title: MM130259

description:
Library name: MM130259
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: European American

value: male


title: 22Rv1_CTC_10

status: Public on Mar 16 2026

type: SRA

city: Portland

first: Rosalyn

middle: M

last: Fey

state: OR

address: 3181 S.W. Sam Jackson Park Road

country: USA

institute: Oregon Health & Science University

description: Library name: 22Rv1_CTC_10

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed with zUMIs.
Assembly: hg38
Supplementary files format and content: merged FASTQ, index and barcode files.
Supplementary files format and content: counts files and gene names file.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: 22Rv1 human prostate cancer cells were cultured in RPMI-1640 media/10% FBS. A375 human melanoma cancer cells were cultured in DMEM media/10% FBS.

extract_protocol:
Cells were stored in a lysis buffer containing poly-ethylene glycol, Triton X-100, RNAse inhibitor, a custom oligo strand, dNTPs, and nuclease free water at -80°C until ready for library preparation according to the Smart-seq3 protocol.  The freeze/thaw aided in cell lysis
Libraries were prepared according to the Smart-seq3 protocol (doi: 10.1038/s41587-020-0497-0)

tag: cell line

tag: cell type

value: prostate


title: Y1.5_Naive_ATAC-seq_Rep1

city: New York

first: Luis

middle: F

last: Soto-Ugaldi

state: NY

institute: The Rockefeller University

description:
Library name: Sample 12
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).

library_source: genomic

data_processing:
FastQ files were aligned with BWA using mm10 genome reference
Reads were filtered with Samtools -F 1804 -f 2
Peaks were detected using Macs3 using -bed as input format
BigWig files were generated using genomicRanges R package. Score represents CPM normalized values
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigWig files

molecule: genomic DNA

organism: Mus musculus

source_name: Skin

extract_protocol:
ATAC-seq was performed on 100,000 FACS-purified cells as previously described (Buenrostro et al., 2013). Briefly, cells were lysed in ATAC lysis buffer for five minutes, then treated with Tn5 transposase (Illumina) for 30 minutes. Sequencing libraries were prepared according to manufacturer guidelines (Illumina), with up to eight uniquely-barcoded samples included per sequencing run. Libraries were sequenced on an Illumina NextSeq500 or NovaSeq 6000.
PCR amplified library from genomic DNA

tag: tissue

value: Skin

value: Epidermal Stem Cell

tag: genotype

value: wildtype

tag: treatment

value: non-treated


title: MM130246

city: New Orleans

first: Hong-Wen

last: Deng

state: LA

institute: Tulane University

description:
Library name: MM130246
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

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.

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.

value: peripheral blood

value: monocytes

tag: population

value: African American

tag: Sex

tag: age

tag: bmi

tag: smoke

tag: alcohol drinking


title: C1 mouse tissue, CST treated

city: San Diego

first: Satadeepa

last: Kal

address: 9500 GILMAN Dr

institute: UCSD

description:
Library name: C1
Mus musculus mouse tissue, group C group, CST treated
B16F10_mouse_Tumor.csv

library_source: transcriptomic

data_processing:
Reads were quantified using Salmon, counts imported using tximport, differential expression via DESeq2, and visualization using pHeatmap and pVolcano.
Assembly: Genome assemblies were performed using GRCh38.p14 for human and GRCm39 for mouse.
Supplementary files format and content: normalised count with gene name for each sample

molecule: total RNA

source_name: mouse tissue

extract_protocol:
RNA was extracted using the Qiagen Rneasy column extraction method following the manufacturer's protocol.
Libraries were made using the KAPA mRNA HyperprepKit according to the manufacturer's guidelines.

value: mouse tissue

value: CST treated

tag: batch

value: C group


title: 22Rv1_CTC_9

description: Library name: 22Rv1_CTC_9


title: MM130249

description:
Library name: MM130249
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: C5 mouse tissue, CST treated

description:
Library name: C5
Mus musculus mouse tissue, group C group, CST treated
B16F10_mouse_Tumor.csv


title: Y1_PIMQ_ATAC-seq_Rep3

description:
Library name: Sample 10
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).

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


title: Y1_PIMQ_ATAC-seq_Rep4

description:
Library name: Sample 11
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).


title: S1 mouse tissue, Saline control

description:
Library name: S1
Mus musculus mouse tissue, group S group, Saline control
B16F10_mouse_Tumor.csv

value: Saline control

value: S group


title: m1128-DKO

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: Library name: m1128-DKO

data_processing:
RNA libraries were sequenced using a NovaSeq 6000 system and the NovaSeq 6000 S2 Reagent Kit (100 cycles, paired end run) with an average of 3 * 10^7 reads per RNA sample (Illumina, San Diego, CA, USA). Trimmed reads (adapter trimming tool: ea-utils: fastq-mcf) were aligned to the murine reference genome using the open source short-read aligner STAR (v2.4.2a).
Illumina RTA v3.1.5 was used for basecalling and Illumina bcl2fastq2 was used for fastq file generation
Feature Count /Read Summarization performed by Rsubread_2.16.1
Assembly: GRCm39 (ENSMBL GRCm39 release 109)
Supplementary files format and content: Excel file containing feature counts

source_name: cardiomyocyte

growth_protocol: Animals were housed with a 14 h light / 10 h dark cycle with free access to food and water.

