapters and low-quality reads was performed using fastp (version 0.21.0). Reads after trimming were used for mapping to the mm10 reference genome and for read counting in the STAR (version 2.5.3a)-RSEM (version 1.3.3) pipeline.
Assembly: mm10
Supplementary files format and content: text file includes raw counts for each Sample

value: Hippocampus

value: control


title: SCC3

description: Library name: SCCc-Me3


title: DSS Distal, replicate 2, RNA_seq

description: Library name: DD2


title: DSS Distal, replicate 3, RNA_seq

description: Library name: DD3


title: SCC-GFP-1

description: Library name: SCC-GFP-B2


title: SCC2

description: Library name: SCCb-Me3


title: ATAC_FOP3

description: Library name: ATAC_FOP3


title: patient with HCM,Peripheral blood,sample8

value: Whole blood

value: Female

value: hypertrophic cardiomyopathy (HCM)

value: 1 :Hypertension low potassium

value: 2 :Image of left ventricular lateral wall trabecular muscle increased, a small amount of pericardial effusion

value: 3 :Scoliosis

value: 4 :Left atrial enlargement, mitral regurgitation

value: 5 :ECG showed left ventricular high voltage, some lead ST-T abnormalities


title: patient with HCM,Peripheral blood,sample12

value: Male

value: obstructive hypertrophic cardiomyopathy


title: DSS Distal, replicate 1, RNA_seq

description: Library name: DD1

value: colon


title: patient with HCM,Peripheral blood,sample5

value: 1 :interventricular septum thickening, left ventricular outflow tract faster

value: 2 :Large left atrium

value: 3 :ST-T changes

value: 4 :Myocardial amyloidosis

value: 5 :Hyperlipidemia


title: SCC1

description: Library name: SCCa-Me3

value: skin cancer

value: Epidermal  SCC cells


title: arcZpmut, rep3

city: Jena

first: Marcel

last: Sprenger

address: Winzerlaer Straße 2

department: Institute of Microbiology

country: Germany

institute: Friedrich Schiller University

description:
Library name: arcZpmut-3
column name arcZpmut, rep3

data_processing:
CLC Genomics Workbench v22.0.2
using default parameters for RNA sequencing
Assembly: NCBI accession CP015137.1
Supplementary files format and content: Expression Browser_only arcZ variants.xlsx
Supplementary files format and content: xlsx files include total counts, TPM, CPM and RPKM values

organism: Dickeya solani

growth_protocol: D. solani was grown overnight in LB. The following day bacteria were diluted in fresh media and grown to OD 0.5. RNA samples were collected and transcription was stopped by adding 0.5 volumes of ice-cold methanol.

extract_protocol:
Total RNA was isolated by hot phenol extraction. Prepared RNA was DNAse digested and cleaned up using standard nucleic acid precipitation procedures. Depletion of ribosomal RNA was performed using biotinylated oligo probes for ribosomal RNA (PMID: 32317317). Integrity of the prepared RNA was tested using a Bioanalyzer.
cDNA libraries were prepared using the NEBNext UltraExpress RNA Library Prep Kit for Illumina (NEB, E3330L) according to the manufacturer's instructions. Library quality was assessed on an Agilent 2100 Bioanalyzer and pooled libraries were sequenced on a NextSeq 1000 system with 100 nt single-read mode.

value: arcZpmut

tag: time

value: 0 min


title: SCC-IgG

description: Library name: SCC-IgG

tag: cell type


title: ATAC_WT2

description: Library name: ATAC_WT2

value: mouse embryonic fibroblasts

tag: genotype

value: Acvr1+/+ (wild-type)


title: IFE-3

description: Library name: IFE-Ctrl-3-Me3

value: Skin epidermis

value: Epidermal cells

value: wile-type


title: arcZpmut, rep2

description:
Library name: arcZpmut-2
column name arcZpmut, rep2


title: IFE-1

description: Library name: IFE-Ctrl-1-Me3


title: IFE-2

description: Library name: IFE-Ctrl-2-Me3


title: Ctrl Proximal, replicate 4, RNA_seq

description: Library name: CP4


title: SCC-GFP-2

description: Library name: SCC-GFP-B3


title: Ctrl Proximal, replicate 5, RNA_seq

description: Library name: CP5


title: IgG

description: Library name: IFE-IgG


title: arcZpmut, rep1

description:
Library name: arcZpmut-1
column name arcZpmut, rep1


title: Ctrl Proximal, replicate 3, RNA_seq

description: Library name: CP3


title: MCD, scRNAseq

city: Guangzhou

first: Huizhen

last: Lin

address: Shatai Nan Road

institute: Southern medical university

description: Library name: J1904184

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using in Cell Ranger software 10X.
Assembly: Assembly: mm10
Supplementary files format and content: Tar archives include tab-separated values files and matrix files (barcodes.tsv, features.tsv/genes.tsv, matrix.mtx).

