title: HOB cultured on HA coating metal day21_3

description: Library name: N3_4


title: MM130591

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: MM130591
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: MM130617

description:
Library name: MM130617
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: MM130620

description:
Library name: MM130620
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: HOB cultured on HA coating metal day0_1

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

country: Japan

institute: Hokkaido University

description: Library name: N0_2

library_source: transcriptomic

data_processing:
The RNA-seq libraries (4 Gb per sample, 150 bp × 2 paired-end, 3 samples per condition) were sequenced on an Illumina NovaSeq 6000 platform and then trimmed for quality. The resulting fastq files were aligned to the reference genome using HISAT2. Reads were counted (FeatureCount v2.06) and the number of fragments per 1 million bases of the transcription sequence of each gene was calculated based on the gene and read length. Significance was set up using the Benjamini-Hochberg approach as p <0.05 for false discovery rate (FDR) . The gene ontology and pathway enrichment analyses and GSEA were performed on the differential expression data using NovoMagic online tools (Novogene, Singapore).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

growth_protocol: Human osteoblasts were cultrured using basal medium including 10% growth supplement and 1% penicillin/streptomycin.

extract_protocol:
Osteoblasts RNA was purified using TRIzol Reagent and RNA extraction kit (NucleoSpin®) according to the manufacturere's protocol
The libraries were generated from high-quality RNA (1 μg) of each sample using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA) and then subjected for sequencing (Illumina NovaSeq 6000, Illumina, Inc. San Diego, CA, USA). The sequence data of 150 bp × 2 paired ends of 6G bases/sample (3 samples for each condition) were trimmed and mapped via HISAT2 v2.0.5. Reads were counted (FeatureCount v1.55.0-p3) and the number of fragments per 1 million bases of the transcription sequence of each gene was calculated based on the gene and read length. Significance was set up using the Benjamini-Hochberg approach as p <0.05 for false discovery rate (FDR) . The gene ontology and pathway enrichment analyses and GSEA were performed on the differential expression data using NovoMagic online tools (Novogene, Singapore).

treatment_protocol: Osteoblasts were seeded onto circular plates fabricated from Ti–6Al–4V alloy and onto plates coated with nano-HA. The osteoblasts were then cultured in growth medium, and were harvested and evaluated on day0  and 21.

value: Osteoblast


title: HOB cultured on HA coating metal day0_2

description: Library name: N0_3


title: GWAT_male_IAS_replicate.5

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_M_IAS_818

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

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

tag: treatment

value: IAS

tag: time

value: 12 weeks old

tag: animal id


title: MM130610

description:
Library name: MM130610
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: Colo_biol_rep_2

city: Burjassot, Valencia

first: Irene

last: Moreno Sanguino

address: Cam. del Cementerio, 1

department: Plant Biology

country: Spain

institute: Univeristy of Valencia, Faculty of Pharmacy

description: Library name: Colo_R2

data_processing:
nf-core rnaseq pipeline doi:10.5281/zenodo.1400710
Biological quality assessment and significant differential expression were performed in RStudio with the DESeq2 package (Love et al., 2014).
Assembly: ARAPORT 11
Supplementary files format and content: quant.genes_*.sf file includes raw counts and TPM for each sample

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Seedlings

extract_protocol:
Total RNA was extracted using the Mini Total RNA Kit (Plants)® (IBI Scientific) from 12 das seedlings of Col-0 and the sORF1511-ox line #7, each condition comprising two biological replicates, with each replicate consisting of five pooled seedlings. 200 ng of RNA per sample were used.
Library construction mRNA stranded (polyA enrichment) Illumina

value: Seedlings

tag: genotype

value: WT


title: MM130618

description:
Library name: MM130618
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: MM130611

description:
Library name: MM130611
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: GWAT_male_TWD_replicate.2

description: Library name: G_M_TWD_683

treatment_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.

