title: MM130464

description:
Library name: MM130464
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: MM130452

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: MM130452
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: Y1_PIMQ_lowH3K27ac_Rep1

city: New York

first: Luis

middle: F

last: Soto-Ugaldi

state: NY

institute: The Rockefeller University

description:
Library name: Sample 14
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Y1_IMQ_rep1_H3K27ac_MERGE_sorted_RPKM.bw

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

organism: Mus musculus

source_name: Skin

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

value: Skin

value: Epidermal Stem Cell

tag: genotype

value: wildtype

tag: treatment

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


title: PGF-BCR_S7

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

description: Library name: PGF-BCR_S7

library_source: transcriptomic

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

molecule: polyA RNA

source_name: Human bone marrow

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

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

value: Human bone marrow

tag: cell line

value: BMMNCs

value: Allogenic stem cell transplantation


title: MM130451

description:
Library name: MM130451
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: Il17 Mock 7dpi 5

city: Manhattan

first: Chaitra

last: Sreenivasaiah

address: 227 E 30th St

department: Applied Bioinformatics Laboratory

institute: NYU Langone Health

description: Library name: TOI 54

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

molecule: total RNA

source_name: nasal lavages

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

value: nasal lavages

value: PBS


title: PGF-TCR_S1

description: Library name: PGF-TCR_S1

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


title: Il1 Spn 21dpi 5

description: Library name: TOI 48

value: Spn-infected


title: MM130456

description:
Library name: MM130456
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: Il17 Mock 7dpi 3

description: Library name: TOI 52


title: PGF-BCR_S9

description: Library name: PGF-BCR_S9


title: MM130458

description:
Library name: MM130458
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: Y1_Naive_lowH3K27ac_Rep1

description:
Library name: Sample 10
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Y1_Ctrl_rep1_H3K27ac_MERGE_sorted_RPKM.bw

value: non-treated


title: Y1_Naive_lowH3K27ac_Rep2

description:
Library name: Sample 12
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Y1_Ctrl_rep2_H3K27ac_MERGE_sorted_RPKM.bw


title: Y1_PIMQ_highH3K4me1_Rep2

description:
Library name: Sample 7
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Y1_IMQ_rep2_H3K4me1_MERGE_sorted_RPKM.bw


title: PGF-BCR_S5

description: Library name: PGF-BCR_S5


title: MM130447

description:
Library name: MM130447
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: MM130463

description:
Library name: MM130463
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: Y1_Naive_highH3K27ac_Rep2

description:
Library name: Sample 11
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Y1_Ctrl_rep2_H3K27ac_MERGE_sorted_RPKM.bw


title: Y1_PIMQ_highH3K4me1_Rep1

description:
Library name: Sample 5
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Y1_IMQ_rep1_H3K4me1_MERGE_sorted_RPKM.bw


title: Y1_PIMQ_lowH3K4me1_Rep1

description:
Library name: Sample 6
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Y1_IMQ_rep1_H3K4me1_MERGE_sorted_RPKM.bw


title: MM130446

description:
Library name: MM130446
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: PGF-TCR_S11

description: Library name: PGF-TCR_S11


title: Y1_PIMQ_lowH3K4me1_Rep2

description:
Library name: Sample 8
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Y1_IMQ_rep2_H3K4me1_MERGE_sorted_RPKM.bw


title: PGF-TCR_S12

description: Library name: PGF-TCR_S12


title: Y1_Naive_lowH3K4me1_Rep1

description:
Library name: Sample 2
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Y1_Ctrl_rep1_H3K4me1_MERGE_sorted_RPKM.bw


title: Il1 Spn 7dpi 5

description: Library name: TOI 42


title: Il1 Spn 21dpi 6

description: Library name: TOI 49


title: Y1_Naive_lowH3K4me1_Rep2

description:
Library name: Sample 4
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Y1_Ctrl_rep2_H3K4me1_MERGE_sorted_RPKM.bw