extract_protocol:
Total RNA from left ventricular tissue was isolated using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany).
The RNA sequencing library was generated from 100 ng of total RNA using the NEBNext® Single Cell/Low Input RNA Library Prep Kit (New England BioLabs, Frankfurt, Germany) according to the manufacturer’s instructions.

treatment_protocol: The present study used mice with embryonic, cardiomyocyte-selective deletion of Rhot1 and Rhot2 (DKO) and controls.

value: cardiomyocyte

value: DKO


title: MM130254

description:
Library name: MM130254
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: male


title: MM130236

description:
Library name: MM130236
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: D180_Naive_ATAC-seq_Rep3

description:
Library name: Sample 3
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).

value: Skin


title: HepG2-NTCP cells, McccDNA transfected

city: Shanghai

first: Yumeng

last: Li

address: 131 Dong'an Road

country: China

institute: Fudan University

description: Library name: Sample 1

data_processing:
MNase-seq data were processed using Cutadapt (v1.9.1) to filter out sequences with a base quality score below 20.
The filtered reads were aligned to HBV genome of genotype D (subtype ayw; GenBank accession no. V01460.1) using Bowtie2 (v2.3.5.1)
The aligned reads were further filtered and sorted with SAMtools (v1.7).
Nucleosome distribution was analyzed using DANPOS3 software and the results were visualized with IGV.
Assembly: HBV genome of genotype D (subtype ayw; GenBank accession no. V01460.1)
Supplementary files format and content: wig,Dpos peak-calling algorithm for each nucleosome positioning and comparation between two samples

source_name: liver

growth_protocol: DMEM, 10% fetal bovine serum, 10 mM HEPES, 1x penicillin/streptomycin. Cells were cultured at 37˚C at 5% CO2.

extract_protocol:
Cell  were digested with trypsin, washed twice with PBS. The cells were then resuspended in PBS at a concentration of 10E6 cells/mL, with a reaction volume of 200 μL per sample. MNase lysis buffer (20 mM Tris-HCl, pH 7.5, 0.1% Triton X-100, 10 mM NaCl, 2 mM CaCl2) was added, and the cells were lysed on ice for 10 minutes. MNase (NEB, M0247S) was diluted to the appropriate concentration with MNase storage buffer, and samples were incubated at 37°C for 20 minutes. The reaction was stopped by adding 6.25 μL of 0.5 M EGTA, followed by 43 μL of PBS containing 1 mM EGTA. The mixture was then treated with RNase, and the reaction was stopped by adding a buffer containing 0.15% SDS and 0.25 mg/mL proteinase K. Subsequently, the samples were extracted with saturated phenol/chloroform, and nucleic acids were precipitated with ethanol. The DNA pellet was dissolved in ddH2O. Nucleosomal DNA monomers were purified by gel extraction, dissolved in TE buffer.
MNase-seq libraries ware prepared using TIANSeq DirectFast Library Kit（illumina）from TIANGEN following manufacture's protocols.

value: liver

value: human hepatoma cell

value: transfected with McccDNA


title: MM130253

description:
Library name: MM130253
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: peripheral blood


title: HepG2 cell, PAOA, MPRA mRNA barcode reads replicate 3

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

institute: Guangzhou National Laboratory

description: MPRA RNA barcode reads used for regulatory activity analysis

data_processing:
For plasmid library, Read 1 sequences were trimmed by cutadapt with the parameters --discard-untrimmed -m 80 -g GGCCTAACTGGCCGGTACCCTGAGTACTGTATGGGCGGGTACC, read 2 were trimmed by cutadapt with parameters --discard-untrimmed -l 20 -g TCACCATGGTGGCTTTACCAACAG. Then Read 1 sequences were mapped to 107bp variants sequences using bwa mem with parameters -L 100 -k 8 -O 5. Reads retained with  mapping score >0.95. Paired Read 2 sequences from the plasmid library corresponding to the retained Read 1 were used to construct oligo-barcode pairs.
For both cDNA and DNA libraries, read1 sequences were trimmed from the beginning using cutadapt with parameters --discard-untrimmed -l 20 -g CTTGGCAATCCGGTACTTAGCGCATCTAAC. The reverse complement of the subsequent 20 bp sequences was treated as barcode sequences.
Summarizing the total barcodes associated with each oligo from cDNA and DNA libraries seperately, following the MPRAprofiler protocol as described by Lu et al., 2021, Nature Communications.
Enhancers were identified using DESeq2 with an adjusted p-value < 0.05 and a log₂ fold change > 0. For enhancer variants, calculated the count ratio between the reference and alternative alleles, using the median ratio of four DNA replicates as a control, then normalized all RNA ratios and performed a Student’s t-test to calculate p-values. Benjamini-Hochberg method was applied to adjust the p-values for multiple testing, and variants with an adjusted p-value < 0.05 were designated as significant differentially active variants.
Assembly: hg38
Supplementary files format and content: Variant and barcode pairs used for mapping barcodes to variants.
Supplementary files format and content: MPRA cDNA and DNA barcode reads used for regulatory activity analysis
Library strategy: MPRA