value: TWD


title: HOB cultured on no coating metal day0_1

description: Library name: C0_1


title: MM130614

description:
Library name: MM130614
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: GWAT_male_IAS_replicate.4

description: Library name: G_M_IAS_804


title: GWAT_male_TWD_replicate.1

description: Library name: G_M_TWD_621


title: For Patient p42, p6110, p6109, p6107, p60, p18,p46,p43

city: Philladephia

first: Hairu

last: Yang

address: Philadelphia, PA 19104

department: Division of Gastroenterology and Hepatology

institute: University of Pennsylvania Perelman School of Medicine

description: Library name: HTS_S082

data_processing:
Raw sequencing data were processed using the Cell Ranger software suite (10x Genomics) for sample demultiplexing, alignment to the human reference genome (GRCh38, Ensembl: http://useast.ensembl.org/Homo_sapiens), and quantification of unique molecular identifiers (UMIs). Feature barcoding count matrices, including antibody-derived tags (ADTs) and hashtag oligonucleotides (HTOs), were generated using the 10x Genomics Cloud Analysis service. Sample demultiplexing based on HTOs was performed using the HTODemux function implemented in Seurat v5.0.1. Quality control was performed to exclude low-quality cells and technical artifacts. Epithelial cells with fewer than 200 detected genes or more than 20% mitochondrial gene content were removed, while a 15% mitochondrial gene content threshold was applied to non-epithelial cell types. Doublets were identified and excluded using the scDblFinder package73. RNA expression data were normalized and batch-corrected using the Harmony package74.
Assembly: human reference genome (GRCh38, Ensembl: http://useast.ensembl.org/Homo_sapiens
Supplementary files format and content: LynchMAIT.rds
Library strategy: CITE-seq

source_name: colon

extract_protocol:
Single-cell suspensions (~200,000 cells per sample) were resuspended in staining buffer composed of PBS with 2% bovine serum albumin (BSA, Sigma, Cat# P7030 ). Samples were centrifuged at 300–350 × g for 5 minutes at 4 °C, and the supernatant was carefully discarded. Cell pellets were then resuspended in 12.5 μL staining buffer supplemented with Fc receptor blocking reagent TruStain FcX™ (BioLegend, Cat# 422302) and incubated on ice for 10 minutes. Following Fc blocking, 12.5 μL of a 2X barcoded antibody cocktail was added directly to each tube. This cocktail contained a panel of oligonucleotide-conjugated antibodies for CITE-seq and a unique hashing antibody for each sample (Table S9). Cells were gently mixed and incubated on ice for 30 minutes. Post-incubation, cells were washed three times in staining buffer and a final time in staining buffer lacking BSA. Cells were filtered through a 70 μm strainer (Fisher Scientific, Cat# 22-363-548) to remove aggregates, then counted. Equal numbers of cells from each sample were pooled, centrifuged, and resuspended in PBS for subsequent loading onto the 10x Genomics Chromium Controller
The pooled cells were subjected to droplet-based single-cell encapsulation and library preparation using the Chromium Single Cell 3’ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions. Feature barcoding technology was used to simultaneously capture gene expression (GEX), antibody-derived tags (ADT), and hashtag oligos (HTO). Reverse transcription, cDNA amplification, and library construction for gene expression, ADT, and HTO components were performed as per the 10x Genomics user guide.

value: colon


title: BLEO-IPF Nintedanib Sample 4016716695

status: Public on Mar 18 2026

city: Hørsholm

first: Henrik

last: Hansen

address: Hørsholm Kongevej 11

department: Histology & NGS

country: Denmark

institute: Gubra

description: Library name: 4016716695

data_processing:
All downstream analyses were performed using R version 3.6.0.
Assembly: Reads were aligned to the GRCm38 release 96 Ensembl Mus musculus genome using STAR version 2.7.0f.
Supplementary files format and content: comma-delimited text file contains raw counts for each Sample.

source_name: Lung

extract_protocol:
The inferior lobe samples were homogenised in lysis buffer, and RNA was purified using NucleoSpin® RNA binding strips (cat. no. 740698.5, Macherey-Nagel, Dueren, Germany). RNA purity and concentration were measured using a NanoDrop 2000.
cDNA libraries were prepared using NEBNext® Ultra II Directional RNA library prep Kit for Illumina® (cat. no. E7760L, New England Biolabs, Ipswich, MA). cDNA libraries were sequenced to a depth of approximately 15 million reads per sample (single-end, 75 bp reads) on a NextSeq 500 System (Illumina, San Diego, CA) using the NextSeq 500/550 High Output Kit version 2.5 (cat. no. 20024906, Illumina).

