title: cKO_no SFN3

description:
Library name: 146-2
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.

value: cerebral cortex


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_PBR1_R2

status: Public on Jun 16 2026

type: SRA

city: Boston

first: Nilay

last: Sethi

state: Massachusetts

address: 450 Brookline Avenue, D742

department: MCO

country: USA

institute: Dana-Farber cancer institute

description:
Library name: cutrun2_dT29_PBR1_R2
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target PBRM1/PBR1; R condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_PBR1_R2_1.fq.gz and cutrun2/dT29_PBR1_R2_2.fq.gz.

library_source: genomic

data_processing:
Sequencing reads were demultiplexed and delivered as compressed FASTQ files.
Read quality was assessed and adapter/low-quality sequence was removed as needed.
Human ATAC-seq, CUT&RUN, and RNA-seq reads were aligned to the hg38 reference genome.
Assay-specific downstream analyses were performed to generate accessibility, occupancy, peak, and expression outputs.
Assembly: hg38
Supplementary files format and content: Tar.gz archive containing processed data files for this study, including per-sample processed outputs generated from ATAC-seq, CUT&RUN, and RNA-seq datasets.

molecule: genomic DNA

organism: Homo sapiens

source_name: colon

growth_protocol: HT29-dTAG and LS180 human colon cancer cells were maintained under standard cell-culture conditions at 37 C in a humidified incubator with 5% CO2.

extract_protocol:
For ATAC-seq, nuclei were prepared and transposed using standard assay workflows. For CUT&RUN, chromatin-protein complexes were captured and digested using standard CUT&RUN procedures. For RNA-seq, total RNA was isolated using standard RNA extraction methods.
Sequencing libraries were prepared using standard Illumina-compatible ATAC-seq, CUT&RUN, and RNA-seq library construction workflows.

treatment_protocol: For the main time-course datasets, cells were treated with DMSO or SOX9-degradation/recovery conditions and harvested at the indicated time points (DMSO, D2, D4, D5, D7, D10, and D13). Additional samples include ARID1A/ARID1B perturbation and SOX9-variant conditions as noted in the sample descriptions.

tag: tissue

value: colon

tag: cell line

tag: cell type

value: epithelial cell

tag: genotype

value: PBRM1 perturbation

tag: treatment

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; R condition/time point; CUT&RUN target PBRM1/PBR1

tag: batch


title: cKO_no SFN2

city: Baltimore

first: Akira

last: Sawa

state: Maryland

address: 600 N Wolfe St Meyer 3-166

institute: Johns Hopkins University

description:
Library name: Astro7
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.

library_source: transcriptomic

data_processing:
FastQC was used to check the quality of reads. Reads were aligned to the mouse genome (mm10) using STAR with the following optional parameters: --runThreadN 8 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts. Count from ReadsPerGene table generated from STAR was used for further analysis
Assembly: mm10
Supplementary files format and content: csv file includes raw count of each sample

molecule: total RNA

organism: Mus musculus

source_name: cerebral cortex

extract_protocol:
RNA was extracted from isolated astrocytes by using the picopure RNA isolation kit (Applied Biosystems).
Samples were checked for quality/quantity on Fragment Analyzer and Qubit prior to library prep (RQN > 7; 100-400 ng per sample). NEBNext Poly(A) Magnetic Isolation Module (NEB #E7490) and NEBNext Ultra II RNA Library Prep Kit for Illumina (Cat# E7775) were used to generate libraries.Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.

treatment_protocol: Cortical astrocytes were acutely isolated from adult cortices by MACS cell separation. Briefly, cortical tissue samples were obtained from adult mice following saline perfusion and cortical dissection, homogenized using a papain dissociation kit (Miltenyi Biotec #130-107-677), incubated with Fc blocking antibody and magnetic anti-ACSA-2 microbeads (Miltenyi Biotec #130-097-679), bound to MACS LS columns (Miltenyi Biotec #130-042-201) placed on a magnetic stand, washed 3 times with 0.5% BSA buffer to remove unbound cells, and eluted for downstream application.

tag: Sex

value: male

tag: age

value: cKO

tag: diet

value: no SFN

tag: celltype

value: astrocyte


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_IgG_R1

description:
Library name: cutrun2_dT29_IgG_R1
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target IgG control; R condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_IgG_R1_1.fq.gz and cutrun2/dT29_IgG_R1_2.fq.gz.

value: IgG control

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; R condition/time point; CUT&RUN target IgG control


title: cKO_SFN1

description:
Library name: 143-7
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.

value: SFN


title: cKO_no SFN1

description:
Library name: 141-1
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_IgG_DM2

description:
Library name: cutrun2_dT29_IgG_DM2
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target IgG control; DM/DMSO condition; source directory cutrun2; paired FASTQ files cutrun2/dT29_IgG_DM2_1.fq.gz and cutrun2/dT29_IgG_DM2_2.fq.gz.

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; DM/DMSO condition; CUT&RUN target IgG control


title: C2C12 n=3, mouse cells transfected with miR-339 mimic

city: Stockholm

first: Nicolas

last: Pillon

address: Solnavägen 9

country: Sweden

institute: Karolinska Institutet

description: Library name: P29458_1018

data_processing:
Quality and adapter trimming of reads was performed using Cutadapt (v3.5). Sample quality was assessed using FastQC (v0.11.8) and MultiQC (v1.14). Reads were aligned to the Ensembl GRCh38/GRCm38 reference genome using STAR (v2.7.9d). Counts for each gene were obtained using featureCounts (v1.5.1).
Assembly: GRCh38/GRCm38
Supplementary files format and content: CSV file, raw counts following featureCounts
Supplementary files format and content: CSV file, raw counts following featureCounts

source_name: skeletal muscle

growth_protocol: Mouse C2C12 muscle cells were obtained from the American Type Culture Collection (ATCC® CRL-1772™). Primary cells were isolated from vastus lateralis skeletal muscle biopsies derived from six healthy individuals (two females, four males, 35±17 years old, BMI 22.6±1.9 kg/m2). The ethical committee at Karolinska Institutet approved the protocols. Mouse and human cells were cultured and differentiated as described (Abdelmoez et al, 2020). Differentiation was monitored under the microscope and the absence of mycoplasma contamination was routinely confirmed by PCR.

extract_protocol:
On the fifth day of differentiation, cells were harvested for gene expression analysis using QIAzol Lysis Reagent.
Libraries were generated using TruSeq Stranded Total RNA (Illumina) following manufacturer's instructions.

treatment_protocol: Muscle cells were transfected on the first and third day of differentiation, with either miR-339-5p mirVana® miRNA mimic (Thermo Fisher Scientific, MC12347) or negative Control #1 mirVana™ miRNA mimic (Thermo Fisher Scientific, 4464059). Transfections were performed using Lipofectamine RNAiMAX as transfection reagent. In primary human skeletal muscle cells, transfection was performed with 25 nM miRNA mimics for 5 hours. For C2C12, miRNA mimics were used at a final concentration of 200 nM for 24h.

value: skeletal muscle

value: skeletal myotube

value: miR-339-5p overexpression


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_IgG_DM1

description:
Library name: cutrun2_dT29_IgG_DM1
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target IgG control; DM/DMSO condition; source directory cutrun2; paired FASTQ files cutrun2/dT29_IgG_DM1_1.fq.gz and cutrun2/dT29_IgG_DM1_2.fq.gz.


title: C2C12 n=3, mouse cells transfected with negative control miRNA mimic

description: Library name: P29458_1017

value: control


title: C2C12 n=2, mouse cells transfected with miR-339 mimic

description: Library name: P29458_1016


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_BRD9_R2

description:
Library name: cutrun2_dT29_BRD9_R2
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target BRD9; R condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_BRD9_R2_1.fq.gz and cutrun2/dT29_BRD9_R2_2.fq.gz.

value: BRD9 perturbation

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; R condition/time point; CUT&RUN target BRD9


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_BRD9_DM2

description:
Library name: cutrun2_dT29_BRD9_DM2
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target BRD9; DM/DMSO condition; source directory cutrun2; paired FASTQ files cutrun2/dT29_BRD9_DM2_1.fq.gz and cutrun2/dT29_BRD9_DM2_2.fq.gz.

value: colon

value: epithelial cell

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; DM/DMSO condition; CUT&RUN target BRD9


title: C2C12 n=1, mouse cells transfected with miR-339 mimic

description: Library name: P29458_1014


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_BRD9_DM1

description:
Library name: cutrun2_dT29_BRD9_DM1
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target BRD9; DM/DMSO condition; source directory cutrun2; paired FASTQ files cutrun2/dT29_BRD9_DM1_1.fq.gz and cutrun2/dT29_BRD9_DM1_2.fq.gz.


title: TCD4eff, miceEOMES-TKO, IgG-treated#3

city: Toulouse

first: Anne

middle: S

last: Dejean

state: Midi-Pyrenees

address: CHU Purpan – BP 3028

country: France

institute: Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)

description: Library name: S673-TCD4eff

data_processing:
Raw sequencing reads were processed using the nf-core RNAseq pipeline v.3.9 developed using Nextflow. Briefly, this pipeline trims adapters and removes low-quality sequences using Cutadapt v.3.4 wrapped with Trimgalore v.0.6.7. Then, STAR v.2.7.10a aligns trimmed reads to the Mus musculus GRCm39 genome assembly and the annotation from Ensembl release 107.
Finally, Salmon v.1.5.2 quantifies reads with parameter --libType=ISR.
Assembly: Mus musculus GRCm39 genome assembly
Supplementary files format and content: raw.count.tsv:data table containing rawcount with tabulation as separator

source_name: spleen

extract_protocol:
total RNA was extracted by using the RNeasy Micro Kit (Qiagen) and its quality was assessed on the Agilent TapeStation system.
High-quality RNA was used to prepare libraries starting from 11 ng of purified RNA and the “Ribo-Zero™ Plus and rRNA Depletion” Kit (Illumina) following the manufacturer’s instructions.

value: spleen

value: LT CD4eff (Thy1neg)

value: Eomes-TKO

value: IgG


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_ARD1_T2

description:
Library name: cutrun2_dT29_ARD1_T2
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target ARID1A/ARD1; T condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_ARD1_T2_1.fq.gz and cutrun2/dT29_ARD1_T2_2.fq.gz.

value: ARID1A perturbation

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; T condition/time point; CUT&RUN target ARID1A/ARD1


title: TCD4eff, miceEOMES-TKO, a41BB-treated#2

description: Library name: S663-TCD4eff


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_ARD1_T1

description:
Library name: cutrun2_dT29_ARD1_T1
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target ARID1A/ARD1; T condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_ARD1_T1_1.fq.gz and cutrun2/dT29_ARD1_T1_2.fq.gz.


title: TCD4eff, miceEOMES-TKO, IgG-treated#2

description: Library name: S656-TCD4eff


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_ARD1_R2

description:
Library name: cutrun2_dT29_ARD1_R2
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target ARID1A/ARD1; R condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_ARD1_R2_1.fq.gz and cutrun2/dT29_ARD1_R2_2.fq.gz.