growth_protocol: HepG2 or LX-2 cells were cultured in DMEM supplemented with 10% FBS, 100 U/mL penicillin and 100 µg/mL streptomycin, in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
Cells were harvested using the Quick DNA/RNA Miniprep Kit (ZYMO, D7001) for simultaneous DNA and RNA extraction, with an additional DNase treatment (TaKaRa) to ensure DNA-free RNA.
For each biological replicate, 240 µg of RNA and 48 µg of DNA were used for RNA/DNA-Lib construction, by using SuperScript II (for cDNA synthesis) and NEBNext® High-Fidelity 2X PCR Master Mix (for PCR amplification).

treatment_protocol: For HepG2 MPRA, the MPRA plasmid libraries were transfected into cells followed with or without PAOA treatment (0.2 mM PA and 1.0 mM OA) for 24h; For LX-2 MPRA, the MPRA plasmid libraries were transfected into cells followed with or without TGF-β₁ treatment (20 ng/mL) for 36h.

value: hepatocyte cell line

value: WT

value: Palmitic acid and oleic acid (PAOA)


title: Y1_PIMQ_ATAC-seq_Rep2

description:
Library name: Sample 9
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).

value: Epidermal Stem Cell

value: wildtype


title: Y1_Naive_ATAC-seq_Rep2

description:
Library name: Sample 5
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).

value: non-treated


title: 22Rv1_CTC_5

description: Library name: 22Rv1_CTC_5

value: prostate


title: Y1_Naive_ATAC-seq_Rep4

description:
Library name: Sample 7
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).


title: 22Rv1_CTC_6

description: Library name: 22Rv1_CTC_6


title: MM130239

description:
Library name: MM130239
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: m1092-DKO

description: Library name: m1092-DKO

value: cardiomyocyte


title: MM130238

description:
Library name: MM130238
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: 22Rv1_CTC_7

description: Library name: 22Rv1_CTC_7


title: MM130231

description:
Library name: MM130231
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: MM130245

description:
Library name: MM130245
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_ATAC-seq_Rep1

description:
Library name: Sample 4
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).


title: cells for DC timeline study, date 202302 (batch 0)

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

description:
Library name: 202302_0_Nextseq
SmartSeq2

data_processing:
Make fastq and demultiplex with bcl2fastq 2.20
Alignment with STAR
Counted with htseq-count.
Assembly: GRCm39

source_name: see CSV file

growth_protocol: Spleen and lymph nodes from OT-1-Thy1.1 mice were collected and placed into cold PBS on ice. The tissues were torn apart into ~ 0.2 mm3 pieces with forceps and scissors and next incubated in the Tissue Digestion Buffer at 37 °C, 110 g for 30 min in an Eppendorf ThermoMixer (Eppendorf, Hamburg, Germany). Cell suspensions were transferred into a 50 mL tube through a 100 μm cell strainer (Corning Inc., Corning NY, USA) with a 1 mL syringe plunger. Lymph nodes were washed through the cell strainer using cold PBS (Thermo Fisher Scientific, Waltham MA, USA), while the spleen was washed through the cell strainer using the Red Blood Cell Lysis Solution and then washed twice using cold PBS. Cell counting was done on a hemocytometer by adding 0.4 % Trypan Blue solution (Thermo Fisher Scientific, Waltham MA, USA) to cell suspensions.

extract_protocol:
After seeding into U40 nanowell slides, CD8+ T cells, DCs, and doublets were picked by the 30 µm glass capillary under the automatic picking mode of CellCelector (Sartorius AG, Niedersachsen, Germany). Three channels (i.e. brightfield, FITC for CD8+ T cells labelled with CellTrace CFSE, and TRITC for DCs labelled with CellTrace Yellow) were selected for scanning to validate cell type. Captured cells with 0.1 uL DNase/RNase-Free Water were dispensed into a 384-well Frame-Star plate containing 1.1 μL lysis buffer. The lysis plate was cooled down to 4 °C at the rack tray during cell capture and was stored at −80 °C for subsequent procedures.
The library was prepared following Smart-seq2 protocol 58. Briefly, cells were picked into 384 well lysis plates followed by reverse transcription, template switching and 23 cycles of PCR to generate and amplify the cDNA. MANTIS automated liquid handler (Tecan, Zürich, Switzerland) was used during the process. cDNA was normalised to 0.1-1 ng/µl according to the qualification by Quant-iT™ PicoGreen™ dsDNA Assay Kit (Thermo Fisher Scientific, Waltham MA, USA) via automated liquid handling robot Mosquito (SPT Labtech, Melbourn, Cambridgeshire, UK). TruePrep DNA Library Prep Kit V2 (Vazyme #TD503, Nanjing, China) with 15 cycles of amplification were used for tagmenting immune cells. Purification was conducted to remove primer by Agencourt Ampure XP (Beckman Coulter, Brea CA, USA) magnetic beads at a ratio of 0.7x two times. Libraries were quantified using Bioanalyzer 2100 (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: Enriched DCs were incubated with 5 ug/mL OVA257-263 (AnaSpec, Fremont CA, USA) inside a humidified 5 % CO2 incubator maintained at 37 °C for 0, 5, 10, 20, and 30 min (OVA257-263 was added at different times to ensure the incubation for each group ended at the same time). Culture media was added to achieve a 1 in 5 dilution of OVA257-263, after which the DCs were pelleted and resuspended in FACS buffer. 12 single cells from each group were sorted by BD LSRFortessa to a 384-well Frame-Star plate containing 1.2 μL lysis buffer. The plate was stored at −80 °C for subsequent procedures.

