title: Fed4h, wild type mouse liver, isolated total primary hepatocytes, RNAPII (Input)

description: Library name: Fed4h total hepatocyte, INPUT

data_processing:
Raw fastq files were trimmed to remove adapter sequences and low-quality bases using Trim Galore (v0.6.7) with “--stringency 5” setting.
Trimmed reads were aligned to mm10 reference genome using bowtie2 (v2.4.5) with default parameters.
The resulting SAM files were converted to BAM files using samtools (v1.6) view with "-f 2 -q 10” setting.
Duplicates were removed using samtools rmdup.
CPM normalized coverage tracks were generated using the bamCoverage tool from the deepTools (v3.5.1) suite with the “--extendReads --normalizeUsing CPM” option.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature and quenched with glycine. Chromatin was sonicated using Bioruptor Pico device (Diagenode).
ChIP-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs, #E7645) with NEBNext® Multiplex Oligos for Illumina® single Index Primers Set 1 and Set 2 (New England Biolabs, #E7335 and #E7500)

treatment_protocol: Mice were fed for 4h or fasted for 16-24h prior to hepatocyte isolation.

value: Liver

value: Total primary hepatocyte

tag: strain

value: Wild type

value: Fed 4h

tag: chip antibody


title: WT_1

status: Public on Apr 10 2026

type: SRA

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

country: USA

institute: Weill Cornell Medical College

description: Library name: bc2089

library_source: genomic

data_processing:
Data was aligned using pbmm2 to mm10 genome
Methylation values were extracted using pb-CpG-tools
Assembly: mm10
Supplementary files format and content: PacBio bam files with methylation calls and kinetics

molecule: genomic DNA

organism: Mus musculus

source_name: spleen

extract_protocol:
DNA was extracted following the manufacturers protocol
libraries were constructed following the manufacturers protocol (SMRT-Seq, PacBio)

tag: tissue

value: spleen

tag: Sex

value: female

tag: cell type

value: CD19+ enriched B cells

tag: genotype

value: WT ( CD19Cre+/-, SPENwt/wt, ICN2-/- )


title: Bone marrow LSK cells from wild type mice

city: Tokyo

first: Ayako

last: Nakamura-Ishizu

address: 8-1 Kawadacho Setagayaku

country: Japan

institute: Tokyo Womens Medical University

description: Library name: WT_Ad_R

library_source: transcriptomic single cell

data_processing:
Sample data was processed by Cell Ranger software generated by 10x Genomics Chromium instruments.
Assembly: Mouse mm10
Supplementary files format and content: .h5 file containing gene, barcode, UMI counts

molecule: polyA RNA

source_name: bone marrow

extract_protocol:
flow cytometry
Library was produced according to 10X genomics Chromium next GEM single cell multiome ATAC + Gene expression protocol

value: bone marrow

value: LSK cells

value: wild type


title: fetal liver LSK cells from Thpo KO  mice

description: Library name: KO_FL_R

source_name: liver

value: liver

value: knock out


title: AG14980, Wildtype, 10 µM PDS for 24h, ATACseq rep2

city: Tübingen

first: Yingguang Frank

last: Chan

address: Max Planck Ring 9

department: Chan group

country: Germany

institute: Friedrich Miescher Laboratory of the Max Planck Society

description:
Library name: Lym_B_PDS2
B_PDS2

data_processing:
Raw FASTQ reads  were extracted with bcl2fastq (version 2.20). Tn5 and Truseq adapter sequences, G repeats due to sequencing artefacts, and reads shorter than 20 bp were trimmed and removed using cutadapt (version 4.0).  Reads were then aligned to human reference genome version hg38 or composite genome of hg38 and EBV using bwa mem (Version: 0.7.17-r1188). Duplicates were marked and removed using Picard (version 2.18.25). Prior to calling peaks, mitochondrial reads, reads with a mapping quality lower than 20 and reads in hg38 blacklisted regions (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38human/hg38.blacklist.bed.gz) were discarded. ATAC-seq peak calling was performed using MACS2 (version 2.1.1.20160309) with callpeak –format BAMPE --nomodel –min-length 100 narrowPeak parameters. For a given cell type, two types of ATACseq peak sets were generated. Using LCL as an example, to identify differentially accessible regions in each contrast (BS vs WT or PDS vs DMSO), a local peak set was called by pooling equal number reads from each sample. To identify peaks that are differentially accessible in BS and PDS-treated conditions, equal number of reads from WT, BS, DMSO- and PDS-treated samples from the same cell type was pooled to call a global peak set, which was further supplemented by unique peaks in the local peak sets from BS vs WT or PDS vs DMSO contrasts. The number of fragments in each ATACseq peak was quantified with htseq-count (HTSeq version 0.9.1). Subsequently, the count matrix was normalized and differential analysis was carried out in DESeq2 (version 1.30.1) to identify significantly differential signals (adjusted p-value <0.05). Loess normalization method in csaw (version 1.24.3) following differential analysis with edgeR (version 3.32.1) were employed to compare PDS- and DMSO-treated samples.
Assembly: hg38
Supplementary files format and content: narrowPeak, ATAC-seq peaks for each pair of samples called by macs2, which were used in downstream differential anlaysis.
Supplementary files format and content: bedgraph files generated from the filtered bamfile.
Supplementary files format and content: tab-delimited txt file, number of fragments in each peak quantified by Htseq.
Supplementary files format and content: tab-delimited txt file of results of differential analysis

organism: Homo sapiens

growth_protocol: Cell lines from Bloom Syndrome and healthy donors were obtained from Coriell Institute (lymphoblastoid cell lines, LCL: GM16375, AG14980; fibroblast cell lines: GM08505, GM00637). LCLs were cultured in RPMI 1640 medium (Gibco, Cat. #21875) supplemented with 15% fetal bovine serum (FBS, Gibco, UK, Cat. #10500), 1% penicillin-streptomycin (P/S, Gibco, US, Cat #15140) and 1% GlutaMAX-I (Gibco, UK, Cat. #35050).  Fibroblast lines were cultured in 1X DMEM (Gibco, UK, Cat. #11960) supplemented with, 1% minimum essential medium non-essential amino acids (MEM NEAA, Gibco, UK, Cat. #11140) and 1% P/S and 10% or 15% FBS, respectively. Cell passaging was performed according to recommendations by Coriell Institute. All cells were cultured at 37°C under 5% CO2.

extract_protocol:
fibroblasts were first trypsinised (Sigma-Aldrich, Cat. #SLCH3385), pelleted at 300 g for 5 min and washed once with cold 1x Dulbecco's phosphate buffered saline (PBS, Gibco, Cat. #14190). Lymphoblastoid cells were pelleted at 300 g for 5 min and washed once with cold 1x PBS.
50, 000 cells were subjected to ATACseq preparation essentially as described in Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396

treatment_protocol: Pyridostatin (PDS, Sigma-Aldrich, Cat. #SML2690) stocks (2.5 mM) were prepared by dissolving it in DMSO (Sigma-Aldrich, Cat. #D2650). For LCLs, wildtype cells from cell line AG14980 were treated with 10 µM PDS vs. 0.4% DMSO (control) for 24 h at the concentration of 1 million cells per ml. Cells were then cultured with gentle rotation at 100 rpm to ensure the equal exposure of cells to the treatment. For fibroblasts, wildtype cells (GM00637) at 60% confluency were treated with 10 µM PDS vs. 0.4% DMSO for 24 h.

tag: cell line

value: lymphoblastoid

value: Wildtype

tag: treatment

value: 10 µM PDS for 24h


title: Mouse 3

city: South San Francisco

first: Kimberle

last: Shen

state: CA

address: 1 Dna way

institute: Genentech

description: Library name: Mouse 3

library_source: transcriptomic

data_processing:
SAW pipeline version V7.0.0
Deepcell cell segmentation
Assembly: mm10
Supplementary files format and content: Cell segmented .gef file
Library strategy: Spatial Transcriptomics

molecule: total RNA

source_name: brain coronal hemisphere

extract_protocol:
Fresh frozen and mounted in OCT
STOMICS Gene Expression kit

value: brain coronal hemisphere

value: brain

value: WT

value: Injected


title: AG14980, Wildtype, 0.4%DMSO for 24h, ATACseq rep2

description:
Library name: Lym_B_DMSO2
B_DMSO2

value: 0.4%DMSO for 24h


title: WT_3

description: Library name: bc2066

value: spleen


title: Fast16h, wild type mouse liver, isolated periportal (PP) hepatocytes, RNAPII (ChIP)

city: Bronx

first: Jeffrey

middle: E

last: Pessin

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

description: Library name: Fast16h periportal (PP) hepatocyte, ChIP

source_name: Liver

value: Liver

value: Periportal primary hepatocyte

value: Wild type

value: Fasted 16h

value: RNAPII subunit B1 (Rpb1) NTD (Cell Signaling, #14958)


title: Fast24h, wild type mouse liver, isolated total primary hepatocytes, RNAPII (Input)

description: Library name: Fast24h total hepatocyte, INPUT

value: Total primary hepatocyte

value: Fasted 24h


title: AG14980, Wildtype, 10 µM PDS for 24h, ATACseq rep1

description:
Library name: Lym_B_PDS1
B_PDS1


title: Fed4h, wild type mouse liver, isolated pericentral (PC) hepatocytes, RNAPII (ChIP)

description: Library name: Fed4h pericentral (PC) hepatocyte, ChIP

value: Pericentral primary hepatocyte

value: Fed 4h


title: WT_4

description: Library name: bc2083

value: female

value: CD19+ enriched B cells

value: WT ( CD19Cre+/-, SPENwt/wt, ICN2-/- )


title: Fed4h, wild type mouse liver, isolated periportal (PP) hepatocytes, RNAPII (ChIP)

description: Library name: Fed4h periportal (PP) hepatocyte, ChIP


title: Fast24h, wild type mouse liver, isolated total primary hepatocytes, RNAPII (ChIP)

description: Library name: Fast24h total hepatocyte, ChIP


title: Bone marrow LSK cells from Thpo KO mice

description: Library name: KO_Ad_R

value: bone marrow

value: LSK cells

value: knock out


title: WT_2

description: Library name: bc2058


title: AG14980, Wildtype, 10 µM PDS for 24h, ATACseq rep3

description:
Library name: Lym_B_PDS3
B_PDS3

value: lymphoblastoid

value: Wildtype

value: 10 µM PDS for 24h


title: GM00637, Wildtype, 0.4%DMSO for 24h, ATACseq rep1

description:
Library name: Fib_K_DMSO1
K_DMSO1

value: fibroblast

value: 0.4%DMSO for 24h


title: AG14980, Wildtype, 0.4%DMSO for 24h, ATACseq rep1

description:
Library name: Lym_B_DMSO1
B_DMSO1


title: Fast16h, wild type mouse liver, isolated pericentral (PC) hepatocytes, RNAPII (ChIP)

description: Library name: Fast16h pericentral (PC) hepatocyte, ChIP

value: Liver

value: Wild type

value: Fasted 16h


title: N2_1

description: Library name: bc2074

value: spleen

value: Notch2 ( CD19Cre+/-, SPENwt/wt, ICN2+/- )


title: fetal liver LSK cells from wild type mice

description: Library name: WT_FL_R

value: liver

value: wild type


title: GM12878 ATAC-seq library, BRM014 (10uM) , 24h , replicate 1

city: Atlanta

first: Alexander

middle: O. D.

last: Gulka

state: Georgia

address: 1510 Clifton Rd NE

institute: Emory University

description: Library name: GM12878_ATAC_BRM014_10uM_24h_rep1

data_processing:
Data were processed using the Encyclopedia Of DNA Elements (ENCODE) ATAC-seq Pipeline, (v2.2.0, https://github.com/ENCODE-DCC/atac-seq-pipeline), executed using Singularity containers. Briefly, adapter trimming was performed using cutadaptwith parameters -e 0.1 -m 5 and reads were aligned to the hg38 reference genome using Bowtie2 [106]. Reads were filtered using SAMtools, PCR duplicates were flagged and removed using Picard, and peaks and signal tracks were generated using MACS2.
Assembly: hg38
Supplementary files format and content: Processed data files  consist of pooled ATAC-seq signal tracks (fold-change over background) generated by combining all biological replicates for each experimental condition, in bigwig format.