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; R condition/time point; CUT&RUN target ARID1A/ARD1


title: TCD4eff, miceEOMES-TKO, IgG-treated#1

description: Library name: S634-TCD4eff


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_ARD1_R1

description:
Library name: cutrun2_dT29_ARD1_R1
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target ARID1A/ARD1; R condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_ARD1_R1_1.fq.gz and cutrun2/dT29_ARD1_R1_2.fq.gz.


title: TCD4eff, miceEOMES-TKO, a41BB-treated#1

description: Library name: S633-TCD4eff


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_ARD1_DM2

description:
Library name: cutrun2_dT29_ARD1_DM2
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target ARID1A/ARD1; DM/DMSO condition; source directory cutrun2; paired FASTQ files cutrun2/dT29_ARD1_DM2_1.fq.gz and cutrun2/dT29_ARD1_DM2_2.fq.gz.

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; DM/DMSO condition; CUT&RUN target ARID1A/ARD1


title: TCD4eff-Eomes-GFPpos, miceEOMESGFP, a41BB-treated#3

description: Library name: S59-TCD4eff-GFPpos

value: LT CD4eff (Thy1neg)-GFPpos

value: Eomes-GFP


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_ARD1_DM1

description:
Library name: cutrun2_dT29_ARD1_DM1
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target ARID1A/ARD1; DM/DMSO condition; source directory cutrun2; paired FASTQ files cutrun2/dT29_ARD1_DM1_1.fq.gz and cutrun2/dT29_ARD1_DM1_2.fq.gz.


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample DMSO_SOX9_2

description:
Library name: cutrun1_DMSO_SOX9_2
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SOX9; DMSO control; source directory cutrun1; paired FASTQ files cutrun1/DMSO_SOX9_2_1.fq.gz and cutrun1/DMSO_SOX9_2_2.fq.gz.

value: SOX9 degradation and recovery time course; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; DMSO control; CUT&RUN target SOX9


title: TCD4eff-Eomes-GFPneg, miceEOMESGFP, a41BB-treated#3

description: Library name: S59-TCD4eff-GFPneg

value: LT CD4eff (Thy1neg)-GFPneg


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample DMSO_SOX9_1

description:
Library name: cutrun1_DMSO_SOX9_1
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SOX9; DMSO control; source directory cutrun1; paired FASTQ files cutrun1/DMSO_SOX9_1_1.fq.gz and cutrun1/DMSO_SOX9_1_2.fq.gz.


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample DMSO_SMARCC1_1

description:
Library name: cutrun1_DMSO_SMARCC1_1
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SMARCC1/C1; DMSO control; source directory cutrun1; paired FASTQ files cutrun1/DMSO_SMARCC1_1_1.fq.gz and cutrun1/DMSO_SMARCC1_1_2.fq.gz.

value: SOX9 degradation and recovery time course; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; DMSO control; CUT&RUN target SMARCC1/C1


title: TCD4eff-Eomes-GFPneg, miceEOMESGFP, a41BB-treated#2

description: Library name: S47-TCD4eff-GFPneg


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample DMSO_SMARCC1_2

description:
Library name: cutrun1_DMSO_SMARCC1_2
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SMARCC1/C1; DMSO control; source directory cutrun1; paired FASTQ files cutrun1/DMSO_SMARCC1_2_1.fq.gz and cutrun1/DMSO_SMARCC1_2_2.fq.gz.


title: TCD4eff, miceEOMESGFP, IgG-treated#1

description: Library name: S43-TCD4eff


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample DMSO_IgG_2

description:
Library name: cutrun1_DMSO_IgG_2
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target IgG control; DMSO control; source directory cutrun1; paired FASTQ files cutrun1/DMSO_IgG_2_1.fq.gz and cutrun1/DMSO_IgG_2_2.fq.gz.

value: IgG control

value: SOX9 degradation and recovery time course; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; DMSO control; CUT&RUN target IgG control


title: TCD4eff-Eomes-GFPpos, miceEOMESGFP, a41BB-treated#1

description: Library name: S30-TCD4eff-GFPpos


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample DMSO_IgG_1

description:
Library name: cutrun1_DMSO_IgG_1
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target IgG control; DMSO control; source directory cutrun1; paired FASTQ files cutrun1/DMSO_IgG_1_1.fq.gz and cutrun1/DMSO_IgG_1_2.fq.gz.

value: colon

value: epithelial cell


title: TCD4eff-Eomes-GFPneg, miceEOMESGFP, a41BB-treated#1

description: Library name: S30-TCD4eff-GFPneg

value: spleen


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D7_SOX9_2

description:
Library name: cutrun1_D7_SOX9_2
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SOX9; day 7; source directory cutrun1; paired FASTQ files cutrun1/D7_SOX9_2_1.fq.gz and cutrun1/D7_SOX9_2_2.fq.gz.

value: SOX9 degradation and recovery time course; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 7; CUT&RUN target SOX9


title: ML (metronidazole liver)

city: Houston

first: Mengyu

last: Chang

state: TX

address: 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

description: Library name: SC557_2

library_source: transcriptomic single cell

data_processing:
Raw reads were processed with Cell Ranger 7.1.0 (cellranger multi) using the 10x Mouse Fixed RNA Profiling probe-set reference (v1.x). For quality control, outlier cells were identified on a per-sample basis using median absolute deviation (MAD) thresholds. Outlier cells were defined based on total counts or feature counts (>4 MADs), the percentage of counts in the top 20 genes (>5 MADs), or mitochondrial RNA fraction (>5 MADs or >10%). Doublets were identified using Scrublet and filtered out. After filtering, we used the Seurat v.5.3.0 for data normalization, dimensionality reduction and clustering. Differentially expressed genes were determined using a fast Wilcoxon rank-sum test (presto v.1.0.0).
Assembly: mm10 (GRCm38)
Supplementary files format and content: This file is an HDF5-formatted matrix generated by the 10x Genomics Cell Ranger pipeline. It contains the filtered gene–barcode count matrix for the sample after removing low-quality cells and features. The file includes gene annotations, cell barcodes, and the UMI count matrix used for downstream single-cell RNA-seq analyses.

source_name: liver

extract_protocol:
SPF mice were treated with either control water or metronidazole-containing water for three weeks. Mice were anesthetized via intraperitoneal injection of an anesthesia mixture at 3.75 μL/g body weight (final concentrations: ketamine, 112.5 mg/kg; xylazine, 22.5 mg/kg). Liver perfusion was performed via the inferior vena cava towards the portal vein to remove blood from hepatic tissue. Following perfusion, livers were excised and dissociated into single-cell suspensions using the Liver Dissociation Kit (Miltenyi, 130-105-807). The resulting cell suspensions were filtered through a 70 µm cell strainer and centrifuged at 300 × g for 10 minutes at 4 °C. To enrich immune cells, suspensions were incubated with CD45 MicroBeads (Miltenyi) and processed by magnetic-activated cell sorting (MACS) according to the manufacturer’s protocol. Cells were then labeled with Live/Dead Aqua and anti-CD45–APC antibody, followed by fixation (10x Genomics, 1000414). Fluorescence-activated cell sorting (FACS) was used to isolate Aqua⁻ CD45⁺ cells from each liver. For each treatment group, sorted cells from three individual mice were pooled to generate one representative sample for downstream single-cell RNA sequencing.
Single-cell gene expression libraries were prepared separately for each of the three samples using the Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples (10x Genomics; User Guide CG000527), following the manufacturer’s instructions. Briefly, fixed single-cell suspensions were incubated with the Gene Expression Probe Kit (PN-1000496) and hybridized at 42 °C for 16-24 h. After probe hybridization, samples were labeled with unique sample barcodes, pooled, and mixed with the single-cell master mix. The pooled suspension was then loaded onto the Chromium X instrument for GEM generation and barcoding. Libraries were constructed using the Single Cell Fixed RNA Hybridization & Library Kit (PN-1000415). Final libraries were quality-checked and sequenced on an Illumina NovaSeq 6000. Sequencing was performed with read lengths of R1 = 28 bp (cell barcode + UMI), i7 = 10 bp, i5 = 10 bp, R2 = 90 bp (target sequence), targeting ~50,000-100,000 reads per cell.

value: liver

value: immune cells from liver

value: WT

value: metronidazole


title: CL (control liver)

description: Library name: SC557_1

value: control


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D7_SMARCC1_2

description:
Library name: cutrun1_D7_SMARCC1_2
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SMARCC1/C1; day 7; source directory cutrun1; paired FASTQ files cutrun1/D7_SMARCC1_2_1.fq.gz and cutrun1/D7_SMARCC1_2_2.fq.gz.

value: SOX9 degradation and recovery time course; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 7; CUT&RUN target SMARCC1/C1


title: TCD4eff, miceEOMESGFP, IgG-treated#2

description: Library name: S58-TCD4eff

value: LT CD4eff (Thy1neg)

value: IgG


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D7_SMARCC1_1

description:
Library name: cutrun1_D7_SMARCC1_1
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SMARCC1/C1; day 7; source directory cutrun1; paired FASTQ files cutrun1/D7_SMARCC1_1_1.fq.gz and cutrun1/D7_SMARCC1_1_2.fq.gz.


title: KO4

city: Chongqing

first: Xiao

last: Wen

address: Medical College Road

department: Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)

country: China

institute: Chongqing Medical University

description: Library name: Sample9

data_processing:
DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

source_name: Liver

extract_protocol:
Total RNA was extracted using total RNA isolation reagent according to the manufacturer's instructions. RNA purity and quantification were identified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA), and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Transcriptome libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep kit according to the manufacturer's instructions.

value: Liver

value: High fat -high fructose diet (HFFD) for 4 months


title: Human histone-mark CUT&RUN multi-time-point sample D2_H3K27Ac_1

description:
Library name: histone_mark_cutrun_D2_H3K27Ac_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27Ac; day 2; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D2_H3K27Ac_1_1.fq.gz and histone_mark_cutrun/D2_H3K27Ac_1_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 2; CUT&RUN target H3K27Ac


title: Human histone-mark CUT&RUN multi-time-point sample D13_H3K9me3_2

description:
Library name: histone_mark_cutrun_D13_H3K9me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K9me3; day 13; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D13_H3K9me3_2_1.fq.gz and histone_mark_cutrun/D13_H3K9me3_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 13; CUT&RUN target H3K9me3


title: TCD4eff-Eomes-GFPpos, miceEOMESGFP, a41BB-treated#2

description: Library name: S47-TCD4eff-GFPpos

value: LT CD4eff (Thy1neg)-GFPpos

value: Eomes-GFP


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D4_SOX9_2

description:
Library name: cutrun1_D4_SOX9_2
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SOX9; day 4; source directory cutrun1; paired FASTQ files cutrun1/D4_SOX9_2_1.fq.gz and cutrun1/D4_SOX9_2_2.fq.gz.

value: colon

value: epithelial cell

value: SOX9 degradation and recovery time course; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 4; CUT&RUN target SOX9


title: KO3

description: Library name: Sample8


title: Human histone-mark CUT&RUN multi-time-point sample D13_H3K4me1_1

description:
Library name: histone_mark_cutrun_D13_H3K4me1_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me1; day 13; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D13_H3K4me1_1_1.fq.gz and histone_mark_cutrun/D13_H3K4me1_1_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 13; CUT&RUN target H3K4me1