title: MM130439

description:
Library name: MM130439
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: PGF-BCR_S6

description: Library name: PGF-BCR_S6


title: Il1 Spn 21dpi 4

description: Library name: TOI 47


title: Il1 Spn 7dpi 4

description: Library name: TOI 41


title: Y1_Naive_highH3K4me1_Rep2

description:
Library name: Sample 3
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Y1_Ctrl_rep2_H3K4me1_MERGE_sorted_RPKM.bw


title: Il1 Spn 21dpi 3

description: Library name: TOI 46


title: Il1 Spn 7dpi 3

description: Library name: TOI 40


title: PGF-BCR_S1

description: Library name: PGF-BCR_S1


title: PBMCs, 500nMTHC, 6hr, rep3 scATAC

city: Chapel Hill

first: Manickam

last: Ashokkumar

state: NC

address: 120 Mason Farm Rd

department: Department of Medicine

institute: The University of North Carolina at Chapel Hill

description: Library name: Donor3_500nMTHC_6hr_PBMCs_scATAC

library_source: transcriptomic single cell

data_processing:
Cell Ranger  v.7.1.0
seurat
seurat doublet discrimination and removal of cells with high mitochondrial read counts
seurat merge to combine all 8 datasets retaining sample metadata
seurat sctransform to generate normalized count matrix
Assembly: GRCh38 + HIV (NL4-3-△6-drEGFP-IRES-thy1.2)
Supplementary files format and content: A .h5 binary file.

molecule: nuclear RNA

source_name: Primary cells

growth_protocol: Cells grown in RPMI supplemented with 10% FBS, L-Glutamine, HEPES, PenStrep, and Sodium Pyruvate.

extract_protocol:
Nuclei were isolated following 10X Genomics protocol  (https://cdn.10xgenomics.com/image/upload/v1747848350/support-documents/CG000365_DemonstratedProtocol_NucleiIsolation_ATAC_GEX_Sequencing_Rev_D.pdf) 10X Genomic's Chromium Next GEM Single Cell Multiome ATAC + Gene Expression
Libraries for scATAC and scRNA were constructed using 10X Genomic's Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit following manufacture's protocol.

treatment_protocol: Treatment with 500nM THC for 3, 6 and 12h. Methanol (0.015% V/V) was used as vehicle control.

value: Primary cells

value: THC


title: PGF-BCR_S12

description: Library name: PGF-BCR_S12


title: MM130437

description:
Library name: MM130437
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: PGF-BCR_S11

description: Library name: PGF-BCR_S11


title: MM130441

description:
Library name: MM130441
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: MM130440

description:
Library name: MM130440
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: PGF-BCR_S2

description: Library name: PGF-BCR_S2


title: PGF-BCR_S4

description: Library name: PGF-BCR_S4


title: PGF-BCR_S3

description: Library name: PGF-BCR_S3


title: MM130450

description:
Library name: MM130450
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: PBMCs, 500nMTHC, 12hr, rep1 scATAC

description: Library name: Donor1_500nMTHC_12hr_PBMCs_scATAC


title: Y1_Naive_highH3K4me1_Rep1

description:
Library name: Sample 1
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
Y1_Ctrl_rep1_H3K4me1_MERGE_sorted_RPKM.bw

value: Skin

value: Epidermal Stem Cell


title: PBMCs, 500nMTHC, 6hr, rep2 scATAC

description: Library name: Donor2_500nMTHC_6hr_PBMCs_scATAC


title: PBMCs, 500nMTHC, 0hr, rep3 scATAC

description: Library name: Donor3_500nMTHC_0hr_PBMCs_scATAC

value: Methanol


title: MM130423

description:
Library name: MM130423
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: Il1 Spn 21dpi 2

description: Library name: TOI 45


title: MM130428

description:
Library name: MM130428
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: PBMCs, 500nMTHC, 6hr, rep1 scATAC