growth_protocol: GM12878 cells were cultured in suspension using RPMI-1640 medium (Thermo Scientific, A1049101) supplemented with 2 mM L-glutamine (Thermo Scientific, 25030081), 15% fetal bovine serum (FBS; Fisher Scientific, 10-082-147), and 100U/mL penicillin/streptomycin (Fisher Scientific, 15-140-122). HepG2 cells were cultured in Eagle’s Minimal Essential Medium (ATCC, 30-2003) supplemented with 10% FBS and 100U/mL penicillin/streptomycin.  HepG2 cells were passaged using Trypsin-EDTA (Fisher Scientific, 25-200-072). All cells were maintained at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Cells were harvested by centrifugation at 500 x g for 5 min, resuspended in cold base media (GM12878: RPMI-1640; HepG2: EMEM) supplemented with 10% DMSO, and immediately flash-frozen in liquid nitrogen to minimize recovery of chromatin accessibility following inhibitor removal. Frozen samples were rapidly thawed in a 37°C water bath and cells were pelleted by centrifugation. After washing with cold 1x PBS, cells were resuspended in cold nuclear permeabilization buffer (1x PBS, 5% w/v bovine serum albumin, 0.2% w/v IGEPAL CA-630, 1mM dithiothreitol, 1x cOmplete EDTA-free Protease Inhibitor Cocktail) and nuclei were extracted by incubation with rocking for 5 minutes at 4°C. Nuclei were pelleted and resuspended in tagmentation buffer (33mM Tris-acetate pH 7.8, 66mM potassium acetate, 11mM magnesium acetate, 16% v/v dimethylformamide).
50,000 nuclei were tagmented for 1h at 37°C with Tn5 (Illumina, 20034197). Tagmented DNA was purified using the MinElute PCR Purification Kit (Qiagen, 28004) and amplified by 7-8 cycles of PCR using NEBNext High-Fidelity Q5 polymerase (New England Biolabs, M0541). Amplified libraries were size-selected using SPRIselect beads (Beckman Coulter, B23318), quantified using a Qubit fluorometer (Thermo Fisher Scientific) with dsDNA High Sensitivity Assay reagents (Thermo Fisher Scientific, Q32854), and library size distributions was evaluated using High Sensitivity D1000 ScreenTapes on an Agilent 4200 TapeStation system.  Libraries were sequenced (150bp paired-end) on an Illumina NovaSeq platform.

treatment_protocol: BRM014 (MedChemExpress, HY-119374) was prepared as a 10mM stock in dimethyl sulfoxide (DMSO) and used at a final concentration of 10µM unless otherwise indicated. Vehicle controls were treated with an equivalent concentration of DMSO. ACBI1 (opnMe, ACBI1) was similarly prepared as a 10mM stock in DMSO and used at a final concentration of 1µM. For stimulus experiments, cells were treated with  interferon gamma (Genscript, Z02986, 100ng/mL) or dexamethasone (MedChemExpress, HY-14648, 500nM) for 1 or 6h. For BAFinh pretreatment, 10µM BRM014 was added to cells 30min prior to the addition of either 100ng/mL IFN-γ or 500nM Dex for 1h or 6h.

value: Lymphoblastoid cell line

tag: timepoint

tag: inhibitor/protac concentration


title: AG14980, Wildtype, none,ATACseq control, genomic sequencing data

description:
Library name: Lym_WT_B_gDNA
genomic sequencing data used as control for ATACseq data from AG14980


title: HL_G3_9C

city: Giessen

first: Vijay

middle: Kumar

last: Singh

address: Feulgenstrasse 12

department: Department of Pediatric Oncology, Hematology, and Immunodeficiencies

description: Library name: Sample 70

data_processing:
CLC Genomics Workbench - Qiagen Genomic Services
Raw data was de-multiplexed FASTQ files for each sample were generated using the bcl2fastq
Cutadapt (v1.11) extracts adapter and UMI info, then trims adapters and collapses reads by UMI.
Reads were mapped with Bowtie2 (v2.2.2); only perfect matches were kept.
Trimmed sequence reads were mapped to GRCh37 using QIAGEN CLC Genomic service tools. For mapping to the genome, not more than one mismatch is allowed in the first 32 basesof the read. No indels are allowed in mapping.
Read count extraction and normalization were performed using QIAGEN CLC genomic benchwork
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample

source_name: Serum

extract_protocol:
RNA was isolated using the miRNeasy Serum/Plasma Kit (QIAGEN) according to manufacturers insructions.
small RNA libraries for non coding-seq were prepared using the QIAseq miRNA Library Kit following manufacturer's protocols.

value: Serum

value: Classical Hodgkin Lymphoma

value: Post-Induction

tag: time

value: Day 57


title: Fed4h, wild type mouse liver, isolated total primary hepatocytes, RNAPII (ChIP)

description: Library name: Fed4h total hepatocyte, ChIP

value: Total primary hepatocyte

value: Fed 4h

value: RNAPII subunit B1 (Rpb1) NTD (Cell Signaling, #14958)


title: S7

city: Montreal

first: Lisa

middle: M

last: Munter

state: QC

address: 3649 Sir-William-Osler Promenade

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

description:
Library name: Sample_15
column name in Phenix25rawCountMatrix: S7

data_processing:
RNA-seq fastq reads were trimmed using Trimmomatic (version 0.39) to remove low-quality bases and adapters. Trimmed reads were aligned to the mus musculus 10 (mm10) reference genome using STAR (version 2.7.8a) with default parameters to generate .bam files.
Alignments were sorted and duplicates were marked using Picard (version 2.0.1).
Raw and normalized reads were quantified using HTSeq-count and the StringTie (version 1.3.5) respectively.
Differentially expressed genes (DEGs) with a maximum adjusted p-value of 0.05 and at least 1.05 absolute value fold change were identified using DEseq2 (Bioconductor release 3.19).
Samples were hierarchically clustered according to their gene expression profiles across the DEGs. Gene expression was normalized by calculating the z-scores of FPKMs within each gene. Clustering was performed by Euclidean distance using Ward’s method.
Assembly: mm10

source_name: brain

growth_protocol: Standard housing, 1% w/w cholesterol diet, water ad libitum

extract_protocol:
Bulk brain was harvested and RNA extracted using the Qiagen RNeasy Plus Universal Mini Kit
mRNA was enriched from 100-500 ng total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module Kit, and libraries were generated using NEBNext Ultra Directional RNA library kit (New England Biolabs, USA).

treatment_protocol: 30 mg/kg evacetrapib or vehicle for 11 weeks

value: brain

value: C57/bl6 background

value: bulk

value: APPxCETP double transgenic

value: vehicle

tag: batch

value: 1% (w/w) cholesterol diet

tag: dna tags

value: AGTGCGGA-GACAACGG

tag: illumina number


title: S8

description:
Library name: Sample_16
column name in Phenix25rawCountMatrix: S8

value: GCTTCACA-TAGCTTTA


title: AG14980, Wildtype, none, ATACseq rep2

description:
Library name: Lym_WT_B2
B2

value: lymphoblastoid

value: Wildtype


title: S6

description:
Library name: Sample_14
column name in Phenix25rawCountMatrix: S6

value: TCGCTCGG-TCCGATGG


title: HL_G3_8C

description: Library name: Sample 68

value: Serum

value: Classical Hodgkin Lymphoma


title: GM12878 ATAC-seq library, DMSO , 24h , replicate 1

description: Library name: GM12878_ATAC_DMSO_24h_rep1

value: Lymphoblastoid cell line

value: DMSO


title: HL_G3_9A

description: Library name: Sample 69

value: Pre-treatment

value: Day 0


title: HL_G3_8A

description: Library name: Sample 67


title: AG14980, Wildtype, none, ATACseq rep1

description:
Library name: Lym_WT_B1
B1


title: AG14980, Wildtype, none, ATACseq rep3

description:
Library name: Lym_WT_B3
B3


title: Cortex_Illumina_RNAseq_rep3

city: Acton

first: Muhammad

last: Bilal

state: ACT

address: 131 Garran Road

department: Eccles Institute of Neuroscience, The John Curtin School of Medical Research

country: Australia

institute: The Australian National University

description:
Library name: Cortex_Illumina_RNAseq_rep3
Adult mouse cortex; Illumina RNA-seq; biological replicate 3

data_processing:
Oxford Nanopore raw signal files were basecalled with Dorado (v0.7.0), and reads were aligned using minimap2 (v2.28). Transcript- and gene-level abundance estimates were generated using NanoCount (v1.2.1) and IsoQuant (v3.7.0). Illumina paired-end RNA-seq reads (150 bp; R1 and R2) were adapter-trimmed using FASTX-Clipper (FASTX-Toolkit, Hannon Lab) with default parameters, removing AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC from R1 and AGATCGGAAGAGCGTCGTGTAGGGAAAGA from R2. Trimmed Illumina reads were quantified against a decoy-aware reference using Salmon (v1.10.1).
Gene- and transcript-level TPM values and read counts were summarised across biological replicates. TRP channel–annotated genes were extracted for downstream analysis.
Assembly: Mus musculus reference genome GRCm39 with Ensembl release 115 annotation.
Supplementary files format and content: Processed data files include spreadsheets containing gene- and transcript-level TPM values and raw read counts derived from Oxford Nanopore direct RNA-seq and Illumina RNA-seq, annotated with Ensembl gene identifiers and gene symbols.

source_name: cortex

growth_protocol: Adult male C57BL/6J mice (5–6 weeks old) were group-housed under controlled temperature and a 12:12 h reverse light/dark cycle with food and water ad libitum.

extract_protocol:
Mice were deeply anaesthetised and transcardially perfused with ice-cold artificial cerebrospinal fluid prior to tissue collection. Cerebral cortex and dorsal root ganglia were rapidly dissected, snap-frozen, and stored at −80 °C. Total RNA was extracted using TRI Reagent followed by purification with the Direct-zol™ RNA Microprep Kit, including on-column DNase I treatment.
For Oxford Nanopore sequencing, direct RNA libraries were prepared using the Oxford Nanopore Direct RNA Sequencing Kit (SQK-RNA004), with Induro Reverse Transcriptase and SUPERase·In added during library preparation, and sequenced on MinION or PromethION instruments. For Illumina sequencing, strand-specific poly(A)+ RNA libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit and sequenced as 150-bp paired-end reads on an Illumina NovaSeq 6000.

treatment_protocol: No experimental treatment was applied. All samples were obtained from untreated wild-type animals.

value: cortex

value: Male

tag: developmental stage

value: 5-6 weeks old

value: brain tissue

value: wild type

value: untreated


title: Cortex_Illumina_RNAseq_rep1

description:
Library name: Cortex_Illumina_RNAseq_rep1
Adult mouse cortex; Illumina RNA-seq; biological replicate 1


title: S4

description:
Library name: Sample_12
column name in Phenix25rawCountMatrix: S4

value: brain

value: C57/bl6 background

value: bulk

value: CETP transgenic

value: vehicle

value: 1% (w/w) cholesterol diet

value: CCTCCTTT-CGCGAAAG


title: GM16375, BLM-/-, none, ATACseq control, genomic sequencing data

description:
Library name: Lym_BS_A_gDNA
genomic sequencing data used as control for ATACseq data from GM16375

value: lymphoblastoid

value: BLM-/-


title: Cortex_Illumina_RNAseq_rep2

description:
Library name: Cortex_Illumina_RNAseq_rep2
Adult mouse cortex; Illumina RNA-seq; biological replicate 2


title: CD8+CD90.1+CD44+CD62L- transgenic TCRTAG CD8 T cells isolated 30d post activation in LMTAG infected spleens, rep 3

city: Nashville

first: Mary

last: Philip

state: TN

address: 777 PRB, 2220 Pierce Ave

department: Medicine

institute: Vanderbilt University Medical Center

description: Library name: 8781-MP-0031

data_processing:
Adaptors were trimmed from raw sequencing reads with TrimGalore v0.6.10 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and Cutadapt v2.6 51. Trimmed reads were mapped with STAR v2.7.9a 52 to the mouse reference genome (GRCm38.p6) and fragments per gene were counted with featureCounts v2.0.1 53 with respect to Gencode vM25 comprehensive gene annotations.
The quality of the sequenced reads was assessed with FastQC and QoRTs.
Sequenced reads were aligned with default parameters to the mouse reference genome (GRCm38.p6) using STAR v2.7.6a.
Gene expression estimates were obtained with featureCounts v2.0.1 using composite gene models from Gencode vM25
Hidden  batch effects were estimated using the svaseq function from sva v3.54.060, and the top 3 surrogate variables were accounted for in DESeq2.
Assembly: GRCm38.p6
Supplementary files format and content: raw counts and batch corrected variance-stabilized (log2) counts

extract_protocol:
CD8 T cells were sorted directly into Trizol LS and frozen. Total RNA was extraced from sorted cells using the Rneasy Micro kit (Qiagen)and amplified using the SMART-Seq v4 UltraLow Input RNA Kit (Clontech).
Libraries were prepared using NEBNext polyA mRNA sample kits (NEB).