value: see CSV file


title: 22Rv1_CTC_4

description: Library name: 22Rv1_CTC_4


title: m1101-Control

description: Library name: m1101-Control

value: control


title: 22Rv1_CTC_2

description: Library name: 22Rv1_CTC_2


title: m1091-Control

description: Library name: m1091-Control


title: 22Rv1_CTC_1

description: Library name: 22Rv1_CTC_1


title: 22Rv1_CTC_3

description: Library name: 22Rv1_CTC_3


title: HepG2 cell, PAOA, MPRA DNA barcode reads replicate 2

description: MPRA DNA barcode reads used for regulatory activity analysis


title: Y1_Naive_ATAC-seq_Rep3

description:
Library name: Sample 6
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).


title: MM130234

description:
Library name: MM130234
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: European American

value: male


title: m1124-DKO

description: Library name: m1124-DKO

value: DKO


title: D180_Naive_ATAC-seq_Rep2

description:
Library name: Sample 2
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).

value: Skin


title: m1046-DKO

description: Library name: m1046-DKO


title: Lsd1_ko2

city: Boston

first: Zhe

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

data_processing:
Visualization Pipeline for RNAseq (Viper) analysis tool developed by Center for Functional Cancer Epigenetics (CFCE) at Dana-Farber Cancer Institute was used to generate standard outputs.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include normalized FPKM matrices for each Sample .

source_name: Mammary tumor cells from MMTV-PyMT female mouse

extract_protocol:
YFP+ mammary tumor cells were sorted from MMTV-PyMT female mice with the corresponding genotypes 2-3 months after intraductal injection of Ad-K8-Cre, and RNA was harvested from the sorted cells using Trizol reagent.
RNA libraries were prepared for sequencing using Low Input mRNA Library (Clontech SMARTer) v4 kit

value: Sorted YFP+ PyMT mammary tumor cells 2-3 months after intraductal injection of Ad-K8-Cre adenovirus to MMTV-PyMT;Lsd1+/+;R26Y

value: female

tag: condition

value: 2-3 month after Ad-K8-Cre intraductal injection

value: Lsd1 knockout


title: m1026-DKO

description: Library name: m1026-DKO


title: m1066-Control

description: Library name: m1066-Control


title: MM130230

description:
Library name: MM130230
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: peripheral blood


title: m1067-DKO

description: Library name: m1067-DKO


title: m1022-Control

description: Library name: m1022-Control


title: HepG2 cell, PAOA, MPRA mRNA barcode reads replicate 2

value: hepatocyte cell line

value: WT

value: Palmitic acid and oleic acid (PAOA)


title: MM130223

description:
Library name: MM130223
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: cells for doublet study, date 202302 (batch 3)

description:
Library name: 202302_3_Nextseq
SmartSeq2


title: MM130219

description:
Library name: MM130219
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: HepG2 cell, control, MPRA mRNA barcode reads replicate 2

description: MPRA RNA barcode reads used for regulatory activity analysis

value: Control


title: HepG2 cell, PAOA, MPRA mRNA barcode reads replicate 1


title: Lsd1_wt2

value: wild-type for Lsd1


title: 69, DKO, d1

description: Library name: 69

value: cardiomyocyte


title: m1064-Control

description: Library name: m1064-Control

value: control


title: D180_Naive_ATAC-seq_Rep1

description:
Library name: Sample 1
50-bp paired-end FASTQ files were aligned to the mm10 genome from the GENCODE (v.30) database using BWA-mem with parameters -M -T 10 in paired-end mode. All BAM files showed >90% mapping rate. BAM files were filtered using samtools -F 1804 -f 2 -q 30 to remove unmapped reads, secondary alignments, optical duplicates, and reads that failed platform or vendor quality checks or had low mapping quality. PCR duplicates were identified and marked by Picard and removed using Samtools. BAM files were filtered to only consider alignments mapping from Chr 1-19 and ChrX. Other alignments mapping to scaffolds or blacklist (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed using bedtools intersect. Normalized bigWig files were calculated using the coverage function from the rtracklayer package and normalized by Counts Per Million (CPM). Deeptools bamcompare was used to generate log2 ratio bigWigs of post-inflamed vs control conditions. Forward and reverse reads from BAM files were separated to generate TAG files in BED format. Offsets were adjusted such that reads mapped to the plus strand were shifted by +4, while reads mapped to the reverse strand were shifted by -5. Peaks were called for each replicate with MACS3 using as input the TAG files with the parameters -f BED --nomodel --shift -75 --extsize 150 -g 2652783500 (mouse genome length in bp).