description: Library name: Donor1_500nMTHC_6hr_PBMCs_scATAC


title: Il1 Spn 7dpi 2

description: Library name: TOI 39


title: PGF-GEX1_S9

description: Library name: PGF-GEX1_S9

value: Human bone marrow


title: PGF-GEX1_S7

description: Library name: PGF-GEX1_S7

value: BMMNCs


title: MM130427

description:
Library name: MM130427
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: PGF-GEX1_S6

description: Library name: PGF-GEX1_S6

value: Allogenic stem cell transplantation


title: PBMCs, 500nMTHC, 0hr, rep2 scATAC

description: Library name: Donor2_500nMTHC_0hr_PBMCs_scATAC


title: MM130421

description:
Library name: MM130421
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: Il1 Spn 7dpi 6

description: Library name: TOI 43


title: PBMCs, 500nMTHC, 0hr, rep1 scATAC

description: Library name: Donor1_500nMTHC_0hr_PBMCs_scATAC


title: PGF-GEX1_S5_2

description: Library name: PGF-GEX1_S5_2


title: Il1 Spn 7dpi 1

description: Library name: TOI 38


title: PBMCs, 500nMTHC, 6hr, rep3 scRNA

description: Library name: Donor3_500nMTHC_6hr_PBMCs_scRNA

data_processing:
Cell Ranger v.7.1.0
seurat
seurat doublet discrimination and removal of cells with high mitochondrial read counts
seurat merge to combine all 8 datasets retaining sample metadata
seurat sctransform to generate normalized count matrix
Assembly: GRCh38 + HIV (NL4-3-△6-drEGFP-IRES-thy1.2)
Supplementary files format and content: A .h5 binary file

tag: donor id

tag: cell subtype

value: Mixture of latently infected CD4 T cells and autologous PBMCs (at a ratio of 1:3)


title: Il1 Mock 21dpi 6

description: Library name: TOI 37

value: nasal lavages


title: Il1 Mock 21dpi 2

description: Library name: TOI 33

value: PBS


title: Il1 Mock 21dpi 4

description: Library name: TOI 35


title: PBMCs, 500nMTHC, 0hr, rep3 scRNA

description: Library name: Donor3_500nMTHC_0hr_PBMCs_scRNA


title: Il1 Mock 21dpi 5

description: Library name: TOI 36


title: MM130426

description:
Library name: MM130426
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: MM130416

description:
Library name: MM130416
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: MM130420

description:
Library name: MM130420
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: PGF-GEX1_S8

description: Library name: PGF-GEX1_S8


title: PBMCs, 500nMTHC, 3hr, rep1 scATAC

description: Library name: Donor1_500nMTHC_3hr_PBMCs_scATAC


title: Il1 Mock 7dpi 6

description: Library name: TOI 31


title: MM130418

description:
Library name: MM130418
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: Il1 Mock 21dpi 3

description: Library name: TOI 34


title: PGF-GEX1_S3

description: Library name: PGF-GEX1_S3


title: MM130414

description:
Library name: MM130414
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: MM130415

description:
Library name: MM130415
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: PGF-GEX1_S4

description: Library name: PGF-GEX1_S4


title: PGF-GEX1_S12

description: Library name: PGF-GEX1_S12


title: Il1 Mock 7dpi 5

description: Library name: TOI 30


title: PBMCs, 500nMTHC, 0hr, rep2 scRNA

description: Library name: Donor2_500nMTHC_0hr_PBMCs_scRNA


title: MM130411

description:
Library name: MM130411
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: PBMCs, 500nMTHC, 6hr, rep2 scRNA