value: spleen

value: primary cells

value: CD8 T cell

value: Listeria monocytogenes

value: Favret


title: GM16375, BLM-/-, none, ATACseq rep3

description:
Library name: Lym_BS_A3
A3


title: HL_G3_7A

description: Library name: Sample 65

value: Serum

value: Classical Hodgkin Lymphoma

value: Pre-treatment

value: Day 0


title: S5

description:
Library name: Sample_13
column name in Phenix25rawCountMatrix: S5

value: brain

value: C57/bl6 background

value: APPxCETP double transgenic

value: CCGGAATT-AAGTATGC


title: GM16375, BLM-/-, none, ATACseq rep2

description:
Library name: Lym_BS_A2
A2


title: S3

description:
Library name: Sample_11
column name in Phenix25rawCountMatrix: S3

value: bulk

value: CETP transgenic

value: vehicle

value: 1% (w/w) cholesterol diet

value: GCCTCTAT-GCTGATTT


title: DRG_Illumina_RNAseq

description:
Library name: DRG_Illumina_RNAseq
Adult mouse DRG; Illumina RNA-seq; biological replicate 1

source_name: dorsal root ganglion

value: dorsal root ganglion

value: Male

value: 5-6 weeks old

value: sensory ganglion tissue

value: wild type

value: untreated


title: S2

description:
Library name: Sample_10
column name in Phenix25rawCountMatrix: S2

value: CTTTAACT-AATCGTCA


title: HL_G3_7C

description: Library name: Sample 66

value: Serum

value: Classical Hodgkin Lymphoma

value: Post-Induction

value: Day 57


title: HL_G3_6C

description: Library name: Sample 64


title: S1

description:
Library name: Sample_9
column name in Phenix25rawCountMatrix: S1

value: brain

value: C57/bl6 background

value: TTTCCATC-CATTCGGA


title: H

description:
Library name: Sample_8
column name in Phenix25rawCountMatrix: H

value: bulk

value: APPxCETP double transgenic

value: Evacetrapib

value: TACTGTGA-CTGGACAC


title: CD8+CD90.1+CD44+CD62L+ transgenic TCRTAG CD8 T cells isolated 30d post activation in LMTAG infected spleens, rep 3

description: Library name: 8781-MP-0028

value: spleen

value: primary cells

value: CD8 T cell

value: Listeria monocytogenes

value: Favret


title: CD8+CD90.1+CD44+CD62L- transgenic TCRTAG CD8 T cells isolated 30d post activation in LMTAG infected spleens, rep 2

description: Library name: 8781-MP-0030


title: CD8+CD90.1+CD44+CD62L- transgenic TCRTAG CD8 T cells isolated 30d post activation in LMTAG infected spleens, rep 1

description: Library name: 8781-MP-0029


title: GM16375, BLM-/-, none, ATACseq rep1

description:
Library name: Lym_BS_A1
A1

value: lymphoblastoid

value: BLM-/-


title: SSB.Pixentrone.1hr.B2

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

country: China

institute: Huaqiao University

data_processing:
SiNGLe method: The genomic site mapping was performed the same way as in the SSiNGLe-ILM protocol (https://protocolexchange.researchsquare.com/article/pex-920/v2) with the two additional filtering steps. One, PCR duplicates were removed. Two, a read-pair was used only if the first base of the read 2 aligned to the reference sequence. The coordinate of  the first aligning base of the read 2 was assigned as the position of the SSB site.
Assembly: hg19(GRCh37) for the human reads mapping
Supplementary files format and content: All BED files contain coordinates of SSBs mapped to human genomes. The 4th columns show the number of reads representing the SSBs.
Library strategy: SSiNGLe

source_name: chronic myelogenous leukemia cell line

extract_protocol:
Three million human chronic myeloid leukemia K562 cells were seeded at 1 million cells per 1 ml of culture medium in each well of 6-well plates. The cells were grown in RPMI 1640 (Gibco, Billings, MT, USA) supplemented with 10% heat-inactivated fetal bovine serum (ExCell Bio, Montevideo, Uruguay) and 1% penicillin-streptomycin (Gibco) at 37 oC in 5% CO2. After 16 h, the cells were separately treated with 0.1%DMSO, 100 μM etoposide (AbMole), 100 μM teniposide (Merck), 10 μM mitoxantrone (Merck), 10 μM m-amsacrine hydrochloride (Merck), 10 μM pixentrone, 0.1 μM, 1 μM, 10 μM, 20 μM or 100 μM doxorubicin (Merck), and 20 μM epirubicin (Selleck) for 1 hour. All drugs were dissolved in DMSO, and each treatment was done in three independent biological replicas. After the drug treatment, DNA was isolated with the TIANamp Genomic DNA Kit (TIANGEN Biotech, DP304) according to the manufacturer’s protocol
SSiNGLe method

value: chronic myelogenous leukemia cell line

value: treated with 10 μM pixentrone

value: 1 hr


title: HL_G3_5C

description: Library name: Sample 62

value: Serum

value: Classical Hodgkin Lymphoma

value: Post-Induction

value: Day 57


title: CD8+CD90.1+CD44+CD62L+ transgenic TCRTAG CD8 T cells isolated 30d post activation in LMTAG infected spleens, rep 2

description: Library name: 8781-MP-0027


title: G

description:
Library name: Sample_7
column name in Phenix25rawCountMatrix: G

value: brain

value: C57/bl6 background

value: bulk

value: APPxCETP double transgenic

value: 1% (w/w) cholesterol diet

value: AGTACAAG-GCAATGGG


title: SSB.Pixentrone.1hr.B1


title: HL_G3_5A

description: Library name: Sample 61

value: Pre-treatment

value: Day 0


title: SSB.Mitoxantrone.1hr.B2

value: treated with 10 μM mitoxantrone


title: SSB.Mitoxantrone.1hr.B3


title: CD8+CD90.1+KLRG1-CD62L+ transgenic TCRTAG CD8 T cells isolated 5d post activation in LMTAG infected spleens, rep 4

description: Library name: 8781-MP-0025

value: spleen

value: primary cells

value: CD8 T cell

value: Listeria monocytogenes

value: Favret


title: F

description:
Library name: Sample_6
column name in Phenix25rawCountMatrix: F

value: Evacetrapib

value: TGTCCAAA-ACAACCAA


title: SSB.Mitoxantrone.1hr.B1

value: chronic myelogenous leukemia cell line

value: 1 hr


title: HL_G3_6A

description: Library name: Sample 63

value: Serum

value: Classical Hodgkin Lymphoma


title: HL_G3_4A

description: Library name: Sample 59


title: CD8+CD90.1+KLRG1-CD62L+ transgenic TCRTAG CD8 T cells isolated 5d post activation in LMTAG infected spleens, rep 3

description: Library name: 8781-MP-0024


title: CD8+CD90.1+KLRG1-CD62L+ transgenic TCRTAG CD8 T cells isolated 5d post activation in LMTAG infected spleens, rep 2

description: Library name: 8781-MP-0023


title: CD8+CD90.1+CD44+CD62L+ transgenic TCRTAG CD8 T cells isolated 30d post activation in LMTAG infected spleens, rep 1

description: Library name: 8781-MP-0026


title: HL_G3_3C

description: Library name: Sample 58

value: Post-Induction

value: Day 57


title: SSB.Pixentrone.1hr.B3

value: treated with 10 μM pixentrone


title: E

description:
Library name: Sample_5
column name in Phenix25rawCountMatrix: E

value: brain

value: C57/bl6 background

value: bulk

value: APPxCETP double transgenic

value: 1% (w/w) cholesterol diet

value: CCCTTCGG-CTGCCTTC


title: C

description:
Library name: Sample_3
column name in Phenix25rawCountMatrix: C

value: CETP transgenic

value: TATCAGTA-AGTAGTAA


title: D

description:
Library name: Sample_4
column name in Phenix25rawCountMatrix: D

value: Evacetrapib

value: CGAGTCAG-TACTAAGG


title: SSB.Etoposide.1hr.B3

value: chronic myelogenous leukemia cell line

value: treated with 100 μM etoposide


title: HL_G3_3A

description: Library name: Sample 57

value: Serum

value: Pre-treatment

value: Day 0


title: CD8+CD90.1+KLRG1-CD62L+ transgenic TCRTAG CD8 T cells isolated 5d post activation in LMTAG infected spleens, rep 1

description: Library name: 8781-MP-0022

value: spleen

value: primary cells

value: CD8 T cell

value: Listeria monocytogenes

value: Favret


title: B

description:
Library name: Sample_2
column name in Phenix25rawCountMatrix: B

value: brain

value: C57/bl6 background

value: bulk

value: CAAGAAGT-CCTAGTCG


title: HL_G3_4C

description: Library name: Sample 60

value: Classical Hodgkin Lymphoma

value: Post-Induction

value: Day 57


title: SSB.Etoposide.1hr.B1

value: chronic myelogenous leukemia cell line

value: 1 hr


title: CD8+CD90.1+KLRG1+CD62L- transgenic TCRTAG CD8 T cells isolated 5d post activation in LMTAG infected spleens, rep 3

description: Library name: 8781-MP-0020


title: A

description:
Library name: Sample_1
column name in Phenix25rawCountMatrix: A

value: CETP transgenic

value: Evacetrapib

value: 1% (w/w) cholesterol diet

value: ACACGTAT-CGATGTAA


title: HL_G3_2A

description: Library name: Sample 55

value: Serum

value: Pre-treatment

value: Day 0


title: pig_3_dpi_1_control

city: Pirbrigh

first: liu

last: yang

address: Ash Rd

country: United Kingdom

institute: The Pirbright Institute

description: Library name: sample_23

data_processing:
Twenty good qiality samples were examined to explore their scRNA-seq profiles. Their BCL files were demultiplexed using the mkfastq function in Cell Ranger v7.1.0.  The reads were mapped to the Sus scrofa reference genome (assembly 11.1, GCA_000003025.6) using STAR v2.7.2a in Cell Ranger. Unique molecular identifier (UMI) counting was implemented with Cell Ranger count. Subsequent data processing and analyses were performed in R v4.3.2.
Assembly: Sscrofa11.1
Supplementary files format and content: 10X unfiltered (raw) feature h5 matrix files

organism: Sus scrofa

source_name: lung tissue

extract_protocol:
Eighteen samples were prepared for single cell transcriptomic analysis using the 10X 3’ Gene expression kit.  Samples were diluted to 10,000 cells and partitioned using the Chromium iX Controller, the Next GEM chip G and the single cell 3’ kit v3.1 library preparation kit (10x Genomics, Pleasanton, California, United States).
Sequencing library quality was determined using the Qubit DNA BR kit (Life Technologies, UK), Illumina library quantitation kit (NEB, US) and the Tapestation D5000 DNA BR kit (Agilent, US).  Sequencing libraries were pooled randomly across 2 NextSeq 2000 P4 100 cycle kit (Illumina, San Diego, California, United States), each with 1% PhiX spikes, aiming for approximately 200 million reads per sample.  Runs formats aligned with manufacturers recommendations

value: lung tissue

value: myeloid cells, T,B and NK-like T cells, non immune structural cells


title: HL_G3_1A

description: Library name: Sample 53


title: HL_G3_2C

description: Library name: Sample 56


title: SSB.Epirubicin_HCl.1hr.B1

value: treated with 20 μM epirubicin


title: CD8+CD90.1+KLRG1+CD62L- transgenic TCRTAG CD8 T cells isolated 5d post activation in LMTAG infected spleens, rep 4

description: Library name: 8781-MP-0021

value: spleen

value: primary cells

value: CD8 T cell

value: Listeria monocytogenes

value: Favret


title: SSB.Epirubicin_HCl.1h.B3

value: chronic myelogenous leukemia cell line


title: HL_G3_1C

description: Library name: Sample 54

value: Classical Hodgkin Lymphoma

value: Post-Induction

value: Day 57


title: HL_G2_12C

description: Library name: Sample 52


title: SSB.Etoposide.1hr.B2

value: treated with 100 μM etoposide

value: 1 hr


title: CD8+CD90.1+KLRG1+CD62L- transgenic TCRTAG CD8 T cells isolated 5d post activation in LMTAG infected spleens, rep 2

description: Library name: 8781-MP-0019


title: pig_11_dpi_1_PRCV

description: Library name: sample_24


title: SSB.Epirubicin_HCl.1hr.B2


title: pig_6_dpi_1_control

description: Library name: sample_22


title: CD8+CD90.1+P4-6CD25high transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 2

description: Library name: 8781-MP-0016


title: CD8+CD90.1+P4-6CD25high transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 3

description: Library name: 8781-MP-0017


title: HL_G2_12A

description: Library name: Sample 51

value: Serum


title: CD8+CD90.1+P4-6CD25high transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 1

description: Library name: 8781-MP-0015


title: SSB.Doxorubicin_HCl.20_1hr.B2

value: treated with 20 μM doxorubicin


title: pig_31_dpi_1_H1N1

description: Library name: sample_19


title: HL_G2_11A

description: Library name: Sample 49

value: Pre-treatment

value: Day 0


title: SSB.Doxorubicin_HCl.20_1hr.B1


title: HL_G2_11C

description: Library name: Sample 50


title: CD8+CD90.1+KLRG1+CD62L- transgenic TCRTAG CD8 T cells isolated 5d post activation in LMTAG infected spleens, rep 1

