title: Replicate 4, AVP-flox;Cre, Tamoxifen

description: Library name: Sample 8

value: Kidney

value: IMCD


title: Replicate 1, AVP-flox, Tamoxifen

status: Public on Aug 05 2025

type: SRA

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

country: USA

institute: NHLBI

description: Library name: Sample 1

library_source: transcriptomic

data_processing:
RNA-seq raw sequencing reads were aligned by STAR to the mouse Ensembl genome (release 113). Transcript per million (TPM) and expected counts were generated by RSEM. Computational analyses were performed on the National Institutes of Health Biowulf High-Performance Computing platform
Assembly: Ensemble release 113
Supplementary files format and content: RNA_rawTPM.txt

molecule: total RNA

organism: Mus musculus

source_name: Kidney

growth_protocol: Mice were maintained in NHLBI/NIH mouse facicility

extract_protocol:
RNA was extracted using Direct-zol RNA MicroPrep kit
Trizol-extracted RNA was proceeded to cDNA generation using the SMART-Seq HT Kit (Takara Bio). cDNA was generated using 1 ng of total RNA with 11 PCR cycles. 1 ng of the resulting cDNA was “tagmented” and barcoded by using the Nextera XT DNA Sample Preparation Kit (Illumina) to generate sequencing libraries for high throughput sequencing. Libraries were purified by AmPure XP magnetic beads (Beckman Coulter), and quantified using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). An equal amount of index libraries were pooled and sequenced (paired-end 50 bp) on an Illumina platform.

tag: tissue

tag: cell type

tag: genotype

value: AVP-flox

tag: treatment

value: Tamoxifen


title: PM, Control, replicate 3

city: New York

first: Fang

last: Li

state: NY

department: Medicine

institute: Columbia University Irving Medical Center

description:
Element Biosciences AVITI sequencer
Ctl3

data_processing:
Raw sequencing reads were mapped to the mouse genome version GRCm39 (M33) using Salmon (version 1.10.2) to obtain transcript abundance counts. MultiQC was used to generate quality control reports based on Salmon read mapping results.
The transcript-level count information was summarized to the gene level using tximport (version 1.28.0).
Differential expression was assessed using DESeq2 (version 1.40.0). Genes with an absolute fold change > 1.5 and false discovery rate (FDR)-adjusted P value < 0.05 were considered as differentially expressed (DE).
Assembly: mm10
Supplementary files format and content: tab-delimited text file for salmon counts
Supplementary files format and content: tab-delimited text file for DESeq2 normalized counts by rld

source_name: PM

extract_protocol:
Total RNAs were extracted from PMs (female mice: 3 Ctl and 3 LipaTg) using the Quick-RNA miniprep plus kit (Zymo).
With a minimum of 150 ng input RNA, strand-specific, poly(A)+ libraries were prepared and sequenced at 20 million 100-bp paired-end reads per sample.

value: PM

value: LysMCre-/-, LipaTg/wt, Ldlr-/-

tag: Sex

value: Female


title: PM, Lipa overexpression, replicate 1

description:
Element Biosciences AVITI sequencer
LipaTg1

value: LysMCre+/-, LipaTg/wt, Ldlr-/-


title: pDC-A, WT, rep3

city: New York City

first: Boris

last: Reizis

state: New York

address: 550 1st Ave

department: Pathology

institute: NYU Grossman School of Medicine

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. The FASTQ files were further processed using Seq-N-Slide pipeline.
The sequencing reads were adapter and quality trimmed with Trimmomatic and then aligned to the mouse genome (build mm10/GRCm38) using the splice-aware STAR aligner.
The FeatureCounts program was utilized to generate counts for each gene based on the number of aligned reads that overlap its exons.
These counts were then normalized and used to test for differential expression using negative binomial generalized linear models implemented by the DESeq2 R package.
Assembly: mm10/GRCm38
Supplementary files format and content: CSV file contains raw counts for all genes and samples.

molecule: polyA RNA

source_name: Spleen

extract_protocol:
RNA was purified from cells using RNeasy Micro kit w/ gDNA Eliminator column (QIAgen Cat# 74034).
Low input Clontech SMART- Seq HT with Nxt HT

value: Spleen

value: Sca1- CD69- pDC

value: WT


title: mGCs from EM group, treated additionally with 100 nM 14, 15-EET for 24 hours,Rep-3

city: Hangzhou

first: Xiang

last: Lin

state: Zhejiang province

address: No. 3 Qingchun East Road, Shangcheng District, Hangzhou, 310000, China

department: Assisted Reproduction Unit, Department of Obstetrics and Gynecology;

country: China

institute: Sir Run Run Shaw Hospital, Zhejiang University School of Medicine;

description: Library name: EET-3

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: Mus musculus GRCm39 release-109
Supplementary files format and content: tsv files include count values for each sample

source_name: granulosa cell

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer's instructions
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA

value: granulosa cell


title: Replicate 2, AVP-flox, Tamoxifen

description: Library name: Sample 2


title: NDF-degron, Spt16, ChIP_DMSO2h_Rep2

city: Piscataway

first: Jia

last: Fei

state: NJ

address: 604 Allison Rd

department: Department of Molecular Biology and Biochemistry

institute: Rutgers University

library_source: genomic

data_processing:
ChIP-Seq sequencing data were trimmed with Fastp and Trim Galore! Programs and aligned to the hg19 reference genome using Bowtie2. Spike-in reads were mapped to the dm3 genome build. PCR duplicates were removed with the samtools. Normalized bigwig files and metagene analysis were prepared by Homer or Deeptools. Spike-in normalizations were performed as suggested by the manufacturer.
Assembly: hg19
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Human iPSC cells were cultured in Essential 8 medium 1 (Gibco) following the vendor’s instruction. Rock inhibitor Y23672 (Selleck Chemicals) with a final concentration of 10 μM was used during cell passaging. Cells were kept in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
For ChIP-seq, cells were crosslinked with 1% formaldehyde (Sigma) for 10 min, after quenching and lysis, chromatin was sonicated with a Covaris S220 focused-ultrasonicator.
ChIP-seq libraries were prepared with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB E7645S) according to kit instructions.

treatment_protocol: For auxin-inducible degron experiments, 0.5 mM 3-indoleacetic acid (IAA) (Sigma) or 0.1% (v/v) DMSO were added to the culture media of degron cells, for the specified duration. For 1,6-Hexanediol treatment, for ChIP-seq experiments, cells were treated with 1.5% 1,6-Hexanediol for 10 minutes.

tag: chip antibody

value: SPT16 (Cell Signaling, 12191S)

tag: cell line

value: hiPSC

value: NDF-degron

value: DMSO 2 hr


title: NDF-degron, Spt16, ChIP_DMSO2h_Rep1


title: HASMC, PA_3

city: Ann Arbor

first: Yaozhong

last: Liu

state: MICHIGAN

address: 2800 Plymouth Road

department: Internal Medicine

institute: University of Michigan

description:
Library name: PA_3
10111-YL-24

data_processing:
The reads were trimmed using Cutadapt v2.3. Reads were mapped to the reference genome GRCh38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq (Dobin). FastQC (Andrews, 2010) (v0.11.8) was run on .bam files in a post-alignment step, including both aligned and un-aligned reads, to ensure data quality.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Human aortic smooth muscle cells (HASMC)

growth_protocol: HASMCs were cultured in SMC Growth Medium 2 (Lonza). Cells were passaged at a 1:3 ratio, and passages 4 to 6 were used for experiments. Prior to incubation, HASMCs at 80-90% confluence were incubated in Opti-MEM™ Reduced Serum Medium for 24 hours.

extract_protocol:
Total RNA was extracted from cells using RNeasy Mini Kit (QIAGEN, Germany).
RNA library preparation and sequencing were performed by the DNA sequencing core at the University of Michigan. Briefly, cDNA libraries were prepared using the Illumina NEBNext Ultra RNA Library Prep Kit and sequencing was performed on the NovaSeq X platform to generate 151-base pair paired-end reads. An average of 34 million paired-reads were generated per sample.

treatment_protocol: For the palmitic acid (PA) incubation study, a 10% BSA (10% wt/vol) solution was prepared by dissolving fatty acid free BSA (Sigma) in sterile saline and stored at 4°C. PA was dissolved in saline at a 50 mM stock concentration and stored at -20°C. For each experiment, PA was thawed at 70°C and dissolved in 10% BSA to 5 mM. This solution was then added to Opti-MEM serum-reduced medium to obtain a final concentration of 250 µM. The control group was mixed with saline instead of PA to maintain a consistent BSA concentration.

value: PA

tag: batch


title: PM, Control, replicate 2

description:
Element Biosciences AVITI sequencer
Ctl2


title: mouse 8-Cell embryo - Control3

city: 温州

first: kefan

last: zheng

address: 瓯海区茶山街道温州医科大学

institute: wenzhou medical university

description: Library name: Sample3

data_processing:
Remove adapters from raw Cut&Tag data using fastp v 0.23.4
Cut-tag reads were aligned to the NCBI GRCm39 using Bowtie version 2.5.4
to create cut-tag coverage plots,the locations of the mapped cut-tag reads were extended to 50bp represent sequenced fragments,renormalizes and reformatted in the bigwig file format
Peaks were called using MACS v3.0.3 with the significance cut-off q-value <= 0.001
bigWig files were generated using deeptools v3.5.5
Assembly: GRCm39
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: mouse 8-Cell embryo

growth_protocol: mouse embryos were maintained in KsOM and cultured in an incubator at 37°C with 5% CO₂

extract_protocol:
Cells were bound to concanavalin A-coated magnetic beads and permeabilized with the nonionic detergent digitonin
ChIP-seq libraries were prepared using Hyperactive® Universal CUT&Tag Assay Kit for Illumina.By using a primary antibody against H3K18ac, along with a corresponding secondary antibody and Protein A/G, the transposase fused to Protein A/G is precisely directed to cleave DNA sequences near the target protein. During the cleavage process, adaptor sequences are simultaneously added to both ends of the DNA fragments. The fragments were then amplified by 18 cycles of PCR to generate libraries suitable for high-throughput sequencing.