description: Library name: Donor2_500nMTHC_6hr_PBMCs_scRNA


title: Il1 Mock 7dpi 4

description: Library name: TOI 29


title: PGF-GEX1_S2

description: Library name: PGF-GEX1_S2


title: Il1 Mock 21dpi 1

description: Library name: TOI 32


title: PBMCs, 500nMTHC, 6hr, rep1 scRNA

description: Library name: Donor1_500nMTHC_6hr_PBMCs_scRNA


title: PBMCs, 500nMTHC, 3hr, rep1 scRNA

description: Library name: Donor1_500nMTHC_3hr_PBMCs_scRNA


title: PGF-GEX1_S11

description: Library name: PGF-GEX1_S11


title: PGF-GEX1_S1

description: Library name: PGF-GEX1_S1


title: PBMCs, 500nMTHC, 12hr, rep1 scRNA

description: Library name: Donor1_500nMTHC_12hr_PBMCs_scRNA


title: Il1 Mock 7dpi 3

description: Library name: TOI 28


title: MM130408

description:
Library name: MM130408
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: Il1 Mock 7dpi 1

description: Library name: TOI 26


title: Virus transduction control, virus batch BL4

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: B68_BL4_LRLG_control_N711_S504_S60

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: Cell culture

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

value: Cell culture

value: kidney cell line

tag: batch


title: PBMCs, 500nMTHC, 0hr, rep1 scRNA

description: Library name: Donor1_500nMTHC_0hr_PBMCs_scRNA

value: Primary cells


title: Virus transduction control, virus batch BL2

description: Library name: B66_BL2_LRLG_control_N711_S502_S58


title: MM130404

description:
Library name: MM130404
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: peripheral blood


title: NPC differentiation, day8, replicate 2, H3K4me3

city: Gent

first: Eva

last: D'haene

address: Corneel Heymanslaan 10

department: Department of Biomolecular Medicine

country: Belgium

institute: Ghent University

description: Library name: NPC diff d8 rep2, H3K4me3

data_processing:
Read processing and peak calling was performed using a dedicated nextflow CUT&RUN pipeline available through nf-core (https://doi.org/10.5281/zenodo.5653535). Briefly, raw reads were trimmed, QC filtered and aligned to the hg38 reference genome using Bowtie2 (v2.4.4). Upon Q-score filtering, duplicate removal and CPM normalization, peaks in target samples were called with SEACR (v1.3) using corresponding IgG samples as controls. A consensus peak list per sample was obtained by requiring the presence of peaks in both replicates.
Assembly: hg38
Supplementary files format and content: bigwig files with cpm normalized signal tracks
Library strategy: CUT&Run

source_name: NPC

growth_protocol: iPSCs were differentiated towards NPCs using the STEMdiff™ SMADi Neural Induction Kit following the monolayer protocol provided by the manufacturer (Catalog #08581), which directs differentiation by blocking TGF-β/BMP-dependent SMAD signalling. NPCs were seeded at a density of 4 × 105 cells per well in a Geltrex coated 12-well plate in STEMdiff™ SMADi Neural Induction medium over 8 or 12 days, with media changes each day. For the 12 day protocol the cells were split at day 6, for the 8 day protocol no split was performed.