description: Library name: 8781-MP-0018


title: Pig_35_DPI_12_H1N1

description: Library name: sample_18

value: lung tissue

value: myeloid cells, T,B and NK-like T cells, non immune structural cells


title: pig_14_dpi_12_PRCV

description: Library name: sample_21


title: CD8+CD90.1+P4-6CD25low transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 3

description: Library name: 8781-MP-0014

value: spleen


title: Pig_10_DPI_12_PRCV

description: Library name: sample_17


title: SSB.Doxorubicin_HCl.1_1hr.B3

value: treated with 1 μM doxorubicin


title: SSB.Doxorubicin_HCl.20_1hr.B3


title: pig_23_dpi_1_H1N1

description: Library name: sample_20


title: SSB.Doxorubicin_HCl.1_1hr.B2


title: CD8+CD90.1+P4-6CD25low transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 1

description: Library name: 8781-MP-0012

value: primary cells

value: CD8 T cell


title: HL_G2_10A

description: Library name: Sample 47


title: Pig_29_DPI_12_H1N1

description: Library name: sample_16


title: SSB.Doxorubicin_HCl.1_1hr.B1


title: CD8+CD90.1+P4-6CD25low transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 2

description: Library name: 8781-MP-0013

value: Listeria monocytogenes

value: Favret


title: SSB.Doxorubicin_HCl.10_1hr.B3

value: chronic myelogenous leukemia cell line

value: treated with 10 μM doxorubicin


title: Pig 32 – H1N1 12 DPI

description: Library name: sample_15


title: HL_G2_10C

description: Library name: Sample 48

value: Classical Hodgkin Lymphoma

value: Post-Induction

value: Day 57


title: CD8+CD90.1+P1-3 transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 2

description: Library name: 8781-MP-0009


title: CD8+CD90.1+P1-3 transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 3

description: Library name: 8781-MP-0010


title: Pig 8 – PRCV 12 DPI

description: Library name: sample_12


title: HL_G3_10C

description: Library name: Sample 46

value: Serum


title: HL_G2_8C

description: Library name: Sample 42


title: CD8+CD90.1+P1-3 transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 1

description: Library name: 8781-MP-0008


title: HL_G2_8A

description: Library name: Sample 41


title: SSB.Doxorubicin_HCl.10_1hr.B1

value: 1 hr


title: SSB.Doxorubicin_HCl.10_1hr.B2


title: Pig 30 – H1N1 12 DPI

description: Library name: sample_14


title: HL_G3_10A

description: Library name: Sample 45

value: Pre-treatment


title: Pig 7 – PRCV 12 DPI

description: Library name: sample_11


title: SSB.Doxorubicin_HCl.100_1hr.B2

value: treated with 100 μM doxorubicin


title: Pig 21 – PRCV 1 DPI

description: Library name: sample_13

value: lung tissue


title: CD8+CD90.1+P1-3 transgenic TCRTAG CD8 T cells isolated 2d post activation in LMTAG infected spleens, rep 4

description: Library name: 8781-MP-0011


title: Pig 4 – control 1 DPI

description: Library name: sample_10

value: myeloid cells, T,B and NK-like T cells, non immune structural cells


title: HL_G2_7C

description: Library name: Sample 40


title: SSB.Doxorubicin_HCl.100_1hr.B1


title: CD8+CD90.1+CD69+CFSE+ transgenic TCRTAG CD8 T cells isolated 12h post activation in LMTAG infected spleens, rep 2

description: Library name: 8781-MP-0005

value: spleen


title: SSB.Doxorubicin_HCl.100_1hr.B3


title: CD8+CD90.1+CD69+CFSE+ transgenic TCRTAG CD8 T cells isolated 12h post activation in LMTAG infected spleens, rep 3

description: Library name: 8781-MP-0006


title: CD8+CD90.1+CD69+CFSE+ transgenic TCRTAG CD8 T cells isolated 12h post activation in LMTAG infected spleens, rep 1

description: Library name: 8781-MP-0004


title: CD8+CD90.1+CD44low transgenic TCRTAG CD8 T cells from spleen, rep 3

description: Library name: 8781-MP-0003


title: SSB.Doxorubicin_HCl.0.1_1hr.B3

value: treated with 0.1 μM doxorubicin


title: HL_G2_6C

description: Library name: Sample 38


title: HL_G2_6A

description: Library name: Sample 37

value: Day 0


title: Pig_27_DPI_1_H1N1

description: Library name: sample_09


title: HL_G2_5C

description: Library name: Sample 36


title: Pig_13_DPI_1_PRCV

description: Library name: sample_08


title: Pig_9_DPI_12_PRCV

description: Library name: sample_05


title: CD8+CD90.1+CD44low transgenic TCRTAG CD8 T cells from spleen, rep 2

description: Library name: 8781-MP-0002

value: primary cells

value: CD8 T cell


title: SSB.DMSO.1hr.B3

value: treated with DMSO


title: Pig_34_DPI_1_H1N1

description: Library name: sample_07


title: Pig_20_DPI_1_PRCV

description: Library name: sample_06


title: SSB.Doxorubicin_HCl.0.1_1hr.B2

value: chronic myelogenous leukemia cell line


title: HL_G2_7A

description: Library name: Sample 39


title: SSB.DMSO.1hr.B2


title: HL_G2_5A

description: Library name: Sample 35


title: SSB.Doxorubicin_HCl.0.1_1hr.B1


title: Pig_2_DPI_12_control

description: Library name: sample_04


title: CD8+CD90.1+CD44low transgenic TCRTAG CD8 T cells from spleen, rep 1

description: Library name: 8781-MP-0001

value: Favret


title: SSB.DMSO.1hr.B1


title: HL_G2_4C

description: Library name: Sample 34

value: Classical Hodgkin Lymphoma


title: HL_G2_9C

description: Library name: Sample 44

value: Post-Induction


title: mLTC-1 murine Leydig cell line, 100µM MSNBA, replicate 5

city: Nouzilly

first: Pascal

last: Froment

address: INRAE Nouzilly

department: UMR 7247 INRAE/CNRS/Université de Tours/IFCE

country: France

institute: INRAE

description: Library name: SMX09_11

data_processing:
Quality control and preprocessing of data were performed by SciLicium (Rennes, France).
The first read contains 16 bases that must have a quality score higher than 10. The first 6 bp correspond to a unique sample-specific barcode and the following 10 bp to a unique molecular identifier (UMI).
The second reads were aligned to the mus musculus reference transcriptome from the UCSC website (release mm10) using BWA version 0.7.4.4 with the parameter “-l 24”
Assembly: mm10
Supplementary files format and content: Expression file in tab-separated format. Contains for each sample (row), the number of unique umis (unique molecular identifier) associated with 26,214 genes (columns).

growth_protocol: The immortalized Leydig cell line (mLTC-1) was cultured in Roswell Park Memorial Institute medium (RPMI 1640) (Corning, Manassas, USA), supplemented with antibiotics (100 IU/mL penicillin, 100 μg/mL streptomycin  (Sigma-Aldrich, l'Isle d'Abeau Chesnes, France), 10% fetal bovine serum (FBS), and 1% L-Glutamine (200 mM, Gibco 25030081). Cells were incubated at 37°C in a humidified atmosphere with 5% CO2. The culture medium was changed every 48 hours, and cells were maintained until reaching 70% sub-confluency.

extract_protocol:
mRNA have been extracted using Macherey-Nagel NucleoSpin RNA Plus (#740984.250) kit, following manufacturer's recommendations.
The sequencing libraries were built by tagmentation using 50 ng of ds cDNA with the Illumina Nextera XT Kit (Illumina, #FC-131-1024) following the manufacturer’s recommendations.

treatment_protocol: Cells were treated with 100 µM N-[4-(methylsulfonyl)-2-nitrophenyl]-1,3-benzodioxol-5-amine (treatment) or DMSO (control) for 24h before RNA extraction


title: Pig_5_DPI_1_control

description: Library name: sample_03


title: CD8+CD90.1+CD69+CFSE+ transgenic TCRTAG CD8 T cells isolated 12h post activation in LMTAG infected spleens, rep 4

description: Library name: 8781-MP-0007

value: Listeria monocytogenes


title: L7- MMP1 RIP

city: Toronto

first: Gobi

last: Thillainadesan

state: Ontario

address: 2075 Bayview Ave., S1-18

department: Biology

institute: Sunnybrook Research Institute

description: Column L7

data_processing:
Adapters were trimmed using cutadapt
RNA immunoprecipitated sequences were aligned to the genome using HISAT2. Analysis was partly done on the high-performance computing platforms Graham (https://docs.alliancecan.ca/wiki/Graham) and Niagra (https://docs.alliancecan.ca/wiki/Niagra) in support with Compute Canada (www.computecanada.ca).
Counts were quantitated using SamTools.
Analysis was partly done on the high-performance computing platforms Graham (https://docs.alliancecan.ca/wiki/Graham) and Niagra (https://docs.alliancecan.ca/wiki/Niagra) in support with Compute Canada (www.computecanada.ca).
Assembly: hg38
Supplementary files format and content: Tab-delimited raw count data.

source_name: Breast

growth_protocol: Cells were grown in DMEM with 10%FBS at 37C and 5%CO2.

extract_protocol:
RNA was extracted using RNeasy kit (Qiagen cat# 74004) according manufacturer's recommendation.
NEBnext Ultra (New England Biolabs: E7760S) was used to sequence.

treatment_protocol: Cells were treated with P4G11 ꞵ1 Integrin, E7-s (Developmental Systems Hybridoma Bank, Iowa City, IA) antibody in serum free media overnight (16hrs).

value: Breast

value: cancer

value: wt

value: G11 antibody treatment


title: Cortex_Nanopore_directRNA_rep3

description:
Library name: Cortex_Nanopore_directRNA_rep3
Adult mouse cortex; Nanopore direct RNA-seq; biological replicate 3

value: cortex

value: Male

value: 5-6 weeks old

value: brain tissue

value: wild type

value: untreated


title: mLTC-1 murine Leydig cell line, 100µM MSNBA, replicate 4

description: Library name: SMX09_9


title: WT Sample FMB

city: Jerusalem

first: Itamar

last: Harel

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

description: Library name: WT_FMB

data_processing:
Quality control and adapter trimming of the fastq sequence files were performed with FastQC (v0.11.8), fastx-toolkits (v0.0.13), Trim Galore! (v0.6.4), and Cutadapt (3.4). Options were set to remove Illumina TruSeq adapters and end sequences to retain high-quality bases with phred score > 20 and a remaining length > 20 bp. Successful processing was verified by re-running FastQC. Reads was mapped and quantified to the killifish genome Nfu_20140520 using STAR 2.7.6a. Differential gene expression analysis was performed using the edgeR package (v3.32.1).
Assembly: Nfu_20140520
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Nothobranchius furzeri

source_name: fibroblast

extract_protocol:
Fibroblast cultures in a 10 cm plate at 90% confluency were harvested by incubating them for 5 min in ice-cold PBS, and then adding  1 mL of TRI Reagent. RNA purification was performed using Direct-zol RNA Miniprep Kit (Zymo Research # R2052) according to the manufacturer's instructions. RNA concentration and quality were determined by using an Agilent 2100 bioanalyzer (Agilent Technologies).
Library preparation was performed using KAPA mRNA HyperPrep Kit (ROCHE-08105936001) according to the recommended protocols. Library quantity and pooling were measured by Qubit (dsDNA HS, Q32854), size selection at 4% agarose gel. Library quality was measured by Tape Station (HS, 5067-5584). Libraries were sequenced by NextSeq 2000 P2, 100 cycle,75 bp single end (Illumina, 20024906) with  ~30 million reads per sample for vgll3.

value: fibroblast

value: WT


title: WT Sample F4B

description: Library name: WT_F4B


title: mLTC-1 murine Leydig cell line, 100µM MSNBA, replicate 3

description: Library name: SMX09_8


title: HL_G2_3A

description: Library name: Sample 31

value: Serum

value: Pre-treatment

value: Day 0


title: L8- Rabbit IgG RIP

description: Column L8


title: sci-RNA-seq3_Arabidopsis_Day0_to_Day4_Biological_Replicate_2_Technical_Replicate_2

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
Library name: Arabidopsis_Day2_to_Day3_Biological_Replicate_2_Technical_Replicate_2
sci-RNA-seq3

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed as described in https://github.com/JunyueC/sci-RNA-seq3_pipeline
Demultiplexing, barcoded processing, and gene counting were preformed as described in https://github.com/JunyueC/sci-RNA-seq3_pipeline
Assembly: Arabidopsis TAIR10
Supplementary files format and content: Seurat object

molecule: nuclear RNA

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol:
5 day old seedlings grown on soil were exposed to light and harvested at different time points during de-etiolation.
Plants were grown on vermiculite under well-watered conditions for 29 days, before being subject to drought stress

