title: HD_2

city: Créteil

first: Sophie

last: Hue

address: 1 rue du général Sarrail

country: France

institute: Henri Mondor APHP

data_processing:
BCL files from Illumina were processed using 10x Genomics Cell Ranger 3.1.0, using cellranger mkfastq and cellranger count commands. Reads were mapped on GRCh37 (hg19) transcriptome. The 12 fastq files correspond to the output for cellranger mkfastq command while the 3 matrices files correspond to the output of cellranger count command. The count matrix is the unfiltered (raw) one, as used in the publication. Each raw count matrix was load using Seurat.  Empty droplets were removed using the emptyDrops function from the package DropletsUtils version 1.6.1. A false discovery rate (FDR) of 1E-3 was set to define empty droplets. Cells having less than 6 log number of unique molecular identifiers (UMI) or less than 500 genes were filtered out. Doublet cells were removed using scDblFinder package (version 1.1.8) and scds package (1.2.0) in hybrid mode. For scDblFinder eponymous function, the size.factors.norm parameter value was defined using DESeq2::sizeFactors function, DESeq2 version 1.26.0. For the cxds_bcds_hybrid function from the scds package, default setting was used and a hybrid_score greater than 1 was used to define double cells.  Then, cells having more than 20 % of UMI related to mitochondrial genes or more than 50 % related to ribosomal genes were filtered out. UMI count matrix for remaining cells was normalized using LogNormalize method implemented in Seurat::NormalizeData function. Single cells were annotated for cell type using Seurat::AddModuleScore and cell type-specific marker gene sets provided as supplementary table along with the publication. For the 2D projection, 3000 highly variable features (HVFs) were identified using Seurat::FindVariableFeatures. Then, a PCA with 100 components was generared from these 3000 HVFs, using Seurat::RunPCA. A tSNE was generated using 20 components from the PCA, using the Seurat::RunTSNE function.
Assembly: hg19
Supplementary files format and content: Raw count matrix provided by Cell Ranger

source_name: hair follicle cells

growth_protocol: Data are directly obtained from patients’ cells.

extract_protocol:
Human scalp samples were digested in 4 mg/ml Dispase (Stem Cell) overnight. Individual HFs were then pulled out one by one using forceps. To obtain single-cell suspension for scRNAseq, the isolated HFs were digested in 0.05% Trypsin-EDTA (Gibco) for 30 mins at room temperature, washed in DMEM + 10 % FBS, and filtered through a 100 μm cell strainer.
HF cells were sorted (BD InfluxTM Cell Sorter) using a nuclear labeling DRAQ7TM Far-Red Fluorescent Live-Cell Impermeant DNA Dye (Abcam, ref:  ab109202). Cells were collected in 20% FBS-RPMI solution. Around 25,000 cells were loaded into one channel of the Chromium system using the V3.1 single-cell reagent kit (10X Genomics) to generate single-cell GEMs. Following capture and lysis, cDNAs were synthesized, and then amplified by PCR for 12 cycles as per the manufacturer’s protocol (10X Genomics). The amplified cDNAs were used to generate Illumina sequencing libraries that were each sequenced on one flow cell Nextseq500 Illumina.

treatment_protocol: HS patients were recruited from FolHYDRA study and enrolled from the dermatology department of the Henri Mondor Teaching hospital between June 2022 and December 2023. The Clinical Investigation Center performed skin biopsies. This monocentric, prospective study was conducted in accordance with the declaration of Helsinki and was approved by the appropriate ethics committee (CPP Noth-West IV: 2021-A02352-39, 13/01/2022). All patients gave written informed consent before study enrolment. For scRNA-Seq analysis, hair follicle (HFs) samples were from discarded plastic surgery specimens from two healthy individuals and five HS patients axillary or pubis area.

value: hair follicle cells

tag: prelevement area

value: pubis

tag: phenotype

value: healthy

tag: hurley score


title: AD-C8_08

status: Public on Jun 02 2025

type: RNA

city: Baltimore

first: Shawn

last: Kwatra MD

state: MD

address: 1550 Orleans Street

department: Dermatology

country: USA

institute: Johns Hopkins School of Medicine

data_processing: Gene expression analysis was conducted for 770 neuroinflammatory-related genes using nCounter’s Human Neuroinflammation Panel and a panel of 30 genes focused on Mrgpr genes and cytokines. Nsolver Analysis Software 4.0 was used to complete quality control, background thresholding, and normalization of the raw expression data. 1 sample was flagged for mRNA content; thus, 119/120 samples were used for subsequent statistical analysis. Background thresholding to the geometric mean of the average counts for eight negative control samples was completed. Positive control normalization was calculated using the geometric mean of the average counts for six synthetic ssDNA control samples; housekeeping normalization was calculated using the geometric mean of the average counts for 9 selected housekeeping genes.

molecule: total RNA

organism: Homo sapiens

source_name: skin punch biopsy

extract_protocol: RNA was extracted from lesional and non-lesional samples using the RNAeasy FFPE Kit (Qiagen) as per the manufacturer's instructions

tag: race

value: C

tag: age

tag: Sex

value: F


title: genomic DNA from peripheral blood [9611518138_R06C01]

type: genomic

city: Munich

first: Binder

last: Elisabeth

address: Kraepelinstr. 2+10

country: Germany

institute: Max-Planck-Institute Psychiatry

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner setting

data_processing:
The Bioconductor R package minfi was used for the quality control of DNAm data. Failed probes based on a detection P-value larger than 0.01 in >50% of the samples as well and non-specific binding probes a nd probes on X and Y chromosome were removed.
We also excluded probes if single nucleotide polymorphisms (SNPs) were documented in the interval for which the Illumina probe is designed to hybridize. Probes located close (10 bp from query site) to a SNP which had a minor allele frequency of ≥0.05, as reported in the 1,000 Genomes Project, were also removed
The data were then normalized with functional normalization. Batch effects were identified using the Empirical Bayes’ method ComBat . Batch corrected M-values after ComBat were used for all further statistical analyses

label: cy3, cy5

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from peripheral blood

tag: genetic sex (male=1, female=2)

tag: weighted life events


title: A51

type: SRA

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

description: Library name: A51

library_source: transcriptomic

data_processing:
Reads were aligned to Rat genome Rnor6.0 with HISAT2.
counts generated for Rnor 6.0 v101 with featureCounts from the subread package.
Counts were normalized with voom and differential expression tested with limma.
Assembly: Rnor6.0
Supplementary files format and content: Text file of voom normalized expression for each gene and each sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Glomerular

growth_protocol: Male Wistar Rats , ~150-175g

extract_protocol:
On Day 11 or 21, rats were sacked, kidneys harvested and glomeruli were isolated by sieve method. Total RNA was extracted.
The mRNA libraries were generated using the following kits and conditions:
NEBNext® Ultra™ II Directional (stranded) RNA Library Prep Kit for Illumina (NEB #E7760L)
NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB #E7490)
NEBNext Multiplex Oligos for Illumina Unique Dual Index Primer Pairs (NEB #6442S/L)
Library input amount: 200ng total RNA (quantified using Qubit Fluorometer) and total RNA achieved a RIN of >7
Fragmentation: 10 minutes
PCR: 12x
Libraries were sequenced with Illumina NovaSeq 6000 flow cell using paired-end 150-bp format to at least 17 million passed-filter clusters/sample (equivalent to 34 million reads)

treatment_protocol: Male Wistar rats were intravenously (IV) injected with puromycin aminonucleoside (PAN) (Sigma-Aldrich, St. Louis, MO) and treatment groups were treated by oral gavage with Pioglitazone, GQ-16, or a sham vehicle daily. A separate group of male Wistar rats were intravenously (IV) injected with Adriamycin (ADR) (Sigma-Aldrich, St. Louis, MO).

tag: tissue

value: Glomerular

tag: strain

value: Wistar

value: male

tag: treatment

value: ADR


title: A52

description: Library name: A52


title: A30

description: Library name: A30


title: HD_1

library_source: transcriptomic single cell

tag: cell type

value: M


title: HS_5

value: axillary

value: III


title: genomic DNA from peripheral blood [9611518138_R01C01]


title: Obese male, anti-PD-1, rep3

city: Bern

first: Carole

last: Bourquin

address: Rosenbühlgasse 27

country: Switzerland

institute: University of Bern

description: Library name: M19

data_processing:
Libraries were sequenced on the HiSeq 4000 System (Illumina) using a 100‐bp single‐end reads protocol.
Quality control was performed with FastQC (v.0.11.5). Reads were mapped with the STAR aligner (v.2.7.0f) to the mouse reference genome (UCSC mm10). Biological quality control was done with PicardTools (v.2.21.6).
Raw counts were obtained using HTSeq (v.0.9.1). Normalization and differential expression analysis were performed with the R package edgeR (v.3.28.1) using the Trimmed Mean of M-values (TMM) normalization method.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: Tumor

growth_protocol: B16-F10 cells were maintained in DMEM supplemented with 10% Fetal Bovine Serum (FBS), 100 U/mL penicillin/streptomycin, 2 mM L-glutamine, 1 mM sodium pyruvate, at 37°C, 5% CO2. B16-F10 cells (2×105) were implanted subcutaneously into the right flank of C57BL/6J mice, and tumor growth was monitored every 2 days.

extract_protocol:
Total RNA was extracted from frozen tumors using TRIzol™ Reagent (Invitrogen #15596018) and purified using the RNA Clean & Concentrator-5 kit (Zymo Research #R1014).
Libraries were prepared with the TruSeq Stranded mRNA kit (Illumina) using 180 ng of total RNA per sample.

treatment_protocol:
C57BL/6J mice were fed with a Western diet (Ssniff #E15746) supplemented with 0.2 % cholesterol until mice showed a 50% weight increase (15 weeks for males and 28 weeks for females (42)). A matching control diet (Ssniff #E157453) was used for experiments on non-obese mice.
After the development of palpable tumors, mice were treated intraperitoneally with 10 mg/kg of anti-PD-1 monoclonal antibody (clone 29F.1A12; BioXCell #BE0273) or isotype control antibody (clone 2A3; BioXCell #BE0089) three times a week.

value: Tumor

tag: cell line

value: Obese

tag: diet

value: Western diet


title: 156-4HC08_07

value: AA


title: HS_4


title: A53

description: Library name: A53


title: Obese male, isotype control, rep3

description: Library name: M17

value: Isotype control


title: 156-3PN14NL_11


title: genomic DNA from peripheral blood [9702496101_R02C02]


title: HS_3

value: hair follicle cells

value: II


title: genomic DNA from peripheral blood [9611518136_R05C02]


title: EtOH-1-BRG1-Cut&TAG

city: Durham

first: Christopher

middle: R

last: Day

state: NC

address: 111 TW Alexander Dr.

department: ERBL

institute: NIH/NIEHS

library_source: genomic

data_processing:
Adaptors were trimmed using Cutadapt and reads were aligned to the hg38 genome assembly using Bowtie2. Samtools was used to sort the reads and deduplication was performed using Picard Tools (http://broadinstitute.github.io/picard). Coverage files were generated using bamCoverage.
Assembly: hg38
Supplementary files format and content: bigwig files
Library strategy: CUT&Tag

growth_protocol: MCF-7 cells (ATCC) were grown in MEM supplemented with 10% FBS (Sigma), 2mM Glutamine and 1X Pen/strep (Gibco).

extract_protocol:
CUT&Tag was performed following the Bench top CUT&Tag V.3 protocol (Kaya-Okur, Wu et al. 2019). Briefly, we used 100K nuclei isolated from E2, BPA, or vehicle treated MCF7 cells. 10 µL BioMag-Plus Concanavalin (Bangs Laboratories) were used per reaction to immobilize the nuclei. Then we added 1:50 mouse ERα (sc-8005, Santa Cruz), 1:25 rabbit FOXA1 (#53528, Cell Signaling Technology), 1:50 mouse H3K27ac (#MA5-23516, Invitrogen), 1:40 Rabbit BRG1 (#NB100-2594, Novus Biologicals) or 1:25 rabbit MED1 (#51613, Cell Signaling Technology) antibody and incubated for 2 hours. After one hour of secondary antibody incubation 1.25μL of CUTANA pAG-Tn5 adapter complex was used to load the enzyme to the antibody bound regions. One hour of tagmentation at 37°C was followed by DNA extraction using MinElute PCR Purification Kit (Qiagen).
Extracted DNA was subjected to PCR amplification using unique primers sets (Nextera XT v2 Full set (N7-S5)). Number of PCR cycles were determined specifically to prevent overamplification. We amplified ERα, FOXA1, H3K27ac, or MED1 with 14, 15, 15 or 17 PCR cycles, respectively. Libraries were size selected using AMPure XP Beads (Beckman Coulter) with 1.3X ratio. We quantified and assessed the quality of the libraries with Qubit Flex and Tapestation and then sequenced the libraries with 50 bp paired-end reads on Illumina high output NovaSeq SP.