extract_protocol:
Mouse liver tissue was digested, passed through a 70 mm cell strainer. The cells were resuspended for density gradient centrifugation with 30% Percoll and 70% Percoll. Cells were incubated with CD45 antibody and 7-AAD at 4°C for 30 minutes, washed with PBS and sorted into single CD45+ cells using a flow cytometer.
Libraries were constructed for 3’ gene expression by fragmentation, end repair, adapter ligation, and indexing. Sequencing was performed on the Illumina Novaseq 6000 platform, achieving a depth of 39,000 reads per cell..

value: liver

value: hepatic CD45+ cells

tag: treatment

value: MCD diet


title: RNA_FOP3

description: Library name: RNA_FOP3

value: Acvr1R206H/+ (FOP mutant)


title: arcZ5, rep3

description:
Library name: arcZ5-3
column name arcZ5, rep3


title: Ctrl Proximal, replicate 2, RNA_seq

description: Library name: CP2

value: colon


title: ND, scRNAseq

description: Library name: J1904183

value: Normal diet


title: Cre-pos-OSR BCR

city: Saint Louis

first: Gwendalyn

middle: J

last: Randolph

state: Missouri

address: 660 South Euclid Ave

department: Immunolgoy

institute: Washington University in St. Louis

description: 10x Genomics

data_processing:
Illumina base call (BCL) files converted to FASTQ using "cellranger mkfastq"
Expression data processed with "cellranger count"
Assembly: mm10-2020-A
Supplementary files format and content: Processed Seurat RDS object
Library strategy: BCR-seq

source_name: omentum sheet region

extract_protocol:
Whole mesenteries and omenta from eight lipoatrophic AdiponectinCre/+ RosaDTAfl/+ female mice that received fat transplant surgery referred to as distal adipocyte receiving lipoatrophic mice (DARL) and their littermates that have standard fat depots that received sham surgery referred to as peritoneal adipocyte-replete control mice post-sham surgery (PARC) mice 8 weeks post-surgery were pinned on Sylgard dishes and kept hydrated in PBS. The adipose region in PARC mice and the corresponding area in DARL mice were carefully separated from the membranous sheet region for each omentum and mesentery using a scalpel and placed in RPMI with 5% FBS on ice. Each sheet or adipose region collected from each mouse was minced and digested separately using 1 mg/mL collagenase IV,  0.1 mg/mL DNAse, and 0.5% BSA for 30 minutes on a shaker. The samples were centrifuged and resuspended for downstream processing. Following digestion of the omentum and mesentery from PARC and DARL mice, the samples were washed and filtered with 100 m filters and stained for CD45+, DAPI, and TER-119. Samples were kept on ice until sorted on the FACSAria II with a 100-m nozzle (Becton Dickinson). Cells stained with DAPI were gated out during cell sorting to remove dead cells. Similarly, cells stained positive for TER-119 were excluded to remove red blood cells from our cell quantifications to increase the collection of desired cells. Approximately equal quantities of CD45+ and CD45- cells were submitted for 10X Genomics single-cell RNA sequencing via the McDonald Genome Institute Core.
10X Genomics Chromium Single Cell 5' Library and Gel Bead Kit