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter.
Library construction was performed following the sci-RNA-seq3 workflow
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter.
Library construction was performed following the sci-RNA-seq3 workflow

value: leaf

tag: age

value: mature rosttes


title: Pig_1_DPI_12_control

description: Library name: sample_02

value: lung tissue

value: myeloid cells, T,B and NK-like T cells, non immune structural cells


title: HL_G2_2A

description: Library name: Sample 29

value: Classical Hodgkin Lymphoma


title: HL_G2_9A

description: Library name: Sample 43


title: Pig_33_DPI_12_H1N1

description: Library name: sample_01


title: mLTC-1 murine Leydig cell line, control, replicate 6

description: Library name: SMX09_10

value: Control


title: mLTC-1 murine Leydig cell line, control, replicate 5

description: Library name: SMX09_7


title: HL_G2_2C

description: Library name: Sample 30

value: Post-Induction

value: Day 57


title: WT Sample FMA

description: Library name: WT_FMA


title: HL_G2_4A

description: Library name: Sample 33


title: mLTC-1 murine Leydig cell line, 100µM MSNBA, replicate 6

description: Library name: SMX09_12


title: mLTC-1 murine Leydig cell line, control, replicate 4

description: Library name: SMX09_5


title: HL_G2_1C

description: Library name: Sample 28


title: sci-RNA-seq3_Arabidopsis_Day5_to_Day8_Biological_Replicate_2_Technical_Replicate_2

description:
Library name: Arabidopsis_Day5_to_Day8_Biological_Replicate_2_Technical_Replicate_2
sci-RNA-seq3

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed as described in https://github.com/JunyueC/sci-RNA-seq3_pipeline
Assembly: Arabidopsis TAIR10
Supplementary files format and content: Seurat object

growth_protocol: Plants were grown on vermiculite under well-watered conditions for 29 days, before being subject to drought stress

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter.
Library construction was performed following the sci-RNA-seq3 workflow


title: WT Sample F4A

description: Library name: WT_F4A


title: HL_G2_1A

description: Library name: Sample 27


title: mLTC-1 murine Leydig cell line, control, replicate 3

description: Library name: SMX09_4


title: HL_G1_13C

description: Library name: Sample 26


title: HL_G1_13A

description: Library name: Sample 25


title: sci-RNA-seq3_Arabidopsis_Day9_Biological_Replicate_2_Technical_Replicate_1

description:
Library name: Arabidopsis_Day9_Biological_Replicate_2_Technical_Replicate_1
sci-RNA-seq3


title: mLTC-1 murine Leydig cell line, 100µM MSNBA, replicate 1

description: Library name: SMX09_3


title: WT Sample F9

description: Library name: WT_F9


title: WT Sample F1

description: Library name: WT_F1


title: Right Central amygdala SNL 4

city: Lubbock

first: Julian

middle: David

last: Cardenas

state: TX

address: 3601 4th Street

department: Pharmacology and Neurosciences

institute: Texas Tech University Health Science Center

description: Library name: snl_cea_right_4

data_processing:
Read quality was assessed using Fastp (v.0.23.4). Reads with a Phred score below 30 were removed (-q 30), and we trimmed 10 low-quality nucleotides from the ends of the reads (-t 10), resulting in reads with a mean length of 91 bp. To align the reads to the reference genome, we utilized Salmon (v.1.10.2). We created a decoy-aware index using the mRatBN7.2 genome release 111 from Ensembl. After building the index, we used the salmon quant command with the -l A flag to automatically identify the library type and the --validatingMappings flag to quantify transcript expression.
Assembly: mRatBN7.2
Supplementary files format and content: Microsoft Excel Spreadsheet includes raw counts for each sample.

organism: Rattus norvegicus

source_name: CeA

extract_protocol:
At the chronic stage of neuropathic pain (4 weeks post-SNL or -sham surgery), rats (SNL, n = 6; sham, n = 6) were euthanized via decapitation. The brains were rapidly extracted and oxygenated in ice-cold ACSF that contained the following (in mM): 125.0 NaCl, 2.6 KCl, 2.5 NaH2PO4, 1.3 CaCl2, 0.9 MgCl2, 21.0 NaHCO3, and 3.5 glucose. Coronal brain slices (1,000 μM) containing the left and right CeA were prepared using a Vibratome (VT1200S, Leica Biosystems, Nussloch, Germany) as described previously (Hein et al., 2021; Presto & Neugebauer, 2022; Thompson et al., 2018). The left and right CeA and BLA were dissected from freshly harvested slices for bulk RNA sequencing analysis.
RNA library preparation and sequencing were performed at the University of Texas at Austin Genomic Facility. Illumina Tag-Seq of polyA enriched total RNA sequencing was performed (single end, 100 bp).

value: CeA


title: Right Central amygdala SNL 6

description: Library name: snl_cea_right_6


title: mLTC-1 murine Leydig cell line, control, replicate 1

description: Library name: SMX09_1


title: Vgll3 Ex3 Sample 3B

description: Library name: Vgll3_null_3B

value: vgll3 Exon3


title: mLTC-1 murine Leydig cell line, 100µM MSNBA, replicate 2

description: Library name: SMX09_6


title: Right Central amygdala SNL 5

description: Library name: snl_cea_right_5


title: Vgll3 Ex3 Sample 4B

description: Library name: Vgll3_null_4B


title: mLTC-1 murine Leydig cell line, control, replicate 2

description: Library name: SMX09_2


title: HL_G1_12A

description: Library name: Sample 23


title: Vgll3 Ex3 Sample 4A

description: Library name: Vgll3_null_4A


title: Gingival tissue, SIIN, Day 7, rep4

city: Cleveland

first: Michael

last: Stolley

state: Ohio

address: 9620 Carnegie Ave N Bldg

department: Department of Inflammation and Immunity

institute: Cleveland Clinic Lerner Research Institute

description:
Library name: sample 21
Stolley_SIIN_D7_4

data_processing:
Raw sequencing reads underwent quality control using fastqc and Trimmomatic and reads were aligned to the mouse genome (mm38) using STAR aligner.
Assembly: mm38
Supplementary files format and content: tab-delimited raw files contains raw counts for each sample

source_name: Gingival tissue

extract_protocol:
Tissues were homogenized in RLT buffer using a Beadblaster (Benchmark) and Omni Bead Ruptor ceramic bead tubes (1.4 mm), and RNA was extracted using a RNeasy mini kit (QIAGEN)
libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina), and sequencing was performed on an Illumina NovaSeq 6000 platform, generating 150 bp paired-end reads. The sequencing depth achieved an average of 30 million reads per sample.

value: Gingival tissue

value: SIIN


title: HL_G1_12C

description: Library name: Sample 24


title: Right Central amygdala SNL 3

description: Library name: snl_cea_right_3


title: Right Central amygdala SNL 2

description: Library name: snl_cea_right_2


title: Vgll3 Ex3 Sample 3A

description: Library name: Vgll3_null_3A

value: fibroblast


title: HL_G1_11C

description: Library name: Sample 22


title: Right Central amygdala SNL 1

description: Library name: snl_cea_right_1


title: Vgll3 Ex3 Sample 1B

description: Library name: Vgll3_null_1B


title: HL_G1_10C

description: Library name: Sample 20


title: Left Central amygdala SNL 2

description: Library name: snl_cea_left_2


title: Gingival tissue, SIIN, Day 7, rep3

description:
Library name: sample 20
Stolley_SIIN_D7_3


title: Gingival tissue, SIIN, Day 3, rep4

description:
Library name: sample 17
Stolley_SIIN_D3_4


title: Left Central amygdala SNL 4

description: Library name: snl_cea_left_4


title: Gingival tissue, SIIN, Day 7, rep1

description:
Library name: sample 18
Stolley_SIIN_D7_1


title: Vgll3 Ex1 Sample 6B

description: Library name: Vgll3_KD_6B

value: vgll3 Exon1


title: Left Central amygdala SNL 3

description: Library name: snl_cea_left_3


title: Gingival tissue, SIIN, Day 7, rep2

description:
Library name: sample 19
Stolley_SIIN_D7_2


title: Vgll3 Ex1 Sample 6A

description: Library name: Vgll3_KD_6A


title: HL_G1_9A

description: Library name: Sample 17

value: Serum


title: HL_G1_9C

description: Library name: Sample 18


title: Vgll3 Ex1 Sample 4A

description: Library name: Vgll3_KD_4A


title: Vgll3 Ex3 Sample 1A

description: Library name: Vgll3_null_1A


title: Gingival tissue, SIIN, Day 3, rep1

description:
Library name: sample 14
Stolley_SIIN_D3_1


title: Left Central amygdala SNL 5

description: Library name: snl_cea_left_5


title: Gingival tissue, SIIN, Day 3, rep3

description:
Library name: sample 16
Stolley_SIIN_D3_3


title: HL_G1_8C

description: Library name: Sample 16


title: HL_G1_11A

description: Library name: Sample 21

value: Pre-treatment


title: Left Central amygdala SNL 6

description: Library name: snl_cea_left_6


title: Gingival tissue, SIIN, Day 3, rep2

description:
Library name: sample 15
Stolley_SIIN_D3_2


title: HL_G1_10A

description: Library name: Sample 19

value: Day 0


title: Vgll3 Ex1 Sample 4B

description: Library name: Vgll3_KD_4B


title: Left Central amygdala SNL 1

description: Library name: snl_cea_left_1


title: HL_G1_8A

description: Library name: Sample 15


title: Gingival tissue, no treatment, rep5

description:
Library name: sample 13
Stolley_No_Tx_5

value: NO TX


title: Vgll3 Ex1 Sample 3B

description: Library name: Vgll3_KD_3B


title: Vgll3 Ex1 Sample 3A

description: Library name: Vgll3_KD_3A


title: Right Central amygdala Sham 6

description: Library name: sham_cea_right_6


title: HL_G1_7C

description: Library name: Sample 14


title: Gingival tissue, no treatment, rep2

description:
Library name: sample 10
Stolley_No_Tx_2


title: HL_G1_6A

description: Library name: Sample 11


title: Right Central amygdala Sham 3

description: Library name: sham_cea_right_3


title: Right Central amygdala Sham 2

description: Library name: sham_cea_right_2


title: Right Central amygdala Sham 1

description: Library name: sham_cea_right_1


title: HL_G1_6C

description: Library name: Sample 12


title: HL_G1_5A

description: Library name: Sample 9


title: Gingival tissue, no treatment, rep1

description:
Library name: sample 9
Stolley_No_Tx_1


title: Right Central amygdala Sham 5

description: Library name: sham_cea_right_5


title: Gingival tissue, gp33, Day 7, rep4

description:
Library name: sample 8
Stolley_gp33_D7_4


title: CD34+ HSPC derived erythroblasts;KMT2D;CUT&RUN;Rep2

city: Suzhou

first: Peng

last: Xu

state: Jiangsu

address: Office3625 Building703, RENAI ROAD No.199, INDUSTRIAL PARK DISTRICT

department: Suzhou Medical College

institute: Soochow University

description: Library name: CD34_KMT2D_R2

data_processing:
Indexed samples were analysed by paired-end NGS, using an Illumina NextSeq Mid-Output (150 cycles) kit. FASTQ files were mapped to hg19 using Bowtie2(v2.2.5).  Reads that could not be uniquely mapped to the human genome were removed by SAMtools (v.0.17). Peaks were called using MACS2 (v.2.1.1). BigWigfiles were generated using DeepTools (v.3.2.0).
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Run

source_name: Human blood

extract_protocol:
10 μl concanavalin beads were added to the samples, followed with gentle rotation for 10 min at room temperature. Beads were resuspended in 100 μl buffer (Dig-wash buffer with 0.05% digitonin ) with 2 μg KMT2D antibody. On ice, 2 μl 100 mM CaCl2 was added to the sample with gentle mixing.rred to a new tube.  Afterward, samples were incubated on ice for 60-180 min. Then 100 μl stop buffer was added to the samples and samples were incubated for 10 min at 37°C followed by centrifugation at 4°C, 12,000 rpm. DNA was extracted by the phenol/chloroform/isopropanol protocol.
Library construction was performed using the DNA Library Prep Kit.