treatment_protocol: MCF7 cells were hormone depleted for 2d prior to treatment. Cells were then treated with 1nM E2, 10uM BPA or vehicle for 8hs.

value: ER+ Breast Cancer

value: 8h EtOH


title: Obese male, anti-PD-1, rep2

description: Library name: M16


title: 156-3PN14L_10

value: F


title: Obese male, isotype control, rep2

description: Library name: M13


title: 156-4AD12NL_06


title: HS_2


title: 156-3PN13NL_04

value: C


title: 156-3PN13L_03


title: genomic DNA from peripheral blood [9611518134_R06C02]


title: HS_1


title: BPA-1-RNAseq

data_processing:
Reads were filtered so that only those with a mean quality score of 20 or greater were kept. Adapter was trimmed using Cutadapt version 3.7. Reads were aligned to the hg38 genome assembly using STAR version 2.6.0c. Counts were obtained using the featureCounts tool from the Subread package version 1.5.1 with the GENCODE basic gene annotation version 44. Differential expression was quantified using the DESeq2 R package version 1.34.0.
Assembly: hg38
Supplementary files format and content: RPKM matrix

source_name: Cell Line

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen). The quantity and quality of the RNA samples were assessed by Tapestation.
Polyadenylated mRNAs were selected using Dynabeads Oligo(dT)25 (Invitrogen #61005) and libraries were prepared with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7760) following manufacturer’s instruction. Libraries were size selected using AMPure XP Beads (Beckman Coulter). Libraries were quantified Qubit Flex and Tapestation and then sequenced with 75 bp single-end reads on Illumina NextSeq high-output.

treatment_protocol: MCF7 cells were hormone depleted for 2d prior to treatment. Cells were then treated with 1nM E2, 10uM BPA or vehicle for 24hs.

value: Cell Line

value: 24h BPA


title: genomic DNA from peripheral blood [9611518134_R03C01]


title: 156-4AD12L_05


title: Obese male, anti-PD-1, rep1

description: Library name: M9


title: BPA-2-RNAseq


title: 156-3PN12NL_02


title: 156-3PN12L_01


title: Non-obese male, isotype control, rep3

description: Library name: M7

value: Non-obese

value: Control diet


title: Non-obese male, anti-PD-1, rep3

description: Library name: M6


title: genomic DNA from peripheral blood [9611518133_R03C01]


title: BPA-3-RNAseq


title: E2-2-RNAseq


title: Non-obese male, anti-PD-1, rep2

description: Library name: M5


title: Non-obese male, isotype control, rep2

description: Library name: M4


title: genomic DNA from peripheral blood [9611518136_R02C02]


title: genomic DNA from peripheral blood [9611518138_R03C02]


title: genomic DNA from peripheral blood [9611518133_R02C02]


title: PS-AA7_09


title: PS-C7_10

value: M


title: genomic DNA from peripheral blood [9611518133_R02C01]


title: genomic DNA from peripheral blood [9611518136_R06C02]


title: genomic DNA from peripheral blood [9611518132_R03C01]


title: Non-obese male, isotype control, rep1

description: Library name: M3


title: AD-C7_08


title: EtOH-1-RNAseq

value: 24h EtOH


title: Non-obese male, anti-PD-1, rep1

description: Library name: M1

value: Tumor


title: genomic DNA from peripheral blood [9611518133_R03C02]


title: 156-4AD01NL_06


title: genomic DNA from peripheral blood [9611518132_R02C01]


title: EtOH-2-RNAseq


title: 156-3HC21_12


title: 156-4AD01L_05


title: E2-1-RNAseq


title: genomic DNA from peripheral blood [9611518119_R04C02]


title: cattle-yak-3

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
Basecall is performed by Guppy v4.3.4 software to convert the off-machine fast5 format data into fastq format. After further filtering short segments ( length < 300bp ) and low-quality reads ( quality score < 7 ) by fastp, the total data set was obtained.
The full-length sequence obtained by minimap2 was compared with the yak reference genome ( version : BosGru3.0 ), and the common sequence was obtained by racon. Subsequently, GMAP ( parameter-cross-species-allow-close-close-indels 0 ) was used to map the shared sequence to the reference genome, and the mapping readings were further folded, min-identity = 90 % and min-coverage = 85 %. In addition, different sequences of only 5 ' exons were combined to obtain non-redundant transcript sequences.
To investigate the functions of new isoforms, Non-Redundant ( Nr ), SwissProt, Kyoto Encyclopedia of Genes and Genomes ( KEGG ), clusters of euKaryotic Orthologous Groups ( KOG ) and Gene Ontology ( GO ) databases were used for annotation.
Assembly: LU_Bosgru_v3.0
Supplementary files format and content: Transcript count value and cpm value of each sample

organism: Bos grunniens x Bos taurus

source_name: longissimus dorsi

extract_protocol:
Total RNA was extracted from each sample using TRIzol ( Invitrogen, Paisley, UK ). Nanodrop-2000 ( Thermo Fisher Scientific, Waltham, MA ) and 1 % agarose gel electrophoresis were used to evaluate the purity, concentration and integrity of total RNA.
1 μg total RNA was used to prepare cDNA library by cDNA-PCR sequencing kit ( SQK-PCS109, Oxford Nanopore Technologies, Oxford, UK ).

value: longissimus dorsi


title: EtOH-3-RNAseq


title: cattle-yak-2


title: 156-3PN08NL_04


title: genomic DNA from peripheral blood [9611518119_R02C02]


title: E2-3-RNAseq


title: genomic DNA from peripheral blood [9611518119_R02C01]


title: BPA-3b-ATAC

data_processing:
Adaptors were trimmed using Cutadapt and reads were aligned to the hg38 genome assembly using Bowtie2. Samtools was used to sort the reads and deduplication was performed using Picard Tools (http://broadinstitute.github.io/picard). Coverage files were generated using bamCoverage. Samtools was also used to separate reads into read lengths of 1-110 bp, nucleosome free, and 150-250 bp, mononucleosome reads.
Assembly: hg38
Supplementary files format and content: bigwig files

extract_protocol:
ATAC-seq samples were prepared following the protocol described in (Orlando, Douglas et al. 2020) with minor modifications. First 50K nuclei were isolated in technical duplicate per sample. DNA was tagmented for 30 min at 37C using the Illumina Tagment DNA kit (20034211). Tagmented DNA was cleaned up using the MinElute PCR Purification Kit (Qiagen).
Extracted DNA was subjected to PCR amplification using unique primers sets (Nextera XT v2 Full set (N7-S5)). The number of PCR cycles used for library amplification was determined by qPCR. Finally, a double-sided size selection was performed using AMPure XP Beads (Beckman Coulter). Libraries quality was assessed using by Tapestation and the technical duplicate of each sample with the most pronounced nucleosome banding was sequenced.

value: 8h BPA


title: cattle-yak-1


title: Obese male, isotype control, rep1

description: Library name: M11

value: Obese

value: Western diet


title: 156-3PN08L_03


title: sALT629, rep 3

city: Ithaca

first: Emma

last: Roszkowski

state: NY

address: 930 Campus Rd

department: Microbiology and Immunology

institute: Cornell University

description: Library name: sALT_3

data_processing:
Paired-end sequence mapping to the H37Rv genome (accession number GCA_000195955.2) was performed with STAR-2.7.10b.
HTSeq v2.02 with H37Rv annotations was used to obtain raw counts.
R was used for read counts normalization and differential expression analysis via DESeq2 v1.44.0.
Assembly: GCA_000195955.2
Supplementary files format and content: txt file for normalized counts

organism: Mycobacterium tuberculosis

source_name: Bacterium

extract_protocol:
Bacteria were isolated by centrifugation and resuspended in Trizol LS (Ambion). Samples were lysed by bead beating and the RNA was isolated by chloroform extraction, isopropanol precipitation, and resuspended in nuclease-free water.
Sequencing was performed by SeqCenter (Pittsburgh, PA) after samples were treated with Invitrogen DNAse (RNAse free). Ribosomal RNA was depleted using custom Mtb specific oligonucleotides and library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation and 10bp unique dual indices (UDI).

treatment_protocol: Bacteria were treated with 25 uM compound or vehicle control for four hours in Middlebrook 7H9 media supplemented with 0.2% glycerol and 10% OADC supplement.

value: Erdman

value: Bacterium

tag: genotype

value: WT

value: sALT629, 25 uM


title: BPA-2b-ATAC

value: ER+ Breast Cancer


title: genomic DNA from peripheral blood [9611518119_R01C02]


title: sALT629, rep 2

description: Library name: sALT_2


title: 156-3PN04NL_12

value: AA


title: BPA-1b-ATAC

value: Cell Line


title: 156-3PN04L_11


title: E2-3b-ATAC

value: 8h E2


title: genomic DNA from peripheral blood [9611518118_R05C02]


title: E2-2b-ATAC


title: isoxyl, rep 3

description: Library name: ISO_3

value: isoxyl, 25 uM


title: genomic DNA from peripheral blood [9611518118_R05C01]


title: sALT629, rep 1

description: Library name: sALT_1


title: 156-3PN03NL_02


title: 156-3PN03L_01


title: genomic DNA from peripheral blood [9611518118_R02C02]


title: E2-1b-ATAC


title: EtOH-3b-ATAC

value: 8h EtOH


title: isoxyl, rep 1

description: Library name: ISO_1


title: genomic DNA from peripheral blood [9611518118_R01C02]


title: 156-10HC16_07

value: F


title: isoniazid, rep 2

description: Library name: INH_2

value: isoniazid, 25 uM


title: genomic DNA from peripheral blood [9611518106_R03C01]


title: isoniazid, rep 3

description: Library name: INH_3


title: 156-3PN07NL_04

value: C


title: PS-AA6_09

value: M


title: genomic DNA from peripheral blood [9611518107_R02C02]


title: genomic DNA from peripheral blood [9611518106_R06C02]


title: isoniazid, rep 1

description: Library name: INH_1


title: EtOH-1b-ATAC


title: BPA-3-MED1-Cut&TAG

extract_protocol:
CUT&Tag was performed following the Bench top CUT&Tag V.3 protocol (Kaya-Okur, Wu et al. 2019). Briefly, we used 100K nuclei isolated from E2, BPA, or vehicle treated MCF7 cells per reaction. 10 ul BioMag-Plus Concanavalin (Bangs Laboratories) were used per reaction to immobilize the nuclei. Then we added 1:50 mouse ERα (sc-8005, Santa Cruz), 1:25 rabbit FOXA1 (#53528, Cell Signaling Technology), 1:50 mouse H3K27ac (#MA5-23516, Invitrogen), or 1:25 rabbit MED1 (#51613, Cell Signaling Technology) antibody and incubated for 2 hours. After one hour of secondary antibody incubation 1.25 ul of CUTANA pAG-Tn5 adapter complex was used to load the enzyme to the antibody bound regions. One hour of tagmentation at 37°C was followed by DNA extraction using MinElute PCR Purification Kit (Qiagen).
Extracted DNA was subjected to PCR amplification using unique primers sets (Nextera XT v2 Full set (N7-S5)). Number of PCR cycles were determined specifically to prevent overamplification. We amplified ERα, FOXA1, H3K27ac, or MED1 with 14, 15, 15 or 17 PCR cycles, respectively. Libraries were size selected using AMPure XP Beads (Beckman Coulter) with 1.3X ratio. We quantified and assessed the quality of the libraries with Qubit Flex and Tapestation and then sequenced the libraries with 50 bp paired-end reads on Illumina high output NovaSeq SP.