value: Lung

value: BLEO-IPF Nintedanib


title: MM130605

description:
Library name: MM130605
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: MM130582

description:
Library name: MM130582
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: HOB cultured on no coating metal day21_3

description: Library name: C3_4


title: GWAT_male_IAS_replicate.3

description: Library name: G_M_IAS_779


title: HOB cultured on no coating metal day21_1

description: Library name: C3_2


title: MM130576

description:
Library name: MM130576
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: MM130597

description:
Library name: MM130597
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: GWAT_male_IAS_replicate.2

description: Library name: G_M_IAS_673


title: dfis, late exponential phase, 37°C, biol rep 3

city: Bochum

first: Franz

last: Narberhaus

address: Universitätsstraße 150

department: Microbial biology

country: Germany

institute: Ruhr University Bochum

description: Library name: fis3_s37

data_processing:
Adapter sequences were removed via cutadapt 1.18 with Python 3.7.9 (options: -j 4 -q 10)
Cleaned reads were mapped with bwa (0.7.17-r1188) mem on default settings.
Duplicate reads were removed with Samtools 1.10.
Differential gene expression was analyzed with DESeq2. A maximal adjusted p-value of 0.05 was used as threshold.
Assembly: NCBI RefSeq: for the chromosome NC_010465.1 from US DOE Joint Genome Institute; Identical to CP000950.1. For the pIB plasmid NZ_CP032567.1 from UC Santa Cruz.
Supplementary files format and content: Files include the binary logarithm of the fold change of each gene in the mutant and the corresponding p values.

organism: Yersinia pseudotuberculosis YPIII

source_name: bacteria

growth_protocol: Y. pseudotuberculosis wild type and the fis mutant were used for RNA-seq transcriptomics analysis. Both strains were grown in LB medium at 25 and 37°C to the early (OD600 0.5) and late exponential growth phase (OD600 1.5).

extract_protocol:
RNA was extracted via hot-phenol method as described in (Pienkoß et al., 2021, DOI: https://doi.org/10.1371/journal.ppat.1009650). Samples were treated with RNase-free DNase.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adapt or ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: growth phase

value: late exponential phase

tag: temperature

value: bacteria

value: dfis


title: MM130602

description:
Library name: MM130602
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: MM130575

description:
Library name: MM130575
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

value: male


title: dfis, late exponential phase, 25°C, biol rep 3

description: Library name: fis3_s25


title: MM130596

description:
Library name: MM130596
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: MM130601

description:
Library name: MM130601
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: GWAT_male_IAS_replicate.1

description: Library name: G_M_IAS_612

value: gonadal white adipose tissue (GWAT)

value: adult


title: MM130572

description:
Library name: MM130572
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: MM130600

description:
Library name: MM130600
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: HAP1 KAT2A KO anti-KAT2A Cut&Run rep1

city: Vienna

first: Paul

last: Batty

address: Zimmermann Platz 10

country: Austria

institute: CCRI

description:
Library name: HAP1 KAT2A KO rep1
Raw data provided for replicates. Merged files of the two replicates for each genotype provided for bigwig files

data_processing:
Trim and preprocess barcodes, TrimGalore 0.6.6-GCC-10.2.0-Python-2.7.18
Read alignment, Bowtie2/2.4.2-GCC-10.2.0
Convert SAM files to BAM files, SAMtools/1.15.1-GCC-11.2.0
Merge BAM files
Sort BAM by read name
Fixmate information in BAM
Sort BAM by position
Remove reads overlapping with CUT&RUN blacklist regions
Index final BAM
Generate bigwig coverage files, BEDTools/2.30.0-GCC-10.3.0
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&RUN

growth_protocol: HAP1 cells were cultured in IMDM (Gibco) supplemented with 10 % (v/v) fetal bovine serum (Gibco, 10270-106), 1 % (v/v) Penicillin–Streptomycin (Fisher Scientific, 11548876), L-Glutamine (Thermo Fisher, 25030024).