treatment_protocol: At the 2-cell stage,embryos were treated with 100uM TMZ(Merck)

value: mouse 8-Cell embryo


title: NDF-degron, Spt16, ChIP_Aux1h_Rep3

value: Auxin 1 hr


title: PM, Control, replicate 1

description:
Element Biosciences AVITI sequencer
Ctl1


title: PM, Lipa overexpression, replicate 3

description:
Element Biosciences AVITI sequencer
LipaTg3


title: mGCs from EM group, cultured in DMEM/F12 with 5% FBS for 24 hours,Rep-3

description: Library name: PBS-3


title: mGCs from EM group, treated additionally with 100 nM 14, 15-EET for 24 hours,Rep-1

description: Library name: EET-1


title: Slc17a5 siRNA-M2+Nit-3

city: Beijing

first: Shaorong

address: Tian Tan Xi Li No. 4

institute: Capital Mecidal University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: Excel file includes RPKM values for each Sample

source_name: bone marrow

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

value: M2 monocyte

value: Slc17a5 knockdown

value: IL4, nitrate


title: NDF-degron, Spt16, ChIP_DMSO1h_Rep3

value: DMSO 1 hr


title: HASMC, PA_1

description:
Library name: PA_1
10111-YL-22

value: Human aortic smooth muscle cells (HASMC)


title: HASMC, BSA_3

description:
Library name: BSA_3
10111-YL-21

value: BSA


title: Slc17a5 siRNA-M2+Nit-2


title: NDF-degron, Spt16, ChIP_Aux2h_Rep1

value: Auxin 2 hr


title: mGCs from EM group, cultured in DMEM/F12 with 5% FBS for 24 hours,Rep-2

description: Library name: PBS-2


title: NDF-degron, Spt16, ChIP_DMSO1h_Rep2


title: Slc17a5 siRNA-M2+Nit-1


title: NDF-degron, Spt16, ChIP_Aux1h_Rep2


title: HASMC, BSA_2

description:
Library name: BSA_2
10111-YL-20


title: Slc17a5 siRNA-M2-3


title: HASMC, BSA_1

description:
Library name: BSA_1
10111-YL-19


title: mGCs from EM group,Rep-5

description: Library name: EM-mGC-5


title: mGCs from EM group, cultured in DMEM/F12 with 5% FBS for 24 hours,Rep-1

description: Library name: PBS-1


title: NDF-degron, Spt16, ChIP_Aux1h_Rep1


title: NDF-degron, Spt16, ChIP_DMSO1h_Rep1


title: DD28 DE

city: Los Angeles

first: Nils

last: Lindstrom

state: California

address: 1425 San Pablo St, BCC 413

institute: University of Southern California

description: Library name: DD28LCL

library_source: transcriptomic single cell

data_processing:
fastq files were demultiplexed and aligned to the genome
Feature-barcode matricies were read into Seurat (v5) using Read10X, as described in the text.
Assembly: Homo sapiens, GRCh38-2024-A
Supplementary files format and content: .rds file of processed single-cells from kidney organoids from differentiation day 28, which include both control and distal-enriched cells.

molecule: nuclear RNA

source_name: Kidney organoid

growth_protocol: Takasato et al., 2016 Nature Protocols

extract_protocol:
6 organoids per condition were pooled and snap-frozen in liquid nitrogen. Nuclei isolation was performed as described in Kim, S., et al, 2024, Dev Cell
10X Genomics Chromium Next GEM Single Cell Multiome Reagents PN-1000283, following 10X Genomics CG000338 Rev E.

treatment_protocol: distal-enriched kidney organoids were treated with LY29 from day 10 to day 12, and CHIR and LDN from day 11 to day 12

value: Kidney organoid

value: iPSCs (male)

value: WT

value: DD28 DE organoids


title: HASMC, PA_2

description:
Library name: PA_2
10111-YL-23


title: mGCs from EM group, treated additionally with 100 nM 14, 15-EET for 24 hours,Rep-2

description: Library name: EET-2

value: granulosa cell


title: DD28 control

description: Library name: DD28ctrl

value: DD28 control organoids


title: Slc17a5 siRNA-M2-2


title: mGCs from EM group,Rep-3

description: Library name: EM-mGC-3


title: mGCs from EM group,Rep-4

description: Library name: EM-mGC-4


title: Slc17a5 siRNA-M1+Nit-3

value: M1 monocyte

value: LPS+IFNg, nitrate


title: mGCs from EM group,Rep-2

description: Library name: EM-mGC-2


title: Slc17a5 siRNA-M2-1


title: Slc17a5 siRNA-M1+Nit-2


title: GCD2-3R

first: qi

last: zhu

state: Beijing

address: 28th Fuxing Road, Beijing, China

institute: Chinese PLA General Hospital

description: Library name: CD2-R3-2

data_processing:
fastp version 0.20.0
hisat2 version 2.2.1
featureCounts(subread) v2.0.1
DESeq2 1.32.0
Assembly: GRCh38.98
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv file include count values for each Sample

source_name: CAR-T cells

extract_protocol:
Qiagen RNeasy Kits for RNA Purification(ID:  74004)
VAHTS  Universal V8 RNA-seq Library Prep Kit for Illumina（NR605）

value: CAR-T cells

value: 3 round of antigen stimulation


title: ZCD2-3R

description: Library name: CD2-R3-3


title: LCD2-3R

description: Library name: CD2-R3-1


title: mGCs from sham surgery group,Rep-5

description: Library name: Con-mGC-5


title: mGCs from EM group,Rep-1

description: Library name: EM-mGC-1


title: Slc17a5 siRNA-M1-3

value: bone marrow

value: LPS+IFNg


title: ZCD2-1R

description: Library name: CD2-R1-3

value: 1 round of antigen stimulation


title: Slc17a5 siRNA-M1+Nit-1

value: Slc17a5 knockdown


title: Slc17a5 siRNA-M1-1


title: ZCD2-0

description: Library name: CD2-R0-3

value: before antigen stimulation


title: Slc17a5 siRNA-M1-2


title: GCD2-1R

description: Library name: CD2-R1-2


title: M2+Nit-3

value: M2 monocyte

value: IL4, nitrate


title: mGCs from sham surgery group,Rep-2

description: Library name: Con-mGC-2


title: GCD2-0

description: Library name: CD2-R0-2


title: MAM326_GFPpos_rep4

type: RNA

city: Lille

first: Roland

middle: P.

last: Bourette

address: Bd du Professeur Jules Leclercq

country: France

description: Gene expression in GFPpositive population

hyb_protocol: The labeled cRNA were purified and 600ng of each cRNA were then hybridized and washed following manufacturer's instructions.

scan_protocol: Microarrays were scanned using Agilent Feature Extraction Software© (FE version 10.7.3.1).

data_processing: Data were extracted using Agilent Feature Extraction Software© (FE version 10.7.3.1).

source_name: MAM326 cell line, GFPpositive cells, replicate 4

label_protocol: Cyanine 3-labeled cRNA were synthesized with the low input QuickAmp labeling kit from 20ng of total RNA. RNA Spike-In were added to all tubes and used as positive controls of labeling and amplification steps.

growth_protocol: Cells were cultured in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum. Cells were incubated at 37°C in a humidified incubator with 5% CO2.

extract_protocol: RNA was extracted using RNeasy Plus Micro kit (QIAGEN, Saint-Quentin Fallavier, France) following the manufacturer's recommendations. Total RNA yield and quality were further assessed on a NanoDrop ND-1000 and an Agilent 2100 bioanalyzer.

treatment_protocol: Cells were harvested using Versene Trypsineand sorted by FACS.


title: MAM326_GFPpos_rep3

source_name: MAM326 cell line, GFPpositive cells, replicate 3


title: MAM326_GFPneg_rep3

description: Gene expression in GFPnegative population

source_name: MAM326 cell line, GFPnegative cells, replicate 3


title: M2+Nit-2


title: mGCs from sham surgery group,Rep-1

description: Library name: Con-mGC-1


title: LCD2-0

description: Library name: CD2-R0-1


title: MAM326_GFPpos_rep2

source_name: MAM326 cell line, GFPpositive cells, replicate 2


title: pool I

city: Vienna

first: Martin

last: Aichinger

address: Dr. Boehringer-Gasse 5-11

country: Austria

institute: Boehringer-Ingelheim

description: Library name: I

data_processing:
Sequence alignment was performed by SevenBridges platform 1.9.1(workflow reversion 13).
Single-cell datasets were analyzed with Seurat package (version 4.2.0) in R in a standard way: first 30 principal components were used for the UMAP embedding, Leiden clustering was performed with the resolution of 0.8. Scrublet (version 0.2.3) was used to detect potential doublet, cells with scrublet score smaller than 0.15 were excluded from the analysis. Automated annotation of the cell types was performed with SingleR package (version 2.0.0). With Seurat, differentially expressed genes were discovered within cell types between treatments.
Assembly: mm10 / custom reference
Supplementary files format and content: Seurat object with the counts of RNA-seq reads and barcodes
Supplementary files format and content: seurat.rds contains a Seurat object with single cell RNA-seq and antibody barcode counts, as well as the cell type annotation.
Supplementary files format and content: reference_adt.fasta contains the sequences of the antibody barcodes for the proteomics analysis
Supplementary files format and content: feature_reference.csv contains the mapping of cell hashing barodes (SampleTag) to the samples and the mapping of antibody barcodes to the proteins they bind to. Sample tag barcodes are re-used between libraries, sample tag and library uniquely define the sample (see "library" column in feature_reference.csv)
Library strategy: CITE-seq

source_name: subcutaneous tumor

growth_protocol: Subcutaneously transplanted syngeneic tumor PDAC tumor model.

extract_protocol:
For CITE-Seq analysis, single cell libraries were generated using the BD Rhapsody system. Single cell suspensions from 3 tumors per group closest to the median were stained for multiplexing and with AbSeq oligo antibodies according to manufacturer’s protocol (BD Doc ID: 214419 Rev 2.0) with slight modifications. In detail, multiplexing of samples was achieved by labelling with the Custom BD Single-Cell Multiplexing MHC I Set (BD 626545), followed by equal pooling of 3 samples each (resulting in 2 pooled samples), Fc blocking with TruStain FcX PLUS antibody (Biolegend 156604) and staining with AbSeq oligo antibody mix (see Table S8). Single cell capture and cDNA synthesis was performed with the BD Rhapsody Single-Cell Analysis System and the Cartridge Reagent Kit (BD 633731), the Cartridge Kit (BD 33733) and the cDNA Kit (BD 633773) according to manufacturer’s protocol (BD Doc ID: 210966 Rev. 1.0). Libraries were generated with the WTA Amplification Kit (BD 633801) according to manufacturer’s protocol “mRNA Whole Transcriptome Analysis (WTA), AbSeq, and Sample Tag Library Preparation” (Doc ID: 23-21752-00). Pooling of libraries of each cartridge was calculated following instructions given in BDs’ “SEQ Calculator v1.2.xlsm” and libraries were sequenced (paired-end) on the Illumina platform.
Libraries were generated with the Targeted Amplification Kit (BD, 633774) and the Mouse Immune Response Panel (BD, 633753) according to manufacturer’s protocol (Doc ID: 214508 Rev. 3.0). Pooling of libraries of each cartridge was calculated following instructions given in BDs’ “SEQ Calculator v1.2.xlsm” and libraries were sequenced (paired-end) on the Illumina platform.