value: Human blood

value: CD34+ HSPC derived erythroblasts


title: Right Central amygdala Sham 4

description: Library name: sham_cea_right_4


title: CD34+ HSPC derived erythroblasts;KMT2D;CUT&RUN;Rep1

description: Library name: CD34_KMT2D_R1


title: Gingival tissue, gp33, Day 7, rep3

description:
Library name: sample 7
Stolley_gp33_D7_3


title: Gingival tissue, no treatment, rep3

description:
Library name: sample 11
Stolley_No_Tx_3


title: HL_G1_7A

description: Library name: Sample 13


title: HUDEP2 cells; IAA treated_rep1;H3K4me1;Cut&Run

description: Library name: IAA_H3K4me1_R1

data_processing:
Indexed samples were analysed by paired-end NGS, using an Illumina NextSeq Mid-Output (150 cycles) kit. FASTQ files were mapped to hg19 using Bowtie2(v2.2.5).  Reads that could not be uniquely mapped to the human genome were removed by SAMtools (v.0.17). Peaks were called using MACS2 (v.2.1.1). BigWigfiles were generated using DeepTools (v.3.2.0).
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Run


title: HUDEP2 cells; IAA treated_rep2;H3K4me1;Cut&Run

description: Library name: IAA_H3K4me1_R2


title: HUDEP2 cells; DMSO treated_rep2;H3K4me1;Cut&Run

description: Library name: DMSO_H3K4me1_R2


title: HL_G1_5C

description: Library name: Sample 10


title: Left Central amygdala Sham 6

description: Library name: sham_cea_left_6


title: Gingival tissue, no treatment, rep4

description:
Library name: sample 12
Stolley_No_Tx_4


title: HUDEP2 cells; DMSO treated_rep1;H3K4me1;Cut&Run

description: Library name: DMSO_H3K4me1_R1


title: Gingival tissue, gp33, Day 7, rep1

description:
Library name: sample 5
Stolley_gp33_D7_1


title: Gingival tissue, gp33, Day 7, rep2

description:
Library name: sample 6
Stolley_gp33_D7_2


title: Gingival tissue, gp33, Day 3, rep4

description:
Library name: sample 4
Stolley_gp33_D3_4


title: Gingival tissue, gp33, Day 3, rep3

description:
Library name: sample 3
Stolley_gp33_D3_3


title: Left Central amygdala Sham 4

description: Library name: sham_cea_left_4


title: Left Central amygdala Sham 5

description: Library name: sham_cea_left_5


title: HL_G1_4C

description: Library name: Sample 8


title: HUDEP2 cells; Washout 24h_re1

description: Library name: Wash24_1

data_processing:
Raw counts of gene transcripts were derived from raw fastq files using the alignment-independent quantification tool, Salmon (https://combine- lab.github.io/salmon/), with standard settings. The raw count matrix was then imported into R-studio and utilized as input for Limma_voom analysis following the vignette of the package for normalization, differential gene expression analysis, and unbiased clustering analysis, including principal component analysis. The output of Limma_voom was used as the input for pre-ranked-based GSEA to enrich functional pathways and gene signatures (https://www.gsea-msigdb.org/gsea/index.jsp).
Assembly: hg19
Supplementary files format and content: Count file

source_name: Blood

extract_protocol:
RNA samples of two biological replicates were extracted from cultured cells, using TRIzol (Ambion by Life technologies, 343,911), following the manufacturer’s instructions. RNA was then sent out for library preparation and next-generation sequencing to a commercial company, Novogene (CA, USA).
According to the manufacturer's instructions, three biologically duplicated RNA samples were extracted from cultured cells using TRIZOL (Ambion by Life technologies, 343911). RNA sample quality was analyzed, and library were prepared and next-generation sequenced by a commercial company, Novogene (California, USA).

value: Blood


title: Gingival tissue, gp33, Day 3, rep1

description:
Library name: sample 1
Stolley_gp33_D3_1


title: HL_G1_2A

description: Library name: Sample 3

value: Classical Hodgkin Lymphoma


title: HUDEP2 cells; Washout 6h_re2

description: Library name: Wash6_2


title: HL_G1_2C

description: Library name: Sample 4


title: Left Central amygdala Sham 3

description: Library name: sham_cea_left_3


title: Left Central amygdala Sham 1

description: Library name: sham_cea_left_1


title: HL_G1_4A

description: Library name: Sample 7


title: HUDEP2 cells; Washout 6h_re1

description: Library name: Wash6_1


title: HUDEP2 cells; 5-Ph-IAA treated rep1

description: Library name: IAA_1


title: Right Basolateral amygdala SNL 5

description: Library name: snl_bla_right_5

source_name: BLA

value: BLA


title: Gingival tissue, gp33, Day 3, rep2

description:
Library name: sample 2
Stolley_gp33_D3_2


title: HL_G1_3C

description: Library name: Sample 6

value: Post-Induction


title: pancreas, Safflower, 8-week on diet, female, K_19

city: New Haven

first: Mandar

middle: Deepak

last: Muzumdar

state: CT

address: 333 Cedar Street

institute: Yale University

description:
Library name: KCO_Safflower_11
column name in KCO_8wk_NormaliizedCounts.csv KCO_Safflower_11

data_processing:
Low-quality bases and adapter sequences were trimmed using Trim Galore (version 0.6.7) and CutAdapt (version 3.5).
Cleaned reads were aligned to the University of California Santa Cruz mouse genome (mm10) using the STAR aligner (version 2.7.9). Gene-level quantification was performed using the -quantMode GeneCounts option in STAR, which generates a matrix of raw read counts for each gene.
Assembly: mm10
Supplementary files format and content: Raw counts processed from sequence-aligned read counts (mm10, gene level) as output from STAR. First row is sample name header, in .txt tab-delimited format. Gene_name is only row descriptor, unsorted by gene, and sample column names are directly from FASTQ file names
Supplementary files format and content: Normalized counts processed from raw counts (mm10, gene level) via DESeq2 in R, in .txt tab-delimited format, absolute normalized counts (linear, not log counts), with UCSC Gene_symbol, ENTREZ_ID as first two columns, first row header contains sample names with simplified name corresponding to GEO sample library name. Genes without any reads are excluded

source_name: pancreas

growth_protocol: All mice were generated by breeding. The original C57BL/6 and 129/Sv mice used to generate the KC and KCO strains were purchased from Jackson Laboratories. KC mice were kept on a C57BL/6 background. KCO were maintained in a hybrid C57BL/6 and 129/Sv background

extract_protocol:
Mouse pancreata were snap frozen in liquid nitrogen and manually pulverized using the BioPulverizer (BioSpec Products 59012MS). Total RNA was extracted from pulverized tissue (20-40 mg), homogenized via QIAshredder column, and purified using the RNeasy Mini Kit (Qiagen) with on column DNAse I digestion, per the manufacturer's protocol.
RNA quality and quantity was assessed using an Agilent Bioanalyzer, and only high-quality RNA samples (RIN>7) were used in downstream analysis. RNA-seq libraries were prepared from mRNA purified from approximately 200ng total RNA with oligo-dT bead polyA selection (Illumina)  and sheared by incubation at 94C in the presence of Mg (Roche Kapa mRNA Hyper Prep Cat# KR1352). Following first-strand synthesis with random primers, second strand synthesis and A-tailing are performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs are ligated to library insert fragments.  Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends.  Strands marked with dUTP are not amplified. Indexed libraries are quantified by qRT-PCR using a commercially available kit (Roch KAPA Biosystems Cat# KK4854) and insert size distribution determined by either the Agilent Bioanalyzer. Samples with a yield of ≥ 0.5 ng/ul and a size distribution of 150-300bp are used for sequencing.
Sequenced (>25M 100-bp paired-end (2x100) reads on NovaSeq 6000 (Illumina)) with the Yale Center for Genome Analysis (YCGA)

treatment_protocol: All mice were put on indicated diet at 6 weeks of age for indicated time. Diets were changed weekly, and pancreate were at terminal time point.

value: pancreas

value: KrasLSL-G12D/+; Pdx1-Cre;Lepob/ob

value: 14 weeks

value: Safflower diet, 8 weeks


title: HUDEP2 cells; DMSO treated rep2

description: Library name: DMSO_2


title: HUDEP2 cells; 5-Ph-IAA treated rep2

description: Library name: IAA_2


title: HL_G1_1A

description: Library name: Sample 1

data_processing:
CLC Genomics Workbench - Qiagen Genomic Services
Raw data was de-multiplexed FASTQ files for each sample were generated using the bcl2fastq
Cutadapt (v1.11) extracts adapter and UMI info, then trims adapters and collapses reads by UMI.
Reads were mapped with Bowtie2 (v2.2.2); only perfect matches were kept.
Trimmed sequence reads were mapped to GRCh37 using QIAGEN CLC Genomic service tools. For mapping to the genome, not more than one mismatch is allowed in the first 32 basesof the read. No indels are allowed in mapping.
Read count extraction and normalization were performed using QIAGEN CLC genomic benchwork
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample


title: Right Basolateral amygdala SNL 3

description: Library name: snl_bla_right_3


title: pancreas, Safflower, 8-week on diet, male, K_16

description:
Library name: KCO_Safflower_8
column name in KCO_8wk_NormaliizedCounts.csv KCO_Safflower_8


title: HUDEP2 cells; DMSO treated rep1

description: Library name: DMSO_1


title: pancreas, Safflower, 8-week on diet, female, K_17

description:
Library name: KCO_Safflower_9
column name in KCO_8wk_NormaliizedCounts.csv KCO_Safflower_9


title: Right Basolateral amygdala SNL 2

description: Library name: snl_bla_right_2


title: OY-25952_S10_tgf_eipa

city: Houston

first: Scott

middle: Andrew

last: Ochsner

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Library name: Sample 10

data_processing:
The STAR software tool was used for aligning sequencing reads to hg38.
Assembly: hg38
Supplementary files format and content: mapped feature counts

growth_protocol: MRC5 cells were maintained in DMEM media supplemented with 10% FBS and antibiotics in cell culture incubator under 5% CO2 at 37˚C

extract_protocol:
total RNA was isolated using QUAGEN RNAsy kit
The Genomic and RNA Profiling Core prepared libraries with 250 ng of RNA and the Illumina TruSeq Stranded mRNA Library Prep kit (p/n 20020594) according to the manufacturer’s protocol. Libraries were quantitated and pooled equimolarly. Sequencing was performed on an Illumina NextSeq 500 platform to around 40 million read pairs per sample.

treatment_protocol: MRC5 cells were stimulated with TGF-𝛃1 (10 ng/ml) in the presence or absence of EIPA (12.5 𝛍M) in DMEM media supplemented with 1% FBS and antibiotics in cell culture incubator under 5% CO2 at 37˚C

value: lung fibroblast


title: Right Basolateral amygdala SNL 1

description: Library name: snl_bla_right_1


title: OY-25955_S12_eipa

description: Library name: Sample 12

value: eipa


title: OY-25951_S9_tgf_eipa

description: Library name: Sample 9


title: HL_G1_3A

description: Library name: Sample 5

extract_protocol:
RNA was isolated using the miRNeasy Serum/Plasma Kit (QIAGEN) according to manufacturers insructions.
small RNA libraries for non coding-seq were prepared using the QIAseq miRNA Library Kit following manufacturer's protocols.


title: pancreas, Safflower, 8-week on diet, female, K_12

description:
Library name: KCO_Safflower_7
column name in KCO_8wk_NormaliizedCounts.csv KCO_Safflower_7


title: OY-25953_S11_eipa

description: Library name: Sample 11


title: pancreas, Safflower, 8-week on diet, female, K_10

description:
Library name: KCO_Safflower_5
column name in KCO_8wk_NormaliizedCounts.csv KCO_Safflower_5


title: Left Basolateral amygdala SNL 6

description: Library name: snl_bla_left_6


title: pancreas, Safflower, 8-week on diet, male, K_11

description:
Library name: KCO_Safflower_6
column name in KCO_8wk_NormaliizedCounts.csv KCO_Safflower_6


title: HUDEP2 cells; dTAG13 treated_rep2

description: Library name: TAG_2


title: HUDEP2 cells; 5-Ph-IAA treated_rep3

description: Library name: IAA_3


title: HUDEP2 cells; dTAG13 treated_rep3

description: Library name: TAG_3


title: pancreas, Safflower, 8-week on diet, male, K_8

description:
Library name: KCO_Safflower_4
column name in KCO_8wk_NormaliizedCounts.csv KCO_Safflower_4


title: OY-25950_S8_tgf_eipa

description: Library name: Sample 8


title: Left Basolateral amygdala SNL 5

description: Library name: snl_bla_left_5


title: HUDEP2 cells; 5-Ph-IAA treated_rep2

description: Library name: IAA_2


title: Left Basolateral amygdala SNL 4

description: Library name: snl_bla_left_4


title: HUDEP2 cells; 5-Ph-IAA treated_rep1

description: Library name: IAA_1


title: Left Basolateral amygdala SNL 2

description: Library name: snl_bla_left_2


title: pancreas, Safflower, 8-week on diet, male, K_3

description:
Library name: KCO_Safflower_3
column name in KCO_8wk_NormaliizedCounts.csv KCO_Safflower_3


title: OY-25949_S7_tgf

description: Library name: Sample 7

value: tgf


title: HUDEP2 cells; DMSO treated_rep3

description: Library name: DMSO_3


title: pancreas, Safflower, 8-week on diet, female, K_1

description:
Library name: KCO_Safflower_1
column name in KCO_8wk_NormaliizedCounts.csv: KCO_Safflower_1