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D4_SOX9_1

description:
Library name: cutrun1_D4_SOX9_1
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SOX9; day 4; source directory cutrun1; paired FASTQ files cutrun1/D4_SOX9_1_1.fq.gz and cutrun1/D4_SOX9_1_2.fq.gz.


title: GEX counts of multiplex sSL0225 containing tissue & timepoint(s) Cerebellum; P4

city: Klosterneuburg

first: Gaia

last: Novarino

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (ISTA)

description:
Library name: sSL0225_GEX
sSL0225_GEX_filtered_feature_bc_matrix.h5
sSL0225_GEX_QC_categories.csv
cb_p4_diet_seurat_RNA_assay.rds

data_processing:
Pre-processing was done per 10X lane (i.e., per multiplexing group of 4-6 samples). Peaks for the snATAC-seq modality were called for each run separately using MACS2 (v2.2.7.1) within Signac. A set of consensus peaks for the snATAC-seq analysis was created according to Signac. CMO demultiplexing information was taken from Cellranger output and added as metadata. Doublets were identified using scDblFinder6 (v1.14.0), separately for snRNA-seq and snATAC-seq modality. snRNA-seq parameters for the scDblFinder function were dims = 50, cluster = TRUE, knownUse = “discard”. snATAC-seq features were first aggregated (aggregateFeatures function, k = 500) and parameters for scDblFinder were dims = 50, aggegateFeatures = TRUE. Cells identified as doublets based on CMO data were included as known doublets (knownDoublets parameter). Quality control metrics such as the percentage of mitochondrial reads, nucleosome signal, and transcription start site (TSS) enrichment were calculated per run. After removing known and estimated doublets outlier thresholds for snRNA-seq read counts (nCount_RNA) or snATAC-seq read counts (nCount_ATAC) were derived using the isOutlier function from the scuttle package7 (v1.10.2) with parameters nmads = 3, type = “both”, log = TRUE. Nuclei falling outside these thresholds or with more than 5% of mitochondrial reads were removed. Complete datasets for each time point/tissue were created by integrating individual Seurat objects representing separate 10X lanes (i.e., multiplexing groups). snRNA-seq data were normalized using SCTransform8,9 from Seurat with parameter vst.flavor = “v2”. Integration of normalized snRNA-seq data was performed according to Seurat using the reciprocal PCA method with the following non-default parameters: SelectIntegrationFeatures(nfeatures = 2500), FindIntegrationAnchors(reduction = “rpca”), IntegrateData(dims = 1:50). Integration of snATAC-seq data was performed at the level of the LSI embedding using IntegrateEmbeddings(dims.to.integrate = 1:50) function with the integration anchors derived from snRNA-seq data. Identification of cell types was performed using the combination of both modalities, snRNA-seq and snATAC-seq. A PCA embedding was derived for the integrated snRNA-seq data, weighted nearest neighbor (WNN) graph was calculated using the FindMultimodalNeighbors function with the integrated LSI and integrated PCA reductions as input and dims_atac = 2:50, dims_rna = 1:50. The resulting WNN graph was used for UMAP visualization of the dataset and identification of clusters
Samples used for multi-omics analyses were de-multiplexed, and the raw sequencing data was converted to FASTQ format using bcl2fastq (v2.20.0.422). Joint processing of the gene expression and ATAC modalities was performed using the cellranger-arc software (v2.0.0). The mm10 reference genome was used for the alignment (refdata-cellranger-arc-mm10-2020-A-2.0.0, obtained from https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-mm10-2020-A-2.0.0.tar.gz). To capture CMO reads, the gene expression modality was separately processed using the cellranger count pipeline (v7.0.0 and v7.1.0), aligning it against the mm10 reference genome (refdata-gex-mm10-2020-A, obtained from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz). Each nucleus was assigned to the sample of origin as part of further demultiplexing, for which a Gaussian mixture model was fitted to the CMO count distributions. The probability that a given CMO read count was derived from background or positive signal was then inferred (as described in2).
Assembly: mm10
Supplementary files format and content: Cellranger output files (GEX): filtered feature matrix (h5 format); QC categories (csv)
Supplementary files format and content: Cellranger output files (ATAC): filtered feature matrix (h5 format); atac fragments (tsv & index); atac peak annotation (tsv & bed)
Supplementary files format and content: Downstream pipeline: integrated seurat object (RDS); pipeline input sample table (xlsx)

molecule: nuclear RNA

source_name: Cerebellum

extract_protocol:
Single nuclei were extracted using the 10X Genomics nuclei isolation kit (Chromium Nuclei Isolation Kit CG000505, Rev A). Samples were pooled after barcoding with cholesterol-modified oligos (CMOs) and a CMO Co-Anchor. Afterwards, single nuclei of pooled samples were encapsulated in Gel-Beads-in  emulsions (GEMs) on a 10X Chromium Controller using Chromium Next GEM Chip J Single Cell kit (PN-1000230), Chromium Next GEM Single Cell Multiome GEM Kit A (PN-1000232), Chromium Next GEM Single Cell Multiome Gel Bead Kit A (PN-1000231) as instructed by the manufacturer.
The library was prepared according to the 10X protocol using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, CG000338 Rev F. The hasthag oligo (HTO) libraries were prepared alongside cDNA amplification. Here, an ADT additive primer was added to the reaction. During cDNA cleanup, supernatant was saved to purify Hash-DNA. HTO libraries were generated using unique combinations of i5 and i7 indices.

value: Cerebellum

value: mixed

value: mixed samples (multiplex)


title: KO2

description: Library name: Sample7


title: KO1

description: Library name: Sample6


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D4_SMARCC1_2

description:
Library name: cutrun1_D4_SMARCC1_2
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SMARCC1/C1; day 4; source directory cutrun1; paired FASTQ files cutrun1/D4_SMARCC1_2_1.fq.gz and cutrun1/D4_SMARCC1_2_2.fq.gz.

value: SOX9 degradation and recovery time course; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 4; CUT&RUN target SMARCC1/C1


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D4_SMARCC1_1

description:
Library name: cutrun1_D4_SMARCC1_1
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SMARCC1/C1; day 4; source directory cutrun1; paired FASTQ files cutrun1/D4_SMARCC1_1_1.fq.gz and cutrun1/D4_SMARCC1_1_2.fq.gz.


title: FLOX5

description: Library name: Sample5


title: Human histone-mark CUT&RUN multi-time-point sample D10_H3K4me3_2

description:
Library name: histone_mark_cutrun_D10_H3K4me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K4me3; day 10; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/D10_H3K4me3_2_1.fq.gz and histone_mark_cutrun/D10_H3K4me3_2_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; day 10; CUT&RUN target H3K4me3


title: FLOX4

description: Library name: Sample4


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D4_IgG_2

description:
Library name: cutrun1_D4_IgG_2
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target IgG control; day 4; source directory cutrun1; paired FASTQ files cutrun1/D4_IgG_2_1.fq.gz and cutrun1/D4_IgG_2_2.fq.gz.

value: IgG control

value: SOX9 degradation and recovery time course; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 4; CUT&RUN target IgG control


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D4_IgG_1

description:
Library name: cutrun1_D4_IgG_1
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target IgG control; day 4; source directory cutrun1; paired FASTQ files cutrun1/D4_IgG_1_1.fq.gz and cutrun1/D4_IgG_1_2.fq.gz.


title: FLOX3

description: Library name: Sample3

value: Liver


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D2_SOX9_2

description:
Library name: cutrun1_D2_SOX9_2
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SOX9; day 2; source directory cutrun1; paired FASTQ files cutrun1/D2_SOX9_2_1.fq.gz and cutrun1/D2_SOX9_2_2.fq.gz.

value: SOX9 degradation and recovery time course; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 2; CUT&RUN target SOX9


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D7_SOX9_1

description:
Library name: cutrun1_D7_SOX9_1
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SOX9; day 7; source directory cutrun1; paired FASTQ files cutrun1/D7_SOX9_1_1.fq.gz and cutrun1/D7_SOX9_1_2.fq.gz.

value: SOX9 degradation and recovery time course; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 7; CUT&RUN target SOX9


title: FLOX2

description: Library name: Sample2

value: High fat -high fructose diet (HFFD) for 4 months


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D2_SOX9_1

description:
Library name: cutrun1_D2_SOX9_1
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SOX9; day 2; source directory cutrun1; paired FASTQ files cutrun1/D2_SOX9_1_1.fq.gz and cutrun1/D2_SOX9_1_2.fq.gz.


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D2_SMARCC1_2

description:
Library name: cutrun1_D2_SMARCC1_2
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SMARCC1/C1; day 2; source directory cutrun1; paired FASTQ files cutrun1/D2_SMARCC1_2_1.fq.gz and cutrun1/D2_SMARCC1_2_2.fq.gz.

value: SOX9 degradation and recovery time course; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 2; CUT&RUN target SMARCC1/C1


title: FLOX1

description: Library name: Sample1


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D2_SMARCC1_1

description:
Library name: cutrun1_D2_SMARCC1_1
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SMARCC1/C1; day 2; source directory cutrun1; paired FASTQ files cutrun1/D2_SMARCC1_1_1.fq.gz and cutrun1/D2_SMARCC1_1_2.fq.gz.


title: C26shCA_3_eWAT

city: Munich

first: Mauricio

last: Berriel Diaz

state: Bavaria

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Cancer

country: Germany

institute: Helmholtz Center Munich

description: Library name: Sample 28

data_processing:
Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and our wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Assembly: mm10
Supplementary files format and content: a single tab-delimited text file include read counts  for each Sample

source_name: eWAT

extract_protocol:
Total RNA was extracted from frozen organs by performing a tissue lysis in TRIzol™ (Life Technologies, #15596018) with Qiagen's TissueLyser II (Qiagen, # 85300).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: eWAT

value: C26 tumor carrying control shRNA


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_SMB1_T1

description:
Library name: cutrun2_dT29_SMB1_T1
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target SMARCB1/SMB1; T condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_SMB1_T1_1.fq.gz and cutrun2/dT29_SMB1_T1_2.fq.gz.

value: colon

value: epithelial cell

value: SMARCB1 perturbation

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; T condition/time point; CUT&RUN target SMARCB1/SMB1


title: C26shCA_2_eWAT

description: Library name: Sample 27


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D13_SOX9_2

description:
Library name: cutrun1_D13_SOX9_2
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SOX9; day 13; source directory cutrun1; paired FASTQ files cutrun1/D13_SOX9_2_1.fq.gz and cutrun1/D13_SOX9_2_2.fq.gz.

value: SOX9 degradation and recovery time course; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 13; CUT&RUN target SOX9


title: KO5

description: Library name: Sample10


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D13_SOX9_1

description:
Library name: cutrun1_D13_SOX9_1
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SOX9; day 13; source directory cutrun1; paired FASTQ files cutrun1/D13_SOX9_1_1.fq.gz and cutrun1/D13_SOX9_1_2.fq.gz.