value: Epidermal Stem Cell

value: wildtype

value: non-treated


title: HepG2 cell, PAOA, MPRA DNA barcode reads replicate 3


title: MM130217

description:
Library name: MM130217
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: European American

value: male


title: HepG2 cell, PAOA, MPRA DNA barcode reads replicate 1


title: m1088-Control

description: Library name: m1088-Control


title: Primary neuron CHX Rep2

city: Chicago

first: Xiaochang

last: Zhang

state: IL

department: Department of Human Genetics

institute: University of Chicago

description:
Library name: Primary neuron CHX Rep2
Primary neurons from E16.5 CD1 mouse dorsal cortices were dissociated with Papain (Worthington),resuspended, and cultured in the Neurobasal medium with GlutaMax, N2, and B27 supplements. On the firstday in vitro, primary neurons were treated with 50 μg/mL cycloheximide (CHX, Sigma-Aldrich, C4859) for 8 hours before RNA extraction Quick-RNA MiniPrep Kit (Zymo) andsequencing (75-bp paired-end). Rep2

data_processing:
Differential expressed gene (DEG) analysis was performed using the STAR-FeatureCounts-DESeq2 workflow. Briefly, short reads were aligned to the reference genome using the STAR aligner with the sameparameters as AS-events detection, and the gene expression quantification was performed using FeatureCounts.DESeq2 was then used to identify DEGs based on the criteria of adjusted p < 0.001 and |log₂FC|>1 as default.
Assembly: mm10
Supplementary files format and content: raw_counts.txt

source_name: Primary neuron

extract_protocol:
RNA was extractedfrom cultured cells using RNeasy Mini Kits (QIAGEN, 74104), RNA extraction Quick-RNA MiniPrep Kit (Zymo)
Sequencing libraries were built by Illumina TruSeqStranded Total RNA Library Prep Kit

value: Primary neuron

value: CHX


title: cells for doublet study, date 202210 (batch 1)

description:
Library name: 202210_1_Nextseq
SmartSeq2

value: see CSV file


title: HepG2 cell, control, MPRA DNA barcode reads replicate 3

value: hepatocyte cell line


title: HepG2 cell, control, MPRA mRNA barcode reads replicate 3

value: WT


title: MM130179

description:
Library name: MM130179
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: peripheral blood


title: MM130180

description:
Library name: MM130180
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: 33, DKO, d1

description: Library name: 33

value: DKO


title: MM130218

description:
Library name: MM130218
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: MM130208

description:
Library name: MM130208
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: MM130216

description:
Library name: MM130216
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: Lsd1_wt1

value: Sorted YFP+ PyMT mammary tumor cells 2-3 months after intraductal injection of Ad-K8-Cre adenovirus to MMTV-PyMT;Lsd1+/+;R26Y

value: female

value: 2-3 month after Ad-K8-Cre intraductal injection

value: wild-type for Lsd1


title: HepG2 cell, control, MPRA DNA barcode reads replicate 1

description: MPRA DNA barcode reads used for regulatory activity analysis

value: Control


title: cells for doublet study, date 202210 (batch 2)

description:
Library name: 202210_2_Nextseq
SmartSeq2


title: MM130165

description:
Library name: MM130165
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: HepG2 cell, control, MPRA mRNA barcode reads replicate 4


title: 56, control, d1

description: Library name: 56

value: cardiomyocyte

value: control


title: Neuro2a_(N2a)_Upf1-siRNA_replicate_1

description:
Library name: MM N2a Upf1 siRNA rep1
Mus musculus Neuro2a cell transfected with Upf1 siRNA by lipo2000 for 48h, biological replicate 1


title: Lsd1_ko1

value: Lsd1 knockout


title: MM130182

description:
Library name: MM130182
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: European American

value: male


title: Ni_72h, scRNA-seq

city: Wuerzburg

first: Marc

last: Schmidt

address: Josef Schneider Str. 2

department: Dept. of Dermatology

institute: University Hospital Wuerzburg

description: SCC0068_2_Schmidt-Goebler_Sample_4_GEX_C11

data_processing:
Samples demultiplexing, reads mapping, and genes counting were perfomred using cellranger-7.0.1 (Nature Communications. 8: 1-12, doi:10.1038/ncomms14049)
Further background removal was performed using Cellbender (Nature Methods, 2023. https://doi.org/10.1038/s41592-023-01943-7) with options --fpr 0.01  --epochs 150
Doublet removal was performed using scDblFinder ( f1000research. doi:10.12688/f1000research.73600.1.)
Downstream analysis of barcodes was peroformed mainly using Seurat (Stuart and Butler et al. Comprehensive Integration of Single-Cell Data. Cell (2019))
Assembly: GRCh38
Supplementary files format and content: Tab separated values files and matrix files

source_name: skin

extract_protocol:
Punch biopsies were rinsed once in 70% ethanol and twice in sterile PBS, freed of fat, and cut into small pieces. Pieces were then incubated overnight at 37°C in RPMI medium containing 10% FCS, 1% penicillin/streptomycin, 8 µg/ml collagenase type IV and 21 µg/ml DNAse I to facilitate cell extraction. Cells were released from the digested tissue using a gentleMACS dissociator (Miltenyi), and isolated single cells separated from undissociated tissue by filtering the cell solution through a 100 µm cell sieve. Subsequently, dead cells were removed using a commercial dead cell removal kit (Miltenyi), and single cell suspensions adjusted to an appropriate concentration suitable for cell labelling and subsequent single cell sequencing using a hemocytometer.
Library was performed according to the manufacturer's instructions (Dual index Chromium Next GEM Single Cell 3’ Reagent Kits v3.1).
Droplet based scRNA-seq

value: skin


title: 55, DKO, d1

description: Library name: 55


title: MM130210

description:
Library name: MM130210
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: Cr2O7_8h, scRNA-seq

description: SCC0068_2_Schmidt-Goebler_Sample_3_GEX_C10


title: 22, control, d1

description: Library name: 22


title: 79, DKO, d1

description: Library name: 79


title: Neuro2a_(N2a)_control-siRNA_replicate_1

description:
Library name: MM N2a Control rep1
Mus musculus Neuro2a cell transfected with control siRNA by lipo2000 for 48h, biological replicate 1


title: Ni_8h, scRNA-seq

description: SCC0068_2_Schmidt-Goebler_Sample_2_GEX_C9


title: cytosolic RNA in LbetaT2 gonadotropes sample 3

city: Haifa

first: Philippa

last: Melamed

address: Technion City

country: Israel

institute: Technion-Israel Institute ofTechnology

description: Library name: Sample_cyt_3

data_processing:
FASTQ, cutadapt, Tophat2, HTseq-count
Assembly: mm10
Supplementary files format and content: Bam

molecule: cytoplasmic RNA

growth_protocol: high glucose DMEM with 10% FCS, incubated at 37C under 5% CO2

extract_protocol:
Separation according to Conrad and Ørom (10.1007/978-1-4939-4035-6_1) - RNA extracted using Trizol and cleaned with RNA clean & concentrator kit, Zymo.
RNA libraries were prepared using SMARTer stranded total RNA-seq kit v2, following manufacturer's instructions.

value: gonadotrope


title: HepG2 cell, control, MPRA mRNA barcode reads replicate 1

description: MPRA RNA barcode reads used for regulatory activity analysis

value: hepatocyte cell line

value: WT


title: cytosolic RNA in LbetaT2 gonadotropes sample 2

description: Library name: Sample_cyt_2


title: HepG2 cell, control, MPRA DNA barcode reads replicate 2


title: MM130157

description:
Library name: MM130157
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: MM130166

description:
Library name: MM130166
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: MM130155

description:
Library name: MM130155
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: Y2_PIMQ_WGBS_Rep2

description:
Library name: Sample 24
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.

data_processing:
Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region
Assembly: GRCm38 (mm10)
Supplementary files format and content: Bigwig

extract_protocol:
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines
Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads.

value: Skin

value: Epidermal Stem Cell

value: wildtype

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


title: 35, DKO, d1

description: Library name: 35

value: DKO


title: MM130178

description:
Library name: MM130178
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: HepG2 cell, control, MPRA DNA barcode reads replicate 4

value: Control


title: Primary neuron DMSO Rep2

description:
Library name: Primary neuron DMSO Rep2
Primary neurons from E16.5 CD1 mouse dorsal cortices were dissociated with Papain (Worthington),resuspended, and cultured in the Neurobasal medium with GlutaMax, N2, and B27 supplements. On the firstday in vitro, primary neurons were treated with 50 μg/mL c  DMSO as controlfor 8 hours before RNA extraction. Rep2

value: Primary neuron

value: DMSO


title: Primary neuron CHX Rep1

description:
Library name: Primary neuron CHX Rep1
Primary neurons from E16.5 CD1 mouse dorsal cortices were dissociated with Papain (Worthington),resuspended, and cultured in the Neurobasal medium with GlutaMax, N2, and B27 supplements. On the firstday in vitro, primary neurons were treated with 50 μg/mL cycloheximide (CHX, Sigma-Aldrich, C4859) for 8 hours before RNA extraction Quick-RNA MiniPrep Kit (Zymo) andsequencing (75-bp paired-end). Rep1

value: CHX


title: Neuro2a_(N2a)_Upf1-siRNA_replicate_2

description:
Library name: MM N2a Upf1 siRNA rep2
Mus musculus Neuro2a cell transfected with Upf1 siRNA by lipo2000 for 48h, biological replicate 2


title: Ctrl_8h, scRNA-seq

description: SCC0068_2_Schmidt-Goebler_Sample_1_GEX_C8


title: 25, control, d1

description: Library name: 25

value: cardiomyocyte

value: control


title: MM130161

description:
Library name: MM130161
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: European American

value: male


title: MM130162

description:
Library name: MM130162
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: Y2_Naive_WGBS_Rep2

description:
Library name: Sample 22
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.

value: Untreated P60 mouse back-skin control


title: Neuro2a_(N2a)_control-siRNA_replicate_2

description:
Library name: MM N2a Control rep2
Mus musculus Neuro2a cell transfected with control siRNA by lipo2000 for 48h, biological replicate 2


title: 29, DKO, d1

description: Library name: 29


title: MM130152

description:
Library name: MM130152
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: Primary neuron DMSO Rep1

description:
Library name: Primary neuron DMSO Rep1
Primary neurons from E16.5 CD1 mouse dorsal cortices were dissociated with Papain (Worthington),resuspended, and cultured in the Neurobasal medium with GlutaMax, N2, and B27 supplements. On the firstday in vitro, primary neurons were treated with 50 μg/mL c  DMSO as controlfor 8 hours before RNA extraction. Rep1


title: Y2_Naive_WGBS_Rep1

description:
Library name: Sample 21
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.


title: Cr2O7_72h, scRNA-seq

description: SCC0068_2_Schmidt-Goebler_Sample_5_GEX_C12

value: skin


title: MM130159

description:
Library name: MM130159
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

value: African American


title: 62, control, d1

description: Library name: 62


title: 13, control, d1

description: Library name: 13


title: MM130150

description:
Library name: MM130150
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: cytosolic RNA in LbetaT2 gonadotropes sample 1

description: Library name: Sample_cyt_1

value: gonadotrope


title: Y1.5_Naive_WGBS_Rep2

description:
Library name: Sample 18
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.

value: Skin

value: Epidermal Stem Cell

value: wildtype


title: A498 ELOVL2 and ELOVL5 double knockdown replicate 2

city: Tsukuba

first: Shotaro

last: Sakka

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description:
Library name: A498_siELOVL2_5_rep2
A498 renal cancer cells, ELOVL2 and ELOVL5 double knockdown, biological replicate 2

data_processing:
Raw sequencing reads were processed and quantified using the CLC Genomics Workbench pipeline.
Gene-level expression values were obtained for all samples.
Normalized expression values were generated and used for downstream comparative analyses among control, ELOVL2 knockdown, ELOVL5 knockdown, and double knockdown groups.
Differential expression-related statistical analyses, including ANOVA-based comparisons, were performed on the processed expression matrix.
Assembly: Homo sapiens reference genome.
Supplementary files format and content: The processed data file contains a gene-by-sample expression matrix including normalized expression values for all 12 samples. Rows correspond to genes/features, and columns correspond to individual samples.
Supplementary files format and content: Additional processed data include statistical analysis results derived from the normalized expression matrix.

growth_protocol: A498 renal cancer cells were maintained under standard cell culture conditions until siRNA transfection.

extract_protocol:
Total RNA was extracted from A498 renal cancer cells after siRNA transfection. RNA quality and quantity were assessed prior to library preparation.
RNA-seq libraries were prepared from total RNA obtained from A498 renal cancer cells transfected with control siRNA or siRNAs targeting ELOVL2, ELOVL5, or both genes. Libraries were validated using a Bioanalyzer (Agilent Technologies) to determine size distribution and concentration. Validated libraries were sequenced on an Illumina NextSeq 500 platform using the paired-end 36-base read option.

treatment_protocol: Cells were transfected with control siRNA or siRNAs targeting ELOVL2, ELOVL5, or both genes and harvested for RNA extraction.

value: ELOVL2 and ELOVL5 double knockdown


title: MM130160

description:
Library name: MM130160
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: chromatin-associated RNA in LbetaT2 gonadotropes sample 3

description: Library name: Sample_crom_3

molecule: nuclear RNA


title: 14, control, d1

description: Library name: 14


title: Y2_PIMQ_WGBS_Rep1

description:
Library name: Sample 23
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.

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


title: Brain Organoid, MTK, Day 60, scRNAseq, biol rep2

city: Shanghai City

first: Yali

address: No.320, Yueyang Avenue

institute: Center for Excellence in Molecular Cell Science

description: GEXSCOPE

library_source: other

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1 contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information.
Assembly: GRCh38
Supplementary files format and content: matrix files

molecule: other

extract_protocol:
Organoids were stored at 4 ℃ GEXSCOPETM Tissue Preservation Solution. Then, we washed samples for 3 times with Hanks Balanced Salt Solution (HBSS) and minced them into 1–2 mm-thick pieces, 2 ml GEXSCOPETM Tissue Dissociation Solution (Singleron Biotechnologies) was added to each sample and allowed for digestion at 37 ℃ for 15 minutes to dissociate the tissue into single cells. Then, we filtrate the samples using 40-μm sterile strainers, followed by centrifuging at 1,000 rpm for 5 minutes. After the centrifugation, the precipitation was resuspended in 1 ml phosphate-buffered saline (PBS; HyClone, Marlborough, United States). Subsequently, 2 ml GEXSCOPETM Red Blood Cell Lysis Buﬀer (Singleron Biotechnologies) was added into the cell suspension and incubated at 25°C for 10 minutes to remove red blood cells. After that, the mixture was centrifuged at 500 × g for 5 minutes, followed by re-suspending the precipitation with PBS.
We used GEXSCOPETM Single Cell RNA Library Kit Tissue (Singleron Biotechnologies) to barcode single cells, capture mRNA from isolated single cells, and generate cDNA libraries for scRNA-seq. Then, individual libraries were diluted to 4 ng/μl, and pooled for sequencing on a Novaseq6000 platform (Illumina, San Diego, USA)

treatment_protocol: The medium with the addition of DMSO or 18.5 μM MTK or 10 μM DEAB was refreshed every day from day 20 to day 60.

value: Human embryonic stem cells

value: WT

value: cerebral differentiation with MTK treatment

tag: time

value: Day 60


title: A498 ELOVL5 knockdown replicate 3

description:
Library name: A498_siELOVL5_rep3
A498 renal cancer cells, ELOVL5 knockdown, biological replicate 3

value: ELOVL5 knockdown


title: Brain Organoid, DMSO, Day 60, scRNAseq, biol rep1

description: GEXSCOPE

value: cerebral differentiation with DMSO treatment


title: Brain Organoid, MTK, Day 60, scRNAseq, biol rep3

description: GEXSCOPE


title: Y1_PIMQ_WGBS_Rep2

description:
Library name: Sample 16
200,000 EpdSCs were FACS purified, washed once with PBS and snap frozen before undergoing DNA extraction. Each biological replicate from each condition consisted of at least two pooled mice. The DNA was sheared in Covaris micro TUBE AFA Fiber Pre-Slit Snap-Cap tubes (SKU: 520045) and cleaned up with the Zymo DNA Clean & Concentrator-5 kit (#D4013) following manufacturer’s guidelines. Sheared gDNA was bisulfite converted following manufacturer's guidelines with the EZ DNA Methylation-Gold Kit (Zymo #D5005), and libraries were prepared using the Accel-NGS Methyl-seq DNA library kit (Swift Biosciences, #30024-SWI). Libraries were cleaned using Agencourt AMPure XP beads (Beckman Coulter, #A63881), and the absence of adapters was confirmed on the Agilent TapeStation HS D5000. The final libraries were sequenced on a NovaSeq platform (Illumina) yielding 150 bp paired-end reads. Raw reads were subjected to adapter and quality trimming using cutadapt (v4.6; parameters: --quality-cutoff 20 --overlap 5 --minimum-length 25; Illumina TruSeq adapter clipped from both reads), followed by trimming of 10 and 5 nucleotides from the 5’ and 3’ end of the first read and 15 and 5 nucleotides from the 5’ and 3’ end of the second read. Trimmed reads were aligned to the mouse genome (mm10) using BSMAP (v2.90; parameters: -v 0.1 -s 16 -q 20 -w 100 -S 1 -u -R). Sorted BAM files were generated and indexed using samtools with the ‘sort’ and ‘index’ commands (v1.10). Duplicates were removed using GATK4 (v4.5.0.0) MarkDuplicates with lenient validation, duplicate removal enabled, and coordinate-sorted input. Methylation rates were called using mcall from the MOABS package (v1.3.9.6; default parameters). All methylation analyses were restricted to autosomes and only CpGs covered by at least 10 and at most 150 reads were considered for downstream analyses.  Replicates were grouped after filtering for coverage by calculating the arithmetic of the remaining positions given their presence in at least one replicate. Region-specific methylation was assessed by calculating average (arithmetic mean) methylation across features using bigWigAverageOverBed from UCSC tools, where a feature was only considered if at least three CpGs were covered within a region.


title: MM130142

description:
Library name: MM130142
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: European American

value: male


title: Brain Organoid, MTK, Day 60, scRNAseq, biol rep1

description: GEXSCOPE


title: Brain Organoid, DEAB, Day 60, scRNAseq, biol rep3

description: GEXSCOPE

value: cerebral differentiation with DEAB treatment


title: chromatin-associated RNA in LbetaT2 gonadotropes sample 1

description: Library name: Sample_crom_1


title: Brain Organoid, DEAB, Day 60, scRNAseq, biol rep2

description: GEXSCOPE


title: MM130153

description:
Library name: MM130153
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

value: African American


title: A498 ELOVL2 and ELOVL5 double knockdown replicate 3

description:
Library name: A498_siELOVL2_5_rep3
A498 renal cancer cells, ELOVL2 and ELOVL5 double knockdown, biological replicate 3