treatment_protocol: Syngenetic PKC7829c11 subcutaneous model were treated with KRAS inhibitor (30mg/kg qd), anti-PD1 (10mg/kg q3/4d)  and their combination.

value: subcutaneous tumor

value: All cell types from a tumor

value: KRAS G12D; p53del

value: mixed sample


title: M2+Nit-1

value: WT


title: MAM326_GFPneg_rep4

source_name: MAM326 cell line, GFPnegative cells, replicate 4


title: MAM326_GFPpos_rep1

source_name: MAM326 cell line, GFPpositive cells, replicate 1


title: MAM326_GFPneg_rep2

source_name: MAM326 cell line, GFPnegative cells, replicate 2


title: mGCs from sham surgery group,Rep-4

description: Library name: Con-mGC-4

value: granulosa cell


title: Z19-3R

description: Library name: 19-R3-3


title: pool H

description: Library name: H


title: pool G

description: Library name: G


title: MEF H3K9me3 Cut and Tag

city: Dallas

first: Nikhil

last: Munshi

address: 5323 Harry Hines Blvd

department: Cardiology

institute: UT Southwestern

description: Library name: Sample5

data_processing:
Paired-end 75 bp read length Fastq files were checked for quality using fastqc (v0.11.5) and fastq_screen (v0.11.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to mouse genome using bowtie2 (v2.3.3.1)
Duplicates were marked using picard-tools (v2.2.1) and blacklist regions were removed using bedtools (v2.7.1)
TN5 shifting of bam files was performed using the open-source Perl script "ATAC_BAM_shiftrt_gappedAlign.pl"
Assembly: mm10
Supplementary files format and content: bigiwg
Library strategy: CUT&Tag

source_name: Mouse Embryonic Fibroblast

growth_protocol: Roughly 150-200k cells were seeded in 1 well of a 6 well dish in 2 mL of DMEM supplemented with 10% FBS and 5% CO2 at 37C

extract_protocol:
Cut and Tag was performed exactly as written in the Henikoff protocol on Protocol.io with no modifications
NEB 2x mastermix was used to amplify sequences containing inserts following the exact steps in the Henikoff protocol

treatment_protocol: One day after plating cells were infected with retrovirus encoding each of the reprogramming cocktails described in the sample header. The cells received a second round of virus one day after the first infection. The cells were then changed to fresh 18s media to promote differentiation. The cells were then grown for 6 days in 18s media prior to sorting for GFP, 50,000 cells were recovered per condition and used to prepare the Cut and Tag libraries.

value: Mouse Embryonic Fibroblast

value: HCN4-GFP reporter


title: mGCs from sham surgery group,Rep-3

description: Library name: Con-mGC-3


title: M2-3


title: PM H3K27me3 Cut and Tag

description: Library name: Sample4

source_name: induced pacemaker myocyte

value: induced pacemaker myocyte

value: GMT + Hand2


title: MAM326_GFPneg_rep1

source_name: MAM326 cell line, GFPnegative cells, replicate 1


title: PM H3K9me3 Cut and Tag

description: Library name: Sample6


title: LCD2-1R

description: Library name: CD2-R1-1

value: CAR-T cells


title: pool F

description: Library name: F


title: G19-3R

description: Library name: 19-R3-2

value: 3 round of antigen stimulation


title: MEF H3K27me3 Cut and Tag

description: Library name: Sample3


title: M2-2

value: bone marrow


title: pool E

description: Library name: E


title: L19-3R

description: Library name: 19-R3-1


title: M2-1


title: Z19-1R

description: Library name: 19-R1-3

value: 1 round of antigen stimulation


title: iPM ATAC

description: Library name: Sample2

data_processing:
Paired-end 75 bp read length Fastq files were checked for quality using fastqc (v0.11.5) and fastq_screen (v0.11.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to mouse genome using bowtie2 (v2.3.3.1)
Duplicates were marked using picard-tools (v2.2.1) and blacklist regions were removed using bedtools (v2.7.1)
TN5 shifting of bam files was performed using the open-source Perl script "ATAC_BAM_shiftrt_gappedAlign.pl"
Assembly: mm10
Supplementary files format and content: bigiwg


title: pool D

description: Library name: D


title: P05P

city: 厦门市

first: 天圣

last: 陈

state: 福建省

address: 印斗路43号集美大学水产学院

institute: 集美大学

description: Library name: sample6

data_processing:
Illumina Casava 1.8 software used for basecalling
Assembly: https://www.ncbi.nlm.nih.gov/genome/10841
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for all Samples

organism: Anguilla japonica

source_name: pituitary

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared usingNEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775L)

value: pituitary

value: female

tag: age

value: pre-matured


title: G19-1R

description: Library name: 19-R1-2


title: M1+Nit-3

value: M1 monocyte

value: LPS+IFNg, nitrate


title: pool C

description: Library name: C

value: subcutaneous tumor

value: All cell types from a tumor

value: KRAS G12D; p53del


title: M1+Nit-2

value: WT


title: L19-1R

description: Library name: 19-R1-1


title: P01P

address: 印斗路43号集美大学水产学院

description: Library name: sample4


title: M1+Nit-1


title: P04P

address: 印斗路43号集美大学水产学院

description: Library name: sample5


title: Z19-0

description: Library name: 19-R0-3

value: before antigen stimulation


title: M1-2

value: LPS+IFNg


title: pool A

description: Library name: A

value: mixed sample


title: Lyve1 KO, heart, MI

city: Oxford

first: Paul

middle: Richard

last: Riley

address: IMS-Tetsuya Nakamura Building, Old Road Campus

country: United Kingdom

institute: University of Oxford

description:
Library name: LKOsample
10X Genomics

data_processing:
Raw data was processed using Cell Ranger, v.8.0.1
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: Heart

extract_protocol:
Chromium GEM-X Single Cell 5' Kit v3, 16 rxns PN-1000699 https://cdn.10xgenomics.com/image/upload/v1710231087/support-documents/CG000733_ChromiumGEM-X_SingleCell5_ReagentKitsv3_UserGuide_RevA.pdf
Library Construction Kit C 16 rxns, PN-1000694

treatment_protocol: Prior to conducting scRNA-Seq, comparing CD45+ enriched cells from neonatal Lyve1 knockout versus WT hearts at P2MI7dpi, the samples were FACS-sorted using 7AAD and CD45 to isolate live CD45+ cells ready for library construction.

value: Heart

value: Lyve1 KO

value: Myocardial infarction P2

value: 9 days


title: A68P

address: 印斗路43号集美大学水产学院

description: Library name: sample3

value: matured


title: A65P

address: 印斗路43号集美大学水产学院

description: Library name: sample2

value: pituitary


title: M1-3

value: bone marrow


title: M1-1


title: G19-0

description: Library name: 19-R0-2

value: CAR-T cells


title: L19-0

description: Library name: 19-R0-1


title: H1299-VGF OE-2

status: Public on Aug 04 2025

city: shenyang

first: Xinyue

last: Sheng

state: liaoning

address: No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning Province, P.R. China

institute: china medical university

description: Library name: H1299-VGF OE-2

data_processing:
Differential expression analysis was conducted using the DESeq2 package. Subsequently, the resulting P values were adjusted using Benjamini and Hochberg’s method to control the false discovery rate. Genes exhibiting differential expression were identified based on a combination of statistical significance (P value < 0.05) and magnitude of change (fold change≥1.5). The acquired biological functions and signaling pathways were annotated and visualized using the Metascape database (www.metascape.org), which included Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, hallmark gene sets, Reactome gene sets, wiki-pathways, canonical pathways, and PANTHER pathway based on specific differentially expressed genes.
Assembly: GRCh38
Supplementary files format and content: csv files include count values for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: A549 NSCLC cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C, NCI-H1299 NSCLC cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Use (Tiangen DP411, CLB+Adlai RN40, CTAB+Adlai RN40, Tiangen DP762-T1C) kit/TRIzol kit to complete the extraction of nucleic acid. Note: plant leaves are preferentially used: (Tiangen DP411 (manufacturer: Tiangen, model: DP411), Tiangen DP762-T1C (manufacturer: Tiangen, model: DP762-T1C)) Plant roots, stems and seeds are preferentially used: (CLB+Adlai RN40, CTAB+Adlai RN40 (manufacturer: Adlai, model: RN40)) kit conventional animal tissuesare preferentially used：TRIzol For other special samples (whole blood, skin and hair), use: (QIAGEN 217044 (manufacturer: QIAGEN. model: 217004), QIAGEN 217184 (manufacturer: QIAGEN. model: 217184), PAXgene Blood miRNA Kit (50) (manufacturer: QIAGEN. model: 763134) reagent kit.
1. mRNAPurificationand Fragmentation (1) First binding of mRNA with beads. Add mRNA Capture Beads into the prepared total RNA samples, mix and incubate at 65℃ to denature RNA. After denaturation, leave at room temperature for 5min to bind mRNA to magnetic beads. Place the tube in a magnetic stand and carefully remove the supernatant after the magnetic bead is fully absorbed to the magnet side.Take the tube out of the magnetic stand, Pipette repeatedly 6 times to mix thoroughly with Wash Buffer and place it on the magnetic stand. After the magnetic bead is fully absorbed to the magnet side, remove the supernatant.Take the tube out of the magnetic stand, add the Tris Buffer to mix thoroughly, and elute the mRNA at 80℃. (2) Second binding of mRNA with beads. Add the Beads Binding Buffer into the centrifugal tube upward, blow and mix, and place at room temperature for 5min to recombine the mRNA onto the magnetic beads. Place the tube on the magneticstand, make the magnetic bead fully adsorbed on the magnet side, and then remove the supernatant. Take the tube out of the magnetic stand, blow and mix it with Wash Buffer, place it on the magnetic stand for 2min, and remove the supernatant. Remove the tube from the magnetic stand, add Frag/Prime Buffer, blow and mix. (3) Fragmentation of mRNA Add the above mRNA products into the PCR instrument, determine the corresponding interrupting conditions according to the quality of the samples, and immediately put them on ice after the completion of interrupting. 2. Synthesis of the first strand cDNA Add the reagent required for reverse transcription of the first strand into the centrifuge tube of the previous reaction, mix and centrifuge, and then put it into the PCR instrument to set the program for the synthesis of the first strand of cDNA. 3. Synthesis of the second strand cDNA(endrepair and add A) Add the reagents of the second strand cDNA synthesis reaction to the first strand product of the synthesized cDNA in turn, mix and centrifuge, and then put them into the PCR instrument to set the procedure for the second.  4. Adapter Ligation The connector and ligase are added to the above reaction products in turn, incubated in a metal bath, and the connector connection reaction is carried out. 5. Clean UpPostLigationandfragmentselection.Add the corresponding volume of (0.6X) mixed magnetic beads to the above reaction products, mix them well, incubate them at room temperature, and then place them on the magnetic stand. After the magnetic beads are adsorbed on one side of the magnetic stand, remove the supernatant.Place the centrifuge tube on the magneticstand, add 80% ethanol freshly prepared, stand for 30s, and remove the supernatant,repeat once. After the second cleaning, centrifuge the supernatant with a 10 ul gun head.Place the centrifugal tube on the magnetic stand, open the tube cover, and dry the air, take off the centrifuge tube, add Nuclease-free Water, mix well, incubate at room temperature, and then put it on the magnetic satnd for standing, suck the supernatant and transfer it into a new centrifuge tube.Add the corresponding volume of (0.6X) mixed magnetic beads to the above centrifuge tube, mix them well, incubate them at room temperature, and then place them on the magnetic stand; suck the supernatant and transfer it to a new centrifuge tube, and add (0 1X) the mixed magnetic beads are incubated at room temperature after mixing.After incubation, put it on the magnetic stand, and discard the supernatant after the separation of the magnetic bead and the supernatant, place the centrifuge tube on the magnetic satnd, add the freshly prepared 80% ethanol, leave it on the magnetic rack for 30s, and remove the supernatant; Repeat this step once.Place the centrifugal tube on the magnetic stand, open the tube cover, and dry the air; Take off the centrifuge stand, add Nuclease-free Water, blow and suck, mix well, and leave at room temperature; Then stand on the magnetic rack, suck the supernatant and transfer it into a new 0.2ml centrifuge tube. 6. Library Amplification Add all kinds of reagents required for PCR reaction into the centrifuge tube, mix well, centrifuge, and put them into the PCR instrument for PCR amplification according to the PCR reaction conditions. 7. Clean UpPostAmplification. Instantaneous centrifugal PCR reaction tube, add corresponding volume of magnetic beads, thoroughly mix; incubate at room temperature, and then put it on a magnetic stand for standing, and carefully remove the supernatant;add freshly prepared 80% ethanol into the reaction tube, stand on the magnetic stand for 30s, remove the supernatant, and repeat this step once. Open the tube cover, add nuclease-free water to elute DNA after the magnetic beads are dried, blow and suck it evenly, leave it at room temperature, stand it on the magneticstand, carefully suck the supernatant into a new centrifuge tube, and sub-pack 1.5 μ L is used for fragment detection in a new 1.5 mL centrifuge tube and stored at- 20 ℃. 8. Library quality inspection The library was inspected by Qsep-400 method, and could be tested on the machine.