title: C26shAA_3_eWAT

description: Library name: Sample 25

value: ADAMTSL4 knockdown in C26 tumor


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D13_SMARCC1_2

description:
Library name: cutrun1_D13_SMARCC1_2
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SMARCC1/C1; day 13; source directory cutrun1; paired FASTQ files cutrun1/D13_SMARCC1_2_1.fq.gz and cutrun1/D13_SMARCC1_2_2.fq.gz.

value: SOX9 degradation and recovery time course; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 13; CUT&RUN target SMARCC1/C1


title: C26shCA_1_eWAT

description: Library name: Sample 26


title: C26shAA_1_eWAT

description: Library name: Sample 23


title: C26shAA_2_eWAT

description: Library name: Sample 24


title: Con_no SFN2

description:
Library name: 143-3
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.

value: cerebral cortex

value: male

value: Con

value: no SFN

value: astrocyte


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D13_SMARCC1_1

description:
Library name: cutrun1_D13_SMARCC1_1
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SMARCC1/C1; day 13; source directory cutrun1; paired FASTQ files cutrun1/D13_SMARCC1_1_1.fq.gz and cutrun1/D13_SMARCC1_1_2.fq.gz.


title: PBSG_2_GC Muscle

description: Library name: Sample 22

source_name: GC Muscle

value: GC Muscle

value: PBSG

value: Non-tumor bearing mice injected with PBS


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D13_IgG_2

description:
Library name: cutrun1_D13_IgG_2
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target IgG control; day 13; source directory cutrun1; paired FASTQ files cutrun1/D13_IgG_2_1.fq.gz and cutrun1/D13_IgG_2_2.fq.gz.

value: IgG control

value: SOX9 degradation and recovery time course; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 13; CUT&RUN target IgG control


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D10_SOX9_2

description:
Library name: cutrun1_D10_SOX9_2
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SOX9; day 10; source directory cutrun1; paired FASTQ files cutrun1/D10_SOX9_2_1.fq.gz and cutrun1/D10_SOX9_2_2.fq.gz.

value: colon

value: SOX9 degradation and recovery time course; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 10; CUT&RUN target SOX9


title: PBSG_1_GC Muscle

description: Library name: Sample 21


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_PBR1_R1

description:
Library name: cutrun2_dT29_PBR1_R1
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target PBRM1/PBR1; R condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_PBR1_R1_1.fq.gz and cutrun2/dT29_PBR1_R1_2.fq.gz.

value: epithelial cell

value: PBRM1 perturbation

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; R condition/time point; CUT&RUN target PBRM1/PBR1


title: Con_SFN1

description:
Library name: Astro2
Paired-End Sequencing was performed using Illumina's NovaSeq6000 S1 200 cycle kit.

value: SFN


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_IgG_T2

description:
Library name: cutrun2_dT29_IgG_T2
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target IgG control; T condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_IgG_T2_1.fq.gz and cutrun2/dT29_IgG_T2_2.fq.gz.

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; T condition/time point; CUT&RUN target IgG control


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_PBR1_DM1

description:
Library name: cutrun2_dT29_PBR1_DM1
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target PBRM1/PBR1; DM/DMSO condition; source directory cutrun2; paired FASTQ files cutrun2/dT29_PBR1_DM1_1.fq.gz and cutrun2/dT29_PBR1_DM1_2.fq.gz.

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; DM/DMSO condition; CUT&RUN target PBRM1/PBR1


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D10_SOX9_1

description:
Library name: cutrun1_D10_SOX9_1
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SOX9; day 10; source directory cutrun1; paired FASTQ files cutrun1/D10_SOX9_1_1.fq.gz and cutrun1/D10_SOX9_1_2.fq.gz.


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D10_SMARCC1_1

description:
Library name: cutrun1_D10_SMARCC1_1
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SMARCC1/C1; day 10; source directory cutrun1; paired FASTQ files cutrun1/D10_SMARCC1_1_1.fq.gz and cutrun1/D10_SMARCC1_1_2.fq.gz.

value: SOX9 degradation and recovery time course; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 10; CUT&RUN target SMARCC1/C1


title: C26shCG_4_GC Muscle

description: Library name: Sample 19

value: C26 tumor carrying control shRNA


title: Human CUT&RUN full time-course SOX9 degradation-recovery sample D10_SMARCC1_2

description:
Library name: cutrun1_D10_SMARCC1_2
CUT&RUN sample from the SOX9 degradation and recovery time-course experiment, full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; target SMARCC1/C1; day 10; source directory cutrun1; paired FASTQ files cutrun1/D10_SMARCC1_2_1.fq.gz and cutrun1/D10_SMARCC1_2_2.fq.gz.


title: C26shCG_5_GC Muscle

description: Library name: Sample 20


title: C26shCG_3_GC Muscle

description: Library name: Sample 18


title: Human LS180 SOX9 variant ATAC-seq sample SOX9_FL_LS180_2

description:
Library name: atacseq4_SOX9_FL_LS180_2
ATAC-seq sample from the LS180 SOX9 variant chromatin accessibility dataset; full-length SOX9; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system; source directory atacseq4; paired FASTQ files atacseq4/SOX9_FL_LS180_2_1.fq.gz and atacseq4/SOX9_FL_LS180_2_2.fq.gz.

value: SOX9 full-length

value: ATAC-seq dataset profiling chromatin accessibility across SOX9 variants; full-length SOX9; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system


title: C26shCG_2_GC Muscle

description: Library name: Sample 17

value: GC Muscle


title: C26shCG_1_GC Muscle

description: Library name: Sample 16


title: Human LS180 SOX9 variant ATAC-seq sample SOX9_379_LS180_2

description:
Library name: atacseq4_SOX9_379_LS180_2
ATAC-seq sample from the LS180 SOX9 variant chromatin accessibility dataset; SOX9-379 variant; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system; source directory atacseq4; paired FASTQ files atacseq4/SOX9_379_LS180_2_1.fq.gz and atacseq4/SOX9_379_LS180_2_2.fq.gz.

value: ATAC-seq dataset profiling chromatin accessibility across SOX9 variants; SOX9-379 variant; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system


title: Human LS180 SOX9 variant ATAC-seq sample SOX9_FL_LS180_1

description:
Library name: atacseq4_SOX9_FL_LS180_1
ATAC-seq sample from the LS180 SOX9 variant chromatin accessibility dataset; full-length SOX9; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system; source directory atacseq4; paired FASTQ files atacseq4/SOX9_FL_LS180_1_1.fq.gz and atacseq4/SOX9_FL_LS180_1_2.fq.gz.


title: C26shAG_5_GC Muscle

description: Library name: Sample 15

value: ADAMTSL4 knockdown in C26 tumor


title: Human LS180 SOX9 variant ATAC-seq sample SOX9_379_LS180_1

description:
Library name: atacseq4_SOX9_379_LS180_1
ATAC-seq sample from the LS180 SOX9 variant chromatin accessibility dataset; SOX9-379 variant; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system; source directory atacseq4; paired FASTQ files atacseq4/SOX9_379_LS180_1_1.fq.gz and atacseq4/SOX9_379_LS180_1_2.fq.gz.


title: C26shAG_4_GC Muscle

description: Library name: Sample 14


title: Human LS180 SOX9 variant ATAC-seq sample SOX9_303_LS180_2

description:
Library name: atacseq4_SOX9_303_LS180_2
ATAC-seq sample from the LS180 SOX9 variant chromatin accessibility dataset; SOX9-303 variant; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system; source directory atacseq4; paired FASTQ files atacseq4/SOX9_303_LS180_2_1.fq.gz and atacseq4/SOX9_303_LS180_2_2.fq.gz.

value: ATAC-seq dataset profiling chromatin accessibility across SOX9 variants; SOX9-303 variant; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system


title: C26shAG_3_GC Muscle

description: Library name: Sample 13


title: Human LS180 SOX9 variant ATAC-seq sample SOX9_303_LS180_1

description:
Library name: atacseq4_SOX9_303_LS180_1
ATAC-seq sample from the LS180 SOX9 variant chromatin accessibility dataset; SOX9-303 variant; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system; source directory atacseq4; paired FASTQ files atacseq4/SOX9_303_LS180_1_1.fq.gz and atacseq4/SOX9_303_LS180_1_2.fq.gz.


title: C26shAG_2_GC Muscle

description: Library name: Sample 12


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_BRD9_T2

description:
Library name: cutrun2_dT29_BRD9_T2
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target BRD9; T condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_BRD9_T2_1.fq.gz and cutrun2/dT29_BRD9_T2_2.fq.gz.

value: BRD9 perturbation

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; T condition/time point; CUT&RUN target BRD9


title: C26shAG_1_GC Muscle

description: Library name: Sample 11


title: Human LS180 SOX9 variant ATAC-seq sample SOX9_228_LS180_2

description:
Library name: atacseq4_SOX9_228_LS180_2
ATAC-seq sample from the LS180 SOX9 variant chromatin accessibility dataset; SOX9-228 variant; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system; source directory atacseq4; paired FASTQ files atacseq4/SOX9_228_LS180_2_1.fq.gz and atacseq4/SOX9_228_LS180_2_2.fq.gz.

value: colon

value: ATAC-seq dataset profiling chromatin accessibility across SOX9 variants; SOX9-228 variant; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system


title: MC38CG_5_GC Muscle

description: Library name: Sample 10

value: GFP expressed in MC38 tumor


title: Human LS180 SOX9 variant ATAC-seq sample SOX9_228_LS180_1

description:
Library name: atacseq4_SOX9_228_LS180_1
ATAC-seq sample from the LS180 SOX9 variant chromatin accessibility dataset; SOX9-228 variant; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system; source directory atacseq4; paired FASTQ files atacseq4/SOX9_228_LS180_1_1.fq.gz and atacseq4/SOX9_228_LS180_1_2.fq.gz.

value: epithelial cell


title: Human LS180 SOX9 variant ATAC-seq sample GFP_pos_LS180_2

description:
Library name: atacseq4_GFP_pos_LS180_2
ATAC-seq sample from the LS180 SOX9 variant chromatin accessibility dataset; GFP-positive control; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system; source directory atacseq4; paired FASTQ files atacseq4/GFP_pos_LS180_2_1.fq.gz and atacseq4/GFP_pos_LS180_2_2.fq.gz.

value: GFP positive control

value: ATAC-seq dataset profiling chromatin accessibility across SOX9 variants; GFP-positive control; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_BRD9_T1

description:
Library name: cutrun2_dT29_BRD9_T1
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target BRD9; T condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_BRD9_T1_1.fq.gz and cutrun2/dT29_BRD9_T1_2.fq.gz.


title: MC38CG_4_GC Muscle

description: Library name: Sample 9


title: Human LS180 SOX9 variant ATAC-seq sample GFP_pos_LS180_1

description:
Library name: atacseq4_GFP_pos_LS180_1
ATAC-seq sample from the LS180 SOX9 variant chromatin accessibility dataset; GFP-positive control; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system; source directory atacseq4; paired FASTQ files atacseq4/GFP_pos_LS180_1_1.fq.gz and atacseq4/GFP_pos_LS180_1_2.fq.gz.