value: 8h BPA


title: BPA-2-MED1-Cut&TAG


title: AD-C6_08


title: isoxyl, rep 2

description: Library name: ISO_2


title: genomic DNA from peripheral blood [9611518059_R06C02]


title: untreated, rep 3

description: Library name: DMSO_3

value: untreated


title: 156-3PN02NL_12


title: 156-3PN07L_03


title: genomic DNA from peripheral blood [9611518059_R06C01]


title: BPA-1-MED1-Cut&TAG


title: PS-C6_10


title: EtOH-2b-ATAC


title: E2-3-MED1-Cut&TAG


title: untreated, rep 1

description: Library name: DMSO_1


title: genomic DNA from peripheral blood [9611518059_R04C02]


title: untreated, rep 2

description: Library name: DMSO_2


title: 156-10PN20NL_02


title: 156-3PN02L_11


title: ESC_ATAC_HP1cKO_72h_rep2

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

description: Library name: ESC_ATAC_HP1cKO_72h_rep2

data_processing:
The ATAC-seq reads were aligned to the mm10 mouse reference genome using the Bowtie2 aligner (Langmead and Salzberg, 2012) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 5-bp windows across the genome using deepTools for presentation as genome browser tracks  (Ramirez et al, 2016).
The seqeunce length was 150 for R1 and 150 for R2 for paired-end data.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Embryonic stem cells

growth_protocol: ESCs were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)) on gelatin-coated plates.

extract_protocol:
Samples were prepared according to the Illumina Nextera protocol
ATAC-seq. Libraries were constructed according to the Illumina Nextera protocol.

value: Embryonic stem cells

value: HP1 cKO


title: 156-10PN20L_01


title: ESC_ATAC_HP1cKO_48h_rep2

description: Library name: ESC_ATAC_HP1cKO_48h_rep2


title: genomic DNA from peripheral blood [9611518058_R06C02]


title: EtOH-2-MED1-Cut&TAG


title: 156-10AD12NL_06


title: ESC_ATAC_HP1WT_rep2

description: Library name: ESC_ATAC_HP1WT_rep2

value: HP1 loxP/loxP


title: 156-10AD12L_05


title: E2-2-MED1-Cut&TAG


title: genomic DNA from peripheral blood [9611518059_R02C02]


title: E2-1-MED1-Cut&TAG


title: ESC_ATAC_HP1cKO_48h_rep1

description: Library name: ESC_ATAC_HP1cKO_48h_rep1


title: genomic DNA from peripheral blood [9611518045_R01C02]


title: EtOH-3-MED1-Cut&TAG


title: ESC_ATAC_HP1WT_rep1

description: Library name: ESC_ATAC_HP1WT_rep1


title: BPA-3-27ac-Cut&TAG


title: genomic DNA from peripheral blood [9611518058_R05C02]


title: genomic DNA from peripheral blood [9611518106_R02C02]


title: ESC_ATAC_HP1cKO_72h_rep1

description: Library name: ESC_ATAC_HP1cKO_72h_rep1


title: genomic DNA from peripheral blood [9611518044_R06C01]


title: 156-10HC05_07


title: PS-AA5_09


title: Decr2 knock down

city: Chicago

first: Thomas

last: Gajewski

state: IL

address: 929 E 57th St

institute: University of Chicago

description:
Library name: TG-Li-10x-4s-SHU-2
10X Genomics

data_processing:
Demultiplexing, barcode processing, and raw counts were generated using Cell Ranger v6.1.2 from 10X Genomics (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Downstream sample processing was carried out in R using Seurat (v4.3).
Assembly: Mouse mm10 (refdata-gex-mm10-2020-A from 10X Genomics)
Supplementary files format and content: Tab separated value files and matrix mtx files

growth_protocol: B16.SIY cells were stably tranduced with control shRNA or Decr2 shRNA lentivirus. The tanduced cells were cultured with 1.5 μg/mL puromycine for 3 days.

extract_protocol:
Tumors were isolated from mice. For TIL isolation, tumors were digested using an enzyme mix containing Collagenase (1mg/mL, Sigma-Aldrich: C5138), DNAse (200 µg/mL, Sigma-Aldrich: D5025), and Hyaluronidase (100 μg/mL, Sigma-Aldrich: H6254) for 30 min at 37oC while rotating. The tumor suspension was filtered through a 50 μm filter and washed with PBS. Tumour and immune cells were pre-enriched using density gradient centrifugation (Ficoll, Sigma-Aldrich). The cell pellet was stained with live/death staining dyev and anti-CD45 antibodies. The CD45+ live cells were sorted by FACs big foot.
Library was performed according to manufacter's instructions (single cell 3' v2 protocol, 10X Genomics)

treatment_protocol: B16.SIY cells were were subcutaneously injected into B6 mice.

value: Tumor

value: Melanoma

value: Decr2 knock down

value: Decr2 KD shRNA lentivirus transduction


title: BPA-2-27ac-Cut&TAG

value: Cell Line

value: ER+ Breast Cancer


title: AD-C5_08


title: BPA-1-27ac-Cut&TAG


title: 156-4AD07NL_06

value: AA


title: genomic DNA from peripheral blood [9611518044_R04C02]


title: E2-3-27ac-Cut&TAG

value: 8h E2


title: genomic DNA from peripheral blood [9611518059_R04C01]


title: E16.5_brain_Anti-G3BP1_rep2

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: Institute of Molecular Medicine, College of Future Technology

institute: Peking University

description: E16.5_brain_editing.tsv.gz;E16.5_brain_TPM.tsv.gz

data_processing:
Reads mapping to abundant RNA types were discarded using BWA-MEM (v0.7.17), retaining unmapped reads for further analysis. The processed reads were aligned to the mouse genome (mm10) via a two-round mapping strategy designed to capture more mismatches for RNA editing candidates, sequentially utilizing HISAT2 (v2.2.1) and BWA-MEM, with GENCODE (vM25) as the transcriptome guide. Unique mapped reads with up to 0.04 mismatches per fragment relative to read length were selected using pysam (v0.22.1) (https://github.com/pysam-developers/pysam) for subsequent analysis. PCR duplicates were removed using Picard (v3.1.1) (https://github.com/broadinstitute/picard).
All usable reads spanning exon-exon junctions were segmented using the GATK (v4.5.0.0) SplitNCigarReads command. Base quality scores were recalibrated using two rounds of GATK BaseRecalibrator and ApplyBQSR commands. RNA variants were identified from BAM files of usable reads via the GATK HaplotypeCaller command. RNA single nucleotide variants were selected using the GATK SelectVariants command. Single nucleotide polymorphisms (SNPs) from dbSNP (v151), the 1000 Genomes Project, and the University of Washington Exome Sequencing Project were removed in SNVs. Raw counts were quantified using Subread featureCounts (v2.0.1) and normalized to transcripts per million (TPM) as gene expression levels.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include TPM
Supplementary files format and content: tab-delimited text including RNA editing data

source_name: Embryo brain

extract_protocol:
Total RNA was extracted following the standard TRIzol protocol (Invitrogen).
RNA-seq library was generated using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, NR604).

value: Embryo brain

value: E16.5 brain

value: WT

value: Fresh frozen

tag: fixation

tag: primary antibody

value: Anti-G3BP1 (Proteintech, 13057-2-AP)

tag: secondary antibody

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)

tag: pag-deaminase

tag: inhouseid


title: 156-4AD07L_05

tag: race

value: F


title: PS-C5_10

value: C

tag: age

value: M


title: EtOH-1-MED1-Cut&TAG

value: 8h EtOH


title: genomic DNA from peripheral blood [9611518044_R03C02]


title: EtOH-3-27ac-Cut&TAG


title: 156-4AD02L_01

tag: Sex


title: EtOH-2-27ac-Cut&TAG


title: genomic DNA from peripheral blood [9611518045_R01C01]

tag: genetic sex (male=1, female=2)


title: 156-10HC04_07


title: EtOH-1-27ac-Cut&TAG


title: E2-2-27ac-Cut&TAG


title: E16.5_brain_Anti-G3BP1_rep1


title: genomic DNA from peripheral blood [9611518044_R01C01]

tag: weighted life events


title: E12.5_brain_Anti-G3BP1_rep1

description: E12.5_brain_editing.tsv.gz;E12.5_brain_TPM.tsv.gz

tag: tissue

value: E12.5 brain


title: E12.5_brain_Anti-G3BP1_rep2

tag: strain


title: genomic DNA from peripheral blood [9611518033_R01C02]


title: E16.5_brain_IgG_rep2

tag: treatment

value: rabbit IgG (CST, 2729S)


title: E2-1-27ac-Cut&TAG

tag: cell type


title: genomic DNA from peripheral blood [9611518033_R03C02]


title: Control

description:
Library name: TG-Li-10x-4s-SHU-4
10X Genomics

value: Tumor

tag: cell line

value: Melanoma

value: Control

value: Control shRNA lentivirus transduction


title: E16.5_brain_IgG_rep1


title: genomic DNA from peripheral blood [9611518032_R04C01]


title: 156-4AD02NL_02

value: AA


title: BPA-3-FoxA1-Cut&TAG

value: Cell Line

value: ER+ Breast Cancer

value: 8h BPA


title: genomic DNA from peripheral blood [9611518031_R05C02]


title: BPA-2-FoxA1-Cut&TAG


title: genomic DNA from peripheral blood [9611518031_R05C01]


title: E12.5_brain_IgG_rep1

value: Embryo brain

value: WT

value: Fresh frozen


title: 156-10PN17NL_12


title: 156-10PN17L_11


title: genomic DNA from peripheral blood [9611518032_R02C02]


title: BPA-1-FoxA1-Cut&TAG


title: E10.5_embryo_FreshFrozen_untreated_rep2

description: E10.5_freshfrozen_embryo_editing.tsv.gz;E10.5_freshfrozen_embryo_TPM.tsv.gz

source_name: Embryo

value: Embryo

value: E10.5 embryo


title: E2-3-FoxA1-Cut&TAG

value: 8h E2


title: 156-10AD02NL_04

value: F


title: E12.5_brain_IgG_rep2

value: E12.5 brain

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: genomic DNA from peripheral blood [9611518031_R03C01]


title: genomic DNA from peripheral blood [9611518031_R02C02]


title: E10.5_embryo_FreshFrozen_untreated_rep1


title: PS-C4_08

value: C

value: M


title: E10.5_embryo_FreshFrozen_Anti-G3BP1_rep2

value: Anti-G3BP1 (Proteintech, 13057-2-AP)


title: E2-2-FoxA1-Cut&TAG


title: 156-10AD02L_03


title: genomic DNA from peripheral blood [9611518014_R02C02]


title: E2-1-FoxA1-Cut&TAG


title: PS-C3_09


title: genomic DNA from peripheral blood [9611518014_R02C01]


title: E10.5_embryo_FreshFrozen_IgG_rep2

value: rabbit IgG (CST, 2729S)


title: PS-AA4_07

value: AA


title: E10.5_embryo_FreshFrozen_Anti-G3BP1_rep1


title: EtOH-2-FoxA1-Cut&TAG

value: Cell Line

value: 8h EtOH


title: PS-AA3_08


title: genomic DNA from peripheral blood [9611518014_R01C02]


title: E10.5_embryo_FreshFrozen_IgG_rep1


title: EtOH-1-FoxA1-Cut&TAG

value: ER+ Breast Cancer


title: genomic DNA from peripheral blood [9611518013_R06C01]


title: E10.5_embryo_Fixed_untreated_rep2

description: E10.5_fixed_embryo_editing.tsv.gz;E10.5_fixed_embryo_TPM.tsv.gz

value: Fixed


title: BPA-3-ERa-Cut&TAG

value: 8h BPA


title: E10.5_embryo_Fixed_untreated_rep1

value: WT


title: genomic DNA from peripheral blood [9611518014_R05C02]


title: genomic DNA from peripheral blood [9611518013_R04C02]


title: E10.5_embryo_Fixed_Anti-G3BP1_rep2

value: Embryo


title: AD-AA1_07


title: EtOH-3-FoxA1-Cut&TAG


title: BPA-2-ERa-Cut&TAG


title: genomic DNA from peripheral blood [9611518013_R02C01]


title: KO2

city: Shanghai

first: Wei

last: Yusheng

state: New York

address: 227,South Road of Chongqian,Shanghai,China

institute: Shanghai Jiao Tong University of Medicine

data_processing:
The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina HiSeqXTen.
The clean reads were then aligned to  genome (mouse version:GRCm38 NCBI; human version:GRCh38 NCBI) using the hisat2. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.HTseqwas used to count gene and lncRNA counts and RPKM method was used to determine the gene expression.
We applied DESeq algorithm to filter the differentially expressed genes, after the protocol significant analysis
Assembly: GRCm38 NCBI;GRCh38 NCBI
Supplementary files format and content: text files include FPKM and TPM values for each Sample