treatment_protocol: NSCLC cells were transfected by empty vector of VGF lentivirus.

value: NSCLC cells

value: VGF-OE

value: VGF lentivirus transfected


title: A10P

address: 印斗路43号集美大学水产学院

description: Library name: sample1

value: female


title: H1299-VGF OE-1

description: Library name: H1299-VGF OE-1


title: H1299-VGF OE-3

description: Library name: H1299-VGF OE-3


title: WT, heart, MI

description:
Library name: WTsample
10X Genomics


title: H1299-CTRL-3

description: Library name: H1299-CTRL-3

value: empty vector lentivirus transfected


title: A549-VGF OE-3

description: Library name: A549-VGF OE-3


title: H1299-CTRL-1

description: Library name: H1299-CTRL-1

value: WT


title: pool B

description: Library name: B

value: subcutaneous tumor

value: All cell types from a tumor

value: KRAS G12D; p53del


title: A549-CTRL-3

description: Library name: A549-CTRL-3


title: H1299-CTRL-2

description: Library name: H1299-CTRL-2


title: A549-VGF OE-2

description: Library name: A549-VGF OE-2


title: A549-CTRL-2

description: Library name: A549-CTRL-2


title: A549-CTRL-1

description: Library name: A549-CTRL-1


title: A549-VGF OE-1

description: Library name: A549-VGF OE-1


title: untreated H3K9me3

city: Kanazawa

first: Tomohisa

last: Baba

address: Kakuma-machi

country: Japan

institute: Kanazawa University

description: Library name: sample 6

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.33 (parameter- TruSeq3-PE.fa:2:40:15, LEADING:10 MINLEN:50).
Trimmed sequence reads were mapped to the NCBI GRCH38  using bowtie2 v2.5.2.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: blood

growth_protocol: RPMI1640 supplemented with 10% FBS

extract_protocol:
DNA sample preparation was conducted using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling).
ChIP-Seq libraries were prepared using NEBNext Ultra II DNA Library prep kit for Illumina.

treatment_protocol: HL-60 cells were treated with 1 μM ATRA and/or 1 μM palbociclib for 48 hours.

value: blood

value: myeloid leukemia


title: input

description: Library name: sample 1


title: ATRA H3K9me3

description: Library name: sample 7


title: palbociclib H3K9me3

description: Library name: sample 8


title: H1, Ectodermal cells, Affected

city: Nantes

first: Marielle

last: OLOUDE

state: Loire et Atlantique

address: 30 Bd Jean Monnet

institute: The Center for Research in Transplantation and Translational Immunology

description:
Library name: H1
Column name in Raw_counts_All_samples.txt: H1

data_processing:
The resulting library, with fragment sizes ranging from 350 to 800 bp, was sequenced on a 100-cycle SP v1.5 run on the NovaSeq 6000 system. The BCL files generated by the sequencer were demultiplexed using bcl2fastq2 ("Bcl2fastq2 Conversion Software v2.20 Software Guide (15051736)"), producing FASTQ files. The resulting FASTQ files were analyzed using the 3’ Sequencing RNA Profiling (SRP) pipeline (Charpentier et al. 2021). This methodology aligns with previous DGEseq analyses performed in various studies (Chaumette et al. 2022; Letellier et al. 2022; Ménoret et al. 2023). The SRP pipeline integrates cutadapt v4.5 (Martin 2011) for read trimming and bwa aln v0.7.17 (Li and Durbin 2009) for alignment to the hg38 human reference genome and transcriptome. A custom Python script integrated into the SRP pipeline was used to parse and count UMIs, generating a raw matrix containing transcript counts, with columns representing samples and rows representing genes. The dataset comprised a total of 28,307 genes and 16 samples, where each sample is in technical replicates (16*2= 32).
Assembly: hg38
Supplementary files format and content: Raw_counts_All_samples.txt

source_name: Ectodermal cells

growth_protocol: Lymphocytes T cells : Whole-blood samples collected from healthy individuals as well as subjects were processed using spin medium gradient centrifugations (pluriSelect) to separate and isolate peripheral blood mononuclear cells (PBMC) for cryopreservation using a standard freezing medium consisting of 90% FBS and 10 % DMSO. At a later point in time, PBMC were plated on 96-well plates together with irradiated allogeneic PBMC in the presence of IL-2 and PHA-L for T cell expansion as in 11. Human T cells were maintained in RPMI1640 supplemented with 10 % human AB serum and 1% penicillin/streptomycin and analyzed at a resting state after 3-4 weeks of expansion. Ectodermal cells : iPSc lines harboring the p.Arg325Trp variant were produced by CRISPR/Cas9 editing of the genome of the commercial iPSC line ASE-9211 (Applied StemCell, Milpitas, USA). iPSc were cultured in mTeSR™1 medium (STEMCELL Technologies) on Matrigel® hESC-Qualified Matrix (Corning) following standard protocols. Cells were seeded onto 24-well plates and differentiated for 7 days using the StemMACS™ Trilineage Differentiation Kit (Miltenyi Biotec) according to the manufacturer's instructions. On day 7, total RNA was extracted using NucleoSpin RNA (Macherey-Nagel), one microgram was then reverse transcribed into cDNA using the ProtoScript II kit (New England BioLabs Inc). The resulting cDNA was subjected to qPCR using Premix Taq™ DNA Polymerase (TaKaRa) and TaqMan Gene Expression Assays (Thermofisher Scientific) for quantification of ectoderm-specific differentiation markers SOX1 and PAX6.

extract_protocol:
Total RNA was harvested using Qiagen's mini miRNeasy kit.
The 3' digital gene expression profiling protocol was performed as previously described (Chaumette et al. 2022). Library preparation was initiated from 10 ng of total RNA per sample. mRNA poly(A) tails were tagged with universal adapters, well-specific barcodes, and unique molecular identifiers (UMIs) during the template-switching reverse transcription process.

treatment_protocol: After cell culture of T lymphocytes, 1 million cells were resuspended in 700 µl Qiazol and conservé à -80°C .

value: Ectodermal cells

value: Affected


title: G8, Ectodermal cells, Affected

description:
Library name: G8
Column name in Raw_counts_All_samples.txt: G8


title: E5, Ectodermal cells, Control

description:
Library name: E5
Column name in Raw_counts_All_samples.txt: E5

value: Control


title: C10, Ectodermal cells, Control

description:
Library name: C10
Column name in Raw_counts_All_samples.txt: C10


title: S37, Lymphocytes T cells, Affected, Rep_2

description:
Library name: S37_Rep_2
Column name in Raw_counts_All_samples.txt: S37_Rep_2

source_name: Lymphocytes T cells

value: Lymphocytes T cells


title: S15, Lymphocytes T cells, Affected, Rep_2

description:
Library name: S15_Rep_2
Column name in Raw_counts_All_samples.txt: S15_Rep_2


title: ASE9211 , Ectodermal cells, Control

description:
Library name: ASE9211
Column name in Raw_counts_All_samples.txt: ASE9211


title: S36, Lymphocytes T cells, Affected, Rep_2

description:
Library name: S36_Rep_2
Column name in Raw_counts_All_samples.txt: S36_Rep_2


title: S36, Lymphocytes T cells, Affected, Rep_1

description:
Library name: S36_Rep_1
Column name in Raw_counts_All_samples.txt: S36_Rep_1


title: S23, Lymphocytes T cells, Affected, Rep_2

description:
Library name: S23_Rep_2
Column name in Raw_counts_All_samples.txt: S23_Rep_2


title: S23, Lymphocytes T cells, Affected, Rep_1

description:
Library name: S23_Rep_1
Column name in Raw_counts_All_samples.txt: S23_Rep_1


title: Control_12, Lymphocytes T cells, Control, Rep_2

description:
Library name: Control_12_Rep_2
Column name in Raw_counts_All_samples.txt: Control_12_Rep_2


title: Control_11, Lymphocytes T cells, Control, Rep_1

description:
Library name: Control_11_Rep_1
Column name in Raw_counts_All_samples.txt: Control_11_Rep_1


title: Control_11, Lymphocytes T cells, Control, Rep_2

description:
Library name: Control_11_Rep_2
Column name in Raw_counts_All_samples.txt: Control_11_Rep_2


title: S15, Lymphocytes T cells, Affected, Rep_1

description:
Library name: S15_Rep_1
Column name in Raw_counts_All_samples.txt: S15_Rep_1