value: omentum sheet region

value: CD45+/CD45- cells

value: Adiponectin Cre+/DTA

value: fat pad transplant


title: Cre-pos-OFR BCR

description: 10x Genomics

source_name: omentum fat region

value: omentum fat region


title: arcZ5, rep2

description:
Library name: arcZ5-2
column name arcZ5, rep2

value: 0 min


title: Ctrl Proximal, replicate 1, RNA_seq

description: Library name: CP1


title: Cre-pos-MFR BCR

description: 10x Genomics

source_name: mesentery fat region

value: mesentery fat region


title: arcZ5, rep1

description:
Library name: arcZ5-1
column name arcZ5, rep1


title: Cre-pos-MSR BCR

description: 10x Genomics

source_name: mesentery sheet region

value: mesentery sheet region


title: Ctrl Distal, replicate 5, RNA_seq

description: Library name: CD5


title: Cre-neg-OSR BCR

description: 10x Genomics

value: Adiponectin Cre-/DTA

value: sham surgery


title: arcZ4, rep3

description:
Library name: arcZ4-3
column name arcZ4, rep3


title: Cre-neg-OFR BCR

description: 10x Genomics


title: Ctrl Distal, replicate 4, RNA_seq

description: Library name: CD4


title: Cre-neg-MSR BCR

description: 10x Genomics


title: arcZ4, rep2

description:
Library name: arcZ4-2
column name arcZ4, rep2


title: Cre-neg-MFR BCR

description: 10x Genomics


title: Cre-pos-OSR TCR

description: 10x Genomics

data_processing:
Illumina base call (BCL) files converted to FASTQ using "cellranger mkfastq"
Expression data processed with "cellranger count"
Assembly: mm10-2020-A
Supplementary files format and content: Processed Seurat RDS object
Library strategy: TCR-Seq


title: Ctrl Distal, replicate 3, RNA_seq

description: Library name: CD3


title: Day7 Proximal, replicate 2, RNA_seq

description: Library name: D7_CP2


title: arcZ4, rep1

description:
Library name: arcZ4-1
column name arcZ4, rep1


title: Cre-pos-OFR TCR

description: 10x Genomics


title: Cre-pos-MFR TCR

description: 10x Genomics


title: arcZ3, rep3

description:
Library name: arcZ3-3
column name arcZ3, rep3


title: Cre-neg-OSR TCR

description: 10x Genomics


title: arcZ3, rep2

description:
Library name: arcZ3-2
column name arcZ3, rep2


title: Cre-neg-MSR TCR

description: 10x Genomics


title: Cre-neg-OFR TCR

description: 10x Genomics


title: arcZ3, rep1

description:
Library name: arcZ3-1
column name arcZ3, rep1


title: Cre-neg-MFR TCR

description: 10x Genomics


title: Newborn Proximal, replicate 1, RNA_seq

description: Library name: NP1

data_processing:
Raw sequencing reads were assessed for quality and adapter contamination prior to alignment.
Clean reads were aligned to the mouse reference genome (mm10) using Bowtie2.
Reads with low mapping quality, mitochondrial reads, and PCR duplicates were removed before downstream analysis. Accessible chromatin regions were identified using MACS2 peak calling.
Peak annotations and downstream analyses were performed using standard bioinformatic workflows. Genome-wide accessibility tracks were generated in bigWig format for visualization in IGV.
Assembly: All ATAC-seq sequencing reads were aligned to the official mouse reference genome assembly. The Mus musculus GRCm38 (mm10) genome build was used as the standard reference for genome mapping and subsequent bioinformatics analysis (default standard for mouse intestinal epigenetic research).
Supplementary files format and content: Processed data files include BED files containing ATAC-seq peak coordinates, bigWig files containing normalized chromatin accessibility signal tracks, and tab-delimited text files containing peak annotations and differential accessibility results. BED files report genomic coordinates of accessible chromatin regions identified by MACS2, while bigWig files provide genome-wide accessibility profiles for visualization. Differential accessibility files include genomic coordinates, fold changes, statistical significance values, and associated gene annotations.

source_name: colonic epithelial cells

extract_protocol:
Colonic epithelial cells were isolated from mouse tissues and processed immediately for ATAC-seq library preparation. Cells were washed with ice-cold PBS and lysed in a detergent-containing lysis buffer to release intact nuclei. Nuclei were collected by centrifugation, washed, and resuspended in transposition reaction buffer for subsequent tagmentation.
ATAC-seq libraries were prepared using the Novoprotein ATAC Library Prep Kit (Novoprotein, China) according to the manufacturer's instructions. Briefly, purified nuclei were incubated with Tn5 transposase at 37°C for 30 min to simultaneously fragment accessible chromatin and insert sequencing adapters. Following transposition, DNA was purified using magnetic beads and amplified by PCR with indexed primers. Amplified libraries were purified, quantified using Qubit fluorometry, and assessed for fragment size distribution using an Agilent Bioanalyzer. Libraries were sequenced on an Illumina platform with paired-end 150-bp reads (PE150).

value: colonic epithelial cells


title: arcZ2, rep3

description:
Library name: arcZ2-3
column name arcZ2, rep3


title: Cre-pos-OFR

description: 10x Genomics

data_processing:
Illumina base call (BCL) files converted to FASTQ using "cellranger mkfastq"
Expression data processed with "cellranger count"
Assembly: mm10-2020-A
Supplementary files format and content: Processed Seurat RDS object


title: Newborn Distal, replicate 2, RNA_seq

description: Library name: ND2


title: arcZ2, rep2

description:
Library name: arcZ2-2
column name arcZ2, rep2