source_name: eye tissue

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: eye tissue

value: KO


title: BPA-1-ERa-Cut&TAG


title: 156-3HC17_05

value: F


title: E10.5_embryo_Fixed_Anti-G3BP1_rep1

value: E10.5 embryo


title: AD-C4_06


title: KO1


title: E10.5_embryo_Fixed_IgG_rep2

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: E2-2-ERa-Cut&TAG

value: 8h E2


title: E10.5_embryo_Fixed_IgG_rep1


title: 156-3HC06_05

value: C


title: 156-10PN12NL_04

value: M


title: AD-C3_10


title: 156-10PN12L_03


title: AD-C2_06


title: WT2


title: WT1


title: rRNA Depleted totalRNA from whole brain from untreated SHR rats (replicate 4, sequencing batch 20)

city: Aurora

last: Saba

state: CO

address: 12850 E. Montview Blvd

department: Skaggs School of Pharmacy and Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

description:
Library name: SHR_4_control_20
SHR_4_batch20

data_processing:
Cutadapt (v1.9.1) trim Illumina adapter, quality, and length, parameters: -q 20 -m 20
Remove rRNA reads by alignment with bowtie2(v2.4.5) to rRNA
genome Alignment Hisat2 (v2.2.1)
Stringtie (v2.2.1) reconstruction
Run Aptardi (v1.4) on each strain reconstructed GTF
Merge aptardi output reconstruction Stringtie(v1.3.5)
Run RSEM (v1.3.3) on reconstruction
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Run RSEM(v1.3.3) on filtered reconstruction
Filter transcripts/genes from RSEM results if one third or more of samples have less than 1 read or  if the length of the mature RNA transcript was less than 200 nucleotides
Apply a regularized log transformation of expected read counts from RSEM (rlog function in DESeq2 package of R)
Remove technical artifacts including batch effects using Removal of Unwanted Variance  (RUVg) with empirically-derived controls (RUVSeq package in R)
Assembly: Rn7.2
Supplementary files format and content: TSV batch corrected/normalized expression values
Supplementary files format and content: GTF of the reconstructed transcriptome

source_name: whole brain

extract_protocol:
RNA was collected from whole brain using the RNeasy Plus Universal Midi kits for RNA sequencing (Qiagen, Valencia, CA, USA).
Libraries were constructed using the Illumina TruSeq Stranded TotalRNA Kit (Illumina, San Diego, CA, USA).

treatment_protocol: Tissue frozen in RNA later.

value: whole brain

value: SHR/OlaIpcv

tag: batch


title: EtOH-3-ERa-Cut&TAG

value: Cell Line


title: E2-3-ERa-Cut&TAG


title: E2-1-ERa-Cut&TAG


title: rRNA Depleted totalRNA from whole brain from untreated SHR rats (replicate 4, sequencing batch 19)

description:
Library name: SHR_4_control_19
SHR_4_batch19


title: 156-10PN11NL_10

value: AA


title: EtOH-2-ERa-Cut&TAG

value: ER+ Breast Cancer

value: 8h EtOH


title: 156-10PN11L_09


title: EtOH-1-ERa-Cut&TAG


title: HiC.12_CTCFWAPLRAD21_IAA_dTAG13

city: Rotterdam

first: Ning Qing

last: Liu

address: Wytemaweg 80

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam

description: Hi-C in E14TG2a (with OsTir1; CTCF-AID-mCherry; WAPL-AID-eGFP; RAD21-FKBP-BFP), after IAA+dTAG13

data_processing:
Raw Hi-C data were mapped with HiC-Pro (Servant et al., 2015), which performs mapping, identification of valid Hi-C pairs, generation of contact matrices and ICE normalization (Imakaev et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: mcool files

growth_protocol: E14Tg2a mouse embryonic stem cells (mESCs) and derived cell lines were cultured in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%; Gibco), 104 U of leukemia inhibitory factor (LIF; Millipore), the MEK inhibitor PD0325901 (1 μM; Selleckchem), the GSK-3β inhibitor CHIR99021 (3 μM; Cayman Chemical) and 1-thioglycerol (1.5 × 10−4 M; Sigma-Aldrich) on 0.1% gelatin-coated plates. The cell lines were passaged every two days.

extract_protocol:
Hi-C data were generated using as a previous published protocol (Rao et al., 2014) with minor modifications (Haarhuis et al., 2017). For each template, 10 million cells were harvested and crosslinked using 2% formaldehyde. Crosslinked DNA was digested in nucleus using MboI, and biotinylated nucleotides were incorporated at the restriction overhangs and joined by blunt-end ligation. The ligated DNA was enriched in a streptavidin pull-down.
Hi-C libraries were prepared using a standard end-repair and A-tailing method.

treatment_protocol: Protein depletion was induced by addition of auxin (IAA) with a final concentration of 500 μM (I5148-10G, Sigma-Aldrich). RAD21 was depleted by adding a final concentration of 500 nM dTAG-13 molecule (requested from Dr. Nathanael S. Gray from Dana-Faber Cancer Institute) (Nabet et al., 2018). Protein degradation was induced at different time points and all samples were collected at the end of the time course.

value: Embyonic stem cell

tag: library type

value: Hi-C

tag: genetic modification

tag: time point


title: HiC.11_CTCFWAPLRAD21_H2O_dTAG13

description: Hi-C in E14TG2a (with OsTir1; CTCF-AID-mCherry; WAPL-AID-eGFP; RAD21-FKBP-BFP), after H2O+dTAG13


title: rRNA Depleted totalRNA from whole brain from untreated SHR rats (replicate 1, sequencing batch 18)

description:
Library name: SHR_1_control_18
SHR_1_batch18


title: HiC.10_CTCFWAPLRAD21_IAA_DMSO

description: Hi-C in E14TG2a (with OsTir1; CTCF-AID-mCherry; WAPL-AID-eGFP; RAD21-FKBP-BFP), after IAA+DMSO

value: IAA+DMSO


title: rRNA Depleted totalRNA from whole brain from untreated LEXF9 rats (replicate 2, sequencing batch 20)

description:
Library name: LEXF9_2.2
LEXF9_2_batch19


title: 18_H82_parental_input

city: Bethesda

first: Nitin

last: Roper

address: 37 Convent Drive

department: Developmental Therapeutics Branch

institute: National Cancer Institute

data_processing:
aw FASTQ files were trimmed with the Trimmomatic software to remove low quality reads. Trimmed FASTQ files were subsequently checked for quality using FastQC. Trimmed reads with high quality were then aligned to the hg19 genome using the BWA aligner. Aligned (unsorted) reads were sorted using samtools followed by duplicate marking using picard-tools. For viewing in the genome browser, scaled bigwig coverage tracks were generated for each alignment file using the scale option of the BAMscale tool.
Assembly: hg19

extract_protocol:
ChIP was carried out following manufacture’s protocol (Active Motif #53008) for cross-linking, cell lysis, sonication, immunoprecipitation with H3K27ac antibody (Abcam #ab4729) until washing with magnetic beads.
ChIP libraries were constructed following manufacture’s protocol (Illumina)

value: small cell lung cancer

tag: chip antibody

value: H3K27ac (Abcam #ab4729)

value: parental


title: 17_H82_parental_H3K27Ac_2


title: 156-10PN09L_11

extract_protocol: RNA was extracted from lesional and non-lesional samples using the RNAeasy FFPE Kit (Qiagen) as per the manufacturer's instructions

value: F


title: rRNA Depleted totalRNA from whole brain from untreated LEXF9 rats (replicate 2, sequencing batch 19)

description: Library name: LEXF9_2.1


title: 156-10PN09NL_12


title: HiC.09_CTCFWAPLRAD21_H2O_DMSO

description: Hi-C in E14TG2a (with OsTir1; CTCF-AID-mCherry; WAPL-AID-eGFP; RAD21-FKBP-BFP), after H2O+DMSO


title: HiC.08_CTCFWAPL_96h

description: Hi-C in E14TG2a (with OsTir1; CTCF-AID-mCherry; WAPL-AID-eGFP), after 96h of IAA

value: OsTir1; CTCF-AID-mCherry; WAPL-AID-eGFP


title: 16_H82_parental_H3K27Ac_1


title: 156-10PN07NL_02


title: HiC.07_CTCFWAPL_24h

description: Hi-C in E14TG2a (with OsTir1; CTCF-AID-mCherry; WAPL-AID-eGFP), after 24h of IAA


title: 15_H82_NOTCH1_no_dox_input


title: 156-10AD20NL_04


title: 156-10PN07L_01


title: 14_H82_NOTCH1_no_dox_H3K27Ac_2


title: HiC.06_CTCFWAPL_6h

description: Hi-C in E14TG2a (with OsTir1; CTCF-AID-mCherry; WAPL-AID-eGFP), after 6h of IAA


title: rRNA Depleted totalRNA from whole brain from untreated LEXF7B rats (replicate 3, sequencing batch 20)

description:
Library name: LEXF7B_3
LEXF7B_3_batch20


title: HiC.05_CTCFWAPL_0h

description: Hi-C in E14TG2a (with OsTir1; CTCF-AID-mCherry; WAPL-AID-eGFP), after 0h of IAA


title: 13_H82_NOTCH1_no_dox_H3K27Ac_1


title: 156-10AD20L_03


title: 156-10 PN14NL_02


title: rRNA Depleted totalRNA from whole brain from untreated LEXF7B rats (replicate 2, sequencing batch 19)

description:
Library name: LEXF7B_2
LEXF7B_2_batch19


title: 12_H82_NOTCH1_dox_input


title: HiC.04_WAPL_96h

description: Hi-C in E14TG2a (with OsTir1; WAPL-AID-eGFP), after 96h of IAA

value: OsTir1; WAPL-AID-eGFP


title: 156-10 PN14L_01

value: C


title: rRNA Depleted totalRNA from whole brain from untreated LEXF7B rats (replicate 1, sequencing batch 18)

description:
Library name: LEXF7B_1
LEXF7B_1_batch18


title: 11_H82_NOTCH1_dox_H3K27Ac_2


title: HiC.03_WAPL_24h

description: Hi-C in E14TG2a (with OsTir1; WAPL-AID-eGFP), after 24h of IAA; re-analysis of GSM3992962


title: 109-18PN01NL_12


title: rRNA Depleted totalRNA from whole brain from untreated LEXF6B rats (replicate 2, sequencing batch 19)

description:
Library name: LEXF6B_2
LEXF6B_2_batch19


title: 10_H82_NOTCH1_dox_H3K27Ac_1


title: HiC.02_WAPL_6h

description: Hi-C in E14TG2a (with OsTir1; WAPL-AID-eGFP), after 6h of IAA


title: rRNA Depleted totalRNA from whole brain from untreated LEXF8A rats (replicate 2, sequencing batch 19)

description: Library name: LEXF8A_2


title: rRNA Depleted totalRNA from whole brain from untreated LEXF6B rats (replicate 1, sequencing batch 20)

description:
Library name: LEXF6B_1
LEXF6B_1_batch20


title: 9_CORL88_TAS1440_input


title: HiC.01_WAPL_0h

description: Hi-C in E14TG2a (with OsTir1; WAPL-AID-eGFP), after 0h of IAA; re-analysis of GSM3992961


title: 109-18PN01L_11


title: rRNA Depleted totalRNA from whole brain from untreated LEXF8A rats (replicate 1, sequencing batch 18)

description:
Library name: LEXF8A_1
LEXF8A_1_batch18


title: rRNA Depleted totalRNA from whole brain from untreated LEXF5 rats (replicate 2, sequencing batch 19)

description:
Library name: LEXF5_2
LEXF5_2_batch19


title: rRNA Depleted totalRNA from whole brain from untreated LEXF5 rats (replicate 1, sequencing batch 18)

description:
Library name: LEXF5_1
LEXF5_1_batch18


title: Adjacent Non-tumor Tissue

city: qingyuan

first: Zhongzhong

last: Guo

address: No.35, Yinquan North Road, Qingcheng District, Qingyuan Guangdong, China, 511518.

institute: The Affiliated Qingyuan Hospital (Qingyuan People's Hospital), Guangzhou Medical University

description: Library name: p1

data_processing:
For the raw data from sequencing, adapter sequences were removed using cutadapt, low-quality reads were filtered out with FastX - Toolkit, and reads containing excessive N bases were eliminated to obtain clean data. Clean reads were aligned to the human hg19 reference genome using the BWA software with default parameters. The Clean Data was aligned to all mature miRNA sequences of the species in the miRBase21 database to calculate their expression levels. EdgeR was employed to analyze inter - group differences and compute P - values.
Assembly: human hg19
Supplementary files format and content: An Excel spreadsheet containing miRNA expression levels in RPM values.