title: Control_8, Lymphocytes T cells, Control, Rep_2

description:
Library name: Control_8_Rep_2
Column name in Raw_counts_All_samples.txt: Control_8_Rep_2


title: Control_10, Lymphocytes T cells, Control, Rep_1

description:
Library name: Control_10_Rep_1
Column name in Raw_counts_All_samples.txt: Control_10_Rep_1


title: Control_9, Lymphocytes T cells, Control, Rep_2

description:
Library name: Control_9_Rep_2
Column name in Raw_counts_All_samples.txt: Control_9_Rep_2


title: Control_9, Lymphocytes T cells, Control, Rep_1

description:
Library name: Control_9_Rep_1
Column name in Raw_counts_All_samples.txt: Control_9_Rep_1


title: combination H3K9me3

description: Library name: sample 9


title: Control_6, Lymphocytes T cells, Control, Rep_2

description:
Library name: Control_6_Rep_2
Column name in Raw_counts_All_samples.txt: Control_6_Rep_2


title: Control_7, Lymphocytes T cells, Control, Rep_2

description:
Library name: Control_7_Rep_2
Column name in Raw_counts_All_samples.txt: Control_7_Rep_2


title: Control_5, Lymphocytes T cells, Control, Rep_2

description:
Library name: Control_5_Rep_2
Column name in Raw_counts_All_samples.txt: Control_5_Rep_2


title: S37, Lymphocytes T cells, Affected, Rep_1

description:
Library name: S37_Rep_1
Column name in Raw_counts_All_samples.txt: S37_Rep_1


title: Control_4, Lymphocytes T cells, Control, Rep_2

description:
Library name: Control_4_Rep_2
Column name in Raw_counts_All_samples.txt: Control_4_Rep_2


title: Control_6, Lymphocytes T cells, Control, Rep_1

description:
Library name: Control_6_Rep_1
Column name in Raw_counts_All_samples.txt: Control_6_Rep_1


title: Control_5, Lymphocytes T cells, Control, Rep_1

description:
Library name: Control_5_Rep_1
Column name in Raw_counts_All_samples.txt: Control_5_Rep_1


title: Control_7, Lymphocytes T cells, Control, Rep_1

description:
Library name: Control_7_Rep_1
Column name in Raw_counts_All_samples.txt: Control_7_Rep_1


title: Control_3, Lymphocytes T cells, Control, Rep_2

description:
Library name: Control_3_Rep_2
Column name in Raw_counts_All_samples.txt: Control_3_Rep_2


title: Control_12, Lymphocytes T cells, Control, Rep_1

description:
Library name: Control_12_Rep_1
Column name in Raw_counts_All_samples.txt: Control_12_Rep_1


title: Control_10, Lymphocytes T cells, Control, Rep_2

description:
Library name: Control_10_Rep_2
Column name in Raw_counts_All_samples.txt: Control_10_Rep_2


title: Caco-2, DFC, Deoxygenated medium, 13DPS, Rep2

city: Odense M

first: Jens

middle: Sivkær

last: Pettersen

state: Danmark

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

description: Library name: DFC_DO_2

library_source: other

data_processing:
Raw paired-end reads were aligned to the human genome assembly hg38 using STAR (version 2.7.11a)
Primary alignments were filtered, sorted, and indexed using samtools (version 1.19).
Using featureCounts from the subread package (version 2.0.6.), read counts within exons were counted, with multimapping reads included and counted fractionally.
Assembly: GRCh38/hg38
Supplementary files format and content: File contains read counts for all protein-coding features of hg38 in all samples (file format: csv). The file also contain EnsemblIDs, Gene names, length, as well as logFC, logCPM, F, PValue and FDR from the edgeR differential gene expression analysis.

molecule: other

growth_protocol: Caco-2 cells were maintained in DMEM supplemented with 20 % heat-inactivated  fetal bovine serum (HI-FBS) and antibiotics (1 % penicillin-streptomycin, (Stock: 10,000 units/mL Penicillin and 10,000 µg/mL Streptomycin)) in humidified atmosphere with 5 % CO2 and 37 C, either in cell culture inserts, or in dual channel flow chambers (DFCs).

extract_protocol:
Cells were lysed with ice-cold lysis buffer (4 M GITC, 0.02 mM Tris-HCl, 10 mM NaAcetate, 25 mM EDTA, 0.1% Triton X-100, 2 mM DTT) and RNA was extracted by a phenol-chloroform extraction.
Ribosomal RNA was depleted uisng NEBNext rRNA Depletion Kit (Human/Mouse/Rat). RNA libraries were then prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit.

treatment_protocol: At 7 days post-seeding (DPS) in DFCs, medium was serum-reduced to 2 % HI-FBS, and cells were perfused with either normoxic medium or deoxygenated medium (< 1 %). Cells cultured statically in cell culture inserts with also serum reduced at 7 DPS.

value: human epithelial colorectal adenocarcinoma cell line

value: Cultured in dual flow chamber system, with deoxygenated medium, for 13DPS


title: Control_3, Lymphocytes T cells, Control, Rep_1

description:
Library name: Control_3_Rep_1
Column name in Raw_counts_All_samples.txt: Control_3_Rep_1


title: Caco-2, DFC, Deoxygenated medium, 13DPS, Rep3

description: Library name: DFC_DO_3


title: Caco-2, DFC, Deoxygenated medium, 13DPS, Rep1

description: Library name: DFC_DO_1


title: Control_1, Lymphocytes T cells, Control, Rep_1

description:
Library name: Control_1_Rep_1
Column name in Raw_counts_All_samples.txt: Control_1_Rep_1


title: Control_2, Lymphocytes T cells, Control, Rep_2

description:
Library name: Control_2_Rep_2
Column name in Raw_counts_All_samples.txt: Control_2_Rep_2


title: Control_1, Lymphocytes T cells, Control, Rep_2

description:
Library name: Control_1_Rep_2
Column name in Raw_counts_All_samples.txt: Control_1_Rep_2


title: Caco-2, DFC, 13DPS, Rep2

description: Library name: DFC_O_2

value: Cultured in dual flow chamber system, with normoxic medium, for 13DPS


title: Caco-2, DFC, 13DPS, Rep3

description: Library name: DFC_O_3


title: Control_8, Lymphocytes T cells, Control, Rep_1

description:
Library name: Control_8_Rep_1
Column name in Raw_counts_All_samples.txt: Control_8_Rep_1


title: Caco-2, TW, 13DPS, Rep3

description: Library name: TW_3

value: Cultured in transwell insert, statically, for 13DPS


title: Caco-2, TW, 13DPS, Rep2

description: Library name: TW_2


title: tkov3-hec1bbko-final-set2

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 440 Brookline Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

description: Library name: A10

data_processing:
Gene essentiality analysis was performed using MAGeCK v.0.5.9.5, with "mageck test -k tkov3_A9-10_BG01-04.txt --control-sgrna tkov3_nontargeting.txt --pdf-report -n bko_b2 -t tkov3-hec1bbko-final-set1,tkov3-hec1bbko-final-set2 -c tkov3-hec1bbko-baseline-set1,tkov3-hec1bbko-baseline-set2" for BKO and "mageck test -k tkov3_A9-10_BG01-04.txt --control-sgrna tkov3_nontargeting.txt --pdf-report -n tkov3_hec1b -t tkov3-hec1b-final -c tkov3-hec1b-initial" for HEC1B.
Assembly: Other, referenced to tkov3_ref_list.txt
Supplementary files format and content: tkov3_A9-10_BG01-04_count.txt, txt file,  raw median normalized mapped sgRNA counts
Supplementary files format and content: bko_b2.gene_summary.txt, txt file, RRA scored gene file tkov3_hec1b.gene_summary.txt, txt file, RRA scored gene file
Library strategy: CRISPR Screen

source_name: HEC1B BKO

extract_protocol:
Genomic DNA was isolated using QIAamp DNA Blood Maxi Kit following manufacturer’s instructions
sgRNA library was amplified from genomic DNA using Illumina-compatible index primers and sequenced by NovaSeq platform aiming for 300-500 times read coverage.

value: HEC1B BKO


title: tkov3-hec1bbko-final-set1

description: Library name: BG04


title: tkov3-hec1bbko-baseline-set2

description: Library name: A9


title: tkov3-hec1bbko-baseline-set1

description: Library name: BG03


title: tkov3-hec1b-initial

description: Library name: BG01


title: tkov3-hec1b-final

description: Library name: BG02


title: Kasumi-1 cells, shHASPIN_2

city: San Diego

first: Dong-Er

last: Zhang

address: 3855 Health Sciences Dr

institute: UCSD

data_processing:
FASTQs were aligned to Human genome (hg38.p13) using STAR (2.7.10a) in two-pass mode.
BAMs were sorted using samtools (v1.10) sort.
Raw counts were quantified using featurecounts (v2.0.0) with corresponding hg38.p13 genome annotation.
Assembly: hg38.p13
Supplementary files format and content: Normalized counts

growth_protocol: Kasumi-1 cells are cultured in RPMI-1640 supplemented with 10% Fetal Bovine Serum, 100 U/ml penicillin, and 100 µg/ml streptomycin at 37°C and 5% CO2. After transduction, 1.0 µg/ml Puromycin is added to culture media.