title: Human LS180 SOX9 variant ATAC-seq sample GFP_neg_LS180_2

description:
Library name: atacseq4_GFP_neg_LS180_2
ATAC-seq sample from the LS180 SOX9 variant chromatin accessibility dataset; GFP-negative control; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system; source directory atacseq4; paired FASTQ files atacseq4/GFP_neg_LS180_2_1.fq.gz and atacseq4/GFP_neg_LS180_2_2.fq.gz.

value: GFP negative control

value: ATAC-seq dataset profiling chromatin accessibility across SOX9 variants; GFP-negative control; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system


title: Human LS180 SOX9 variant ATAC-seq sample GFP_neg_LS180_1

description:
Library name: atacseq4_GFP_neg_LS180_1
ATAC-seq sample from the LS180 SOX9 variant chromatin accessibility dataset; GFP-negative control; only LS180 cell-line dataset in this submission; all other retained human datasets use the HT29-dTAG cell-line system; source directory atacseq4; paired FASTQ files atacseq4/GFP_neg_LS180_1_1.fq.gz and atacseq4/GFP_neg_LS180_1_2.fq.gz.


title: MC38CG_2_GC Muscle

description: Library name: Sample 7


title: MC38CG_1_GC Muscle

description: Library name: Sample 6


title: Human ARID1A/ARID1B perturbation ATAC-seq sample Pos_Ctrl_A2

description:
Library name: atacseq3_Pos_Ctrl_A2
ATAC-seq sample from the ARID1A/ARID1B perturbation chromatin accessibility dataset; positive control; source directory atacseq3; paired FASTQ files atacseq3/Pos_Ctrl_A2_1.fq.gz and atacseq3/Pos_Ctrl_A2_2.fq.gz.

value: positive control

value: ATAC-seq dataset profiling chromatin accessibility after ARID1A and ARID1B perturbation; positive control


title: MC38AG_5_GC Muscle

description: Library name: Sample 5

value: ADAMTSL4 overexpressed in MC38 tumor


title: Human ARID1A/ARID1B perturbation ATAC-seq sample Pos_Ctrl_A1

description:
Library name: atacseq3_Pos_Ctrl_A1
ATAC-seq sample from the ARID1A/ARID1B perturbation chromatin accessibility dataset; positive control; source directory atacseq3; paired FASTQ files atacseq3/Pos_Ctrl_A1_1.fq.gz and atacseq3/Pos_Ctrl_A1_2.fq.gz.


title: MC38AG_4_GC Muscle

description: Library name: Sample 4

value: GC Muscle


title: C2C12 n=2, mouse cells transfected with negative control miRNA mimic

description: Library name: P29458_1015

value: skeletal muscle

value: skeletal myotube

value: control


title: MC38AG_3_GC Muscle

description: Library name: Sample 3


title: MC38AG_2_GC Muscle

description: Library name: Sample 2


title: Human ARID1A/ARID1B perturbation ATAC-seq sample NTC_C2

description:
Library name: atacseq3_NTC_C2
ATAC-seq sample from the ARID1A/ARID1B perturbation chromatin accessibility dataset; non-targeting control; source directory atacseq3; paired FASTQ files atacseq3/NTC_C2_1.fq.gz and atacseq3/NTC_C2_2.fq.gz.

value: non-targeting control

value: ATAC-seq dataset profiling chromatin accessibility after ARID1A and ARID1B perturbation; non-targeting control


title: AnpKO H2AZ siRNA  rep 3

city: Rochester

first: Patrick

last: Murphy

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

description: RNA-Seq

data_processing:
CUT&Tag aligned with bowtie2, duplicate reads were removed, and individual bigWig files were created with DeepTools bamCoverage. bigWig files were merged with deepTools bigWigMerge. More details available in the Methods section of the associated manuscript
RNA-Seq aligned with STAR. Read counts were converted to FPKM values, using the Mm10 NCBI RefSeq gene annotation file.
Assembly: mm10
Supplementary files format and content: bigWig - read accumulation
Supplementary files format and content: txt - FPKM expression table

source_name: MEF

extract_protocol:
gentle trypsin extraction
RNA-Seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (cat: 20020598), according to the standard methods, and total RNA was purified using the Zymo Research Direct-zol RNA Miniprep kit (cat: R2051). Libraries were sequenced in 150 bp paired-end sequencing mode on an Illumina NextSeq550 high-throughput DNA Sequencer. CUT&Taglibraries were generated using approximately 100,000 cells. Cells were incubated with Convanavalin A-coated magnetic beads (Bang Laboratories, BP531), and then primary antibodies were added to incubate overnight at 4 °C. After incubation, secondary antibodies (incubated at RT for 1 h) and pA-Tn5 adapter complex (incubated at RT for 1 h) were added. Then, tagmentation took place for 1 h, and DNAs were extracted using phenol–chloroform–isoamyl alcohol. Libraries were prepared using NEBNext HiFi 2XPCR Master mix and cleaned up using Ampure XP beads (Beckman Coulter A63880).
CUT&Tag and RNA-Seq

value: MEF


title: Human ARID1A/ARID1B perturbation ATAC-seq sample Neg_Ctrl_B2

description:
Library name: atacseq3_Neg_Ctrl_B2
ATAC-seq sample from the ARID1A/ARID1B perturbation chromatin accessibility dataset; negative control; source directory atacseq3; paired FASTQ files atacseq3/Neg_Ctrl_B2_1.fq.gz and atacseq3/Neg_Ctrl_B2_2.fq.gz.

value: colon

value: negative control

value: ATAC-seq dataset profiling chromatin accessibility after ARID1A and ARID1B perturbation; negative control


title: MC38AG_1_GC Muscle

description: Library name: Sample 1


title: AnpKO H2AZ siRNA  rep 2

description: RNA-Seq


title: Human ARID1A/ARID1B perturbation ATAC-seq sample NTC_C1

description:
Library name: atacseq3_NTC_C1
ATAC-seq sample from the ARID1A/ARID1B perturbation chromatin accessibility dataset; non-targeting control; source directory atacseq3; paired FASTQ files atacseq3/NTC_C1_1.fq.gz and atacseq3/NTC_C1_2.fq.gz.

value: epithelial cell


title: AnpKO H2AZ siRNA  rep 1

description: RNA-Seq


title: Human ARID1A/ARID1B perturbation ATAC-seq sample ARID1B_KD_E1

description:
Library name: atacseq3_ARID1B_KD_E1
ATAC-seq sample from the ARID1A/ARID1B perturbation chromatin accessibility dataset; ARID1B knockdown; source directory atacseq3; paired FASTQ files atacseq3/ARID1B_KD_E1_1.fq.gz and atacseq3/ARID1B_KD_E1_2.fq.gz.

value: ARID1B knockdown

value: ATAC-seq dataset profiling chromatin accessibility after ARID1A and ARID1B perturbation; ARID1B knockdown


title: Human ARID1A/ARID1B perturbation ATAC-seq sample ARID1A_KD_D2

description:
Library name: atacseq3_ARID1A_KD_D2
ATAC-seq sample from the ARID1A/ARID1B perturbation chromatin accessibility dataset; ARID1A knockdown; source directory atacseq3; paired FASTQ files atacseq3/ARID1A_KD_D2_1.fq.gz and atacseq3/ARID1A_KD_D2_2.fq.gz.

value: ARID1A knockdown

value: ATAC-seq dataset profiling chromatin accessibility after ARID1A and ARID1B perturbation; ARID1A knockdown


title: MC38CG_3_GC Muscle

description: Library name: Sample 8

value: GFP expressed in MC38 tumor


title: WT_H2AZ_siRNA biol rep 3

description: RNA-Seq


title: Human ARID1A/ARID1B perturbation ATAC-seq sample ARID1A_KD_D1

description:
Library name: atacseq3_ARID1A_KD_D1
ATAC-seq sample from the ARID1A/ARID1B perturbation chromatin accessibility dataset; ARID1A knockdown; source directory atacseq3; paired FASTQ files atacseq3/ARID1A_KD_D1_1.fq.gz and atacseq3/ARID1A_KD_D1_2.fq.gz.


title: WT_H2AZ_siRNA biol rep 2

description: RNA-Seq


title: Human ARID1A/ARID1B perturbation ATAC-seq sample ARID1AB_KD_F2

description:
Library name: atacseq3_ARID1AB_KD_F2
ATAC-seq sample from the ARID1A/ARID1B perturbation chromatin accessibility dataset; combined ARID1A and ARID1B knockdown; source directory atacseq3; paired FASTQ files atacseq3/ARID1AB_KD_F2_1.fq.gz and atacseq3/ARID1AB_KD_F2_2.fq.gz.

value: ARID1A/ARID1B combined knockdown

value: ATAC-seq dataset profiling chromatin accessibility after ARID1A and ARID1B perturbation; combined ARID1A and ARID1B knockdown


title: ANP32E.KO_NT_siRNA biol rep 3

description: RNA-Seq


title: ANP32E.KO_NT_siRNA biol rep 1

description: RNA-Seq


title: Human matched ATAC-seq full time-course sample DMSO_1

description:
Library name: atacseq_DMSO_1
ATAC-seq sample from the chromatin accessibility time-course matched to the main RNA-seq and CUT&RUN SOX9 degradation/recovery sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; DMSO control; source directory atacseq; paired FASTQ files atacseq/DMSO_1_1.fq.gz and atacseq/DMSO_1_2.fq.gz.

value: SOX9 degradation/recovery time course

value: ATAC-seq chromatin accessibility time-course matched to the main RNA-seq and SOX9 degradation/recovery CUT&RUN sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; DMSO control

value: atacseq


title: WT_NT_siRNA biol rep 3

description: RNA-Seq


title: Human matched ATAC-seq full time-course sample D7_2

description:
Library name: atacseq_D7_2
ATAC-seq sample from the chromatin accessibility time-course matched to the main RNA-seq and CUT&RUN SOX9 degradation/recovery sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 7; source directory atacseq; paired FASTQ files atacseq/D7_2_1.fq.gz and atacseq/D7_2_2.fq.gz.

value: ATAC-seq chromatin accessibility time-course matched to the main RNA-seq and SOX9 degradation/recovery CUT&RUN sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 7


title: WT_NT_siRNA biol rep 2

description: RNA-Seq


title: Human matched ATAC-seq full time-course sample D7_1

description:
Library name: atacseq_D7_1
ATAC-seq sample from the chromatin accessibility time-course matched to the main RNA-seq and CUT&RUN SOX9 degradation/recovery sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 7; source directory atacseq; paired FASTQ files atacseq/D7_1_1.fq.gz and atacseq/D7_1_2.fq.gz.


title: Human matched ATAC-seq full time-course sample D4_2

description:
Library name: atacseq_D4_2
ATAC-seq sample from the chromatin accessibility time-course matched to the main RNA-seq and CUT&RUN SOX9 degradation/recovery sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 4; source directory atacseq; paired FASTQ files atacseq/D4_2_1.fq.gz and atacseq/D4_2_2.fq.gz.

value: ATAC-seq chromatin accessibility time-course matched to the main RNA-seq and SOX9 degradation/recovery CUT&RUN sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 4


title: Human matched ATAC-seq full time-course sample D4_1

description:
Library name: atacseq_D4_1
ATAC-seq sample from the chromatin accessibility time-course matched to the main RNA-seq and CUT&RUN SOX9 degradation/recovery sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 4; source directory atacseq; paired FASTQ files atacseq/D4_1_1.fq.gz and atacseq/D4_1_2.fq.gz.


title: WT_H3K27ac biol rep 3

description: CUT&Tag

value: MEF

value: WT-DMSO


title: Human matched ATAC-seq full time-course sample D2_2

description:
Library name: atacseq_D2_2
ATAC-seq sample from the chromatin accessibility time-course matched to the main RNA-seq and CUT&RUN SOX9 degradation/recovery sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 2; source directory atacseq; paired FASTQ files atacseq/D2_2_1.fq.gz and atacseq/D2_2_2.fq.gz.

value: colon

value: ATAC-seq chromatin accessibility time-course matched to the main RNA-seq and SOX9 degradation/recovery CUT&RUN sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 2


title: WT_H3K27ac biol rep 2

description: CUT&Tag


title: Human matched ATAC-seq full time-course sample D2_1

description:
Library name: atacseq_D2_1
ATAC-seq sample from the chromatin accessibility time-course matched to the main RNA-seq and CUT&RUN SOX9 degradation/recovery sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 2; source directory atacseq; paired FASTQ files atacseq/D2_1_1.fq.gz and atacseq/D2_1_2.fq.gz.

value: epithelial cell


title: WT_H3K27ac biol rep 1

description: CUT&Tag


title: Human matched ATAC-seq full time-course sample D13_1

description:
Library name: atacseq_D13_1
ATAC-seq sample from the chromatin accessibility time-course matched to the main RNA-seq and CUT&RUN SOX9 degradation/recovery sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 13; source directory atacseq; paired FASTQ files atacseq/D13_1_1.fq.gz and atacseq/D13_1_2.fq.gz.

value: ATAC-seq chromatin accessibility time-course matched to the main RNA-seq and SOX9 degradation/recovery CUT&RUN sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 13


title: Human matched ATAC-seq full time-course sample D10_2

description:
Library name: atacseq_D10_2
ATAC-seq sample from the chromatin accessibility time-course matched to the main RNA-seq and CUT&RUN SOX9 degradation/recovery sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 10; source directory atacseq; paired FASTQ files atacseq/D10_2_1.fq.gz and atacseq/D10_2_2.fq.gz.

value: ATAC-seq chromatin accessibility time-course matched to the main RNA-seq and SOX9 degradation/recovery CUT&RUN sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 10


title: ANP32E.KO-DMSO_H3K9me3 biol rep 1

description: CUT&Tag


title: WT-DAC_H3K9me3 biol rep 3

description: CUT&Tag

value: WT-DAC


title: NCMT3

city: Suzhou

first: Wenbo

last: Jia

state: Jiangsu Province

address: No.199 Ren'ai Road

institute: Soochow University

description: Library name: 6

data_processing:
Paired-end reads were harvested from sequencer, and were quality controlled by Q30.
After 3’adaptor-trimming and low-quality reads removing by cutadapt software (v1.9.1)[3], the high-quality clean reads were aligned to the reference genome (UCSC hg19) with bwa software (v0.7.12)[4].
Then, circle-map software (v1.1.4)[5] was used to detect circular DNA within all samples, and samtools (v0.2)[6] software was used to get raw soft-clipped read counts of the break point.
Then edgeR (v0.6.9)[7] software was used to perform normalization and differentially expressed circular DNA filter by p-value and fold change.
bedtools (v2.27.1)[8] software was used to annotate the circular DNAs. GO and Pathway enrichment analysis were performed based on the differentially expressed circular DNA associated genes.
Assembly: HG38
Supplementary files format and content: Column A-E: eccDNA genomic position & length. Column F-K: split read counts of each sample. Column L-Q: normalized split read counts by edgeR packages. Column R-AF: gene annotation information of eccDNA.

extract_protocol:
Total RNA was extracted using Trizol reagent
Briefly, tissue samples or cell pellets were suspended in L1 solution (Plasmid Mini AX ;A&A Biotechnology) and supplemented with Proteinase K before incubation overnight at 50°C with agitation. After Lysis, samples were alkaline treated, followed by precipitation of proteins and separation of chromosomal DNA from circular DNA through an ion exchange membrane column (Plasmid Mini AX;A&A Biotechnology). Column-purified DNA was treated with FastDigest MssI (Thermo Scientifific) to remove mitochondrial circular DNA and incubated at 37°C for 16 h. Remaining linear DNA was removed by exonuclease (Plasmid-Safe ATP-dependent DNase, Epicentre) at 37°C in a heating block and enzyme reaction was carried out continuously for 1 week, adding additional ATP and DNase every 24 h (30 units per day) according to the manufacturer’s protocol (Plasmid-Safe ATP-dependent DNase, Epicentre). circular DNA-enriched samples was used as template for phi29 polymerase amplification reactions (Genseq® RCA DNA Amplification Kit) at 30 Cfor 2 days (46–48 h), followed by purification using MinElute Reaction Cleanup Kit (Qiagen). Purified DNA was subjected to library preparation with GenSeq® Rapid DNA Lib Prep Kit (GenSeq Inc.).


title: Human matched ATAC-seq full time-course sample D10_1

description:
Library name: atacseq_D10_1
ATAC-seq sample from the chromatin accessibility time-course matched to the main RNA-seq and CUT&RUN SOX9 degradation/recovery sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 10; source directory atacseq; paired FASTQ files atacseq/D10_1_1.fq.gz and atacseq/D10_1_2.fq.gz.


title: NCMT1

description: Library name: 4


title: CA3

description: Library name: 3


title: WT-DMSO_H3K9me3 biol rep 3

description: CUT&Tag


title: WT-DMSO_H3K9me3 biol rep 2

description: CUT&Tag


title: CA2

description: Library name: 2


title: WT-DMSO_H3K9me3 biol rep 1

description: CUT&Tag


title: CA1

description: Library name: 1


title: ANP32E-KO-DAC_RNA-Seq biol rep 3

description: RNA-Seq


title: purified monolayer hiPSC-cardiomyocytes, day10, nucleofected 3A12, biol rep 3

city: Chicago

first: Zachary

middle: Thomas

last: Weber

state: Illinois

department: Human Genetics

institute: University of Chicago

description: Library name: CM-2D-348-3A12-Nucleofected-03

data_processing:
Reads were aligned to the GRCh38/hg38 human transcriptome reference with NCBI refseq transcript models. Library strand orientation was confirmed using kallisto and count matrices were generated by HTSeq-count. Differential expression analyses were performed in R using the limma, and edgeR packages.
Assembly: Human GRCh38
Supplementary files format and content: Tab separated HTSeq-count files assigning reads to gene counts

molecule: polyA RNA

growth_protocol: Cardiomyocytes were generated by standard methods using small molecule modulation of WNT signaling. Briefly, when hiPSCs reached 90% confluency, differentiation was initiated using 6 mM CHIR99021 for 24 hours in cardiomyocyte differentiation medium 3 (CDM3): RPMI 1640 supplemented with 2mM L-glutamine, 213 mg/mL L-ascorbic acid 2-phosphate, and 500mg/mL recombinant human albumin. Media containing CHIR99201 was exchanged for fresh CDM3 at 24 hours. On day 3 cells were treated with 2 uM Wnt-C59 in CDM3. On day 5, Wnt-C59-containing media was changed for CDM3 and subsequently exchanged every two days until cells matured into beating monolayers.

extract_protocol:
Cardiomyocytes were dissociated for 1-2 hours in a dissociation solution containing 200 units / ml Collagenase IV,10 mM HEPES pH 7.4, 2 mM Thiazovivin, and 30 mM N-Benzyl-p-Toluenesulfonamide and passed through a 70 um cell strainer. Cardiomyocytes were isolated using column-based purification, and allowed to recover for 48 hours on matrigel coated plates before lysis and RNA isolation.
Differentiated and purified hiPSC-cardiomyocytes were washed in Dulbecco’s phosphate-buffered saline solution (DPBS) without calcium or magnesium and RNA was extracted using Qiagen RNeasy mini kit. Libraries were prepared using the NEBNext low input RNA library prep kit for Illumina with NEBNext Illumina index primers and adapters. Sequencing of the RNA-Seq libraries was performed on an Illumina NovaSeq 6000 platform.

value: cardiomyocyte

tag: sample group


title: ANP32E-KO-DAC_RNA-Seq biol rep 2

description: RNA-Seq


title: purified monolayer hiPSC-cardiomyocytes, day10, nucleofected 3A12, biol rep 2

description: Library name: CM-2D-348-3A12-Nucleofected-02


title: ANP32E-KO-DAC_RNA-Seq biol rep 1

description: RNA-Seq


title: WT-DAC_RNA-Seq biol rep 3

description: RNA-Seq


title: purified monolayer hiPSC-cardiomyocytes, day10, nucleofected 3A12, biol rep 1

description: Library name: CM-2D-348-3A12-Nucleofected-01


title: purified monolayer hiPSC-cardiomyocytes, day10, nucleofected 4G7, biol rep 3

description: Library name: CM-2D-348-4G7-Nucleofected-03


title: WT-DAC_RNA-Seq biol rep 2

description: RNA-Seq


title: WT-DAC_RNA-Seq biol rep 1

description: RNA-Seq


title: purified monolayer hiPSC-cardiomyocytes, day10, nucleofected 4G7, biol rep 2

description: Library name: CM-2D-348-4G7-Nucleofected-02


title: purified monolayer hiPSC-cardiomyocytes, day10, nucleofected 4G7, biol rep 1

description: Library name: CM-2D-348-4G7-Nucleofected-01


title: ANP32E-KO-DMSO_RNA-Seq biol rep 2

description: RNA-Seq


title: purified monolayer hiPSC-cardiomyocytes, day10, nucleofected 3A7, biol rep 3

description: Library name: CM-2D-348-3A7-Nucleofected-03


title: ANP32E-KO-DMSO_RNA-Seq biol rep 1

description: RNA-Seq


title: purified monolayer hiPSC-cardiomyocytes, day10, nucleofected 3A7, biol rep 2

description: Library name: CM-2D-348-3A7-Nucleofected-02


title: WT-DMSO_RNA-Seq biol rep 1

description: RNA-Seq


title: WT-DMSO_RNA-Seq biol rep 2

description: RNA-Seq


title: purified monolayer hiPSC-cardiomyocytes, day10, nucleofection control, biol rep 3

description: Library name: CM-2D-348-WT-Nucleofected-03

value: WT


title: ANP32E.KO-DAC_H2AZ_Expt3 biol rep 3

description: CUT&Tag


title: purified monolayer hiPSC-cardiomyocytes, day10, nucleofection control, biol rep 2