source_name: Adjacent Non-tumor Tissue

extract_protocol:
Total RNA was extracted from the samples using the MagZol Reagent kit (Magen Company). The RNA concentration was detected by a nanodrop instrument, and the RNA fragment distribution was analyzed by an Agilent 2200 instrument.
The NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) kit was used to construct small RNA libraries.

value: Adjacent Non-tumor Tissue


title: 8_CORL88_TAS1440_H3K27Ac_2


title: Breast cancer

description: Library name: b1

source_name: Breast cancer

value: Breast cancer


title: 7_CORL88_TAS1440_H3K27Ac_1


title: PS-C2_12

data_processing: Gene expression analysis was conducted for 770 neuroinflammatory-related genes using nCounter’s Human Neuroinflammation Panel and a panel of 30 genes focused on Mrgpr genes and cytokines. Nsolver Analysis Software 4.0 was used to complete quality control, background thresholding, and normalization of the raw expression data. 1 sample was flagged for mRNA content; thus, 119/120 samples were used for subsequent statistical analysis. Background thresholding to the geometric mean of the average counts for eight negative control samples was completed. Positive control normalization was calculated using the geometric mean of the average counts for six synthetic ssDNA control samples; housekeeping normalization was calculated using the geometric mean of the average counts for 9 selected housekeeping genes.


title: PS-AA2_11


title: rRNA Depleted totalRNA from whole brain from untreated LEXF2C rats (replicate 2, sequencing batch 19)

description:
Library name: LEXF2C_2
LEXF2C_2_batch19

value: whole brain


title: 6_CORL88_TAS1440_GSI_input


title: 5_CORL88_TAS1440_GSI_H3K27Ac_2


title: 156-4AD05NL_06


title: rRNA Depleted totalRNA from whole brain from untreated LEXF2C rats (replicate 1, sequencing batch 20)

description:
Library name: LEXF2C_1
LEXF2C_1_batch20


title: 156-4AD05L_05


title: SW620_N_EXO_2

city: Chengdu

first: Yang

last: Zhang

state: Sichuan

address: No. 37 Guo Xue Alley

institute: West China Hospital of Sichuan University

hyb_protocol: Add RNA Spike Control Oligos to the sample according to the standard procedure of Affymetrix Flashtag kit. After configuring Poly-A Tailing Master Mix, add it to Total RNA, and perform tail addition at 37 ℃ for 15 minutes. Use 5 x FlashTag Biotin HSR Ligation Mix, T4 DNA Ligase for biotin ligation. Add the biotinylated sample to the corresponding model chip and place it in the GeneChip Hybridization Oven 645 for chip hybridization at a specific temperature and speed; After reaching the specified time, use the GeneChip Fluidics Station 450 to wash and dye according to the corresponding protocol.

scan_protocol: Flurorescence signal was scanned by using GeneChip 3000 7G scanner.

data_processing:
Scanned signal was processed following a standard instruction of ThermoScientific Affymetrix pipeline.
The scanner captures fluorescence signals and converts them into signal values for each probe using GCOS software, generating CEL files
Scanned signal was processed following a standard instruction of ThermoScientific Affymetrix pipeline. Raw data (CEL files) were generated using AGCC. Signal summarization and normalization were performed using Affymetrix Expression Console software with the RMA+DABG algorithm (Robust Multi-array Average with Detection Above Background).
The reported values represent log2-transformed signal intensities derived from RMA normalization. These values quantify the relative expression levels of miRNA probes, where higher values indicate stronger hybridization signals.

label: biotin

source_name: extracellular vesicles isolated from SW620 cells cultured under normoxic conditions

growth_protocol: SW620 cells were purchased from the cell bank of the Chinese Academy of Science (Shanghai, China) and human umbilical vein endothelial cells (HUVECs) were purchased from Procell (Wuhan, China). SW620 cells were cultured under normoxic (20% oxygen concentration) or hypoxic conditions (1% oxygen concentration) in DMEM (Cytiva, USA) plus 10% fetal bovine serum (Excell Bio, HK) and 1% penicillin/ streptomycin (Beyotime, China) for 48h.

extract_protocol: SW620 cell supernatant were collected and EVs were isolated by ultrafiltration plus size exclusion chromatography

value: Colorectal cancer cell line

value: Normoxia


title: AD-AA2_10

value: AA


title: 156-3HC10_09


title: 4_CORL88_TAS1440_GSI_H3K27Ac_1


title: rRNA Depleted totalRNA from whole brain from untreated SHR rats (replicate 4, sequencing batch 18)

description:
Library name: SHR_4_control_18
SHR_4_batch18

value: SHR/OlaIpcv


title: rRNA Depleted totalRNA from whole brain from untreated LEXF2B rats (replicate 2, sequencing batch 19)

description:
Library name: LEXF2B_2
LEXF2B_2_batch19


title: 3_CORL88_DMSO_input

value: DMSO


title: 2_CORL88_DMSO_H3K27Ac_2


title: rRNA Depleted totalRNA from whole brain from untreated LEXF1A rats (replicate 2, sequencing batch 19)

description:
Library name: LEXF1A_2
LEXF1A_2_batch19


title: rRNA Depleted totalRNA from whole brain from untreated LEXF2C rats (replicate 3, sequencing batch 20)

description:
Library name: LEXF2C_3
LEXF2C_3_batch20


title: 156-10PN05NL_04


title: 156-10PN05L_03


title: 156-10PN04NL_02

value: M


title: SW620_N_EXO_1

label_protocol: SW620 cells were cultured under normoxic (20% oxygen concentration) or hypoxic conditions (1% oxygen concentration) in DMEM (Cytiva, USA) plus 10% fetal bovine serum (Excell Bio, HK) and 1% penicillin/ streptomycin (Beyotime, China) for 48h.


title: Day 3 fibrosis, biological replicate 3

city: Philadelphia

first: Janice

middle: Lynn

last: Walker

state: PA

address: 1020 Locust Street; 571 JAH

department: Pathology and Genomic Medicine

institute: Thomas Jefferson University

description: Library name: sample 18

data_processing:
Quality control: Raw reads (fastq format) were processed through Novogene in-house perl scripts. The following were removed to obtain clean reads: 1) reads containing adapter, 2) reads containing ploy-N, and 3) low quality reads from raw data. Additionally, Q20, Q30, and GC content were calculated on clean data. All downstream analyses were performed on high quality clean data.
Hisat2 was used to map reads, which were assembled by StringTie (v1.3.3b) and featureCounts (v1.5.0-p3) was utilized to count the reads numbers mapped to each gene. Then the FPKM of each gene was calculated based on: 1)  the length of the gene and  2)mapped read count of gene.
False Delivery Rate was assessed by using Benjamini and Hochberg's approach to adjust P-values  and genes were considered differentially expressed (DEG) with an adjusted P-valuse <=0.05 by DESeq2 software.
Assembly: Reference genome was acquired from genome website. Hisat2 v2.0.5 software and alignment of paired-end clean reads were used to create an index of the reference genome.
Supplementary files format and content: Supplementary files format and content: tab-delimited xls text files include raw counts for each Sample
Supplementary files format and content: Supplementary files format and content: tab-delimited xls files include DEG set for each Sample

organism: Gallus gallus

source_name: Lens

growth_protocol: Post-cataract surgery lens explants were maintained in Media 199 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, and 1% penicillin/stretomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Wound healing regions were separately isolated from fibrotic (ECZ ) regions. RNA was then  isolated from each of these regions of the post-cataract surgery cultures using the Rneasy mini kit (Qiagen). Sequencing libraries were created using total RNA according to Novogene's protocols. Sequencing was performed on an Illumina NovaSeq 6000 platform and 150bp paired-end reads were generated.
Novogene performed the libarary preparation using the following steps: 1) poly-T oligo-attached  magnetic beads were used to purify mRNA, 2)PCR products were purfied on AMPure XP system, 3) The Agilent Bioanalyzer 2100 system  was used to assess library quality. 4) a cBot Cluster Generation System utilizing TruSeq PE Cluster Kit v3-cBot-Hs (Illumia) was used to cluster index-coded samples, and 5) an  Illumina Novaseq platform  was to sequence and create library preparations to generate 150bp paired reads.

value: Lens

tag: time

tag: condition

value: fibrosis


title: 1_CORL88_DMSO_H3K27Ac_1

value: small cell lung cancer

value: H3K27ac (Abcam #ab4729)


title: GM23338_TReg_r2c10, mTeSR1 + DOX, rep2

city: Boston

first: Evan

middle: Michael

last: Appleton

state: MA

address: 75 Kneeland St.

institute: Colossal Biosciences

data_processing:
homer v4.9 read trimming (Transcriptome sequencing)
Bowtie2 v2.2.9 to align reads to hg38 (Transcriptome sequencing)
homer v4.9 peak calling and read count extraction (Transcriptome sequencing)
Custom script for barcode tallying in amplicon sequencing (TFome screening)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample and barcode counts for amplicon sequencing

growth_protocol: All iPSCs maintained in mTeSR1 until differentiation

extract_protocol:
RNA was harvested using Directzol RNA miniprep kit (Transcriptome sequencing) (Zymo) or Directzol RNA microprep kit (amplicon sequencing of TFome screens) (Zymo)
RNA libraries for RNA-seq were prepared using either SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (TFome screening) or NEBNext Ultra II RNA Kit (Transcriptome sequencing) following manufacturer's protocols.

treatment_protocol: Differentiation for 6 days in mTeSR1 and a variety of target cell type-specific media conditions with 1ug/mL DOX

value: iPSC-derived regulatory T-cells

tag: genotype

value: Overexpression of TFs:[ETS1, ETV3, GABPA, Klf9, NFKB1]

value: Induction with 1ug/mL DOX in mTeSR1 Medium

value: Day 6


title: rRNA Depleted totalRNA from whole brain from untreated LEXF11 rats (replicate 1, sequencing batch 20)

description:
Library name: LEXF11_1
LEXF11_1_batch20


title: Day 3 fibrosis, biological replicate 2

description: Library name: sample 17


title: SW620_N_EXO_3

treatment_protocol: SW620 cells were cultured under normoxic (20% oxygen concentration) or hypoxic conditions (1% oxygen concentration) in DMEM (Cytiva, USA) plus 10% fetal bovine serum (Excell Bio, HK) and 1% penicillin/ streptomycin (Beyotime, China) for 48h.