extract_protocol:
For each sample, nuclei from 250,000 cells were isolated in 100 µl nuclear extraction (NE) buffer (20 mM HEPES (Thermo Fisher, 15630-056), 10 mM KCl (Thermo Scientific, AM960-G), 0.1 % Triton X-100 (Sigma, 93443-100ML), 20 % Glycerol (Fisher Scientific, 10692372), 0.5 mM Spermidine (Sigma, S2626-1G) supplemented with Roche cOmplete EDTA-free Protease Inhibitors (Sigma, 11873580001) for 10 min on ice and centrifuged for 3 min at 600 g at room temperature
Samples were resuspended in 100 µl NE buffer and bound to 10 µl of activated ConA beads for 10 min at room temperature. Next, beads were collected with a magnetic rack and resuspended in 50 µl Antibody Buffer (20 mM HEPES, 150 mM NaCl (Fisher Scientific, BP358-1), 0.5 mM Spermidine, 0.02 % Digitonin (Millipore, D141-100MG), 2 mM EDTA supplemented with Roche Complete EDTA-free Protease Inhibitors) supplemented with 1 µl of antibody. Nuclei were incubated overnight on a nutator at 4C. After two washes with 250 µl Digitonin buffer (20 mM HEPES, 150 mM NaCl, 0.5 mM Spermidine, 0.02 % Digitonin supplemented with Roche Complete EDTA-free Proteasome Inhibitor), nuclei were resuspended in 50 µl Digitonin buffer supplemented with 700 ng/µl pAG-Mnase (gift of Joris Van der Veeken, IMP, Vienna), and incubated for 30 min at room temperature. Excess pAG-Mnase was removed with two washes with Digitonin buffer. Finally, nuclei were resuspended in 50 µl Digitonin buffer and pAG-Mnase was activated with 1 µl 100 mM CaCl2 for 1.5 h on ice. The reaction was quenched with 33 µl Stop Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA (VWR, J60767AD), 50 µg/mL RNAse A, 50 µg/mL Glycogen (Merck, 10901393001). Cleaved DNA was allowed to diffuse out by incubating the tubes at 37ºC for 10 min. After separation using a magnetic rack, DNA was isolated using the Monarch DNA Cleanup Kit (NEB, T1030) and eluted in 15 µl Elution Buffer. Next-generation sequencing libraries were prepared from 2 ng DNA using the NEBaNext Ultra II DNA Library prep Kit (NEB, E7645L), pooled and sequenced (PE150) at Azenta, at a depth of 5-10M reads per library.

tag: cell line

value: KAT2A KO

tag: cut&run antibody

value: Anti KAT2A/GCN5 antibody [EPR21146], abcam, ab217876, 1:50


title: HOB cultured on no coating metal day0_2

description: Library name: C0_3

tag: cell type

value: Osteoblast


title: MM130571

description:
Library name: MM130571
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

tag: tissue

tag: population


title: dfis, late exponential phase, 37°C, biol rep 2

description: Library name: fis2_s37


title: GWAT_male_5TBT_replicate.2

description: Library name: G_M_5TBT_646

tag: Sex

value: 12 weeks old


title: HOB cultured on no coating metal day0_3

description: Library name: C0_4


title: GWAT_male_DMSO_replicate.4

description: Library name: G_M_DMSO_713

value: DMSO


title: MM130569

description:
Library name: MM130569
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

tag: age

tag: bmi


title: MM130583

description:
Library name: MM130583
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

tag: smoke

tag: alcohol drinking


title: MM130589

description:
Library name: MM130589
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_male_DMSO_replicate.5

description: Library name: G_M_DMSO_788

tag: strain

tag: developmental stage


title: HAP1 wild type anti-KAT2A Cut&Run rep1

description:
Library name: HAP1 wild type rep1
Raw data provided for replicates. Merged files of the two replicates for each genotype provided for bigwig files

value: Wild type


title: MM130577

description:
Library name: MM130577
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: snMultiome, MUPIT6-X4, ATAC

city: Los Angeles

first: Frederique

last: Ruf-Zamojski

state: CA

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

description: Library name: MUPIT6-X4_ATAC

library_source: genomic single cell

data_processing:
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

source_name: pituitary

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. We followed 2 protocols: the first for individual pituitaries and the second for multiplexed pituitaries. For individual pituitary processing, each sample was homogenized in a dounce glass homogenizer (1ml, VWR cat# 71000-514). For multiplexed processing, several samples were homogenized simmultaneously in the same homogenizer. In all cases, the final homogenate was filtered through a 40 mm cell strainerAn 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 2,000-25,000 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.