extract_protocol:
On day 0, 4, 6 and 8 of differentiation, iPSCs/NPCs were washed twice with room temperature 1X PBS. Cells were lifted from the dish using a cell lifter and gently resuspended using a P1000 pipet. Cells were counted using an automated cell counter, and the appropriate number of cells was taken. For each condition 5 x 10^5 cells were required, however it is recommended to batch process and therefore cells for all conditions were pooled into a 15ml falcon tube. The lysate was transferred to a fresh 15ml falcon tube and spun down at 600 g at RT for 3 min. The supernatant was carefully discarded and nuclei were isolated by addition of Nuclei Extraction Buffer (NEB, 20 mM Hepes (KOH) pH 7.9, 10 mM KCl, 0.5 mM Spermidine, 0.1% Triton X-100, 20% Glycerol, 1mM MnCl2, 1 tablet cOmplete MINI EDTA-free Protease inhibitor (Roche)) (100µl per condition). The samples were incubated for 10 minutes on ice and spun down at 600 x g at 4°C for 3 minutes. Supernatants was removed and 100µl NEB was added per condition.
For these first steps it is recommended to work in batch, pool everything together for all samples of the same datapoint or cell type. Per reaction, 10 μl/sample Concavalin-A conjugated beads were activated by washing twice in 100 μl/sample cold Bead Activation Buffer (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) on a magnetic stand and then resuspended in 11 μl/sample Bead activation Buffer. Freshly 100 μl/sample extracted nuclei were added to the activated beads and incubated at 4°C for 10 min with rotation. Beads-bound nuclei were placed on a magnetic stand and resuspended in Antibody buffer 50 μl/sample (2mM EDTA, 1 tablet cOmplete MINI EDTA-free Protease inhibitor (Roche) in wash buffer). Primary antibodies were added to the beads-bound nuclei and gently mixed, see table S7 (final dilution of 1:50 or 1:100 in 50 μl volume). Mixtures were incubated with rotation at 4°C overnight on a nutator.
After washing twice on a magnetic stand in 250 μl/sample Washing Buffer (WB, 20 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 tablet cOmplete EDTA-free Protease inhibitor), nuclei were resuspended in 50 μl/sample cold Washing Buffer. 2.5 μl of pAG-MNAse (15-1016-EPC Epicypher) was added to the mix and incubated with rotation for 10 min at 4 °C. Next, beads were washed twice in 250 μl/sample cold Washing Buffer on a magnetic strand and resuspended in 50 μl cold Washing Buffer. The samples were equilibrated to 0°C in an ice bath and 1 μl/sample of 100 mM CaCl2 were added to the reaction. After an incubation of 2h at 4°C on a nutator, 33 μl/sample 2X STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg/ml RNAseA, 50 μg/ml Glycogen, 10 ng/ml spike-in DNA) was added and beads were incubated for 10 min at 37°C. The supernatants was extracted and DNA was purified using the CUTANA™ Quick Cleanup DNA Purification Kit, following manufacturer’s instructions. DNA concentration was measured with Qubit (Thermo Fisher Scientific).
Libraries were prepared using the NEBNext Ultra II Library prep Kit (E7645S, New England Biolabs) according to the manufacturer’s protocol using half of the volumes. Adapters were used at a working concentration of 15 μM, 1.5 μM, 0.6 μM based on the DNA input. A cleanup of the adaptor-ligated DNA without size selection was performed making use of AMPure XP beads (1.8X). Libraries (13 μL) were PCR amplified with unique indexes (15 μL NEBNext Ultra II Q5 Master Mix and 1 μL i7 Primer) (New England Biolabs) for 8-15 cycles depending on the start DNA input.
A cleanup of the PCR reaction with size selection was performed making use of AMPure XP beads for the selection of fragments 150bp(0.5X) < DNA fragments < 500bp(1.2X). After cleanup, fragment size and concentration was analyzed by Fragment Analyzer. CUT&RUN library concentrations were measured with the Illumina Kapa Library quantification kit (Roche #07960140001). All pre-made libraries were sequenced at on Illumina NEXTseq2000 platform (150 bp paired-end sequencing). Each replicate was sequenced at a sequencing depth of 10 million reads.

value: NPC


title: NPC differentiation, day8, replicate 1, input

description: Library name: NPC diff d8 rep1, input


title: MM130407

description:
Library name: MM130407
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: MM130402

description:
Library name: MM130402
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: male


title: Il1 Mock 7dpi 2

description: Library name: TOI 27


title: NPC differentiation, day8, replicate 2, H3K4me1

description: Library name: NPC diff d8 rep2, H3K4me1


title: NPC differentiation, day8, replicate 2, H3K27ac

description: Library name: NPC diff d8 rep2, H3K27ac


title: MM130401

description:
Library name: MM130401
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: WT Spn 21dpi 7

description: Library name: TOI 25

value: WT

value: Spn-infected


title: WT Spn 21dpi 4

description: Library name: TOI 22


title: THP-1 macrophage_HSV-1_PGE2_rep3

city: San Diego

first: Pham Thuy Tien

last: Vo

address: 3855 Health Sciences Dr

institute: University of California, San Diego

description: Library name: Sample12

data_processing:
The raw reads were filtered to remove low quality reads and adapters. The filtering process is as follows: (1) Remove reads containing adapters. (2) Remove reads containing N > 10% (N represents the base cannot be determined). (3) Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
The filtered sequenced reads were aligned to the human reference genome hg38 using STAR v2.7.9a with Gencode v38 annotations.
Read count data for each gene was calculated usng RSEM v1.3.1.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes read count data of each gene for each Sample. Gene names are represented as Ensembl Gene IDs.