title: SW620_H_EXO_3

source_name: extracellular vesicles isolated from SW620 cells cultured under hypoxic conditions

value: Hypoxia


title: 156-10AD06NL_08

city: Baltimore

first: Shawn

last: Kwatra MD

address: 1550 Orleans Street

institute: Johns Hopkins School of Medicine

tag: race

value: C

tag: age


title: GM23338_TReg_r2c10, mTeSR1 + DOX, rep1


title: 156-10PN04L_01

tag: Sex


title: rRNA Depleted totalRNA from whole brain from untreated LEXF10B rats (replicate 3, sequencing batch 20)

description:
Library name: LEXF10B_3
LEXF10B_3_batch20

value: whole brain


title: rRNA Depleted totalRNA from whole brain from untreated LEXF1A rats (replicate 3, sequencing batch 19)

description:
Library name: LEXF1A_3
LEXF1A_3_batch19


title: 156-10AD06L_07


title: GM23338_TReg_r2c10, IXFT + DOX, rep2

value: Induction with 1ug/mL DOX in Immunocult XF T-cell Medium


title: Day 3 fibrosis, biological replicate 1

description: Library name: sample 16


title: SW620_H_EXO_1

value: Colorectal cancer cell line


title: Day 2 fibrosis, biological replicate 3

description: Library name: sample 15


title: SW620_H_EXO_2


title: Day 2 fibrosis, biological replicate 2

description: Library name: sample 14


title: rRNA Depleted totalRNA from whole brain from untreated LEXF10B rats (replicate 1, sequencing batch 18)

description: Library name: LEXF10B_1


title: PS-C1_11


title: rRNA Depleted totalRNA from whole brain from untreated FXLE18 rats (replicate 2, sequencing batch 20)

description:
Library name: FXLE18_2
FXLE18_2_batch20


title: Day 2 fibrosis, biological replicate 1

description: Library name: sample 13


title: GM23338_Hep_r2c6, mTeSR1 + DOX, rep2

value: iPSC-derived hepatocytes

value: Overexpression of TFs:[HNF4G, HNF4A, TEAD4]


title: PS-AA1_10

value: AA


title: rRNA Depleted totalRNA from whole brain from untreated FXLE18 rats (replicate 1, sequencing batch 20)

description:
Library name: FXLE18_1
FXLE18_1_batch20


title: rRNA Depleted totalRNA from whole brain from untreated LEXF11 rats (replicate 2, sequencing batch 20)

description:
Library name: LEXF11_2
LEXF11_2_batch20


title: GM23338_Hep_r2c6, mTeSR1 + DOX, rep1


title: Day 1 fibrosis, biological replicate 3

description: Library name: sample 12


title: GM23338_Hep_r2c6, WE + DOX, rep2

value: Induction with 1ug/mL DOX in William's E Medium Medium


title: rRNA Depleted totalRNA from whole brain from untreated FXLE17 rats (replicate 3, sequencing batch 20)

description:
Library name: FXLE17_3
FXLE17_3_batch20


title: 156-4AD03L_05

value: F


title: GM23338_Hep_r2c6, WE + DOX, rep1


title: Day 1 fibrosis, biological replicate 2

description: Library name: sample 11

value: Lens

value: fibrosis


title: rRNA Depleted totalRNA from whole brain from untreated LEXF10B rats (replicate 2, sequencing batch 19)

description: Library name: LEXF10B_2


title: rRNA Depleted totalRNA from whole brain from untreated FXLE17 rats (replicate 2, sequencing batch 19)

description:
Library name: FXLE17_2
FXLE17_2_batch19


title: GM23338_TReg_r2c10, IXFT + DOX, rep1


title: GM23338_CD8_r3c2, mTeSR1 + DOX, rep2

value: iPSC-derived cytotoxic T-cells

value: Overexpression of TFs:[ZBTB1, RUNX3, RELA]


title: Day 1 fibrosis, biological replicate 1

description: Library name: sample 10


title: 156-10PN03NL_04


title: 156-4AD03NL_06


title: rRNA Depleted totalRNA from whole brain from untreated FXLE17 rats (replicate 1, sequencing batch 18)

description:
Library name: FXLE17_1
FXLE17_1_batch18


title: GM23338_CD8_r3c2, mTeSR1 + DOX, rep1


title: rRNA Depleted totalRNA from whole brain from untreated FXLE14 rats (replicate 3, sequencing batch 20)

description:
Library name: FXLE14_3
FXLE14_3_batch20


title: 156-10PN03L_03


title: GM23338_CD8_r3c2, IXFT + DOX, rep2


title: AD-C1_12

value: M


title: GM23338_CD8_r3c2, IXFT + DOX, rep1


title: rRNA Depleted totalRNA from whole brain from untreated FXLE14 rats (replicate 2, sequencing batch 19)

description:
Library name: FXLE14_2
FXLE14_2_batch19


title: Day 3 post-wounding, biological replicate 2

description: Library name: sample 8

value: post-wounding


title: 156-10PN01L_01


title: 156-10PN01NL_02


title: Day 2 post-wounding, biological replicate 3

description: Library name: sample 6


title: GM23338_Ast_r1c2, mTeSR1 + DOX, rep2

value: iPSC-derived typeII astrocytes

value: Overexpression of TFs:[ERG, EGR1, FLI1, FOSB]

value: Induction with 1ug/mL DOX in mTeSR1 Medium

value: Day 6


title: Day 3 post-wounding, biological replicate 1

description: Library name: sample 7


title: Day 2 post-wounding, biological replicate 2

description: Library name: sample 5


title: rRNA Depleted totalRNA from whole brain from untreated FXLE13 rats (replicate 2, sequencing batch 19)

description:
Library name: FXLE13_2
FXLE13_2_batch19

value: whole brain


title: 156-10AD03NL_08

value: C


title: GM23338_Ast_r1c2, mTeSR1 + DOX, rep1


title: rRNA Depleted totalRNA from whole brain from untreated FXLE13 rats (replicate 1, sequencing batch 20)

description:
Library name: FXLE13_1
FXLE13_1_batch20


title: rRNA Depleted totalRNA from whole brain from untreated BUF rats (replicate 2, sequencing batch 19)

description:
Library name: BUF_2
BUF_2_batch19

value: BUF/MnaMcwi


title: GM23338_Ast_r1c2, BPhys + DOX, rep2

value: Induction with 1ug/mL DOX in BrainPhys Medium


title: Day 3 post-wounding, biological replicate 3

description: Library name: sample 9


title: Day 1 post-wounding, biological replicate 3

description: Library name: sample 3


title: Day 2 post-wounding, biological replicate 1

description: Library name: sample 4


title: yak-3

organism: Bos grunniens

value: longissimus dorsi


title: 156-10AD03L_07


title: yak-2


title: GM23338_Ast_r1c2, BPhys + DOX, rep1


title: Day 1 post-wounding, biological replicate 2

description: Library name: sample 2


title: GM23338, mTeSR1 + DOX, rep2

value: iPSCs

value: WT


title: rRNA Depleted totalRNA from whole brain from untreated BDIX rats (replicate 2, sequencing batch 19)

description:
Library name: BDIX_2
BDIX_2_batch19

value: BDIX/NemOdaMcwi


title: yak-1


title: rRNA Depleted totalRNA from whole brain from untreated FXLE14 rats (replicate 1, sequencing batch 20)

description:
Library name: FXLE14_1
FXLE14_1_batch20


title: Day 1 post-wounding, biological replicate 1

description: Library name: sample 1

value: Lens


title: GM23338, mTeSR1 + DOX, rep1


title: ATAC_L854F_3

status: Public on Jun 01 2025

city: Bronx

first: Matanel

last: Yheskel

address: 1300 Morris Park

department: Genetics

institute: Albert Einstein College of Medicine

description:
Library name: ATAC_L854F_3
ATAC-Seq for L854F

data_processing:
Raw reads quality controlled and trimmed using rfastp (v 1.6.0) and were aligned using Rsubread (2.10.5) to the dm6 Drosophila melanogaster genome assembly
BigWigs were generated using deeptools (v 3.5.1) bamCoverage function
Assembly: dm6
Supplementary files format and content: bigwig

organism: Drosophila melanogaster

source_name: Brain

extract_protocol:
Used Active Motif ATAC-Seq Kit
Used Active Motif ATAC-Seq Library Prep Kit

value: Brain


title: rRNA Depleted totalRNA from whole brain from untreated BDIX rats (replicate 1, sequencing batch 18)

description:
Library name: BDIX_1
BDIX_1_batch18


title: ATAC_JmjC_3

description:
Library name: ATAC_JmjC_3
ATAC-Seq for JmjC

value: JmjC


title: ATAC_JmjC_2

description:
Library name: ATAC_JmjC_2
ATAC-Seq for JmjC


title: 156-10HC08_09

source_name: skin punch biopsy

value: F


title: ATAC_L854F_4

description:
Library name: ATAC_L854F_4
ATAC-Seq for L854F


title: ATAC_JmjC_4

description:
Library name: ATAC_JmjC_4
ATAC-Seq for JmjC


title: ATAC_JmjC_1

description:
Library name: ATAC_JmjC_1
ATAC-Seq for JmjC


title: ATAC_WT_4

description:
Library name: ATAC_WT_4
ATAC-Seq for WT


title: ATAC_WT_1

description:
Library name: ATAC_WT_1
ATAC-Seq for WT


title: ATAC_WT_3

description:
Library name: ATAC_WT_3
ATAC-Seq for WT


title: SK-NEP-1 cells treated with siNC, replicate 3

first: Cheng

last: Cheng

state: Shanghai

address: NO.1665 Kongjiang Road

institute: Shanghai Jiaotong University School of Medicine affiliated Xinhua Hospital

description: Library name: siNC-3

data_processing:
We preprocessed the raw reads of RNA-seq using fastp with default options, removing low-quality reads. Subsequently, we aligned them to the hg19 reference genome using HISAT v2.2.1 and annotated the genes using GENCODE v19 gene annotation. Next, we converted the SAM files to BAM files and sorted the reads using SAMtools v1.4.1. Consequently, we quantified gene expression using StringTie v2.2.0. The gene expression was normalized to Fragments Per Kilobase Million (FPKM) by R ballgown v2.32.0 package.
Assembly: hg19
Supplementary files format and content: one xlsx file included FPKM values for all samples

source_name: Kidney

extract_protocol:
RNA integrity was assessed using the Fragment Analyzer 5400 (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Kidney

value: Wilms tumor cell line, SK-NEP-6

value: Cell line


title: SK-NEP-1 cells treated with siEHMT2, replicate 3

description: Library name: siEHMT2-3

value: Wilms tumor cell line, SK-NEP-3


title: SK-NEP-1 cells treated with siNC, replicate 2

description: Library name: siNC-2

value: Wilms tumor cell line, SK-NEP-5


title: SK-NEP-1 cells treated with siNC, replicate 1

description: Library name: siNC-1

value: Wilms tumor cell line, SK-NEP-4


title: SK-NEP-1 cells treated with siEHMT2, replicate 2

description: Library name: siEHMT2-2

value: Wilms tumor cell line, SK-NEP-2


title: SK-NEP-1 cells treated with siEHMT2, replicate 1

description: Library name: siEHMT2-1

value: Wilms tumor cell line, SK-NEP-1


title: BRI-2253

first: Soumya

last: Raychaudhuri

address: 75 Francis St

institute: Brigham and Women's Hospital

description: Library name: BRI-2253

data_processing:
The AIM-Seq data was processed using Cell Ranger version 6.1.1 with default parameters and alignment to hg38 reference genome. The donor of origin for each cell was determined using Demuxlet version 1.0 with doublet-prior of 0.168. Cells with null or ambiguous demuxlet result, fewer than 10 counts of the hashtag oligos, or fewer than 50 total RNA counts were filtered. To account for staining differences between the hashtag oligos and different sequencing depths of the two 10X runs, the counts for each hashtag oligo in each 10X run were scaled to have the same median value. Next we added a pseudocount to the hashtag oligo counts and log10 transformed this data. Then we ran Gaussian Mixture models separately for each hashtag oligo with K=2 clusters. Each cell was assigned to a single condition if it was in the high cluster for one oligo and the low clusters for all others, a doublet if it was in the high cluster for more than one oligo, or an empty droplet if it was in the low cluster for all oligos. Empty droplets or doublets based on the hashtag oligo clustering were filtered, as were doublets based on demuxlet. Genes detected in fewer than 10 cells were filtered prior to running TCAT.
Assembly: hg38
Supplementary files format and content: Single-cell RNA, ADT, hashing counts matrices and per-cell metadata, including TCR clonotypes.
Library strategy: TCR-Seq

source_name: Blood

extract_protocol:
PBMCs from 5 healthy donors were quickly thawed and placed in pre-warmed xVIVO15 cell culture medium (Lonza) supplemented with 5% heat-inactivated FBS. To reduce cell clumping, PBMCs were incubated in xVIVO15 containing 50 U/mL of benzonase nuclease (Sigma-Aldrich) for 15 minutes at 37 degrees and filtered using a 70 µm cell strainer. Washed and nuclease treated cells were seeded in a 96 well cell culture plate at a concentration of 2.5 x 106/mL. Peptide stimulations were performed using the CEFX Ultra SuperStim Pool (JPT Peptide Technologies, Product Code: PM-CEFX-1) at a final concentration of 1.25 µg/mL per peptide for 22 hours at 37 degrees and 5% CO2. Recombinant anti-CD28 and anti-CD49d antibodies (BioLegend) were added at a final concentration of 5 µg/mL and 0.625 µg/mL, respectively, to provide co-stimulation for peptide reactive T-cells. Separately mock-stimulated cells were treated with anti-CD28 and anti-CD49d antibodies at the same concentration. Peptide responsive T-cells were detected by the expression of the surface activation markers PD-L1, OX40, and CD137 via flow cytometry. Following the stimulation, peptide treated and mock-stimulated cells were washed in cell staining buffer (PBS + 2mM EDTA + 2% FBS) to end the stimulation. Fc receptor blocking was performed using a 1:50 dilution of Human TruStain FcX (Biolegend) in cell staining buffer for 10 minutes at 4 degrees. Cell viability staining was performed using a 1:500 dilution of Zombie Yellow Fixable Viability Dye (BioLegend) prepared in PBS for 30 minutes at 4 degrees. Surface staining was performed using 1:100 dilutions of BV421 conjugated anti-CD3, FITC conjugated anti-CD4, BV786 conjugated anti-PD-L1, PE conjugated anti-OX40, and APC conjugated anti-CD137 (BioLegend) for 25 minutes at 4 degrees in cell staining buffer. Following cell staining, antigen reactive and non-reactive T-cells were identified using a BD FACSAria II cell sorter and collected in cRPMI medium (100 U/mL penicillin-streptomycin + 2 mM L-glutamine + 10 mM HEPES + 0.1 mM non-essential amino acids + 1 mM sodium pyruvate + .05 mM 2-Mercaptoethanol) supplemented with 20% FBS. Sorted T cell populations were then labeled with 75 uL of TotalSeq oligo conjugated hashing antibody mix, incubated for 30 minutes at 4 degrees with gentle mixing after 15 minutes, and pooled in equal quantities. Staining with the TotalSeq-C Human Universal Cocktail (BioLegend) was then performed according to the manufacturer's instructions. The cells were then resuspended in PBS supplemented with .04% FBS at a final concentration of 500 cells/µL and submitted for single-cell profiling on the Chromium Next GEM instrument.
Library preparation was completed for the hashtag oligos, single-cell rna-seq, cite-seq, and TCR-repertoire sequencing following the manufacturer’s instructions.

value: Blood

value: T

value: TCR


title: BRI-2252

description: Library name: BRI-2252

library_source: other

data_processing:
The AIM-Seq data was processed using Cell Ranger version 6.1.1 with default parameters and alignment to hg38 reference genome. The donor of origin for each cell was determined using Demuxlet version 1.0 with doublet-prior of 0.168. Cells with null or ambiguous demuxlet result, fewer than 10 counts of the hashtag oligos, or fewer than 50 total RNA counts were filtered. To account for staining differences between the hashtag oligos and different sequencing depths of the two 10X runs, the counts for each hashtag oligo in each 10X run were scaled to have the same median value. Next we added a pseudocount to the hashtag oligo counts and log10 transformed this data. Then we ran Gaussian Mixture models separately for each hashtag oligo with K=2 clusters. Each cell was assigned to a single condition if it was in the high cluster for one oligo and the low clusters for all others, a doublet if it was in the high cluster for more than one oligo, or an empty droplet if it was in the low cluster for all oligos. Empty droplets or doublets based on the hashtag oligo clustering were filtered, as were doublets based on demuxlet. Genes detected in fewer than 10 cells were filtered prior to running TCAT.
Assembly: hg38
Supplementary files format and content: Single-cell RNA, ADT, hashing counts matrices and per-cell metadata, including TCR clonotypes.
Library strategy: CITE-seq

molecule: protein

value: ADT/HTO


title: ATAC_L854F_2

description:
Library name: ATAC_L854F_2
ATAC-Seq for L854F


title: BRI-2250

description: Library name: BRI-2250


title: BRI-2249

description: Library name: BRI-2249


title: ATAC_L854F_1

description:
Library name: ATAC_L854F_1
ATAC-Seq for L854F


title: BRI-2248

description: Library name: BRI-2248

value: mRNA


title: BRI-2013_rerun

description: Library name: BRI-2013_rerun


title: BRI-2012

description: Library name: BRI-2012


title: Olfactory Epithelium, WT

city: NY

first: Paul

middle: G

last: Feinstein

address: 695 Park Ave

department: Biology

institute: CUNY Hunter College

description:
Library name: Sample 2
10X Genomics

data_processing:
The 10X Libraries were sequenced on the Illumina NovaSeq6000 sequencer with pair-end reads (28 bp for read 1 (R1) and 90 bp for read 2 (R2)).  The sequencing data were primarily analyzed by the 10X cellranger pipeline (v6.1.1) (https://www.10xgenomics.com/support/software/cell-ranger/downloads)  in two steps. In the first step, cellranger mkfastq demultiplexed samples and generated fastq files; and in the second step, cellranger count aligned fastq files to the reference genome and extracted gene expression UMI counts matrix.  In order to measure both mouse and transgene gene expression, we built a custom reference genome by integrating the OR1A1 transgene sequence into the mouse reference (GRCm39) using cellranger mkref.
Assembly: mm39 (GRCm39)
Supplementary files format and content: Tab-separated value (tsv) files
Supplementary files format and content: Matrix (mtx) files

source_name: Olfactory Epithelium

extract_protocol:
Olfactory epithelia were dissected out and minced with spring scissors in HBSS on ice. The minced tissues were incubated with  10 U/ml disease, 230 U/ml collagenase type II and 77 μg/ml DNase I in HBSS for 30 min at 37°C. Filter the cell suspension through a 40 μm strainer and a 10 μm strainer. Washed with Hibernate-A, 10% FBS two times and finally, cells were resuspended with 0.04% BSA in PBS.
Library construction was performed according to the manufacturer’s instructions (single cell 3’ reagent kit v3.1). Briefly, dissociated cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in emulsion (GEM). The ploy-A RNA from the cell lysate continued in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcode cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction, Illumina Read2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Olfactory Epithelium

value: 8 weeks

value: Female

value: WT


title: ATAC_WT_2

description:
Library name: ATAC_WT_2
ATAC-Seq for WT

value: Brain


title: Olfactory Epithelium, 5x21 OR1A1 beta

description:
Library name: Sample 1
10X Genomics

value: 9 weeks


title: CPC, middle

city: Wenzhou

first: Jun

last: Ying

address: Wenzhou Medical University, University Town, Chashan, Wenzhou, Zhejiang, P.R China

institute: Wenzhou Medical University

description:
Library name: Sample 5
PC_2

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: skin

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: skin

value: C-PC


title: CPC, early

description:
Library name: Sample 4
PC_1


title: negative control, late

description:
Library name: Sample 3
NC_3


title: HeLa cells, DMSO treat, 72h

city: Kashiwa

first: Akihiro

last: Ohashi

state: Chiba

address: 6-5-1 Kashiwanoha

department: Exploratory Oncology Research and Clinical Center

country: Japan

institute: National Cancer Center Japan

description: Library name: Sample 1

data_processing:
Sequence read was mapped to human genome using STAR (v2.6.1c).
Multimapped reads were removed.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including expression level for each sample

source_name: Cervix

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% Fetal Bovine Serum and penicillin/Streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy Mini kit (QIAGEN).
RNA-seq was performed by Filgen, Inc.

treatment_protocol: HeLa cells were treated with DMSO or Olaparib for 72 h.

value: Cervix

value: HeLa cells

value: epithelial cell

value: DMSO


title: HeLa cells, Olaparib treat, 72h

description: Library name: Sample 2

value: Olaparib


title: BRI-2011

description: Library name: BRI-2011

value: Blood

value: T


title: JIMT1_rep3

city: Nanjing

first: Nignjun

last: Duan

address: 300 Guangzhou Road

institute: JSPH

description: Library name: JIMT1_rep3

data_processing:
RNA-seq reads were aligned to the hg38 build of the human genome reference using STAR 2.4.2a.
The GENCODE v19 annotation was used for the STAR alignment and all other quantifications.
Gene level read count values were calculated using RNA-SeQC v1.1.8.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

value: Breast; Mammary gland, epithelial


title: BRI-2009

description: Library name: BRI-2009

value: ADT/HTO


title: BRI-2010_rerun

description: Library name: BRI-2010_rerun

value: TCR


title: negative control, middle

description:
Library name: Sample 2
NC_2


title: JIMT1_rep1

description: Library name: JIMT1_rep1


title: JIMT1_rep2

description: Library name: JIMT1_rep2


title: BRI-2008

description: Library name: BRI-2008

value: mRNA


title: JIMT1 RNApolII rep2

description: Library name: JIMT1 RNApolII rep2

data_processing:
DNA-seq reads were aligned to hg38 build of the human genome using Bowtie2 (v2.2.5).
Aligned reads were filtered and sorted by Samtools (v1.14) and Bedtools (v2.30.0).
SEACR (v1.3) was applied for peak calling.
Assembly: hg38
Supplementary files format and content: bigwig
Supplementary files format and content: bed file includes peak information of each sample
Library strategy: CUT&Tag

extract_protocol:
Cell were harvested by ConA conjugated magnetic beads and permeabilized by Digitonin.
DNA library was prepared using Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme) following manufacturer's protocol.


title: Mature neutrophils cultured without DKK1 ex vivo, sample 3

city: 南京

first: shiji

last: ren

address: 南京鼓楼

institute: Nanjing University

description:
Library name: Sample 6
MAT3

data_processing:
the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina)
Assembly: mm10
Supplementary files format and content: csv files include count values for each sample

source_name: neutrophil

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent/RNeasy Mini Kit (Qiagen), and was qualified by Agilent 2100/2200 Bioanalyzer (Agilent Technologies) and NanoDrop (Thermo Fisher). 1 μg of total RNA was used for following library preparation.
Libraries with different indices were multiplexed and loaded on an Illumina HiSeq/Novaseq instrument (Illumina) according to instructions of the manufacturer.

value: neutrophil


title: Mature neutrophils cultured without DKK1 ex vivo, sample 1

description:
Library name: Sample 4
MAT1


title: negative control, early

description:
Library name: Sample 1
NC_1


title: Mature neutrophils cultured with DKK1 ex vivo, sample 2

description:
Library name: Sample 2
DKK12


title: JIMT1 CTCF rep2

description: Library name: JIMT1 CTCF rep2


title: JIMT1 RNApolII rep1

description: Library name: JIMT1 RNApolII rep1


title: CPC, late

description:
Library name: Sample 6
PC_3


title: Mature neutrophils cultured with DKK1 ex vivo, sample 3

description:
Library name: Sample 3
DKK13


title: Mature neutrophils cultured with DKK1 ex vivo, sample 1

description:
Library name: Sample 1
DKK11


title: JIMT1 H3K27ac rep2

description: Library name: JIMT1 H3K27ac rep2


title: JIMT1 H3K27ac rep1

description: Library name: JIMT1 H3K27ac rep1


title: TP+Ab

city: Seoul

first: Mi-Ock

last: Lee

address: 1 Gwanak-ro

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description:
Library name: Sample 3
10x Genomics

data_processing:
Raw BCL files were demultiplexed into FASTQ format using Cell Ranger v8.0.1 (10x Genomics), and reads were aligned to the mouse reference genome (mm10-2020-A) using the cellranger count pipeline, which also performed UMI quantification and cell barcode filtering.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: dorsal skin

extract_protocol:
To induce AGA, the dorsal skin of 7-week-old male C3H/HeN mice was shaved, followed by subcutaneous injection of testosterone propionate (TP; 0.5mg/day). A CXCL12 neutralizing antibody (5 μg) was administered via subcutaneous injection twice weekly for two consecutive weeks. Skin tissues were collected from the dorsal region of mice (n = 15 per group). Samples were pooled, minced, and enzymatically digested in 0.7 mg/mL collagenase D (Sigma-Aldrich). The resulting suspension was filtered through cell strainers to remove aggregates. Red blood cells were lysed using ACK Lysing Buffer (Gibco), and debris was removed via density gradient centrifugation with Percoll (Sigma-Aldrich). The single-cell suspension was immediately used for single-cell RNA sequencing (scRNA-seq).
Single-cell suspensions were processed using the Chromium GEM-X Single Cell 3’ RNA v4 kit (10x Genomics), following the manufacturer’s protocol. Briefly, cells were partitioned into Gel Beads-in-Emulsion (GEMs) containing barcoded oligonucleotides. Poly(dT) primers captured polyadenylated mRNA from individual cells, enabling the synthesis of barcoded cDNA. The resulting cDNA was amplified to construct 3’ gene expression libraries and sequenced on an Illumina platform at Macrogen (Seoul, Republic of Korea).

value: dorsal skin

value: whole skin

value: 9 weeks old

value: male

value: Androgenetic alopecia (AGA) model treated with CXCL12-neutralizing antibody


title: TP

description:
Library name: Sample 2
10x Genomics

value: Androgenetic alopecia (AGA) model


title: JIMT1 H3K4me3 rep2

description: Library name: JIMT1 H3K4me3 rep2


title: JIMT1 H3K4me3 rep1

description: Library name: JIMT1 H3K4me3 rep1


title: Con

description:
Library name: Sample 1
10x Genomics

value: Negative (vehicle) control


title: JIMT1 H3K27me3 rep1

description: Library name: JIMT1 H3K27me3 rep1


title: SKBR3 RNApolII rep1

description: Library name: SKBR3 RNApolII rep1


title: JIMT1 H3K27me3 rep2

description: Library name: JIMT1 H3K27me3 rep2


title: JIMT1 CTCF rep1

description: Library name: JIMT1 CTCF rep1


title: SKBR3 RNApolII rep2

description: Library name: SKBR3 RNApolII rep2


title: SKBR3 CTCF rep2

description: Library name: SKBR3 CTCF rep2


title: B-cells from young, Rps15-S138F homozygous mutant mouse, biological replicate 4 (Ribo-Seq)

first: Catherine

middle: J.

last: Wu

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
Library name: HOM_sample3_6
Mice aged 3-6 months

data_processing:
Adapters were removed using fastx_clipper from FASTX-Toolkit (Ribo-seq)
UMIs were removed using umi_tools (Ribo-seq)
Ribosomal RNA and tRNA were removed using Bowtie version 1.0.05 (Ribo-seq)
Transcriptomic alignment with STAR (v2.7.0a) (--alignIntronMin 20 --alignIntronMax 100000 --outFilterMismatchNmax 1 --outFilterType BySJout --outFilterMismatchNoverLmax 0.04 --twopassMode Basic)
Ribo-seq reads were further aligned to padded (± 20 nucleotides) canonical protein-coding ORFs using STAR (v2.7.0a) (-alignIntronMin 2 --alignIntronMax 1 --outFilterMismatchNmax ---scoreDelOpen -10000 --scoreInsOpen -10000 1 --outFilterType BySJout --outFilterMismatchNoverLmax 0.04 --twopassMode Basic)
RSEM (v1.2.31) was used for transcript and ORF expression quantitation.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited quantitation files show raw RPF or RNA transcript counts
Library strategy: Ribo-Seq

source_name: B-cells

extract_protocol:
Spleens or femurs of mice were mechanically dissociated into a single cell suspension. B-cells were negatively selected using the MACS Mouse B cell Isolation Kit (Miltenyi Biotec, #130-090-862). Total RNA was extracted with Qiagen RNAeasy kits.
200 ng per sample was used as input into an automated variant of the Illumina TruSeq Stranded mRNA Sample Preparation Kit (which preserves strand orientation of the RNA transcript). Oligo dT beads were used to enrich mRNA from the total RNA sample, followed by heat fragmentation and cDNA synthesis. The resultant 400 bp cDNA underwent dual-indexed library preparation, including ‘A’ base addition, adapter ligation using P7 adapters, and PCR enrichment using P5 adapters.

value: B-cells


title: B-cells from young, Rps15 wildtype mouse, biological replicate 4 (Ribo-Seq)

description:
Library name: WT_sample3_6
Mice aged 3-6 months


title: B-cells from young, Rps15 wildtype mouse, biological replicate 1 (Ribo-Seq)

description:
Library name: WT_sample1_4
Mice aged 3-6 months


title: SKBR3 CTCF rep1

description: Library name: SKBR3 CTCF rep1


title: B-cells from young, Rps15-S138F homozygous mutant mouse, biological replicate 1 (Ribo-Seq)

description:
Library name: HOM_sample1_4
Mice aged 3-6 months


title: B-cells from young, Rps15 wildtype mouse, biological replicate 3 (Ribo-Seq)

description:
Library name: WT_sample2_5
Mice aged 3-6 months


title: SKBR3 H3K27ac rep2

description: Library name: SKBR3 H3K27ac rep2


title: SKBR3 H3K27ac rep1

description: Library name: SKBR3 H3K27ac rep1


title: B-cells from young, Rps15-S138F heterozygous mutant mouse, biological replicate 2 (Ribo-seq)

description:
Library name: HET_sample2_5
Mice aged 3-6 months


title: B-cells from young, Rps15-S138F heterozygous mutant mouse, biological replicate 3 (Ribo-seq)

description:
Library name: HET_sample3_6
Mice aged 3-6 months


title: B-cells from young, Rps15-S138F heterozygous mutant mouse, biological replicate 1 (Ribo-seq)

description:
Library name: HET_sample1_4
Mice aged 3-6 months


title: SKBR3 H3K4me3 rep2

description: Library name: SKBR3 H3K4me3 rep2


title: SKBR3 H3K4me3 rep1

description: Library name: SKBR3 H3K4me3 rep1


title: SKBR3 H3K27me3 rep2

description: Library name: SKBR3 H3K27me3 rep2


title: MDM2 sKO-3

city: Wuhan

first: ZHIYI

last: CHEN

address: WuHan

institute: WuHan University

description:
Library name: sample5
T3

data_processing:
Sequence reads were flitered by fastp
Trimmed sequence reads were mapped to mm39 using STAR
Read count extraction were performed using RSEM
Assembly: mm39
Supplementary files format and content: count maritx for six samples

source_name: testis

extract_protocol:
Total RNA was used as input material for the RNA sample preparations.
Enriching mRNA using mRNA Capture Beads (oligo dT magnetic beads).

value: testis

value: postnatal day 5 (P5)

value: sKO


title: MDM2 sKO-2

description:
Library name: sample4
T2


title: SKBR3 H3K27me3 rep1

description: Library name: SKBR3 H3K27me3 rep1


title: Mature neutrophils cultured without DKK1 ex vivo, sample 2

description:
Library name: Sample 5
MAT2


title: 12402

city: Nashville

first: Jonathan

middle: A

last: Kropski

state: TN

department: Medicine

institute: Vanderbilt University Medical Center

description: Library name: 12402

data_processing:
CellRanger v. 7.0.0
Cellbender v2
Assembly: GRCh38-3.0.0
Supplementary files format and content: raw counts files and post-cellbender filtered counts files in .h5 format

source_name: lung

extract_protocol:
1% collagenase, 1% dispase
10X Genomics 5' scRNA-seq

value: lung


title: B-cells from young, Rps15-S138F homozygous mutant mouse, biological replicate 2 (Ribo-Seq)

description:
Library name: HOM_sample2_5
Mice aged 3-6 months


title: 12026

description: Library name: 12026


title: 10106

description: Library name: 10106


title: IgG

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description: Library name: IgG

data_processing:
Paired-end reads were trimmed using TrimmomaticPE
Trimmed reads were mapped to mouse genome mm10 using Bowtie2
Duplicate reads were removed with MarkDuplicates tools
Peaks were called with the callpeak tool from MACS2 package with following parameters: -f BAMPE -g mm -q 0.05 –nomodel –call-summits -B –SPMR
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Cortices from E12.5 embryos

extract_protocol:
The dissected tissue was then fixed for  in 1% methanol-free formaldehyde in 1X PBS at room temperature. The crosslinking reaction was stopped by adding Glycine to a final concentration of 125mM. The tissue was washed two times lysed in SDS lysis buffer on ice subjected to sonication. The resultant chromatin was centrifuged to remove any debris. The supernatant was collected and diluted in a ChIP dilution buffer.
Library preparation was performed for histone modifications  and transcription factors using TruSeq ChIP library Preparation kit

value: Cortices from E12.5 embryos

value: Knock-in EMX2-3xFlag-V5


title: 3821

description: Library name: 3821


title: 8962

description: Library name: 8962


title: EMX2-V5

description: Library name: EMX2-V5


title: Sgcg nuclei

city: Los Angeles

first: Daniel

last: Helzer

state: CA

address: 610 Charles E. Young Drive East

institute: University of California, Los Angeles

description:
Library name: Sgcg
10x Genomics

data_processing:
data was processed using Cell Ranger (v7.2.0)
Assembly: Mouse mm10
Supplementary files format and content: Hierarchical Data Format (.h5) files containing cell ranger filtered feature x cell count matrices; processed data (QC steps, clustering, annotations, normalization) as .rds files

source_name: skeletal muscle (quadriceps)

extract_protocol:
Quadriceps muscle from 8-12 weeks old female mice were frozen in liquid nitrogen and stored in liquid nitrogen until use. One quadriceps from wildtype, Sgcg, and SgcgTG mice were processed for sequencing. Frozen quadriceps were briefly incubated on ice then submerged in lysis buffer (10 mM Tris-HCl pH 7.4 (T2194; Sigma), 10 mM NaCl (59222C; Sigma), 3 mM MgCl2 (M1028; Sigma), 0.1% NP40 (I8896, Sigma), 1 mM dithiothreitol (646563; Sigma), 1 U/µL Roche RNase inhibitor (3335402001, Sigma)), minced with scissors, then dounced in lysis buffer. Samples were centrifuged at 500 xg for 5 min at 4°C and washed in BSA solution (1% BSA (130-091-376, Miltenyi Biotec) in PBS with 1 U/µL RNase inhibitor). Samples were then centrifuged at 100 xg for 1 min at 4°C to pellet large debris. The supernatant was then filtered through 70 µm and 30 µm filters and centrifuged at 500 xg for 5 min at 4°C. Pellets were resuspended in BSA solution and nuclei were stained with 7-Aminoactinomycin D (7-AAD; 1:100 from 1 mg/mL stock; SML1633, Sigma) for 5 min on ice. Pellets were centrifuged and washed in BSA solution. 7-AAD+ nuclei were isolated by FACS. Sorted nuclei were then permeabilized in permeabilization buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20 (1662404, BioRad), 1% BSA, 0.01% NP40, 0.001% digitonin (BN2006, Thermo Fisher Scientific), 1 mM dithiothreitol, 1 U/µL RNase inhibitor) for 2 min on ice.  Nuclei were diluted in wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 1 mM dithiothreitol, 1 U/µL RNAase inhibitor) and centrifuged at 500 xg for 5 min at 4°C.  Nuclei were resuspended in 1× nuclei buffer (20× nuclei buffer (PN-2000153, 10X Genomics), 1 mM dithiothreitol, 1 U/µL RNase inhibitor), counted, and adjusted to 3000-8000 nuclei/µL.
Library construction was performed according to the manufacturer's instructions (10x genomics); library type 3'GEX

value: skeletal muscle (quadriceps)

value: Sgcg-KO


title: TG nuclei

description:
Library name: TG
10x Genomics

value: Sgcg-KO+SSPN transgenic


title: wildtype nuclei

description:
Library name: WT
10x Genomics

value: wildtype


title: Input

description: Library name: Input


title: DC2,Delta,replicate5

city: Paris

first: Okan

last: Ayas

address: 1 avenue Claude Vellefaux

institute: INSERM

description:
Library name: Sample 39
Column name in raw_counts.tsv : 23_DC2_delta

data_processing:
Sequence reads were aligned to GRCh38 reference genome using Kallisto from Pachter lab
Read counts were imported using tximport in R4.3.2
Counts were normalized and the differentially expression analysis was conducted using DESeq2
The gene functional annotation was performed using ClusterProfiler
Assembly: GRCh38
Supplementary files format and content: raw_counts.tsv contains the raw counts for all samples

source_name: PBMC

growth_protocol: pDC and DC2  were cultured in medium RPMI 1640 with GlutaMAX, 10% of FBS, 1% of MEM nonessential amino acid, 1% of sodium pyruvate and 1% of penicillin-streptomycin

extract_protocol:
ARN extraction was performed using RNeasy mini kit (Qiagen) according to the manufacturer’s protocol
RNA libraries for RNAseq were prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit following manufacturer’s protocol

treatment_protocol: 1 x 105 cells (pDC or DC2) were plated in V-bottom 96-well plates in presence of medium alone (RPMI 1640 medium with GlutaMAX, 10% FBS, 1% of MEM nonessential amino acid, 1% of sodium pyruvate, and 1% of penicillin-streptomycin), the TLR7/TLR8 agonist R848 (Resiquimod), SARS-CoV-2 strain 220/95, Delta or Omicron BA.1, at 100 and 400 genome copies per cell

value: PBMC

value: SARS-CoV-2 Delta


title: DC2,BA.1,replicate4

description:
Library name: Sample 36
Column name in raw_counts.tsv : 20_DC2_BA1

value: SARS-CoV-2 Omicron BA.11


title: DC2,NI,replicate5

description:
Library name: Sample 37
Column name in raw_counts.tsv : 21_DC2_NI

value: Unstimulated


title: DC2,BA.1,replicate5

description:
Library name: Sample 40
Column name in raw_counts.tsv : 24_DC2_BA1