title: OY-25948_S6_tgf

description: Library name: Sample 6


title: Left Basolateral amygdala SNL 3

description: Library name: snl_bla_left_3


title: OY-25947_S5_tgf

description: Library name: Sample 5


title: HUDEP2 cells; DMSO treated_rep2

description: Library name: DMSO_2


title: OY-25946_S4_control

description: Library name: Sample 4

value: control


title: Left Basolateral amygdala SNL 1

description: Library name: snl_bla_left_1


title: HUDEP2 cells; DMSO treated_rep1

description: Library name: DMSO_1


title: OY-25944_S3_control

description: Library name: Sample 3


title: pancreas, HO Safflower, 3-week on diet, male, 1568

description:
Library name: HO_Safflower_4
column name in KC_3wk_NormaliizedCounts.csv: HO_Safflower_4

value: KrasLSL-G12D/+; Pdx1-Cre

value: 9 weeks

value: HO Safflower diet, 3 weeks


title: HUDEP2 cells; KO-Rep2;ATAC

description: Library name: KMT2D-KO-2

data_processing:
Paired-end reads were trimmed for index adapter by cutadapt (paired-end mode, default parameter with ‘-m 6 -O 20’) and aligned to human genome hg19 by BWA (version 0.7.12-r1039, default parameter). Duplicated reads were then marked with Picard (version 2.6.0-SNAPSHOT) and only non-duplicated proper paired reads were kept by samtools (parameter ‘-q 1 -F 1804’ version 1.2) . To evaluate the Cut&Run assay quality, we first separated reads by fragment size <120 bp, or fragment size >150 bp and <2,000 bp and generated bigwig files for visualization. We observed a clear pattern that peaks in tracks with <120 bp were sharper and surrounded by peaks in tracks with >150 bp on IGV (version 2.17.14), which was consistent to the description from the original Cut&Run protocol paper. We then generated bigwig files using all reads that fragment size <2,000 bp.
Assembly: hg19
Supplementary files format and content: bigWig,narrowPeak

source_name: blood

growth_protocol: Immature HUDEP2 cells were expanded in the StemSpan serum-free medium (SFEM; STEMCELL Technologies) supplemented with 1uM dexamethasone, 1ug/mL doxycycline, 50 ng/mL human stem cell factor (SCF), 3 units/mL erythropoietin (EPO), and 1% penicillin–streptomycin.cell lines were placed in a 37 °C incubator containing 5% CO2.

extract_protocol:
Collect cells and add 10% NP40, 10% Tween, and 1% Digitonin to lyse cells. Add Tn5 transposase for fragmentation and collect DNA fragments
Building a library using the Hyperactive ATAC Seq Library Prep Kit with 10ng DNA

treatment_protocol: Collect cells and extract RNA after knocking out KMT2D

value: blood

value: Human blood


title: OY-25394_S2_control

description: Library name: Sample 2


title: HUDEP2 cells; KO-Rep1;ATAC

description: Library name: KMT2D-KO-1


title: Right Basolateral amygdala Sham 5

description: Library name: sham_bla_right_5


title: Right Basolateral amygdala Sham 4

description: Library name: sham_bla_right_4


title: Right Basolateral amygdala Sham 6

description: Library name: sham_bla_right_6


title: Right Basolateral amygdala Sham 3

description: Library name: sham_bla_right_3


title: HFD_EVs 3

city: Nanjing

first: jin

last: wang

address: No. 321 Zhongshan Road

department: Department of Endocrinology

institute: Drum Tower hospital affiliated to Nanjing university medical school

description: Library name: Sample 7

data_processing:
miRNA sequences, tRNA sequences and piRNA sequences were obtained from miRBase v21(Kozomara and Griffiths-Jones, 2014), GtRNAdb (Chan and Lowe, 2016) and piRNA bank (Lakshmi and Agrawal, 2008), respectively. Bowtie was used to align clean reads to these reference sequences for annotation.
Assembly: miRBase v21; GtRNAdb; piRNA bank
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

source_name: adipose tissue

extract_protocol:
EVs were extracted from adipose tissues of chow-fed and high-fat diet mice and processed for RNA extraction by Trizol. All sRNA library construction and deep sequencing were performed by Novogene (Tianjin, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adipose tissue

value: HFD diet


title: HUDEP2 cells; Ctrl-Rep2;ATAC

description: Library name: NT-2


title: Right Basolateral amygdala SNL 4

description: Library name: snl_bla_right_4

value: BLA


title: OY-25385_S1_eipa

description: Library name: Sample 1


title: HUDEP2 cells; Ctrl-Rep1;ATAC

description: Library name: NT-1


title: pancreas, Safflower, 3-week on diet, male, 3_5

description:
Library name: Safflower_4
column name in KC_3wk_NormaliizedCounts.csv: Safflower_4

value: Safflower diet, 3 weeks


title: HUDEP2 cells; IAA treated_24h_rep2

description: Library name: C25_I24_2

data_processing:
Raw counts of gene transcripts were derived from raw fastq files using the alignment-independent quantification tool, Salmon (https://combine- lab.github.io/salmon/), with standard settings. The raw count matrix was then imported into R-studio and utilized as input for Limma_voom analysis following the vignette of the package for normalization, differential gene expression analysis, and unbiased clustering analysis, including principal component analysis. The output of Limma_voom was used as the input for pre-ranked-based GSEA to enrich functional pathways and gene signatures (https://www.gsea-msigdb.org/gsea/index.jsp).
Assembly: hg19
Supplementary files format and content: Tab-delimited text file includes Row counts for each sample

growth_protocol: Immature HUDEP2 cells were expanded in the StemSpan serum-free medium (SFEM; STEMCELL Technologies) supplemented with 1 uM dexamethasone, 1 ug/mL doxycycline, 50 ng/mL human stem cell factor (SCF), 3 units/mL erythropoietin (EPO), and 1% penicillin–streptomycin.The human K562 cell line was maintained in RPMI-1640 medium (Hycita) containing 10% fetal bovine serum (FBS) (Hyclone), 2 mM glutamine (Sigma) and 1% penicillin/streptomycin (Thermo Fisher Scientific). Both cell lines were placed in a 37 ° C incubator containing 5% CO2.

treatment_protocol: Collect cells and extract RNA after adding 5-PH-IAA6, 12, and 24 hours.


title: Right Basolateral amygdala Sham 1

description: Library name: sham_bla_right_1


title: Chow_EVs 4

description: Library name: Sample 4

value: Chow diet


title: HUDEP2 cells; IAA treated_12h_rep2

description: Library name: C25_I12_2


title: pancreas, Safflower, 8-week on diet, male, K_2

description:
Library name: KCO_Safflower_2
column name in KCO_8wk_NormaliizedCounts.csv KCO_Safflower_2

value: pancreas

value: KrasLSL-G12D/+; Pdx1-Cre;Lepob/ob


title: Left Basolateral amygdala Sham 6

description: Library name: sham_bla_left_6


title: HFD_EVs 1

description: Library name: Sample 5


title: Right Basolateral amygdala Sham 2

description: Library name: sham_bla_right_2


title: pancreas, Safflower, 3-week on diet, male, 1880

description:
Library name: Safflower_1
column name in KC_3wk_NormaliizedCounts.csv: Safflower_1


title: HUDEP2 cells; IAA treated_6h_rep2

description: Library name: C25_I6_2


title: pancreas, HO Safflower, 3-week on diet, male, 2342

description:
Library name: HO_Safflower_2
column name in KC_3wk_NormaliizedCounts.csv: HO_Safflower_2


title: pancreas, HO Safflower, 3-week on diet, male, 2288

description:
Library name: HO_Safflower_1
column name in KC_3wk_NormaliizedCounts.csv: HO_Safflower_1


title: pancreas, HO Sunflower, 12-week on diet, male, 877

description:
Library name: HO_Sunflower_M_6
column name in KC_12wk_NormaliizedCounts.csv: HO_Sunflower_M_6

value: 18 weeks

value: HO Sunflower diet, 12 weeks


title: HUDEP2 cells; DMSO treated_rep2

description: Library name: C25_D6_2


title: Chow_EVs 2

description: Library name: Sample 2


title: Left Basolateral amygdala Sham 5

description: Library name: sham_bla_left_5


title: Chow_EVs 1

description: Library name: Sample 1


title: Left Basolateral amygdala Sham 3

description: Library name: sham_bla_left_3


title: pancreas, Sunflower, 12-week on diet, male, 3770

description:
Library name: Sunflower_M_8
column name in KC_12wk_NormaliizedCounts.csv: Sunflower_M_8

value: Sunflower diet, 12 weeks


title: K562 cells; IAA treated_12h_rep2

description: Library name: C13_I12_2


title: pancreas, HO Sunflower, 12-week on diet, male, 663

description:
Library name: HO_Sunflower_M_3
column name in KC_12wk_NormaliizedCounts.csv: HO_Sunflower_M_3


title: Left Basolateral amygdala Sham 4

description: Library name: sham_bla_left_4


title: CTCF_CUT&RUN-Cdiptos-dCas9

city: Boston

first: Wanying

state: MA

address: Karp Family Research Building

department: Hematology

institute: Boston Children's Hospital & Broad Institute

data_processing:
CUT&RUN data were mapped to mouse reference genome mm10 using Bowtie2. First 50 bases of each read were used for mapping. We only use non-redundant reads to eliminate possible duplicates from biased PCR amplification.
Assembly: mm10
Supplementary files format and content: monoclonal bed file
Library strategy: CUT&RUN

growth_protocol: E14Tg2a (karyotype 19, XY; 129/Ola isogenic background) and subclones were cultured in DMEM+Glutamax (ThermoFisher cat 10566-016) supplemented with 15% Fetal Bovine Serum (ThermoFisher SH30071.03), 550µM b-mercaptoethanol (ThermoFisher 21985-023), 1mM Sodium Pyruvate (ThermoFisher 11360-070), 1X non-essential amino-acids (ThermoFisher 11140-50) and 104U of Leukemia inhibitory factor (Millipore ESG1107). Cells were maintained at a density of 0.2-1.5x105 cells / cm² by passaging using TrypLE (12563011) every 24-48h on 0.1% gelatin-coated dishes (Millipore cat ES-006-B) at 37°C and 7% CO2. Medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 3-4 months and tested negative.

extract_protocol: All CUT&RUN libraries were generated following with CUT&RUN protocol

value: embryonic stem cells

value: CTCF-KD

value: dox treatement


title: pancreas, HO Safflower, 3-week on diet, male, 2343

description:
Library name: HO_Safflower_3
column name in KC_3wk_NormaliizedCounts.csv: HO_Safflower_3

value: KrasLSL-G12D/+; Pdx1-Cre

value: 9 weeks


title: CTCF_CUT&RUN-Cdiptos-WT

value: WT

value: no treatment


title: pancreas, Safflower, 3-week on diet, male, 8781

description:
Library name: Safflower_2
column name in KC_3wk_NormaliizedCounts.csv: Safflower_2


title: pancreas, Sunflower, 12-week on diet, male, 3762

description:
Library name: Sunflower_M_6
column name in KC_12wk_NormaliizedCounts.csv: Sunflower_M_6


title: Left Central amygdala Sham 2

description: Library name: sham_cea_left_2

value: CeA


title: Left Basolateral amygdala Sham 1

description: Library name: sham_bla_left_1


title: pancreas, Sunflower, 12-week on diet, male, 1510

description:
Library name: Sunflower_M_1
column name in KC_12wk_NormaliizedCounts.csv: Sunflower_M_1


title: IL10

city: South San Francisco

first: Xinming

last: Tong

state: California

address: 1 DNA Way

institute: Genentech Inv.

description: Library name: SAM24459733

data_processing:
Read count extraction was performed using internal GSNAP-based NGS workflow
Assembly: Genome Reference Consortium Human build 38
Supplementary files format and content: CSV files includes raw counts for each sample

source_name: colon organoid

extract_protocol:
The RNA was isolated using QIAGEN´s RNeasy Plus Mini Kit
Libraries were prepared using the TruSeq RNA Sample Preparation Kit

value: colon organoid


title: Chow_EVs 3

description: Library name: Sample 3

value: adipose tissue


title: K562 cells; DMSO treated_rep2

description: Library name: C13_D6_2

value: Human blood


title: dne_isl1sib_homeo_mchpos_5dpf_atac_2

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description: Library name: dne_isl1sib_homeo_mchpos_5dpf_atac_2

data_processing:
RNA-seq raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner (version 2.7.3a ), using Ensembl 102 gene models. TPM values were generated using RSEM (version v1.3.0 ).
ATAC-seq raw reads were aligned using bowtie2 default parameters.
Assembly: danRer11
Supplementary files format and content: RNA-seq processed read count in csv file
Supplementary files format and content: ATAC-seq processed data in bigwig file format

organism: Danio rerio

source_name: posterior lateral line

growth_protocol: embryos were raised until 5dpf larval stage in E2 embryo medium.