source_name: Peripheral blood

extract_protocol:
Total RNA was harvested using the QIAGEN RNAeasy Mini Kit.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: Peripheral blood

value: Monocyte


title: NPC differentiation, day8, replicate 2, input

description: Library name: NPC diff d8 rep2, input


title: WT Spn 21dpi 6

description: Library name: TOI 24


title: Virus transduction control, virus batch BL3

description: Library name: B67_BL3_LRLG_control_N711_S503_S59


title: WT Spn 21dpi 5

description: Library name: TOI 23


title: MM130399

description:
Library name: MM130399
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: THP-1 macrophage_PGE2_rep3

description: Library name: Sample11


title: MM130397

description:
Library name: MM130397
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: THP-1 macrophage_HSV-1_rep3

description: Library name: Sample10


title: NPC differentiation, day8, replicate 1, H3K27ac

description: Library name: NPC diff d8 rep1, H3K27ac


title: WT Spn 21dpi 2

description: Library name: TOI 20


title: Virus transduction control, virus batch BL1

description: Library name: B65_BL1_LRLG_control_N711_S501_S57


title: NPC differentiation, day6, replicate 2, input

description: Library name: NPC diff d6 rep2, input


title: MM130396

description:
Library name: MM130396
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: WT Spn 7dpi 6

description: Library name: TOI 18


title: NPC differentiation, day8, replicate 1, H3K4me1

description: Library name: NPC diff d8 rep1, H3K4me1


title: MM130394

description:
Library name: MM130394
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: NPC differentiation, day8, replicate 1, H3K4me3

description: Library name: NPC diff d8 rep1, H3K4me3


title: MM130395

description:
Library name: MM130395
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: MM130388

description:
Library name: MM130388
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: MM130393

description:
Library name: MM130393
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: NPC differentiation, day6, replicate 2, H3K27ac

description: Library name: NPC diff d6 rep2, H3K27ac


title: WT Spn 7dpi 4

description: Library name: TOI 16


title: WT Spn 7dpi 5

description: Library name: TOI 17


title: MM130391

description:
Library name: MM130391
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: THP-1 macrophage_HSV-1_PGE2_rep2

description: Library name: Sample8


title: NPC differentiation, day6, replicate 2, H3K4me3

description: Library name: NPC diff d6 rep2, H3K4me3


title: THP-1 macrophage_PGE2_rep2

description: Library name: Sample7


title: WT Spn 21dpi 1

description: Library name: TOI 19


title: NPC differentiation, day6, replicate 2, H3K4me1

description: Library name: NPC diff d6 rep2, H3K4me1


title: WT Spn 21dpi 3

description: Library name: TOI 21


title: NPC differentiation, day6, replicate 1, input

description: Library name: NPC diff d6 rep1, input


title: MM130385

description:
Library name: MM130385
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: THP-1 macrophage_HSV-1_rep2

description: Library name: Sample6


title: THP-1 macrophage_vehicle_rep3

description: Library name: Sample9


title: NPC differentiation, day6, replicate 1, H3K27ac

description: Library name: NPC diff d6 rep1, H3K27ac


title: THP-1 macrophage_vehicle_rep2

description: Library name: Sample5


title: WT Spn 7dpi 3

description: Library name: TOI 15


title: MM130379

description:
Library name: MM130379
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: WT Spn 7dpi 1

description: Library name: TOI 13


title: NPC differentiation, day6, replicate 1, H3K4me1

description: Library name: NPC diff d6 rep1, H3K4me1


title: MM130377

description:
Library name: MM130377
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: THP-1 macrophage_PGE2_rep1