extract_protocol:
RNA was extracted from transduced Kasumi-1 cells 4 days post-selection using Trizol reagent per manufacturer's instructions.
Library was constructed using poly-A enrichment strategy by Novogene. Sequenced with Illumina Novaseq 6000 (Paired-End 150)

value: Acute Myeloid Leukemia

value: HASPIN knockdown


title: Kasumi-1 cells, shHASPIN_3


title: Control_2, Lymphocytes T cells, Control, Rep_1

description:
Library name: Control_2_Rep_1
Column name in Raw_counts_All_samples.txt: Control_2_Rep_1


title: Kasumi-1 cells, shCTRL_3


title: Kasumi-1 cells, shCTRL_2


title: Kasumi-1 cells, shCTRL_1


title: BTRC_53_10X _multiome_snATAC-seq

city: Indianapolis

first: Yunlong

state: IN

address: 410 West 10th Street, HITS 5001

institute: Indiana University School of Medicine

description: BTRC_53 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay

library_source: genomic single cell

data_processing:
For libraries containing 'multiome': Cell Ranger ARC Analysis Cell Ranger ARC (cellranger-arc-2.0.0, http://support.10xgenomics.com/) was utilized to process the raw sequence data derived from the single-cell multiome libraries. Both the ATAC and gene expression FASTQ files were processed with the cellranger-arc count algorithm. The reference refdata-cellranger-arc-GRCh38-2020-A-2.0.0 (10x Genomics) was used. Demultiplexing: Cells from each of the sequencing pools were demultiplexed back into their samples of origin using the tool Demuxlet with default parameters. A Signac object, containing both RNA and ATAC-seq data, was created for each pool from the multiome assay from the hdf5 file from the Cell Ranger output. Data from multiple sequencing runs of the same pool were merged. Sample-level metadata were then added to the Signac objects, which were saved as .rds files.
For libraries containing 'HT': Cell ranger Count Analysis: Cell Ranger Count (cellranger-count-7.0.1, http://support.10xgenomics.com/) was utilized to process the raw sequence data derived from the single-cell multiome libraries. The gene expression FASTQ files were processed with the cellranger count algorithm. The reference refdata-cellranger-GRCh38-2020-A (10x Genomics) was used. The filtered gene-cell barcode matrices were used for further analysis. Demultiplexing: Cells from each of the sequencing pools were demultiplexed back into their samples of origin using the tool Demuxlet with default parameters. The data from the technical replicates were then combined. A Seurat object was created from the data from each pool from the HT assay using the gene expression count matrix from the Cell Ranger output. Data from multiple sequencing runs of the same pool were merged. Sample-level metadata was then added to each Seurat object, which were then saved as .rds files.
Assembly: GRCh38
Supplementary files format and content: .RDS files are Seurat objects containing unnormalized count matrices and metadata for each barcode, including sample assignments and sample-level information, such as age, gender, and AUD classification. For HT RNA-seq objects, gene expression counts are included. For multiome objects, counts for gene expression and chromatin peaks are included.

source_name: caudate nucleus (postmortem brain)

extract_protocol:
For libraries containing 'multiome': 184 fresh-frozen post-mortem caudate brain samples were utilized in the assay. The 184 specimens were divided into 23 pools, with 8 in each pool. The donors in each pool were both condition (with or without AUD) and sex balanced. For each pool, around 20 mg tissue from each donor specimen was collected and combined into a sterilized 2 ml Dounce homogenizer. 2 ml chilled NP40 lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet P40 Substitute, 1mM DTT, 1 U/µl RNase inhibitor) was added to the Dounce homogenizer before the tissues were thawed. The tissues were homogenized 15x using pestle A, and 10x using pestle B, and were transferred into a centrifuge tube to incubate for 2 minutes on ice. After that, 2 ml wash buffer containing PBS, 1% BSA and 1 U/µl RNase inhibitor was added and mixed well. The lysed tissue was centrifuged at 500 rcf for 5 minutes at 4°C, then washed twice more with wash buffer and filtered through 70 µm and then 40 µm cell strainer separately. The pellet was resuspended in 2 ml wash buffer and mixed with 3.6 ml Sucrose Cushion Buffer I (nuclei PURE prep isolation kit, Sigma) containing 1 U/µl RNase inhibitor. 2 ml Sucrose Cushion Buffer I with 1 U/µl RNase inhibitor was added into one 15 ml Beckman Coulter centrifuge tube.  After that, the 5.6 ml nuclei suspensions were gently added to the top of Sucrose Cushion Buffer I without mixing, and followed by centrifuging at 13,000 x rpm (30,000 rcf) (Beckman Coulter ultracentrifuge) with rotor SW40Ti for 45 minutes at 4°C. The purified nuclei pellet was washed by centrifuging at 300 rcf for 5 min at 4°C with wash buffer, and the washed nuclei pellets was resuspended in wash buffer to target ~ 1000 nuclei/μl. For libraries containing HT: Nuclei Isolation for Single-nuclei RNA-seq: 163 fresh-frozen post-mortem caudate brain samples (same individuals as in Multiome assay) were grouped into 17 pools, with roughly 10 in each pool. The donors in each pool were both condition (with or without alcohol use disorder) and sex balanced. For each pool, around 20 mg tissue from each donor specimen was collected and combined into a sterilized 2 ml Dounce homogenizer. 2 ml chilled NP40 lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet P40 Substitute, 1mM DTT, 1 U/µl RNase inhibitor) was added to the Dounce homogenizer before the tissues were thawed. The tissues were homogenized 15x using pestle A, and 10x using pestle B, and were transferred into a centrifuge tube to incubate for 2 minutes on ice. After that, 2 ml wash buffer containing PBS, 1% BSA and 1 U/µl RNase inhibitor was added and mixed well. The lysed tissue was centrifuged at 500 rcf for 5 minutes at 4°C, then washed twice more with wash buffer and filtered through 70 µm and then 40 µm cell strainer separately. The pellet was resuspended in 2 ml wash buffer and mixed with 3.6 ml Sucrose Cushion Buffer I (nuclei PURE prep isolation kit, Sigma).  Zero point two (or One fifth) unit per microliter of RNase inhibitor was used in the buffers. This was followed by centrifuging at 13,000 x rpm (30,000 rcf) (Beckman Coulter ultracentrifuge) with rotor SW40Ti for 45 minutes at 4°C. The purified nuclei pellet was washed by centrifuging at 300 rcf for 5 min at 4°C with wash buffer, and the washed nuclei pellets was resuspended in wash buffer to target ~ 1000 nuclei/μl.
For libraries containing 'multiome': 10X Single-cell Multiome Library Preparation and Sequencing: Paired ATAC and gene expression libraries were generated following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide CG000338_RevB (10X Genomics, Inc). In brief, the isolated nuclei from a pool of samples were first incubated in a transposition mix. The single nuclei master mixture containing tagmented single nuclei suspension was loaded into two well of a Next GEM Chip J, along with the single cell multiome gel beads and partition oil. The chip was then loaded to the Chromium X Controller for GEM generation and barcoding. Barcoded transposed DNA and cDNA were amplified after GEMs being released. At each step, the quality of cDNA, ATAC library and cDNA library was examined by Bioanalyzer 2000. The final single indexed ATAC libraries and the dual indexed gene expression libraries were sequenced on an Illumina Novaseq 6000, with index reads of 10 bp + 24 bp, and 100 bp paired-end reads. The libraries were sequenced twice (2 technical replicates for each BioSample). For libraries containing 'HT': 10X HT Single-nuclei RNA-seq Library Preparation and Sequencing: The Chromium Next GEM single cell 3’ HT reagent kits v3.1 (user guide CG000416, 10X Genomics, Inc.) was used for the single-nuclei RNA-seq assay. The single nuclei suspension from a pool of 10 donor tissue samples were loaded into two wells of a Chromium Next GEM chip M to target 60,000 cell recovery per well. The chip was run on a Chromium X (10x Genomics). Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated. cDNA was synthesized and amplified following cell capture and cell lysis, The quality and quantity of cDNA and resulting libraries were examined by Bioanalyzer. The final libraries were sequenced on an Illumina NovaSeq 6000. 100-bp reads including cell barcode and UMI sequences and 100-bp RNA reads were generated. The libraries were sequenced two or three times for each BioSample.
For libraries containing 'multiome', 10X single nucleus multiome assay (RNA+ATAC-seq). For libraries contatining 'HT', single nucleus RNA-seq.

value: caudate nucleus (postmortem brain)


title: BTRC_104_10X _multiome_snATAC-seq

description: BTRC_104 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_93_10X _multiome_snATAC-seq

description: BTRC_93 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_97_10X _multiome_snATAC-seq

description: BTRC_97 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_95_10X _multiome_snATAC-seq

description: BTRC_95 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: Caco-2, DFC, 13DPS, Rep1

description: Library name: DFC_O_1

value: WT


title: BTRC_99_10X _multiome_snATAC-seq

description: BTRC_99 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_96_10X _multiome_snATAC-seq

description: BTRC_96 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_98_10X _multiome_snATAC-seq

description: BTRC_98 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_89_10X _multiome_snATAC-seq

description: BTRC_89 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_92_10X _multiome_snATAC-seq

description: BTRC_92 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_9_10X _multiome_snATAC-seq

description: BTRC_9 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: Caco-2, TW, 13DPS, Rep1

description: Library name: TW_1


title: BTRC_87_10X _multiome_snATAC-seq

description: BTRC_87 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_86_10X _multiome_snATAC-seq

description: BTRC_86 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_85_10X _multiome_snATAC-seq

description: BTRC_85 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: Kasumi-1 cells, shHASPIN_1


title: BTRC_79_10X _multiome_snATAC-seq

description: BTRC_79 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_76_10X _multiome_snATAC-seq

description: BTRC_76 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_72_10X _multiome_snATAC-seq

description: BTRC_72 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_71_10X _multiome_snATAC-seq

description: BTRC_71 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_6_10X _multiome_snATAC-seq

description: BTRC_6 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_83_10X _multiome_snATAC-seq

description: BTRC_83 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_7_10X _multiome_snATAC-seq

description: BTRC_7 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_58_10X _multiome_snATAC-seq

description: BTRC_58 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_69_10X _multiome_snATAC-seq

description: BTRC_69 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_51_10X _multiome_snATAC-seq

description: BTRC_51 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_5_10X _multiome_snATAC-seq

description: BTRC_5 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_47_10X _multiome_snATAC-seq

description: BTRC_47 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_42_10X _multiome_snATAC-seq

description: BTRC_42 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_44_10X _multiome_snATAC-seq

description: BTRC_44 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_45_10X _multiome_snATAC-seq

description: BTRC_45 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_35_10X _multiome_snATAC-seq

description: BTRC_35 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_34_10X _multiome_snATAC-seq

description: BTRC_34 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_33_10X _multiome_snATAC-seq

description: BTRC_33 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_326_10X _multiome_snATAC-seq

description: BTRC_326 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_318_10X _multiome_snATAC-seq

description: BTRC_318 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_313_10X _multiome_snATAC-seq

description: BTRC_313 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_311_10X _multiome_snATAC-seq

description: BTRC_311 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_309_10X _multiome_snATAC-seq

description: BTRC_309 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_304_10X _multiome_snATAC-seq

description: BTRC_304 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_303_10X _multiome_snATAC-seq

description: BTRC_303 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_30_10X _multiome_snATAC-seq

description: BTRC_30 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_3_10X _multiome_snATAC-seq

description: BTRC_3 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_299_10X _multiome_snATAC-seq

description: BTRC_299 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_57_10X _multiome_snATAC-seq

description: BTRC_57 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_54_10X _multiome_snATAC-seq

description: BTRC_54 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_291_10X _multiome_snATAC-seq

description: BTRC_291 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_29_10X _multiome_snATAC-seq

description: BTRC_29 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_41_10X _multiome_snATAC-seq

description: BTRC_41 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_281_10X _multiome_snATAC-seq

description: BTRC_281 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_284_10X _multiome_snATAC-seq

description: BTRC_284 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_28_10X _multiome_snATAC-seq

description: BTRC_28 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_280_10X _multiome_snATAC-seq

description: BTRC_280 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_282_10X _multiome_snATAC-seq

