title: MM130504

description:
Library name: MM130504
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: MM130508

status: Public on Mar 16 2026

type: SRA

city: New Orleans

first: Hong-Wen

last: Deng

state: LA

country: USA

institute: Tulane University

description:
Library name: MM130508
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

library_source: genomic

data_processing:
Sequencing reads were quality-filtered and aligned to the human reference genome using BSMAP. Methylation levels at CpG sites were calculated as the ratio of methylated reads to total reads covering each site. CpG sites overlapping known SNPs were removed. Rank-based inverse normal transformation was applied for normalization. Reads with >10% unknown bases or >10% of bases with quality scores <20 were further excluded to obtain high-quality data. The cleaned reads were aligned to the GRCh37/hg19 human reference genome using BSMAP, then converted to GRCh38/hg38 using the UCSC LiftOver tool (https://genome.ucsc.edu/cgi-bin/hgLiftOver).
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data files contain tab-delimited matrices of CpG-level DNA methylation beta values. Rows represent CpG loci with genomic coordinates, and columns represent individual samples. Chromosome-specific methylation matrices are provided in compressed format.

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
Genomic DNA was extracted from purified peripheral blood monocytes using the QIAamp DNA Mini Kit (Qiagen) following the manufacturer’s protocol. DNA concentration and purity were evaluated using NanoDrop spectrophotometry and agarose gel electrophoresis.
Monocytes were isolated from peripheral blood mononuclear cells using negative selection. Genomic DNA was extracted and fragmented. Libraries were prepared following bisulfite conversion using the EZ DNA Methylation-Gold kit and sequenced on the Illumina HiSeq 4000 platform.

tag: tissue

value: peripheral blood

tag: cell type

value: monocytes

tag: population

value: African American

tag: Sex

value: male

tag: age

tag: bmi

tag: smoke

tag: alcohol drinking


title: MM130503

description:
Library name: MM130503
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: European American


title: MM130506

description:
Library name: MM130506
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: GWAT_female_50TBT_replicate.2

city: Santa Cruz

first: Carlos

last: Diaz-Castillo

state: California

address: 448 Physical Sciences Building

institute: University of California Santa Cruz

description: Library name: G_F_50TBT_649

library_source: transcriptomic

data_processing:
We uploaded the FASTQ files obtained from the UCI Genomics High Throughput Facility to the Galaxy Platform website (usegalaxy.org). We concatenated FASTQ files for each sample and used FastQC (version 0.12) to assess read quality, multiQC (version 1.27) to generate multi-sample reports, Cutadapt (version 5.0) to remove adapter sequences, RNA Star (version 2.7) to map reads to mouse genes, featureCounts (version 2.0) to count reads, and Intersect (version 1.0) to determine the overlap of genes and isochores in the mouse genome. We used the annotation file “mm39.ncbiRefSeq.gtf.gz” with primary gene transcript annotation for the June 2020 GRCm39/mm39 mouse genome assembly from the UCSC Genome Browser (https://hgdownload.soe.ucsc.edu/downloads.html#mouse) to map reads to splice junctions. After completing all Galaxy Platform operations, we downloaded a table with RNA-seq gene-wise read counts for each gWAT and liver sample, which is included in the processed data file in this submission.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: gonadal white adipose tissue (GWAT)

growth_protocol: We purchased 160 female and 80 male C57BL/6J mice from Jackson Laboratory (strain #000664). At 5 weeks old, we randomly assorted females in 5 equal-size groups. We exposed 5-week-old female mice in each group to the following combinations of treated drinking water and diet for 3.5 weeks: 0.1% DMSO in water and control diet (CD; Envigo Teklad Diets TD.140148) [DMSO group, negative control], 5 nM tributyltin (TBT) and 0.1% DMSO in water and CD [5TBT group], 50 nM TBT and 0.1% DMSO in water and CD [50TBT group], 10 µg/L sodium meta(arsenite) (inorganic arsenic, iAs) and 0.1% DMSO in water and CD [IAS group], and 0.1% DMSO in water and Total Western Diet (TWD; Envigo Teklad Diets TD.110919) [TWD group]. After 3.5 weeks of exposure at 8 weeks of age, we mated exposed female mice with unexposed same-age male mice for a week to produce the first generation (F1) offspring. At 8-11 days, we toeclipped F1 mice. At 3 weeks, we weaned and selected 10 F1 mice per sex and exposure group. We housed mice of the same sex and exposure group together. We fed F1 mice CD between 3-7 weeks and TWD between 7-end. At 12 weeks, we fasted mice for 12 hours, euthanized them with isoflurane, and harvested gonadal white adipose tissue (gWAT) and liver.

extract_protocol:
We extracted RNA from F1 gWAT and liver using a VWR® Micro Homogenizer (catalog number #10032-328) and Qiagen RNeasy Plus kits (catalog number #74034), following the manufacturer’s protocols.
We submitted 100 RNA samples (2 sexes x 2 tissues x 5 experimental groups x 5 replicates per group) to the University of California, Irvine (UCI) Genomics High Throughput Facility for sequencing using Illumina TruSeq Stranded mRNA kits and an Illumina NovaSeq 6000 sequencer. Libraries obtained from were sequenced up to three times to yield approximately 30 million 150-bp paired reads per sample.

value: gonadal white adipose tissue (GWAT)

tag: strain

tag: developmental stage

value: adult

value: female

tag: treatment

tag: time

value: 12 weeks old

tag: animal id


title: MM130493

description:
Library name: MM130493
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: SP014 CT26 KO_rep2 TCR library

city: Memphis

first: Douglas

middle: R

last: Green

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St. Jude Children's Research Hospital

description:
Library name: SP014_KO_rep2_TCR
CT26 tumor infiltrating T cells from BALB/c mice; genotype DPM1_KO; pool2 (hashtags 4,5,8). BioProject PRJNA1435810; BioSample SAMN56455357. Library type: TCR.

data_processing:
FASTQ files were processed using Cell Ranger v7.2.0. Per pool, cellranger multi was run with mm10 (refdata-gex-mm10-2020-A) for gene expression and the 10x VDJ reference (refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0) for TCR. Outputs include filtered feature-barcode matrices (MEX) and VDJ contig annotations and clonotypes. Pools were aggregated using cellranger aggr (aggregation.csv provided).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Processed data are provided as 10x MEX feature-barcode count matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) for each pool. features.tsv.gz includes Gene Expression and Antibody Capture features. Feature barcode definitions are provided as feature_reference.csv and auto_gen_citeseq_features.csv. TCR results are provided as filtered_contig_annotations.csv and clonotypes.csv for each pool. Files are packaged in SP014_GEO_processed.tar.gz.
Supplementary files format and content: SP014_GEO_processed.tar.gz
Library strategy: TCR-Seq

source_name: tumor

growth_protocol: BALB/c mice (5 weeks old) were implanted with CT26 colorectal tumor cells and tumors were harvested for immune profiling.

extract_protocol:
Tumors were dissociated to single cell suspensions. Tumor infiltrating T cells were enriched and sorted by flow cytometry (CD3+ TCRB+ CD4/CD8+) and pooled by genotype.
Single cell libraries were prepared using 10x Genomics Chromium Next GEM Single Cell 5' v2 kits for gene expression and feature barcode hashtags. Paired TCR V(D)J libraries were prepared using the 10x Genomics V(D)J enrichment workflow. Libraries were sequenced as dual-indexed paired-end runs on Illumina NovaSeq 6000.

treatment_protocol: Not applicable.

value: tumor

tag: cell line

value: tumor infiltrating T cells

tag: genotype

tag: batch


title: MM130498

description:
Library name: MM130498
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: SP014 CT26 WT_rep1 HTO library

description:
Library name: SP014_WT_rep1_HTO
CT26 tumor infiltrating T cells from BALB/c mice; genotype WT; pool1 (hashtags 1-4). BioProject PRJNA1435810; BioSample SAMN56455354. Library type: HTO.

data_processing:
FASTQ files were processed using Cell Ranger v7.2.0. Per pool, cellranger multi was run with mm10 (refdata-gex-mm10-2020-A) for gene expression and the 10x VDJ reference (refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0) for TCR. Outputs include filtered feature-barcode matrices (MEX) and VDJ contig annotations and clonotypes. Pools were aggregated using cellranger aggr (aggregation.csv provided).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Processed data are provided as 10x MEX feature-barcode count matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) for each pool. features.tsv.gz includes Gene Expression and Antibody Capture features. Feature barcode definitions are provided as feature_reference.csv and auto_gen_citeseq_features.csv. TCR results are provided as filtered_contig_annotations.csv and clonotypes.csv for each pool. Files are packaged in SP014_GEO_processed.tar.gz.
Supplementary files format and content: SP014_GEO_processed.tar.gz
Library strategy: CITE-seq

value: WT


title: Primary lung tumor, 8wk timepoint, mouse 27563

city: Houston

first: Fredrik

middle: Ivar

last: Thege

state: Texas

address: 6565 MD Anderson Blvd

department: Translational Molecular Pathology

institute: UT MD Anderson Cancer Center

description: Library name: B10_27563_Lu_8wk_N702_S502_S10

data_processing:
Guide sequences from the Onco1 library were matched to FASTQ files to generate raw counts.
Supplementary files format and content: csv-file, table raw guide counts
Library strategy: CRISPR Screen

source_name: Lung

extract_protocol:
Flash frozen tissues or cell pellets were homogenized in ATL buffer and genomic DNA was isolated using the Qiagen DNeasy blood and tissue kit. Plasmid DNA was isolated using Qiagen EndoFree MaxiPrep kit.
A region of genomic or plasmid DNA containing the guide sequences was amplified using direct PCR (NEBNext Ultra II Q5) with dual-indexed primers. Libraries were sequenced using 75 cycle single-end sequencing.

value: Lung

value: Whole lung tissue

value: PPKS


title: bulkRNA-seq, HF187438

city: Los Angeles

first: Frederique

last: Ruf-Zamojski

state: CA

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

description: Library name: HF187438_bulkRNA

data_processing:
Bulk RNA-seq: Pooled libraries were sequenced on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) to a target depth of 35 million read pairs (70 million paired-end reads) per sample using a paired-end 100 base pair run configuration. In order to capture the 8-base UMIs, libraries were sequenced using 16 cycles for the i7 index read and 8 cycles for the i5 index read. Reads were demultiplexed with bcl2fastq2 (v2.20.0) using options --use-bases-mask Y*,I8Y*,I*,Y* --mask-short-adapter-reads 0 --minimum-trimmed-read-length 0 (Illumina, San Diego, CA, USA), and UMIs in the index FASTQ files were attached to the read FASTQ files. Adapters were trimmed with cutadapt (v1.18), and trimmed reads shorter than 20 base pairs were removed 61 . FastQC (v0.11.8) was used to generate pre-alignment QC metrics. STAR (v2.7.0d) was used to index and align reads to release 96 of the Ensembl hg38_gencode v30 genome and gene annotation . Default parameters were used for STAR’s genomeGenerate run mode. RSEM (v1.3.1) was used to quantify transcriptome-coordinate-sorted alignments using a forward probability of 0.5 to indicate a non-strand-specific protocol.
Assembly: GRCh38
Supplementary files format and content: bam

source_name: pituitary

extract_protocol:
Bulk RNA-seq: The tissues were disrupted in Agencourt RNAdvance tissue lysis buffer (Beckman Coulter, Brea, CA) using a tissue ruptor (Omni International, Kennesaw, GA, # 19-040E). Total RNA was extracted in a Biomek FXp automation workstation according to the manufacturer’s instructions for tissue-specific extraction.
Bulk RNA-seq: Universal Plus mRNA-Seq with NuQuant Human Globin AnyDeplete kit from Tecan (# 0521-A01) was used for the generation of RNA-seq libraries derived from poly(A)-selected RNA according to the manufacturer’s instructions. Universal Plus mRNA-Seq libraries contain dual (i7 and i5) 8 bp barcodes and an 8 bp unique molecular identifier (UMI), which enable deep multiplexing of NGS sequencing samples and accurate quantification of PCR duplication levels. Approximately 300ng of total RNA was used to generate the libraries. The Universal Plus mRNA-Seq workflow consists of poly(A) RNA selection, RNA fragmentation, and double-stranded cDNA generation using a mixture of random and oligo(dT) priming, end repair to generate blunt ends, adaptor ligation, strand selection, AnyDeplete workflow to remove unwanted ribosomal and globin transcripts, and PCR amplification to enrich final library species. All library preparations were performed using a Biomek i7 laboratory automation system (Beckman Coulter). Normalized pooled libraries were sequenced on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) to a target depth of 35 million read pairs (70 million paired-end reads) per sample using a paired-end 100 base pair run configuration. To capture the 8-base UMIs, libraries were sequenced using 16 cycles for the i7 index read and 8 cycles for the i5 index read.

value: pituitary


title: SP014 CT26 KO_rep1 HTO library

description:
Library name: SP014_KO_rep1_HTO
CT26 tumor infiltrating T cells from BALB/c mice; genotype DPM1_KO; pool1 (hashtags 1-3). BioProject PRJNA1435810; BioSample SAMN56455356. Library type: HTO.


title: bulkRNA-seq, HF187441

description: Library name: HF187441_bulkRNA


title: D30_PIMQ_lowH2AZ_Rep2

city: New York

first: Luis

middle: F

last: Soto-Ugaldi

state: NY

institute: The Rockefeller University

description:
Library name: Sample 32
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
D30_IMQ_rep2_H2AZ_MERGE_sorted_RPKM.bw

data_processing:
Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Bigwig

source_name: Skin

extract_protocol:
Using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed
Library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000.

value: Skin

value: Epidermal Stem Cell

value: wildtype

value: 2-3 postnatal day 60  murine backskin was treated with Imiquimod for 6 consecutive days


title: bulkRNA-seq, HF5077

description: Library name: HF5077_bulkRNA


title: MM130490

description:
Library name: MM130490
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: peripheral blood

value: monocytes

value: male


title: Il1 Spn 21dpi

city: Manhattan

first: Chaitra

last: Sreenivasaiah

address: 227 E 30th St

department: Applied Bioinformatics Laboratory

institute: NYU Langone Health

description: Library name: TOI 74

data_processing:
Basecalls performed using CASAVA, RNA-Seq reads were mapped to mm10 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools, RNA-Seq read counting performed using HT-seq
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4, Statistics and plotting performed in R v3.3.0
Assembly: mm10
Supplementary files format and content: count tables(txt)

source_name: nasal lavages

extract_protocol:
RNA was extracted using the Rneasy mini kit (Qiagen).
Automated stranded RNA-seq library prep, polyA selection

value: nasal lavages

value: Spn-infected


title: bulkRNA-seq, HF5445

description: Library name: HF5445_bulkRNA


title: SP014 CT26 WT_rep2 GEX library

description:
Library name: SP014_WT_rep2_GEX
CT26 tumor infiltrating T cells from BALB/c mice; genotype WT; pool2 (hashtags 5-8). BioProject PRJNA1435810; BioSample SAMN56455355. Library type: GEX.

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed using Cell Ranger v7.2.0. Per pool, cellranger multi was run with mm10 (refdata-gex-mm10-2020-A) for gene expression and the 10x VDJ reference (refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0) for TCR. Outputs include filtered feature-barcode matrices (MEX) and VDJ contig annotations and clonotypes. Pools were aggregated using cellranger aggr (aggregation.csv provided).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Processed data are provided as 10x MEX feature-barcode count matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) for each pool. features.tsv.gz includes Gene Expression and Antibody Capture features. Feature barcode definitions are provided as feature_reference.csv and auto_gen_citeseq_features.csv. TCR results are provided as filtered_contig_annotations.csv and clonotypes.csv for each pool. Files are packaged in SP014_GEO_processed.tar.gz.
Supplementary files format and content: SP014_GEO_processed.tar.gz


title: D30_PIMQ_highH2AZ_Rep2

description:
Library name: Sample 31
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
D30_IMQ_rep2_H2AZ_MERGE_sorted_RPKM.bw


title: bulkRNA-seq, 4HF-6302-3

description: Library name: 4HF-6302-3_bulkRNA


title: MM130488

description:
Library name: MM130488
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

value: African American


title: MM130494

description:
Library name: MM130494
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: SP014 CT26 KO_rep2 GEX library

description:
Library name: SP014_KO_rep2_GEX
CT26 tumor infiltrating T cells from BALB/c mice; genotype DPM1_KO; pool2 (hashtags 4,5,8). BioProject PRJNA1435810; BioSample SAMN56455357. Library type: GEX.

value: tumor


title: SP014 CT26 WT_rep2 TCR library

description:
Library name: SP014_WT_rep2_TCR
CT26 tumor infiltrating T cells from BALB/c mice; genotype WT; pool2 (hashtags 5-8). BioProject PRJNA1435810; BioSample SAMN56455355. Library type: TCR.

value: tumor infiltrating T cells


title: SP014 CT26 WT_rep2 HTO library

description:
Library name: SP014_WT_rep2_HTO
CT26 tumor infiltrating T cells from BALB/c mice; genotype WT; pool2 (hashtags 5-8). BioProject PRJNA1435810; BioSample SAMN56455355. Library type: HTO.

value: WT


title: MM130487

description:
Library name: MM130487
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: MM130486

description:
Library name: MM130486
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: Il17 Spn 21dpi 4

description: Library name: TOI 71


title: MM130496

description:
Library name: MM130496
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: D30_PIMQ_highH2AZ_Rep1

description:
Library name: Sample 29
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
D30_IMQ_rep1_H2AZ_MERGE_sorted_RPKM.bw


title: SP014 CT26 WT_rep1 TCR library

description:
Library name: SP014_WT_rep1_TCR
CT26 tumor infiltrating T cells from BALB/c mice; genotype WT; pool1 (hashtags 1-4). BioProject PRJNA1435810; BioSample SAMN56455354. Library type: TCR.


title: bulkRNA-seq, 1HM-6058-3

description: Library name: 1HM-6058-3_bulkRNA


title: MM130481

description:
Library name: MM130481
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: Primary lung tumor, 6d timepoint, mouse 27564

description: Library name: B1_27564_Lu_6d_N701_S501_S1

value: Lung


title: MM130484

description:
Library name: MM130484
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: Il17 Spn 21dpi 3

description: Library name: TOI 70


title: snMultiome, PA_004_M, ATAC

description: Library name: PA_004_M_ATAC

library_source: genomic single cell

data_processing:
snMultiome: sn multiome data were processed using the Cell Ranger Arc pipeline 1.0.0. Samples were aligned to the CellRanger GRCh38 reference transcriptome, introns included.
Assembly: GRCh38
Supplementary files format and content: UMI count matrices in Hierarchical Data Format HDF5 for cell barcodes

extract_protocol:
snMultiome: Briefly, and all on ice, RNAse inhibitor (NEB MO314L) was added to the homogenization buffer (0.32 M sucrose, 1 mM EDTA, 10 mM Tris-HCl, pH 7.4, 5mM CaCl2, 3mM Mg(Ac)2, 0.1% IGEPAL CA-630), 50% OptiPrep (Stock is 60% Media from Sigma; cat# D1556), 35% OptiPrep and 30% OptiPrep right before isolation. Each pituitary was homogenized in a dounce glass homogenizer (1ml, VWR cat# 71000-514), and the homogenate filtered through a 40 mm cell strainer. An equal volume of 50% OptiPrep was added, and the gradient centrifuged (SW41 rotor at 9200rpm; 4C; 25min). Nuclei were collected from the interphase, washed, resuspended in 1X nuclei buffer for sn multiome (10X Genomics).
snMultiome: sn Multiome (10x Genomics, Pleasanton, CA) was performed  following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guidelines. Nuclei were filtered and counted on a Nexcelom instrument. The amount of nuclei loaded on the chip was determined based on the 10X Genomics protocol loading table. The 10X chip (Chromium Single Cell Chip kit J  PN-200264) was loaded to target 2,000-10,000 nuclei final. After transposition, linear amplification was performed in the emulsion and cDNA was amplified before the RNA and ATAC library constructions were performed following the Chromium multiome protocol. The library was tagged with an index for multiplexing (Chromium i7 Sample Index Plate N Set A for ATAC PN-3000427; Chromium i7 Sample Dual Index Plate TT Set A for ATAC PN-3000431). Quality control and quantification of the amplified cDNA were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit). Sequencing was carried out at the NYGC on Illumina Novaseq using 98+26 paired-end reads.


title: D30_Naive_lowH2AZ_Rep2

description:
Library name: Sample 28
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
D30_Ctrl_rep2_H2AZ_MERGE_sorted_RPKM.bw

value: non-treated


title: MM130495

description:
Library name: MM130495
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: Primary lung tumor, 4wk timepoint, mouse 29429

description: Library name: B9_29429_Lu_4wk_N702_S501_S9

value: Whole lung tissue

value: PPKS


title: Primary lung tumor, 4wk timepoint, mouse 28673

description: Library name: B5_28673_Lu_4wk_N701_S505_S5


title: D30_Naive_highH2AZ_Rep2

description:
Library name: Sample 27
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
D30_Ctrl_rep2_H2AZ_MERGE_sorted_RPKM.bw

value: Skin


title: Primary lung tumor, 4wk timepoint, mouse 29428

description: Library name: B6_29428_Lu_4wk_N701_S506_S6


title: D30_PIMQ_lowH2AZ_Rep1

description:
Library name: Sample 30
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
D30_IMQ_rep1_H2AZ_MERGE_sorted_RPKM.bw

value: Epidermal Stem Cell


title: bulkRNA-seq, 3HF-5670-3

description: Library name: 3HF-5670-3_bulkRNA

value: pituitary


title: Primary lung tumor, 4wk timepoint, mouse 28671

description: Library name: B7_28671_Lu_4wk_N701_S507_S7


title: SP014 CT26 WT_rep1 GEX library

description:
Library name: SP014_WT_rep1_GEX
CT26 tumor infiltrating T cells from BALB/c mice; genotype WT; pool1 (hashtags 1-4). BioProject PRJNA1435810; BioSample SAMN56455354. Library type: GEX.


title: MM130492

description:
Library name: MM130492
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: European American


title: D30_Naive_lowH2AZ_Rep1

description:
Library name: Sample 26
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
D30_Ctrl_rep1_H2AZ_MERGE_sorted_RPKM.bw

value: wildtype


title: Il17 Spn 21dpi 6

description: Library name: TOI 73


title: snMultiome, PA_004_M, GEX

description: Library name: PA_004_M_GEX


title: bulkRNA-seq, HF1706

description: Library name: HF1706_bulkRNA


title: bulkRNA-seq, HF187440

description: Library name: HF187440_bulkRNA


title: snMultiome, PA_003_F, ATAC

description: Library name: PA_003_F_ATAC


title: MM130476

description:
Library name: MM130476
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: peripheral blood

value: monocytes


title: Il17 Spn 7dpi 5

description: Library name: TOI 66

value: nasal lavages


title: bulkRNA-seq, HF1499

description: Library name: HF1499_bulkRNA


title: Il17 Spn 21dpi 5

description: Library name: TOI 72

value: Spn-infected


title: MM130477

description:
Library name: MM130477
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: male


title: D6_IMQ_highH2AZ_Rep2

description:
Library name: Sample 23
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
D6_IMQ_rep2_H2AZ_MERGE_sorted_RPKM.bw

value: 2-3 postnatal day 60  murine backskin was treated with Imiquimod for 6 consecutive days


title: D6_IMQ_lowH2AZ_Rep2

description:
Library name: Sample 24
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
D6_IMQ_rep2_H2AZ_MERGE_sorted_RPKM.bw


title: Il17 Spn 7dpi 6

description: Library name: TOI 67


title: D30_Naive_highH2AZ_Rep1

description:
Library name: Sample 25
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
D30_Ctrl_rep1_H2AZ_MERGE_sorted_RPKM.bw


title: snMultiome, PA_002_M, ATAC

description: Library name: PA_002_M_ATAC


title: snMultiome, PA_003_F, GEX

description: Library name: PA_003_F_GEX


title: bulkRNA-seq, 2HM-1547-3

description: Library name: 2HM-1547-3_bulkRNA


title: MM130478

description:
Library name: MM130478
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: D6_IMQ_highH2AZ_Rep1

description:
Library name: Sample 21
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
D6_IMQ_rep1_H2AZ_MERGE_sorted_RPKM.bw


title: Il17 Spn 7dpi 4

description: Library name: TOI 65


title: MM130475

description:
Library name: MM130475
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

value: African American


title: snMultiome, PA_002_M, GEX

description: Library name: PA_002_M_GEX


title: MM130472

description:
Library name: MM130472
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130480

description:
Library name: MM130480
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: Il17 Spn 21dpi 2

description: Library name: TOI 69


title: Il17 Spn 7dpi 3

description: Library name: TOI 64


title: D6_Naive_lowH2AZ_Rep1

description:
Library name: Sample 18
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
D6_Ctrl_rep1_H2AZ_MERGE_sorted_RPKM.bw


title: Il17 Spn 21dpi 1

description: Library name: TOI 68


title: Il17 Spn 7dpi 1

description: Library name: TOI 62


title: D6_IMQ_lowH2AZ_Rep1

description:
Library name: Sample 22
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
D6_IMQ_rep1_H2AZ_MERGE_sorted_RPKM.bw


title: snMultiome, PA_001_M, ATAC

description: Library name: PA_001_M_ATAC


title: Il17 Spn 7dpi 2

description: Library name: TOI 63


title: snMultiome, PA_001_M, GEX

description: Library name: PA_001_M_GEX


title: PGF-TCR_S9

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

description: Library name: PGF-TCR_S9

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Paired-end reads were mapped to the hg19 genome with cellranger for gene-level read counts
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting,and csv files of TCR clonality were performed using the cellranger analysis pipeline.
Data normalization, dimension reduction, and differential expression analysis were performed using R and the Seurat R package. Cells were clustered with PhenoGraph.
T cell receptor and B cell receptor VDJ analysis: Cellranger. VDJ of T cells and B cells were infered with cellranger vdj pipeline to get TCR and BCR contig annotations.
Assembly: hg38
Supplementary files format and content: comma-separated files and matrix files
Library strategy: TCR-Seq

molecule: polyA RNA

source_name: Human bone marrow

extract_protocol:
BMMNCs were isolated from each bone marrow aspirate sample by density centrifugation using LSM Lymphocyte Separation Medium.
Libraries of gene expression of BMMNCs and TCR/BCR sequencing for patients were generated using Chromium Single Cell 5' Solution Kit from 10XGenomics v1 and v1.1.

treatment_protocol: Patients with hematologic malignancies were treated with allogenic stem cell transplantation. Patients were evaluated periotically in the clinic, and evaluate if they achieved good graft function or poor graft function by blood counts and bone marrow aspirate/biopsy.

value: Human bone marrow

value: BMMNCs

value: Allogenic stem cell transplantation


title: MM130471

description:
Library name: MM130471
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: D6_Naive_lowH2AZ_Rep2

description:
Library name: Sample 20
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
D6_Ctrl_rep2_H2AZ_MERGE_sorted_RPKM.bw

value: non-treated


title: Y1_PIMQ_highH3K27ac_Rep2

description:
Library name: Sample 15
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Y1_IMQ_rep2_H3K27ac_MERGE_sorted_RPKM.bw


title: MM130468

description:
Library name: MM130468
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: MM130466

description:
Library name: MM130466
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: Il17 Mock 21dpi 5

description: Library name: TOI 60

value: PBS


title: MM130469

description:
Library name: MM130469
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: PGF-TCR_S6

description: Library name: PGF-TCR_S6


title: Il17 Mock 21dpi 2

description: Library name: TOI 57


title: MM130470

description:
Library name: MM130470
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: PGF-TCR_S4

description: Library name: PGF-TCR_S4


title: PGF-TCR_S3

description: Library name: PGF-TCR_S3


title: PGF-TCR_S7

description: Library name: PGF-TCR_S7


title: Il17 Mock 7dpi 6

description: Library name: TOI 55


title: Y1_PIMQ_highH3K27ac_Rep1

description:
Library name: Sample 13
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Y1_IMQ_rep1_H3K27ac_MERGE_sorted_RPKM.bw

value: Skin


title: PGF-TCR_S8

description: Library name: PGF-TCR_S8


title: MM130462

description:
Library name: MM130462
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: D6_Naive_highH2AZ_Rep1

description:
Library name: Sample 17
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
D6_Ctrl_rep1_H2AZ_MERGE_sorted_RPKM.bw

value: Epidermal Stem Cell


title: Il17 Mock 21dpi 6

description: Library name: TOI 61


title: Il17 Mock 21dpi 4

description: Library name: TOI 59


title: Y1_PIMQ_lowH3K27ac_Rep2

description:
Library name: Sample 16
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Y1_IMQ_rep2_H3K27ac_MERGE_sorted_RPKM.bw


title: MM130460

description:
Library name: MM130460
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: MM130467

description:
Library name: MM130467
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: Il17 Mock 21dpi 3

description: Library name: TOI 58


title: MM130459

description:
Library name: MM130459
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: Il17 Mock 7dpi 4

description: Library name: TOI 53


title: Y1_Naive_highH3K27ac_Rep1

description:
Library name: Sample 9
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Y1_Ctrl_rep1_H3K27ac_MERGE_sorted_RPKM.bw


title: PGF-TCR_S5

description: Library name: PGF-TCR_S5


title: Il17 Mock 21dpi 1

description: Library name: TOI 56


title: Il17 Mock 7dpi 2

description: Library name: TOI 51


title: Il17 Mock 7dpi 1

description: Library name: TOI 50


title: PGF-BCR_S8

description: Library name: PGF-BCR_S8

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Paired-end reads were mapped to the hg19 genome with cellranger for gene-level read counts
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting,and csv files of TCR clonality were performed using the cellranger analysis pipeline.
Data normalization, dimension reduction, and differential expression analysis were performed using R and the Seurat R package. Cells were clustered with PhenoGraph.
T cell receptor and B cell receptor VDJ analysis: Cellranger. VDJ of T cells and B cells were infered with cellranger vdj pipeline to get TCR and BCR contig annotations.
Assembly: hg38
Supplementary files format and content: comma-separated files and matrix files


title: PGF-TCR_S2

description: Library name: PGF-TCR_S2