description: Library name: Sample3


title: NPC differentiation, day6, replicate 1, H3K4me3

description: Library name: NPC diff d6 rep1, H3K4me3


title: WT Spn 7dpi 2

description: Library name: TOI 14


title: NPC differentiation, day4, replicate 2, input

description: Library name: NPC diff d4 rep2, input


title: THP-1 macrophage_HSV-1_rep1

description: Library name: Sample2


title: MM130374

description:
Library name: MM130374
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: WT Mock 21dpi 4

description: Library name: TOI 10


title: WT Mock 21dpi 5

description: Library name: TOI 11


title: MM130375

description:
Library name: MM130375
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: MM130371

description:
Library name: MM130371
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: THP-1 macrophage_vehicle_rep1

description: Library name: Sample1


title: THP-1 macrophage_HSV-1_PGE2_rep1

description: Library name: Sample4


title: WT Mock 21dpi 6

description: Library name: TOI 12


title: MM130369

description:
Library name: MM130369
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: NPC differentiation, day4, replicate 2, H3K27ac

description: Library name: NPC diff d4 rep2, H3K27ac


title: Normal, replicate5, snATAC-seq

city: Guangzhou

last: He

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China

department: Department of Basic Research

country: China

institute: Guangzhou National Laboratory

description: 10x Genomics

library_source: genomic single cell

data_processing:
The raw fastq files of snATAC-seq were mapped to Homo sapiens genome assembly GRCh38 (hg38) using cellranger-atac (2.1.0). Unique molecular identifiers (UMI) count matrices and indexed fragments file were imported into Seurat (3.2.0), and Signac(1.14.0)(Stuart et al., 2019) to generate Seurat object to each experiment.
Assembly: hg38
Supplementary files format and content: snATAC-seq clustered rds file
Supplementary files format and content: Filtered barcode, matrix, peaks and fragment files.

source_name: Liver

extract_protocol:
Frozen human liver tissue was homogenized using a Dounce homogenizer in lysis dilution buffer. The homogenate was centrifuged, and the pellet was resuspended in lysis dilution buffer. The nuclei were washed and resuspended in lysis dilution buffer. Nuclei were further purified using the Nuclei Isolation Kit (Sigma, Cat# NUC201) with a 1.8 M sucrose cushion, following the manufacturer's instructions. After centrifugation at 30,000 g (approximately 13,000 rpm) for 45 minutes at 4 °C, the nuclei pellet was collected and resuspended in PBS containing 1% BSA. The nuclei were filtered through a 40 μm cell strainer before loading onto the 10x Genomics Chromium Controller.
snATAC-seq libraries were prepared according to the manufacturer’s instructions of 10XGenomics (PN-1000176)

value: Liver


title: WT Mock 21dpi 2

description: Library name: TOI 8


title: MM130370

description:
Library name: MM130370
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: NPC differentiation, day4, replicate 2, H3K4me3

description: Library name: NPC diff d4 rep2, H3K4me3


title: MM130368

description:
Library name: MM130368
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: Normal, replicate4, snATAC-seq

description: 10x Genomics


title: NPC differentiation, day4, replicate 2, H3K4me1

description: Library name: NPC diff d4 rep2, H3K4me1


title: MM130367

description:
Library name: MM130367
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: WT Mock 21dpi 1

description: Library name: TOI 7


title: NPC differentiation, day4, replicate 1, H3K27ac

description: Library name: NPC diff d4 rep1, H3K27ac


title: Normal, replicate3, snATAC-seq

description: 10x Genomics


title: NPC differentiation, day4, replicate 1, input

description: Library name: NPC diff d4 rep1, input


title: WT Mock 21dpi 3

description: Library name: TOI 9


title: Normal, replicate6, snATAC-seq

description: 10x Genomics


title: WT Mock 7dpi 6

description: Library name: TOI 6