description: Library name: CM-2D-348-WT-Nucleofected-02


title: ANP32E.KO-DAC_H2AZ_Expt3 biol rep 2

description: CUT&Tag


title: purified monolayer hiPSC-cardiomyocytes, day10, nucleofection control, biol rep 1

description: Library name: CM-2D-348-WT-Nucleofected-01


title: ANP32E.KO-DMSO_H2AZ_Expt3 biol rep 4

description: CUT&Tag


title: purified monolayer hiPSC-cardiomyocytes, day 10, biol rep 3

description: Library name: CM-2D-348-03


title: purified monolayer hiPSC-cardiomyocytes, day 10, biol rep 2

description: Library name: CM-2D-348-02


title: ANP32E.KO-DMSO_H2AZ_Expt3 biol rep 3

description: CUT&Tag


title: ANP32E.KO-DAC_H2AZ_Expt3 biol rep 1

description: CUT&Tag


title: purified monolayer hiPSC-cardiomyocytes, day 10, biol rep 1

description: Library name: CM-2D-348-01


title: ANP32E.KO-DMSO_H2AZ_Expt3 biol rep 2

description: CUT&Tag


title: hiPSC-derived Cardiomyocyte, day10, biol rep 3

description: Library name: CM-2D-3

data_processing:
FASTQ reads were evaluated using FASTQC for quality control metrics and trimmed for adapter sequences using cutadpt. Reads were aligned using bowtie2 v2.3.5.
Duplicates were identified using Picard MarkDuplicates, and filtered from alignments using Samtools Filter
Peaks were called using MACS2. NarrowPeak summits were collected and extended to 501-bp fixed-width intervals. Overlapping peaks were prunned by score to obtain final non-overlapping fixed width peak sets.
BigWig files were generated to summarize read coverage using deepTools in Python 3.8
Assembly: Human GRCh38
Supplementary files format and content: BigWig files summarizing read coverage and narrowPeak bed files with 501-bp fixed width peaks extending from called peak summits.

source_name: derived cells

growth_protocol: EHTs were cultured in media containing DMEM low glucose, 10% horse serum, 1% Penicillin/Streptomycin, and 0.1% human insulin. For 72 hours following EHT generation, the cells were supplemented with 5 μg/mL recombinant human TGF-β1. On day 3 after tissue casting, TGF-β1 was removed from culture medium and media was exchanged with 500 μL fresh media per well. EHT media was exchanged every 2 days throughout the course of tissue maturation. EHTs were harvested for downstream applications at day 20 post tissue casting. Input cardiomyocytes used in EHTs were generated by standard methods using small molecule modulation of WNT signaling. Briefly, when hiPSCs reached 90% confluency, differentiation was initiated using 6 mM CHIR99021 for 24 hours in cardiomyocyte differentiation medium 3 (CDM3): RPMI 1640 supplemented with 2mM L-glutamine, 213 mg/mL L-ascorbic acid 2-phosphate, and 500mg/mL recombinant human albumin. Media containing CHIR99201 was exchanged for fresh CDM3 at 24 hours. On day 3 cells were treated with 2 uM Wnt-C59 in CDM3. On day 5, Wnt-C59-containing media was changed for CDM3 and subsequently exchanged every two days until cells matured into beating monolayers.

extract_protocol:
Engineered heart tissues were pooled from 2x 48 well plates and incubated at 37° C for 1.5-2 hours in a dissociation solution containing 1mg/ml Collagenase II,10 mM HEPES pH 7.4, 2 mM Thiazovivin, and 30 mM N-Benzyl-p-Toluenesulfonamide to obtain a single cell suspension. Cells were filtered through 70 um cell strainer. Cells were sorted for eGFP expression using fluorescence-assisted cell sorting to generate eGFP+ cardiomyocyte fractions and eGFP- cardiac fibroblast fractions for library preparation. Input cardiomyocytes were dissociated for 1-2 hours in a dissociation solution containing 200 units / ml Collagenase IV,10 mM HEPES pH 7.4, 2 mM Thiazovivin, and 30 mM N-Benzyl-p-Toluenesulfonamide and passed through a 70 um cell strainer. Cardiomyocytes were isolated using column-based purification before library preparation.
Sorted cells were washed again with 10mL EHT media and resuspended in 1mL with 2%BSA. The cells were then counted and separated into aliquots of 50,000. Assay for transposase-accessible chromatin sequencing (ATAC-Seq) was performed as described by Grandi, F. C. et al. 2022. Briefly, 50k cells were collected at 500g for 5min at 4°C and gently resuspended in 50 ml ice-cold lysis buffer: 10 mM Tris–HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin. Lysis proceeded for 3min on ice and was neutralized with 1ml of ice-cold lysis buffer excluding detergents digitonin and NP40. Following neutralization, permeabilized nuclei were pelleted at 4°C and resuspended in 50µl transposition master mix: 25µl (2X) Illumina TD buffer, 16.5 ml PBS, 5 ml H2O, 0.5 ml 1% digitonin, 0.5 ml 10% Tween-20, and 2.5 ml Illumina TDE1 enzyme, and incubated for 30min at 37°C on a thermomixer. Tagmentation was terminated and DNA collected using Zymo Clean and Concentrator-5 following the manufacturers recommendations. Libraries were barcoded with 5 cycles of preamplification, and the PCR reaction was paused for quantification using NEBNext Library Quant Kit for Illumina. Diluted final libraries were mixed and sequenced on an Illumina Nova-Seq 6000 using paired end 50bp reads.

value: derived cells


title: ANP32E.KO-DMSO_H2AZ_Expt3 biol rep 1

description: CUT&Tag


title: WT-DAC_H2AZ_Expt2 biol rep 3

description: CUT&Tag


title: hiPSC-derived Cardiomyocyte, day10, biol rep 1

description: Library name: CM-2D-1


title: WT-DAC_H2AZ_Expt2 biol rep 2

description: CUT&Tag


title: WT-DAC_H2AZ_Expt2 biol rep 1

description: CUT&Tag


title: WT-DMSO_H2AZ_Expt2 biol rep 3

description: CUT&Tag


title: Engineered Heart Tissue, Cardiomyocte Fraction, day 30, biol rep1

description: Library name: EHT-CM-1


title: WT-DMSO_H2AZ_Expt2 biol rep 2

description: CUT&Tag


title: Muscle, ID ELMIH066, After_exercise, Group 4

city: Amsterdam

first: Georges

last: Janssens

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

description: Library name: Sample_93

data_processing:
Analysis for read mapping was performed in R v4.1.0 and Bioconductor v3.13. Reads were subjected to quality control FastQC v0.11.15 and trimmed using Trimmomatic v0.36 and aligned using HISAT2 v2.1.0 to the GRCh38 (v94) human genome reference assembly. Counts were obtained using HTSeq (v0.11.0, default parameters) using the corresponding GTF taking into account the directions of the reads. Statistical analyses were performed using the edgeR v3.34.1 and limma/voom v 3.48.344 R packages. All genes with more than 2 counts in at least 4 of the samples were kept. Count data were transformed to log2-counts per million (logCPM), normalized by applying the trimmed mean of M-values method and precision weighted using voom. Genes were reannotated using the Ensembl genome database (v104) and the biomaRt package.
Assembly: GRCh38 (v94)
Supplementary files format and content: Count data, 93 human muscle samples with annotation of 58735 Ensembl Gene IDs

source_name: Muscle

extract_protocol:
Human muscle tissues were homogenized with a 5 mm steel bead using a TissueLyser II (QIAGEN) for 5 min at frequency of 30 times/second. RNA was extracted according to the instructions of the RNaesy Mini Kit (QIAGEN). Contaminating genomic DNA was removed using RNase-Free DNase (QIAGEN). RNA was quantified with a NanoDrop 2000 spectrophotometer (Thermo Scientific; Breda, The Netherlands) and stored at -80°C until use.
RNA libraries were prepared and sequenced with the Illumina platform by Genome Scan (Leiden, The Netherlands). The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used. NovaSeq control software NCS v1.6 was used.

value: Muscle


title: purified monolayer hiPSC-cardiomyocytes, day10, nucleofected 3A7, biol rep 1

description: Library name: CM-2D-348-3A7-Nucleofected-01


title: Muscle, ID ELMIH120, Before_exercise, Group 4

description: Library name: Sample_92


title: ANP32E.KO_H2AZ_Expt1 biol rep 3

description: CUT&Tag


title: Muscle, ID ELMIH005, Before_exercise, Group 4

description: Library name: Sample_91


title: ANP32E.KO_H2AZ_Expt1 biol rep 2

description: CUT&Tag


title: Muscle, ID ELMIH131, After_exercise, Group 2

description: Library name: Sample_90


title: ANP32E.KO_H2AZ_Expt1 biol rep 1

description: CUT&Tag


title: Muscle, ID ELMIH084, After_exercise, Group 2

description: Library name: Sample_89


title: hiPSC-derived Cardiomyocyte, day10, biol rep 2

description: Library name: CM-2D-2


title: WT_H2AZ_Expt1 biol rep 3

description: CUT&Tag


title: Human ARID1A/ARID1B perturbation ATAC-seq sample Neg_Ctrl_B1

description:
Library name: atacseq3_Neg_Ctrl_B1
ATAC-seq sample from the ARID1A/ARID1B perturbation chromatin accessibility dataset; negative control; source directory atacseq3; paired FASTQ files atacseq3/Neg_Ctrl_B1_1.fq.gz and atacseq3/Neg_Ctrl_B1_2.fq.gz.

value: negative control

value: ATAC-seq dataset profiling chromatin accessibility after ARID1A and ARID1B perturbation; negative control


title: Engineered Heart Tissue, Fibroblast Fraction, day 30, biol rep1

description: Library name: EHT-FB-1

value: cardiac fibroblast


title: Human ARID1A/ARID1B perturbation ATAC-seq sample ARID1B_KD_E2

description:
Library name: atacseq3_ARID1B_KD_E2
ATAC-seq sample from the ARID1A/ARID1B perturbation chromatin accessibility dataset; ARID1B knockdown; source directory atacseq3; paired FASTQ files atacseq3/ARID1B_KD_E2_1.fq.gz and atacseq3/ARID1B_KD_E2_2.fq.gz.

value: ARID1B knockdown

value: ATAC-seq dataset profiling chromatin accessibility after ARID1A and ARID1B perturbation; ARID1B knockdown


title: WT_H2AZ_Expt1 biol rep 2

description: CUT&Tag

value: MEF


title: Muscle, ID ELMIH102, Before_exercise, Group 2

description: Library name: Sample_88


title: Muscle, ID ELMIH030, Before_exercise, Group 2

description: Library name: Sample_87


title: Human ARID1A/ARID1B perturbation ATAC-seq sample ARID1AB_KD_F1

description:
Library name: atacseq3_ARID1AB_KD_F1
ATAC-seq sample from the ARID1A/ARID1B perturbation chromatin accessibility dataset; combined ARID1A and ARID1B knockdown; source directory atacseq3; paired FASTQ files atacseq3/ARID1AB_KD_F1_1.fq.gz and atacseq3/ARID1AB_KD_F1_2.fq.gz.

value: ARID1A/ARID1B combined knockdown

value: ATAC-seq dataset profiling chromatin accessibility after ARID1A and ARID1B perturbation; combined ARID1A and ARID1B knockdown


title: WT_H2AZ_siRNA biol rep 1

description: RNA-Seq


title: Muscle, ID ELMIH050, After_exercise, Group 1

description: Library name: Sample_86


title: WT_H2AZ_Expt1 biol rep 1

description: CUT&Tag


title: Engineered Heart Tissue, Cardiomyocte Fraction, day 30, biol rep2

description: Library name: EHT-CM-2


title: Human matched ATAC-seq full time-course sample DMSO_2

description:
Library name: atacseq_DMSO_2
ATAC-seq sample from the chromatin accessibility time-course matched to the main RNA-seq and CUT&RUN SOX9 degradation/recovery sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; DMSO control; source directory atacseq; paired FASTQ files atacseq/DMSO_2_1.fq.gz and atacseq/DMSO_2_2.fq.gz.

value: colon

value: SOX9 degradation/recovery time course

value: ATAC-seq chromatin accessibility time-course matched to the main RNA-seq and SOX9 degradation/recovery CUT&RUN sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; DMSO control

value: atacseq


title: Muscle, ID ELMIH005, After_exercise, Group 4

description: Library name: Sample_85


title: Muscle, ID ELMIH001, After_exercise, Group 4

description: Library name: Sample_84


city: Shanghai

first: Zhu

last: Ming

address: No. 500, Dongchuan Road

institute: East China Normal University

description: Library name: GUIDE-seq-2_Cas9_VEGFA2_HEK293T_rep2_72h

data_processing:
Tracking-seq/2: Data were analyzed using Offtracker (https://github.com/Lan-lab/offtracker)
GUIDE-seq-2: Data were analyzed using guideseq (https://github.com/tsailabSJ/guideseq)
Assembly: hg38
Supplementary files format and content: BigWig of genome-editing signals

extract_protocol:
Tracking-seq/2: Cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2 antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA. GUIDE-seq-2 were performed according to doi: 10.1101/2025.02.10.637517
Tracking-seq/2: The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit.GUIDE-seq-2 libraries were constructed according to doi: 10.1101/2025.02.10.637517


title: ANP32E.KO_NT_siRNA biol rep 2

description: RNA-Seq


description: Library name: GUIDE-seq-2_Cas9_VEGFA2_HEK293T_rep3_72h


title: WT_NT_siRNA biol rep 1

description: RNA-Seq


description: Library name: GUIDE-seq-2_Cas9_VEGFA2_HEK293T_rep1_72h


title: Muscle, ID ELMIH004, Before_exercise, Group 4

description: Library name: Sample_83


title: GUIDE-seq-2_Cas9_HEK4_HEK293T_rep3_72h

description: Library name: GUIDE-seq-2_Cas9_HEK4_HEK293T_rep3_72h


title: Muscle, ID ELMIH072, After_exercise, Group 3

description: Library name: Sample_82


title: GUIDE-seq-2_Cas9_HEK4_HEK293T_rep2_72h

description: Library name: GUIDE-seq-2_Cas9_HEK4_HEK293T_rep2_72h


title: Muscle, ID ELMIH049, After_exercise, Group 2

description: Library name: Sample_81


title: Human matched ATAC-seq full time-course sample D13_2

description:
Library name: atacseq_D13_2
ATAC-seq sample from the chromatin accessibility time-course matched to the main RNA-seq and CUT&RUN SOX9 degradation/recovery sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 13; source directory atacseq; paired FASTQ files atacseq/D13_2_1.fq.gz and atacseq/D13_2_2.fq.gz.

value: epithelial cell

value: ATAC-seq chromatin accessibility time-course matched to the main RNA-seq and SOX9 degradation/recovery CUT&RUN sample series; full multi-time-point series covering DMSO, D2, D4, D7, D10, and D13; day 13


title: ANP32E.KO-DMSO_H3K9me3 biol rep 3

description: CUT&Tag


title: WT-DMSO_H2AZ_Expt2 biol rep 1

description: CUT&Tag

value: WT-DMSO


title: Muscle, ID ELMIH084, Before_exercise, Group 2

description: Library name: Sample_80


title: GUIDE-seq-2_Cas9_HEK4_HEK293T_rep1_72h

description: Library name: GUIDE-seq-2_Cas9_HEK4_HEK293T_rep1_72h


title: TdCBE_VEGFA2_24h_293_500k_PEI_T5_rep3

description: Library name: TdCBE_VEGFA2_24h_293_500k_PEI_T5_rep3


title: TdCBE_VEGFA2_24h_293_500k_PEI_T5_rep2

description: Library name: TdCBE_VEGFA2_24h_293_500k_PEI_T5_rep2


title: Muscle, ID ELMIH008, Before_exercise, Group 2

description: Library name: Sample_79


title: ANP32E.KO-DMSO_H3K9me3 biol rep 2

description: CUT&Tag


title: Muscle, ID ELMIH100, After_exercise, Group 1

description: Library name: Sample_78


title: TdCBE_VEGFA2_24h_293_500k_PEI_T5_rep1

description: Library name: TdCBE_VEGFA2_24h_293_500k_PEI_T5_rep1


title: WT-DAC_H3K9me3 biol rep 2

description: CUT&Tag

value: WT-DAC


title: Muscle, ID ELMIH099, Before_exercise, Group 1

description: Library name: Sample_77

value: Muscle


title: WT-DAC_H3K9me3 biol rep 1

description: CUT&Tag


title: NCMT2

description: Library name: 5


title: Muscle, ID ELMIH112, Before_exercise, Group 4

description: Library name: Sample_75


title: TdCBE_VEGFA2_24h_293_500k_PEI_mock_rep3

description: Library name: TdCBE_VEGFA2_24h_293_500k_PEI_mock_rep3


title: TdCBE_VEGFA2_24h_293_500k_PEI_mock_rep2

description: Library name: TdCBE_VEGFA2_24h_293_500k_PEI_mock_rep2


title: Muscle, ID ELMIH042, Before_exercise, Group 1

description: Library name: Sample_76


title: TdCBE_VEGFA2_24h_293_500k_PEI_mock_rep1

description: Library name: TdCBE_VEGFA2_24h_293_500k_PEI_mock_rep1


title: Muscle, ID ELMIH018, Before_exercise, Group 4

description: Library name: Sample_74


title: TdCBE_HEK4_24h_293_500k_PEI_T5_rep3

description: Library name: TdCBE_HEK4_24h_293_500k_PEI_T5_rep3


title: Muscle, ID ELMIH021, Before_exercise, Group 3

description: Library name: Sample_73


title: Muscle, ID ELMIH029, After_exercise, Group 2

description: Library name: Sample_72


title: TdCBE_HEK4_24h_293_500k_PEI_T5_rep2

description: Library name: TdCBE_HEK4_24h_293_500k_PEI_T5_rep2


title: Muscle, ID ELMIH041, Before_exercise, Group 2

description: Library name: Sample_71


title: TdCBE_HEK4_24h_293_500k_PEI_T5_rep1

description: Library name: TdCBE_HEK4_24h_293_500k_PEI_T5_rep1


title: TdCBE_HEK4_24h_293_500k_PEI_mock_rep3

description: Library name: TdCBE_HEK4_24h_293_500k_PEI_mock_rep3


title: Muscle, ID ELMIH062, After_exercise, Group 1

description: Library name: Sample_69


title: Hippocampus, 6h, NMEC, rep2

city: Tianjin

first: zhiyue

last: Wu

address: No. 288 Nanjing Road, Heping District, Tianjin, China

institute: Institute of Hematology & Blood Diseases Hospital

description:
Library name: Sample 12
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v7.0.1. (https://www.10xgenomics.com/support/software/cell-ranger/)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hippocampus

extract_protocol:
scRNA-seq was performed with cortex and hippocampus cells from18-day-old C57BL/6N mice. Single-cell dissociation was performed following published protocols with modifications. 1× 107 CFU of NMEC WT strain in 100 μL sterile PBS were injected intravenously in which doses bacteria develop a high level of bacteremia followed by bacterial traversal of the BBB mimicking the pathogenesis of human meningitis. Three or six hours later, mice were transcardially perfused using ice cold Hank’s balanced salt solution (HBSS) and the brains were quickly dissected and placed on ice. Single cell suspensions were performed as previously described. Briefly, brains in ice cold HBSS were minced using a scalpel and then Dounce homogenized 15-20 times each with the loose and tight pestles while simultaneously rotating the pestle. Cell suspension was then passed through pre-wet 70 mm filter, and spun down at 300 g for 5 min in a centrifuge set to 4℃.
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, single cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Escherichia coli (NMEC) infection in mice

value: Hippocampus

value: WT

value: infected, NMEC, 6h


title: TdCBE_HEK4_24h_293_500k_PEI_mock_rep1

description: Library name: TdCBE_HEK4_24h_293_500k_PEI_mock_rep1


title: Hippocampus, 6h, NMEC, rep1

description:
Library name: Sample 11
10x Genomics


title: TdCBE_HEK4_24h_293_500k_PEI_mock_rep2

description: Library name: TdCBE_HEK4_24h_293_500k_PEI_mock_rep2


title: Muscle, ID ELMIH053, Before_exercise, Group 1

description: Library name: Sample_68


title: Isocortex, 6h, NMEC, rep1

description:
Library name: Sample 9
10x Genomics

source_name: Isocortex

value: Isocortex


title: Isocortex, 6h, NMEC, rep2

description:
Library name: Sample 10
10x Genomics


title: PE3_VEGFA3_48h_293_500k_PEI_T5_rep2

description: Library name: PE3_VEGFA3_48h_293_500k_PEI_T5_rep2


title: Muscle, ID ELMIH027, After_exercise, Group 4

description: Library name: Sample_66


title: PE3_VEGFA3_48h_293_500k_PEI_T5_rep1

description: Library name: PE3_VEGFA3_48h_293_500k_PEI_T5_rep1


title: Muscle, ID ELMIH089, Before_exercise, Group 4

description: Library name: Sample_65


title: Isocortex, 3h, NMEC, rep1

description:
Library name: Sample 5
10x Genomics

value: infected, NMEC, 3h


title: Hippocampus, 6h, PBS, rep2

description:
Library name: Sample 4
10x Genomics

value: infected, PBS, 6h


title: PE3_VEGFA3_48h_293_500k_PEI_mock_rep3

description: Library name: PE3_VEGFA3_48h_293_500k_PEI_mock_rep3


title: Muscle, ID ELMIH066, Before_exercise, Group 4

description: Library name: Sample_64


title: Hippocampus, 6h, PBS, rep1

description:
Library name: Sample 3
10x Genomics


title: PE3_VEGFA3_48h_293_500k_PEI_mock_rep2

description: Library name: PE3_VEGFA3_48h_293_500k_PEI_mock_rep2


title: Isocortex, 6h, PBS, rep1

description:
Library name: Sample 1
10x Genomics


title: Muscle, ID ELMIH072, Before_exercise, Group 3

description: Library name: Sample_63