description: BTRC_282 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_276_10X _multiome_snATAC-seq

description: BTRC_276 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_274_10X _multiome_snATAC-seq

description: BTRC_274 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_321_10X _multiome_snATAC-seq

description: BTRC_321 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_273_10X _multiome_snATAC-seq

description: BTRC_273 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_272_10X _multiome_snATAC-seq

description: BTRC_272 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_269_10X _multiome_snATAC-seq

description: BTRC_269 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_267_10X _multiome_snATAC-seq

description: BTRC_267 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_266_10X _multiome_snATAC-seq

description: BTRC_266 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_264_10X _multiome_snATAC-seq

description: BTRC_264 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_302_10X _multiome_snATAC-seq

description: BTRC_302 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_295_10X _multiome_snATAC-seq

description: BTRC_295 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_261_10X _multiome_snATAC-seq

description: BTRC_261 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_262_10X _multiome_snATAC-seq

description: BTRC_262 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_26_10X _multiome_snATAC-seq

description: BTRC_26 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_259_10X _multiome_snATAC-seq

description: BTRC_259 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_256_10X _multiome_snATAC-seq

description: BTRC_256 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_251_10X _multiome_snATAC-seq

description: BTRC_251 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_258_10X _multiome_snATAC-seq

description: BTRC_258 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_245_10X _multiome_snATAC-seq

description: BTRC_245 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_289_10X _multiome_snATAC-seq

description: BTRC_289 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_242_10X _multiome_snATAC-seq

description: BTRC_242 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_241_10X _multiome_snATAC-seq

description: BTRC_241 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_235_10X _multiome_snATAC-seq

description: BTRC_235 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_232_10X _multiome_snATAC-seq

description: BTRC_232 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_234_10X _multiome_snATAC-seq

description: BTRC_234 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_231_10X _multiome_snATAC-seq

description: BTRC_231 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_27_10X _multiome_snATAC-seq

description: BTRC_27 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_230_10X _multiome_snATAC-seq

description: BTRC_230 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_24_10X _multiome_snATAC-seq

description: BTRC_24 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_225_10X _multiome_snATAC-seq

description: BTRC_225 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_227_10X _multiome_snATAC-seq

description: BTRC_227 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_221_10X _multiome_snATAC-seq

description: BTRC_221 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_218_10X _multiome_snATAC-seq

description: BTRC_218 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_216_10X _multiome_snATAC-seq

description: BTRC_216 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: Colon, KO, sample 4

city: Madrid

first: María

last: Mittelbrunn

state: Madrid

address: C/ Nicolás Cabrera, 1

country: Spain

institute: Centro de Biología Molecular Severo Ochoa

data_processing:
RNA-sequencing reads were mapped to the Mus musculus reference genome, GRCm39, using Hisat2 v2.2.1 software.
Reads were then preprocessed with SAMtools v1.13 to transform Sequence Alignment/Map files into Binary Alignment/Map files and sorted.
The number of reads covered by each gene is calculated by HTSeq-Count v1.99.2.
The normalized counts was obtained using DESeq2 v1.40.2.
Assembly: grcm39
Supplementary files format and content: comma-separated value file with the DESeq2 normalized counts for each sample
Supplementary files format and content: comma-separated value file the metadata for each sample

source_name: Colon

extract_protocol:
RNA from mouse colon was purified using the RNeasy Mini Kit (QIAGEN)
cDNA libraries were prepared from total RNA and, then, validated and quantified by an Agilent 4150 Bioanalyzer in BGI Genomics.

value: Colon

value: Tfam fl/fl Cd4 Cre


title: Colon, KO, sample 3


title: BTRC_215_10X _multiome_snATAC-seq

description: BTRC_215 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: Colon, KO, sample 1


title: BTRC_212_10X _multiome_snATAC-seq

description: BTRC_212 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_220_10X _multiome_snATAC-seq

description: BTRC_220 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_214_10X _multiome_snATAC-seq

description: BTRC_214 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_211_10X _multiome_snATAC-seq

description: BTRC_211 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: Colon, control, sample 2

value: Tfam fl/fl


title: Colon, control, sample 1


title: BTRC_210_10X _multiome_snATAC-seq

description: BTRC_210 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: Colon, KO+adoptive transfer, sample 6

value: CD4 T cell therapy


title: BTRC_21_10X _multiome_snATAC-seq

description: BTRC_21 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_228_10X _multiome_snATAC-seq

description: BTRC_228 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: Colon, KO+adoptive transfer, sample 4


title: BTRC_207_10X _multiome_snATAC-seq

description: BTRC_207 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: Colon, KO+adoptive transfer, sample 2


title: BTRC_205_10X _multiome_snATAC-seq

description: BTRC_205 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_204_10X _multiome_snATAC-seq

description: BTRC_204 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: Colon, KO+adoptive transfer, sample 3


title: BTRC_219_10X _multiome_snATAC-seq

description: BTRC_219 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_201_10X _multiome_snATAC-seq

description: BTRC_201 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_20_10X _multiome_snATAC-seq

description: BTRC_20 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: Control group

city: Shanghai

first: Shuo

last: Han

address: 320 Yue Yang Road, Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology

description: Library name: OES00396064

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm 10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: subcutaneous tumor

value: breast cancer

value: PBS


title: BTRC_2_10X _multiome_snATAC-seq

last: Liu

description: BTRC_2 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_197_10X _multiome_snATAC-seq

description: BTRC_197 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_198_10X _multiome_snATAC-seq

description: BTRC_198 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: 4_RT_Female, GEX

city: Milwaukee

first: Joseph

last: Zenga

state: WI

address: 9200 W WISCONSIN AVE

institute: MEDICAL COLLEGE OF WISCONSIN

description: Library name: 4_RT_Female

data_processing:
Raw sequencing reads were processed using CellRanger v8.0.1 to demultiplex reads, align to the GRCh38 reference genome, and quantify unique molecular identifiers (UMIs). Quality control was performed by filtering out cells with fewer than 200 or more than 5,000 features, and cells with >15% mitochondrial gene expression were excluded. The Seurat v5.1.0 toolkit was used to integrate datasets, perform canonical correlation analysis (CCA) to reduce batch effects, and identify variable features. Principal component analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP) were used for dimensionality reduction.
Assembly: GRCm39
Supplementary files format and content: Gene expression matrix: .mtx.gz, Barcodes and features: .tsv.gz, Metadata and annotations: .csv

source_name: jejunum

extract_protocol:
Single-cell suspensions were prepared from jejunum and viable cells were loaded into the 10x Genomics Chromium platform for partitioning. RNA from individual cells was reverse-transcribed and libraries were prepared accoding to the 10x Genomics protocol.
Library preparation was completed at the MCW Mellowes Center (RRID:SCR_022926) with 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kits (10X Genomics, sample dual indexes with cellular and molecular barcodes with VDJ amplification). Target capture of 10,000 cells per sample was used. Prior to sequencing, libraries were quantified and pooled by qPCR (Kapa Library Quantification Kit, Kapa Biosystems).

value: jejunum

value: Radiation Only


title: 5_RT_DIZE_Female, GEX

description: Library name: 5_RT_DIZE_Female

value: Radiation with DIZE


title: Treatment group

description: Library name: OES00396063

value: PCN


title: BTRC_196_10X _multiome_snATAC-seq

description: BTRC_196 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: 165_RT_DIZE_Male, GEX

description: Library name: 165_RT_DIZE_Male


title: BTRC_195_10X _multiome_snATAC-seq

description: BTRC_195 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: 164_RT_Male, GEX

description: Library name: 164_RT_Male


title: 163_NI_Male, GEX

description: Library name: 163_NI_Male

value: Non Irradiated


title: 24159FL-25-16

first: William

middle: T.

last: Pu

state: Ma

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: Library name: KO2_TBX5_2

data_processing:
Fastq files were analyzed using the Nextflow CUT&RUN pipeline with standard settings. Alignment was performed using the mm10 genome with bowtie2. Peaks called using Seacr were retained for diffbind analysis.
Assembly: mm10
Supplementary files format and content: Processed data files are bigwigs produced by the bed_to_bigwig process in nextflow.
Library strategy: CUT&Run

source_name: Atria

growth_protocol: Chd4 flox/flox mice were crossed and pups were used in the experiment.

extract_protocol:
Nuclei were extracted following the protocol described in detail in the methods. Briefly, snap-frozen atria were homogenized in homogenization buffer. Nuclei were filtered and counted. 500K nuclei were used in each CUT&RUN reaction.
Library construction was performed following the Epicypher CUT&RUN library prep protocol without modifications.

treatment_protocol: P2 mice were injected with a full dose of AAV9:Nppa-Cre or AAV9:Nppa-EGFP to produce CHD4 atrial KO or control mice.

value: Atria

value: whole atria

value: chd4 AKO (atrial KO)

tag: cut&run antibody

value: Novus 55931


title: Colon, KO+adoptive transfer, sample 1


title: BTRC_190_10X _multiome_snATAC-seq

description: BTRC_190 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay

value: caudate nucleus (postmortem brain)


title: BTRC_191_10X _multiome_snATAC-seq

description: BTRC_191 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_183_10X _multiome_snATAC-seq

description: BTRC_183 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: 24159FL-25-14

description: Library name: KO2_H3k27ac

value: Active motif 39133


title: BTRC_182_10X _multiome_snATAC-seq

description: BTRC_182 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_180_10X _multiome_snATAC-seq

description: BTRC_180 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: 24159FL-25-12

description: Library name: KO1_TBX5_2


title: Control_4, Lymphocytes T cells, Control, Rep_1

description:
Library name: Control_4_Rep_1
Column name in Raw_counts_All_samples.txt: Control_4_Rep_1

value: Lymphocytes T cells

value: Control


title: 3_NI_Female, GEX

description: Library name: 3_NI_Female


title: BTRC_176_10X _multiome_snATAC-seq

description: BTRC_176 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: 24159FL-25-10

description: Library name: KO1_H3k27ac


title: BTRC_179_10X _multiome_snATAC-seq

description: BTRC_179 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: 24159FL-25-11

description: Library name: KO1_TBX5_1

value: R+D Systems AF5918


title: BTRC_223_10X _multiome_snATAC-seq

description: BTRC_223 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_193_10X _multiome_snATAC-seq

description: BTRC_193 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: 24159FL-25-09

description: Library name: KO1_IgG

value: Epicypher Neg. ctl.