extract_protocol:
mcherry+ cells were FACsorted after Trypsin larvae dissociation. For RNA-seq, cells were sorted into Trizol and RNA was extracted using phenol/chloroform extraction method. For ATAC-seq, nuclei were extracted and tagmentation performed as described in Buenrostro, Jason D et al., Nat. Methods (2013) and Corces, M. R. et al., Nat. Methods (2017).
RNA libraries for RNA-seq were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing following manufacturer's protocols. For ATAC-seq, DNA fragments were purified using the Monarch PCR & DNA Cleanup Kit following manufacturer's instructions. Libraries were constructed using Illumina Nextera Dual Indexing as described in Corces, M. R. et al., Nat. Methods (2017).

treatment_protocol: 300uM neomycin treatment was done at 5dpf (not in homeostasis samples) for 30min, then samples were extensively washed with E2 embryo medium and let to recover for 1 hr or 3hr depending on the sample.

value: posterior lateral line

value: neuromast cells

value: isl1apsi97 sibling

value: homeostasis


title: dne_isl1sib_homeo_mchpos_5dpf_atac_3

description: Library name: dne_isl1sib_homeo_mchpos_5dpf_atac_3


title: K562 cells; IAA treated_6h_rep2

description: Library name: C13_I6_2


title: IL2

description: Library name: SAM24459732


title: K562 cells; IAA treated_24h_rep2

description: Library name: C13_I24_2


title: pancreas, HO Safflower, 12-week on diet, male, 1234

description:
Library name: HO_Safflower_M_4
column name in KC_12wk_NormaliizedCounts.csv: HO_Safflower_M_4

value: pancreas

value: 18 weeks

value: HO Safflower diet, 12 weeks


title: HUDEP2 cells;NT_rep3_Input

description: Library name: 1345275_PXU041_R1

data_processing:
For ChIP-Seq, raw sequencing data were aligned to the mouse genome mm9 and the drosophila genome dm6 using Bowtie2 (ref. 51; v2.3.2). To identify ChIP-enriched regions, SICER52 (v1.1) was used. For ChIP–seq of KMT2D, the window size of 50 bp, the gap size of 50 bp and the false discovery rate (FDR) threshold of 0.05 were used. For ChIP–seq of histone modifications (H3K4me1 and H3K27ac), the window size of 200 bp, the gap size of 200 bp and the FDR threshold of 10−3 were used. Reads on indicated regions were collected to calculate reads per kilobase million as a measure of signal intensity.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: Human bone marrow

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Antibody were added to the sonication samples, followed with gentle rotation for 16 hours at 4°C, Beads added after that,followed with gentle rotation for 6 hours at 4°C. beads transfered to a new tube. Using wash buffer to wash beads, then, samples were incubated in SDS elution buffer for 6 hours. separate beads and supernatant, DNA was in supernatant and then extracted by the phenol/chloroform/isopropanol protocol. Library construction was performed using the DNA Library Prep Kit.

value: Human bone marrow

value: erythroblast cells

value: NT

tag: antibody

value: no


title: HUDEP2 cells;KO_rep2_Input

description: Library name: 1480045_PXU046_R1

value: KO


title: dne_isl1sib_3hneo_mchpos_5dpf_atac_3

description: Library name: dne_isl1sib_3hneo_mchpos_5dpf_atac_3

value: 30min neomycin (300uM)


title: HUDEP2 cells;NT_rep2_Input

description: Library name: 1480044_PXU045_R1


title: TFF3

description: Library name: SAM24459729


title: KGF

description: Library name: SAM24459728


title: dne_isl1sib_3hneo_mchpos_5dpf_atac_2

description: Library name: dne_isl1sib_3hneo_mchpos_5dpf_atac_2


title: pancreas, HO Sunflower, 12-week on diet, male, 897

description:
Library name: HO_Sunflower_M_4
column name in KC_12wk_NormaliizedCounts.csv: HO_Sunflower_M_4

tag: strain

value: KrasLSL-G12D/+; Pdx1-Cre

value: HO Sunflower diet, 12 weeks


title: pancreas, HO Safflower, 12-week on diet, male, 688

description:
Library name: HO_Safflower_M_3
column name in KC_12wk_NormaliizedCounts.csv: HO_Safflower_M_3


title: TGFa

description: Library name: SAM24459726

value: colon organoid


title: HUDEP2 cells;KO_rep1_Input

description: Library name: 1480041_PXU042_R1


title: EGF

description: Library name: SAM24459725


title: pancreas, Sunflower, 12-week on diet, male, 3748

description:
Library name: Sunflower_M_4
column name in KC_12wk_NormaliizedCounts.csv: Sunflower_M_4

value: Sunflower diet, 12 weeks


title: HUDEP2 cells;NT_rep1_Input

description: Library name: 1480040_PXU041_R1


title: pancreas, HO Safflower, 12-week on diet, male, 685

description:
Library name: HO_Safflower_M_2
column name in KC_12wk_NormaliizedCounts.csv: HO_Safflower_M_2


title: pancreas, Safflower, 12-week on diet, male, 1314

description:
Library name: Safflower_M_5
column name in KC_12wk_NormaliizedCounts.csv: Safflower_M_5

value: Safflower diet, 12 weeks


title: pancreas, HO Safflower, 12-week on diet, male, 683

description:
Library name: HO_Safflower_M_1
column name in KC_12wk_NormaliizedCounts.csv: HO_Safflower_M_1


title: Ctrl

description: Library name: SAM24459724


title: dne_isl1sib_3hneo_mchpos_5dpf_atac_1

description: Library name: dne_isl1sib_3hneo_mchpos_5dpf_atac_1

value: posterior lateral line

value: neuromast cells


title: dne_isl1sib_1hneo_mchpos_5dpf_atac_3

description: Library name: dne_isl1sib_1hneo_mchpos_5dpf_atac_3

value: isl1apsi97 sibling


title: HUDEP2 cells; KO_rep3;GATA1;ChIP-seq

description: Library name: 1345266_PXU032_R1


title: Organoid B

description: Library name: SAM24472169


title: pancreas, Safflower, 12-week on diet, male, 736

description:
Library name: Safflower_M_4
column name in KC_12wk_NormaliizedCounts.csv: Safflower_M_4

value: pancreas


title: HUDEP2 cells; NT_rep3;GATA1;ChIP-seq

description: Library name: 1345262_PXU028_R1


title: dne_isl1sib_1hneo_mchpos_5dpf_atac_2

description: Library name: dne_isl1sib_1hneo_mchpos_5dpf_atac_2


title: dne_isl1sib_1hneo_mchpos_5dpf_atac_1

description: Library name: dne_isl1sib_1hneo_mchpos_5dpf_atac_1


title: dne_isl1sib_homeo_mchpos_5dpf_atac_1

description: Library name: dne_isl1sib_homeo_mchpos_5dpf_atac_1

value: homeostasis


title: HUDEP2 cells; NT_rep2;GATA1;ChIP-seq

description: Library name: 1480028_PXU029_R1


title: pancreas, CD, 12-week on diet, male, 962

description:
Library name: CD_M_5
column name in KC_12wk_NormaliizedCounts.csv: CD_M_5

value: 18 weeks

value: CD, 12 weeks


title: pancreas, Safflower, 12-week on diet, male, 733

description:
Library name: Safflower_M_3
column name in KC_12wk_NormaliizedCounts.csv: Safflower_M_3


title: dne_isl1mut_homeo_mchpos_5dpf_atac_3

description: Library name: dne_isl1mut_homeo_mchpos_5dpf_atac_3

value: isl1apsi97 mutant


title: dne_isl1mut_homeo_mchpos_5dpf_atac_2

description: Library name: dne_isl1mut_homeo_mchpos_5dpf_atac_2


title: HUDEP2 cells; NT_rep1;GATA1;ChIP-seq

description: Library name: 1480024_PXU025_R1

value: Human bone marrow

value: erythroblast cells

value: NT


title: DiffD7.A

description: Library name: SAM24459019


title: HUDEP2 cells; KO_rep2;GATA1;ChIP-seq

description: Library name: 1480029_PXU030_R1

value: KO


title: pancreas, Safflower, 12-week on diet, male, 726

description:
Library name: Safflower_M_2
column name in KC_12wk_NormaliizedCounts.csv: Safflower_M_2

value: KrasLSL-G12D/+; Pdx1-Cre


title: pancreas, Safflower, 12-week on diet, male, 721

description:
Library name: Safflower_M_1
column name in KC_12wk_NormaliizedCounts.csv: Safflower_M_1


title: dne_isl1mut_homeo_mchpos_5dpf_atac_1

description: Library name: dne_isl1mut_homeo_mchpos_5dpf_atac_1


title: DiffD5.B

description: Library name: SAM24459018


title: HUDEP2 cells; KO_rep1;GATA1;ChIP-seq

description: Library name: 1480025_PXU026_R1


title: dne_isl1mut_3hneo_mchpos_5dpf_atac_3

description: Library name: dne_isl1mut_3hneo_mchpos_5dpf_atac_3

value: 30min neomycin (300uM)


title: DiffD5.A

description: Library name: SAM24459017

value: colon organoid


title: Organoid A

description: Library name: SAM24472168


title: pancreas, CD, 12-week on diet, male, 431

description:
Library name: CD_M_4
column name in KC_12wk_NormaliizedCounts.csv: CD_M_4


title: HUDEP2 cells; KO_rep3;H3K27ac;ChIP-seq

description: Library name: 1345265_PXU031_R1


title: DiffD7.B

description: Library name: SAM24459020


title: DiffD3.B

description: Library name: SAM24459016


title: dne_isl1mut_3hneo_mchpos_5dpf_atac_2

description: Library name: dne_isl1mut_3hneo_mchpos_5dpf_atac_2


title: DiffD3.A

description: Library name: SAM24459015


title: pancreas, CD, 12-week on diet, male, 395

description:
Library name: CD_M_2
column name in KC_12wk_NormaliizedCounts.csv: CD_M_2


title: HUDEP2 cells; NT_rep3;H3K27ac;ChIP-seq

description: Library name: 1345261_PXU027_R1


title: dne_isl1mut_1hneo_mchpos_5dpf_atac_3

description: Library name: dne_isl1mut_1hneo_mchpos_5dpf_atac_3


title: dne_isl1mut_3hneo_mchpos_5dpf_atac_1

description: Library name: dne_isl1mut_3hneo_mchpos_5dpf_atac_1


title: pancreas, CD, 12-week on diet, male, 390

description:
Library name: CD_M_1
column name in KC_12wk_NormaliizedCounts.csv: CD_M_1


title: Right Basolateral amygdala SNL 6

description: Library name: snl_bla_right_6

value: BLA


title: DiffD1.B

description: Library name: SAM24459014


title: HUDEP2 cells; NT_rep2;H3K27ac;ChIP-seq

description: Library name: 1480020_PXU021_R1


title: HUDEP2 cells; KO_rep2;H3K27ac;ChIP-seq

description: Library name: 1480021_PXU022_R1


title: dne_isl1mut_1hneo_mchpos_5dpf_atac_2

description: Library name: dne_isl1mut_1hneo_mchpos_5dpf_atac_2


title: DiffD1.A

description: Library name: SAM24459013


title: HUDEP2 cells; KO_rep1;H3K27ac;ChIP-seq

description: Library name: 1480017_PXU018_R1


title: HL_G1_1C

city: Giessen

first: Vijay

last: Singh

address: Feulgenstrasse 12

description: Library name: Sample 2

source_name: Serum

value: Serum

value: Classical Hodgkin Lymphoma

value: Post-Induction

value: Day 57


title: dne_isl1mut_1hneo_mchpos_5dpf_atac_1

description: Library name: dne_isl1mut_1hneo_mchpos_5dpf_atac_1

value: posterior lateral line

value: neuromast cells


title: B12 Low treated splenic CD11b+ Cells

city: Miami

first: Luisa

last: Cimmino

state: Florida

address: 1501 NW 10th Ave, BRB 711

institute: University of Miami

data_processing:
The demultiplexing, barcode processing and aggregation were made using the Cell Ranger software v2.1.1
Assembly: m38
Supplementary files format and content: Tab-separate values file and matrix files

source_name: Splenic Cd45.2+CD11b+ Cells

extract_protocol:
Viably frozen single cell suspensions of splenic cells were FACS sorted on CD45.2+CD11b+DAPI. Cells were resuspended in 10% FBS in PBS.
Library preparation was performed according to manufacturer's instruction (single cell 3' v2 protocol, 10x Genomics).

value: Splenic Cd45.2+CD11b+ Cells

value: Low B12


title: HUDEP2 cells; NT_rep1;H3K27ac;ChIP-seq

description: Library name: 1480016_PXU017_R1