value: pituitary

tag: multiplex batch


title: MM130580

description:
Library name: MM130580
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: For Patient  p6102, p6103, p6104, p6100, p41, p7, p44, p45, p05, p57, p54, p16

description: Library name: HTS_S060

value: colon


title: HAP1 TAF5L KO anti-KAT2A Cut&Run rep2

description:
Library name: HAP1 TAF5L KO rep2
Raw data provided for replicates. Merged files of the two replicates for each genotype provided for bigwig files

value: TAF5L KO


title: GWAT_male_50TBT_replicate.4

description: Library name: G_M_50TBT_760

tag: treatment

tag: time

tag: animal id


title: GWAT_male_DMSO_replicate.3

description: Library name: G_M_DMSO_703


title: MM130581

description:
Library name: MM130581
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: For Patient p17, p38, p39, p6100

description: Library name: HTS_S050


title: MM130579

description:
Library name: MM130579
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_male_DMSO_replicate.1

description: Library name: G_M_DMSO_573


title: GWAT_male_5TBT_replicate.5

description: Library name: G_M_5TBT_822


title: MM130584

description:
Library name: MM130584
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: MM130562

description:
Library name: MM130562
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: GWAT_male_5TBT_replicate.4

description: Library name: G_M_5TBT_733


title: MM130574

description:
Library name: MM130574
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: GWAT_male_DMSO_replicate.2

description: Library name: G_M_DMSO_627


title: snMultiome, MUPIT5-X4, GEX

description: Library name: MUPIT5-X4_GEX

library_source: transcriptomic single cell


title: MM130557

description:
Library name: MM130557
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: HAP1 KAT2A KO anti-KAT2A Cut&Run rep2

description:
Library name: HAP1 KAT2A KO rep2
Raw data provided for replicates. Merged files of the two replicates for each genotype provided for bigwig files

tag: genotype


title: dfis, exponential phase, 37°C, biol rep 3

description: Library name: fis3_e37

tag: growth phase

value: exponential phase

tag: temperature

value: bacteria

value: dfis


title: snMultiome, MUPIT4-X4, GEX

description: Library name: MUPIT4-X4_GEX


title: MM130556

description:
Library name: MM130556
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

tag: cell type

value: monocytes

value: European American


title: HAP1 TAF5L KO anti-KAT2A Cut&Run rep1

description:
Library name: HAP1 TAF5L KO rep1
Raw data provided for replicates. Merged files of the two replicates for each genotype provided for bigwig files

tag: cell line

tag: cut&run antibody


title: dfis, exponential phase, 25°C, biol rep 3

description: Library name: fis3_e25


title: GWAT_male_5TBT_replicate.3

description: Library name: G_M_5TBT_726

tag: tissue

value: gonadal white adipose tissue (GWAT)

tag: Sex

value: male


title: snMultiome, MUPIT3-X4, ATAC

description: Library name: MUPIT3-X4_ATAC


title: MM130566

description:
Library name: MM130566
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

tag: population

tag: age

tag: bmi


title: dfis, late exponential phase, 25°C, biol rep 2

description: Library name: fis2_s25

value: late exponential phase


title: dfis, exponential phase, 37°C, biol rep 2

description: Library name: fis2_e37


title: GWAT_male_5TBT_replicate.1

description: Library name: G_M_5TBT_639

tag: strain

value: adult


title: snMultiome, MUPIT2-X4, ATAC

description: Library name: MUPIT2-X4_ATAC


title: HAP1 wild type anti-KAT2A Cut&Run rep2

description:
Library name: HAP1 wild type rep2
Raw data provided for replicates. Merged files of the two replicates for each genotype provided for bigwig files

value: Anti KAT2A/GCN5 antibody [EPR21146], abcam, ab217876, 1:50


title: MM130552

description:
Library name: MM130552
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

tag: smoke

tag: alcohol drinking


title: GWAT_male_50TBT_replicate.5

description: Library name: G_M_50TBT_767

tag: developmental stage

tag: treatment

value: 12 weeks old


title: snMultiome, MUPIT6-X4, GEX

description: Library name: MUPIT6-X4_GEX

tag: multiplex batch


title: dfis, exponential phase, 25°C, biol rep 2

description: Library name: fis2_e25

tag: genotype


title: GWAT_female_TWD_replicate.1

description: Library name: G_F_TWD_616

value: female

value: TWD

tag: time

tag: animal id


title: dfis, late exponential phase, 37°C, biol rep 1

description: Library name: fis1_s37

tag: growth phase

tag: temperature

tag: cell type


title: Primary pancreas tumor, 8wk timepoint, mouse 28638

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: B36_28638_Pa_8wk_N705_S504_S36

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: Pancreas

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.

tag: tissue

value: Pancreas

tag: cell line

value: Whole pancreas tissue

value: PPKS

tag: batch


title: MM130567

description:
Library name: MM130567
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

tag: population

tag: Sex

tag: age


title: snMultiome, MUPIT5-X4, ATAC

description: Library name: MUPIT5-X4_ATAC

value: pituitary


title: Primary pancreas tumor, 8wk timepoint, mouse 28652

description: Library name: B35_28652_Pa_8wk_N705_S503_S35


title: GWAT_female_TWD_replicate.5

description: Library name: G_F_TWD_806

tag: strain


title: GWAT_female_IAS_replicate.4

description: Library name: G_F_IAS_800

value: IAS


title: GWAT_male_50TBT_replicate.2

description: Library name: G_M_50TBT_650


title: GWAT_female_IAS_replicate.3

description: Library name: G_F_IAS_774


title: GWAT_female_TWD_replicate.4

description: Library name: G_F_TWD_687


title: snMultiome, MUPIT4-X4, ATAC

description: Library name: MUPIT4-X4_ATAC


title: dfis, exponential phase, 37°C, biol rep 1

description: Library name: fis1_e37

value: exponential phase

value: bacteria

value: dfis


title: Primary pancreas tumor, 8wk timepoint, mouse 28651

description: Library name: B39_28651_Pa_8wk_N705_S507_S39


title: dfis, exponential phase, 25°C, biol rep 1

description: Library name: fis1_e25


title: Primary pancreas tumor, 6d timepoint, mouse 28676

description: Library name: B84_28676_Pa_6d_N714_S504_S75


title: snMultiome, HM64, ATAC

description: Library name: HM64_ATAC


title: MM130555

description:
Library name: MM130555
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: European American

tag: bmi

tag: smoke

tag: alcohol drinking


title: GWAT_male_50TBT_replicate.3

description: Library name: G_M_50TBT_657

value: gonadal white adipose tissue (GWAT)

tag: developmental stage

value: adult

value: male

tag: treatment


title: GWAT_female_IAS_replicate.2

description: Library name: G_F_IAS_671

tag: time

value: 12 weeks old


title: Primary pancreas tumor, 6d timepoint, mouse 29836

description: Library name: B82_29836_Pa_6d_N714_S502_S73

tag: genotype


title: MM130565

description:
Library name: MM130565
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: MM130554

description:
Library name: MM130554
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: MM130541

description:
Library name: MM130541
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: MM130560

description:
Library name: MM130560
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: GWAT_male_50TBT_replicate.1

description: Library name: G_M_50TBT_601

tag: animal id


title: Primary pancreas tumor, 8wk timepoint, mouse 28665

description: Library name: B38_28665_Pa_8wk_N705_S506_S38


title: GWAT_female_DMSO_replicate.4

description: Library name: G_F_DMSO_709

value: female

value: DMSO


title: Primary pancreas tumor, 8wk timepoint, mouse 28666

description: Library name: B37_28666_Pa_8wk_N705_S505_S37

value: Pancreas

value: Whole pancreas tissue


title: dfis, late exponential phase, 25°C, biol rep 1

description: Library name: fis1_s25

tag: growth phase

value: late exponential phase

tag: temperature


title: snMultiome, MUPIT3-X4, GEX

description: Library name: MUPIT3-X4_GEX

tag: tissue

value: pituitary

tag: multiplex batch


title: GWAT_female_TWD_replicate.3

description: Library name: G_F_TWD_684

value: TWD


title: snMultiome, HM1076, GEX

description: Library name: HM1076_GEX


title: GWAT_female_TWD_replicate.2

description: Library name: G_F_TWD_680


title: Primary pancreas tumor, 4wk timepoint, mouse 28674

description: Library name: B33_28674_Pa_4wk_N705_S501_S33

tag: cell line

tag: cell type

value: PPKS

tag: batch


title: GWAT_female_DMSO_replicate.1

description: Library name: G_F_DMSO_569

tag: Sex


title: MM130551

description:
Library name: MM130551
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

tag: population

tag: age


title: Primary pancreas tumor, 4wk timepoint, mouse 28658

description: Library name: B32_28658_Pa_4wk_N704_S508_S32


title: snMultiome, MUPIT2-X4, GEX

description: Library name: MUPIT2-X4_GEX


title: snMultiome, MUPIT-X4, GEX

description: Library name: MUPIT-X4_GEX


title: GWAT_female_IAS_replicate.5

description: Library name: G_F_IAS_817

tag: strain

value: IAS


title: snMultiome, MUPIT-X4, ATAC

description: Library name: MUPIT-X4_ATAC


title: Primary pancreas tumor, 8wk timepoint, mouse 28663

description: Library name: B34_28663_Pa_8wk_N705_S502_S34


title: Primary pancreas tumor, 6d timepoint, mouse 29843

description: Library name: B81_29843_Pa_6d_N714_S501_S72


title: MM130550

description:
Library name: MM130550
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

tag: bmi

tag: smoke

tag: alcohol drinking


title: GWAT_female_IAS_replicate.1

description: Library name: G_F_IAS_608

tag: developmental stage

tag: treatment

tag: time


title: snMultiome, HM64, GEX

description: Library name: HM64_GEX


title: MM130544

description:
Library name: MM130544
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: monocytes


title: MM130542

description:
Library name: MM130542
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: MM130548

description:
Library name: MM130548
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: MM130528

description:
Library name: MM130528
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_5TBT_replicate.4

description: Library name: G_F_5TBT_727

tag: animal id


title: Primary pancreas tumor, 4wk timepoint, mouse 28675

description: Library name: B30_28675_Pa_4wk_N704_S506_S30

tag: genotype


title: Primary pancreas tumor, 6d timepoint, mouse 29834

description: Library name: B83_29834_Pa_6d_N714_S503_S74

tag: tissue


title: GWAT_female_5TBT_replicate.3

description: Library name: G_F_5TBT_724


title: GWAT_female_DMSO_replicate.5

description: Library name: G_F_DMSO_785


title: MM130539

description:
Library name: MM130539
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: MM130524

description:
Library name: MM130524
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_5TBT_replicate.2

description: Library name: G_F_5TBT_645


title: Primary pancreas tumor, 4wk timepoint, mouse 28668

description: Library name: B28_28668_Pa_4wk_N704_S504_S28


title: snMultiome, HM5938, GEX

description: Library name: HM5938_GEX


title: MM130530

description:
Library name: MM130530
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, 8wk timepoint, mouse 28123

description: Library name: B17_28123_Lu_8wk_N703_S501_S17

value: Lung

value: Whole lung tissue


title: Primary lung tumor, 8wk timepoint, mouse 28158

description: Library name: B16_28158_Lu_8wk_N702_S508_S16


title: Primary pancreas tumor, 6d timepoint, mouse 29842

description: Library name: B80_29842_Pa_6d_N712_S508_S71


title: GWAT_female_DMSO_replicate.3

description: Library name: G_F_DMSO_695

value: gonadal white adipose tissue (GWAT)

value: adult


title: GWAT_female_DMSO_replicate.2

description: Library name: G_F_DMSO_623

value: 12 weeks old


title: Primary pancreas tumor, 6d timepoint, mouse 29831

description: Library name: B79_29831_Pa_6d_N712_S507_S70


title: snMultiome, HM5938, ATAC

description: Library name: HM5938_ATAC


title: snMultiome, HM1076, ATAC

description: Library name: HM1076_ATAC


title: MM130536

description:
Library name: MM130536
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

value: male


title: bulkRNA-seq, HM5715

description: Library name: HM5715_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

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.


title: MM130514

description:
Library name: MM130514
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: MM130540

description:
Library name: MM130540
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: snMultiome, HF5822, GEX

description: Library name: HF5822_GEX


title: bulkRNA-seq, HM187443

description: Library name: HM187443_bulkRNA


title: snMultiome, HF5751, GEX

description: Library name: HF5751_GEX


title: GWAT_female_5TBT_replicate.5

description: Library name: G_F_5TBT_820

value: female


title: Primary pancreas tumor, 4wk timepoint, mouse 28670

description: Library name: B31_28670_Pa_4wk_N704_S507_S31

value: Pancreas

value: Whole pancreas tissue


title: MM130529

description:
Library name: MM130529
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: snMultiome, HF5350, ATAC

description: Library name: HF5350_ATAC

value: pituitary


title: GWAT_female_50TBT_replicate.5

description: Library name: G_F_50TBT_763


title: snMultiome, HF5822, ATAC

description: Library name: HF5822_ATAC


title: Primary lung tumor, 8wk timepoint, mouse 28118

description: Library name: B11_28118_Lu_8wk_N702_S503_S11


title: MM130519

description:
Library name: MM130519
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: snMultiome, HF5350, GEX

description: Library name: HF5350_GEX


title: GWAT_female_5TBT_replicate.1

description: Library name: G_F_5TBT_637


title: MM130527

description:
Library name: MM130527
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: MM130505

description:
Library name: MM130505
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: bulkRNA-seq, HM163

description: Library name: HM163_bulkRNA


title: bulkRNA-seq, HM5787

description: Library name: HM5787_bulkRNA


title: bulkRNA-seq, HM5818

description: Library name: HM5818_bulkRNA


title: MM130523

description:
Library name: MM130523
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: GWAT_female_50TBT_replicate.1

description: Library name: G_F_50TBT_600


title: Primary lung tumor, 8wk timepoint, mouse 28133

description: Library name: B15_28133_Lu_8wk_N702_S507_S15


title: MM130520

description:
Library name: MM130520
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: snMultiome, HF5751, ATAC

description: Library name: HF5751_ATAC


title: SP014 CT26 KO_rep2 HTO 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_HTO
CT26 tumor infiltrating T cells from BALB/c mice; genotype DPM1_KO; pool2 (hashtags 4,5,8). BioProject PRJNA1435810; BioSample SAMN56455357. 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

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

value: tumor infiltrating T cells


title: Primary pancreas tumor, 4wk timepoint, mouse 28669

description: Library name: B29_28669_Pa_4wk_N704_S505_S29

value: PPKS


title: Primary lung tumor, 6d timepoint, mouse 27569

description: Library name: B4_27569_Lu_6d_N701_S504_S4


title: bulkRNA-seq, HF5621

description: Library name: HF5621_bulkRNA


title: SP014 CT26 KO_rep1 TCR library

description:
Library name: SP014_KO_rep1_TCR
CT26 tumor infiltrating T cells from BALB/c mice; genotype DPM1_KO; pool1 (hashtags 1-3). BioProject PRJNA1435810; BioSample SAMN56455356. 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


title: Primary lung tumor, 6d timepoint, mouse 27567

description: Library name: B3_27567_Lu_6d_N701_S503_S3


title: GWAT_female_50TBT_replicate.4

description: Library name: G_F_50TBT_757


title: bulkRNA-seq, HF5446

description: Library name: HF5446_bulkRNA


title: Primary lung tumor, 6d timepoint, mouse 27565

description: Library name: B2_27565_Lu_6d_N701_S502_S2


title: MM130513

description:
Library name: MM130513
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


title: Primary lung tumor, 8wk timepoint, mouse 27568

description: Library name: B13_27568_Lu_8wk_N702_S505_S13


title: Primary lung tumor, 8wk timepoint, mouse 28176

description: Library name: B12_28176_Lu_8wk_N702_S504_S12


title: Primary lung tumor, 8wk timepoint, mouse 28121

description: Library name: B14_28121_Lu_8wk_N702_S506_S14


title: bulkRNA-seq, HM187442

description: Library name: HM187442_bulkRNA


title: GWAT_female_50TBT_replicate.3

description: Library name: G_F_50TBT_653


title: MM130497

description:
Library name: MM130497
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: monocytes


title: Primary lung tumor, 4wk timepoint, mouse 29432

description: Library name: B8_29432_Lu_4wk_N701_S508_S8

value: Lung


title: bulkRNA-seq, HM1674

description: Library name: HM1674_bulkRNA


title: SP014 CT26 KO_rep1 GEX library

description:
Library name: SP014_KO_rep1_GEX
CT26 tumor infiltrating T cells from BALB/c mice; genotype DPM1_KO; pool1 (hashtags 1-3). BioProject PRJNA1435810; BioSample SAMN56455356. Library type: GEX.

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: bulkRNA-seq, HM187439

description: Library name: HM187439_bulkRNA


title: MM130509

description:
Library name: MM130509
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: bulkRNA-seq, HF5566

description: Library name: HF5566_bulkRNA