title: BTRC_174_10X _multiome_snATAC-seq

description: BTRC_174 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: 24159FL-25-08

description: Library name: WT2_TBX5_2

value: chd4 flox/flox (control)


title: 24159FL-25-06

description: Library name: WT2_H3k27ac


title: G1, Ectodermal cells, Affected

description:
Library name: G1
Column name in Raw_counts_All_samples.txt: G1

value: Ectodermal cells

value: Affected


title: 24159FL-25-07

description: Library name: WT2_TBX5_1


title: BTRC_171_10X _multiome_snATAC-seq

description: BTRC_171 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_172_10X _multiome_snATAC-seq

description: BTRC_172 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_170_10X _multiome_snATAC-seq

description: BTRC_170 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: 24159FL-25-05

description: Library name: WT2_IgG


title: 24159FL-25-13

description: Library name: KO2_IgG


title: BTRC_169_10X _multiome_snATAC-seq

description: BTRC_169 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: 24159FL-25-02

description: Library name: WT1_H3k27ac


title: 24159FL-25-03

description: Library name: WT1_TBX5_1


title: 24159FL-25-15

description: Library name: KO2_TBX5_1


title: 24159FL-25-04

description: Library name: WT1_TBX5_2


title: BTRC_17_10X _multiome_snATAC-seq

description: BTRC_17 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_168_10X _multiome_snATAC-seq

description: BTRC_168 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: 24159FL-25-01

description: Library name: WT1_IgG


title: BTRC_18_10X _multiome_snATAC-seq

description: BTRC_18 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P84 [p84-6]

city: New Haven

first: Jay

last: Humphrey

state: CT

address: 55 Prospect St

department: Department of Biomedical Engineering

institute: Yale University

description:
Library name: Sample 31
p84-6_213_364_S97_L001

data_processing:
Sequenced reads were imported into CLC Genomics Workbench V23 (Qiagen).
Following quality control, reads were trimmed and aligned/mapped to a Mus musculus reference genome.
Reads were then automatically processed using trimmed mean of M values (TMM) normalization, log counts per million (CPM) transformation, and Z-Score normalization to generate principal component analysis (PCA) and heat map plots (Euclidean distance and complete linkage for clustering).
Assembly: GRCm39
Supplementary files format and content: csv files include raw counts for each sample

source_name: Aorta

extract_protocol:
RNA was isolated using an RNeasyMini Kit (Qiagen) according to manufacturer's specifications.
Whole-transcriptome sequencing was performed by The Yale Center for Genome Analysis using a NovaSeq 6000 System (Illumina, Inc.).

value: Aorta

value: WT

tag: developmental stage


title: WT P84 [p84-5]

description:
Library name: Sample 30
p84-5_225_352_S96_L001


title: BTRC_164_10X _multiome_snATAC-seq

description: BTRC_164 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P84 [p84-4]

description:
Library name: Sample 29
p84-4_237_340_S95_L001


title: BTRC_162_10X _multiome_snATAC-seq

description: BTRC_162 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P84 [p84-3]

description:
Library name: Sample 28
p84-3_249_328_S94_L001


title: BTRC_163_10X _multiome_snATAC-seq

description: BTRC_163 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P84 [p84-2]

description:
Library name: Sample 27
p84-2_261_316_S93_L001


title: BTRC_161_10X _multiome_snATAC-seq

description: BTRC_161 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P84 [p84-1]

description:
Library name: Sample 26
p84-1_273_304_S92_L001


title: BTRC_16_10X _multiome_snATAC-seq

description: BTRC_16 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_159_10X _multiome_snATAC-seq

description: BTRC_159 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_173_10X _multiome_snATAC-seq

description: BTRC_173 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_158_10X _multiome_snATAC-seq

description: BTRC_158 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P42 [p42-5]

description:
Library name: Sample 24
p42-5_202_375_S90_L001


title: WT P42 [p42-4]

description:
Library name: Sample 23
p42-4_214_363_S89_L001


title: BTRC_167_10X _multiome_snATAC-seq

description: BTRC_167 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P42 [p42-3]

description:
Library name: Sample 22
p42-3_226_351_S88_L001


title: BTRC_150_10X _multiome_snATAC-seq

description: BTRC_150 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_146_10X _multiome_snATAC-seq

description: BTRC_146 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_147_10X _multiome_snATAC-seq

description: BTRC_147 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_149_10X _multiome_snATAC-seq

description: BTRC_149 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P42 [p42-1]

description:
Library name: Sample 20
p42-1_250_327_S86_L001


title: WT P21 [p21-5]

description:
Library name: Sample 19
p21-5_262_315_S85_L001


title: BTRC_145_10X _multiome_snATAC-seq

description: BTRC_145 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_143_10X _multiome_snATAC-seq

description: BTRC_143 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P21 [p21-4]

description:
Library name: Sample 18
p21-4_274_303_S84_L001


title: BTRC_142_10X _multiome_snATAC-seq

description: BTRC_142 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P21 [p21-3]

description:
Library name: Sample 17
p21-3_286_291_S51_L001


title: BTRC_139_10X _multiome_snATAC-seq

description: BTRC_139 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_137_10X _multiome_snATAC-seq

description: BTRC_137 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P21 [p21-1]

description:
Library name: Sample 15
p21-1_215_362_S81_L001


title: WT P21 [p21-2]

description:
Library name: Sample 16
p21-2_203_374_S82_L001


title: WT P42 [p42-6]

description:
Library name: Sample 25
p42-6_285_292_S91_L001


title: BTRC_136_10X _multiome_snATAC-seq

description: BTRC_136 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_148_10X _multiome_snATAC-seq

description: BTRC_148 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P10 [p10-5]

description:
Library name: Sample 14
p10-5_227_350_S80_L001


title: WT P10 [p10-4]

description:
Library name: Sample 13
p10-4_239_338_S79_L001


title: WT P10 [p10-3]

description:
Library name: Sample 12
p10-3_251_326_S78_L001


title: WT P10 [p10-2]

description:
Library name: Sample 11
p10-2_263_314_S77_L001


title: BTRC_134_10X _multiome_snATAC-seq

description: BTRC_134 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_132_10X _multiome_snATAC-seq

description: BTRC_132 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_131_10X _multiome_snATAC-seq

description: BTRC_131 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P10 [p10-1]

description:
Library name: Sample 10
p10-1_275_302_S76_L001


title: BTRC_128_10X _multiome_snATAC-seq

description: BTRC_128 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P42 [p42-2]

description:
Library name: Sample 21
p42-2_238_339_S87_L001


title: BTRC_125_10X _multiome_snATAC-seq

description: BTRC_125 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P2 [p2-9]

description:
Library name: Sample 9
p2-9_287_290_S75_L001


title: BTRC_127_10X _multiome_snATAC-seq

description: BTRC_127 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P2 [p2-8]

description:
Library name: Sample 8
p2-8_204_373_S74_L001


title: WT P2 [p2-7]

description:
Library name: Sample 7
p2-7_216_361_S73_L001


title: BTRC_124_10X _multiome_snATAC-seq

description: BTRC_124 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_123_10X _multiome_snATAC-seq

description: BTRC_123 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P2 [p2-6]

description:
Library name: Sample 6
p2-6_228_349_S72_L001


title: WT P2 [p2-5]

description:
Library name: Sample 5
p2-5_240_337_S71_L001


title: BTRC_121_10X _multiome_snATAC-seq

description: BTRC_121 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P2 [p2-4]

description:
Library name: Sample 4
p2-4_252_325_S70_L001


title: BTRC_115_10X _multiome_snATAC-seq

description: BTRC_115 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_116_10X _multiome_snATAC-seq

description: BTRC_116 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P2 [p2-2]

description:
Library name: Sample 2
p2-2_276_301_S68_L001


title: BTRC_12_10X _multiome_snATAC-seq

description: BTRC_12 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_112_10X _multiome_snATAC-seq

description: BTRC_112 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: WT P2 [p2-1]

description:
Library name: Sample 1
p2-1_288_289_S67_L001


title: BTRC_11_10X _multiome_snATAC-seq

description: BTRC_11 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_107_10X _multiome_snATAC-seq

description: BTRC_107 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: snATACseq for 12hr Refed mouse Hypothalmus 3

city: Salt Lake City

first: Chris

last: Gregg

state: UT

address: 20 South 2030 East

department: Neurobiology and Anatomy

institute: University of Utah

description:
Library name: C57_snATACseq_FFR_12hrRefed3
snATACseq to identify cell type level accessibility peaks across diet states

data_processing:
CellRanger Fragments files subset with cell types categorized in snRNAseq analysis.
Peaks called with Genrich with the following parameters-r -l 140 -e chrM,chrY -j -d 100 -q 0.05 -v -f.
Assembly: mm10
Supplementary files format and content: NarrowPeak: BED file output by the peak caller Genrich.

source_name: Hypothalamus

extract_protocol:
10x Nuclei Isolation Kit.
10x Genomics Chromium Next GEM Single cell Multiome ATAC preparation.

treatment_protocol: Fed, Fasted 72 hours, Refed 12 hours.

value: Hypothalamus


title: snATACseq for 12hr Refed mouse Hypothalmus 3.1

description:
Library name: C57_snATACseq_FFR_12hrRefed3.1
snATACseq to identify cell type level accessibility peaks across diet states


title: BTRC_106_10X _multiome_snATAC-seq

description: BTRC_106 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: snATACseq for Fed mouse Hypothalmus 3

description:
Library name: C57_snATACseq_FFR_Fed3
snATACseq to identify cell type level accessibility peaks across diet states

value: Fed


title: BTRC_103_10X _multiome_snATAC-seq

description: BTRC_103 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_105_10X _multiome_snATAC-seq

description: BTRC_105 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: snATACseq for Fed mouse Hypothalmus 3.1

description:
Library name: C57_snATACseq_FFR_Fed3.1
snATACseq to identify cell type level accessibility peaks across diet states


title: snATACseq for 12hr Refed mouse Hypothalmus 2.1

description:
Library name: C57_snATACseq_FFR_Refed12hr2.1
snATACseq to identify cell type level accessibility peaks across diet states


title: snATACseq for 12hr Refed mouse Hypothalmus 2

description:
Library name: C57_snATACseq_FFR_Refed12hr2
snATACseq to identify cell type level accessibility peaks across diet states


title: snATACseq for Fasted mouse Hypothalmus 3.3

description:
Library name: C57_snATACseq_FFR_Fasted3.3
snATACseq to identify cell type level accessibility peaks across diet states

value: Fasted


title: BTRC_53_10X _multiome_snRNAseq

description: BTRC_53 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: snATACseq for Fasted mouse Hypothalmus 3

description:
Library name: C57_snATACseq_FFR_Fasted3
snATACseq to identify cell type level accessibility peaks across diet states


title: BTRC_99_10X _multiome_snRNAseq

description: BTRC_99 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: BTRC_102_10X _multiome_snATAC-seq

description: BTRC_102 ' in Seurat object's 'Donor' metadata field, count information in 'ATAC' assay


title: BTRC_104_10X _multiome_snRNAseq

description: BTRC_104 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay