title: MM130882

description:
Library name: MM130882
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: MM130896

status: Public on Mar 16 2026

type: SRA

city: New Orleans

first: Hong-Wen

last: Deng

state: LA

country: USA

institute: Tulane University

description:
Library name: MM130896
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

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

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

tag: tissue

value: peripheral blood

tag: cell type

value: monocytes

tag: population

value: European American

tag: Sex

value: male

tag: age

tag: bmi

tag: smoke

tag: alcohol drinking


title: MM130884

description:
Library name: MM130884
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: AY25

type: genomic

city: BETHESDA

first: Zhichao

last: Wu

state: MD

address: BG 10 RM 4A31 MSC 1500, 10 CENTER DR

department: Center for Cancer Research

institute: NIH/NCI

description: Tumor

hyb_protocol: standard Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: R package minfi v1.40.0

label: Cy5 and Cy3

source_name: ICMT

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was bisulfite-converted with the EZ DNA Methylation Kitm (Zymo Research D5001)

tag: gender

value: M

tag: progression-free survival

tag: progression status

tag: material

value: FFPE

tag: arraytype

value: IlluminaHumanMethylationEPIC


title: ADISSP-1

city: Worcester

first: Marcus

last: Ruscetti

state: MA

address: 364 Plantation Street

department: MCCB

institute: UMass Chan Medical School

description:
Library name: ADISSP-1
Column name in raw counts_All_Samples.txt: Adissp-1

library_source: transcriptomic

data_processing:
Raw FASTQ files were processed using the OneStopRNAseq platform, which performed read alignment, quality control, feature counting, differential gene expression analysis, and other downstream analyses.
Reads were aligned to mm39 with STAR.
Feature counting was performed using featureCounts with the annotation file Mus_musculus.GRCm39.111.gtf.
Assembly: mm39
Supplementary files format and content: Tab-delimited Excel files including raw counts, TPM, and FPKM values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: iWAT

extract_protocol:
Total RNA was extracted from iWAT tissues using TRIzol reagent.
One microgram of total RNA per sample was used to generate RNA-seq libraries in biological triplicates, using KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche, Cat#KK8561). The amplified libraries were sequenced on an Illumina NovaSeq X platform.

value: iWAT

tag: genotype

value: WT mice fed with high-fat diet

tag: treatment

value: ADISSP

tag: batch


title: ADISSP-2

description:
Library name: ADISSP-2
Column name in raw counts_All_Samples.txt: Adissp-2


title: MM130874

description:
Library name: MM130874
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: AZ91

description: Tumor

value: F


title: MM130872

description:
Library name: MM130872
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: FA_3

city: Nanjing City

first: shuting

last: huang

address: No. 109, Longmian Avenue, Jiangning District

country: China

institute: Nanjing Medical University

description: Library name: Sample9

data_processing:
Samples are sequenced on the platform to getimage files, which are transformed by thesoftware of the sequencing platform, and theoriginal data in FASTQ format (Raw Data) isgenerated. Sequencing data contains a numbeof connectors, low-quality Reads, so we usefastp(0.22.0) software to filter the sequencingdata to get high quality sequence (Clean Data)for further analysis
Assembly: WBcel235
Supplementary files format and content: FPKM for each sample

organism: Caenorhabditis elegans

source_name: whole tissue

extract_protocol:
Total RNA was extracted by the chloroformmethod.
RNA-seqlibrary was cunstructed by usingNEBNext Ultra ll RNA Library Prep Kit forlllumina.

value: whole tissue

value: FA


title: AX91

description: Tumor


title: HFD_3

description: Library name: Sample6

value: HFD


title: MM130868

description:
Library name: MM130868
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: MM130869

description:
Library name: MM130869
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: AU59

description: Tumor


title: MM130865

description:
Library name: MM130865
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: LHCNM2, day12-4

city: Freising-Weihenstephan

first: Alexander

last: Bartelt

address: Gregor-Mendel-Str. 2

department: Chair of Translational Nutritional Medicine

country: Germany

institute: Technical University of Munich

description: Library name: Sample24

data_processing:
All workflows used in this study are available via the GitHub repository cited in the publication. Raw FASTQ reads were filtered using fastp to obtain high-quality clean data (Q30 > 90%). Reads were aligned to the reference genome using HISAT2 (v2.2.1), followed by transcript assembly with StringTie (v2.2.3) and gene-level quantification using featureCounts (v2.0.6).
Sequence reads were trimmed for adaptor sequence/low-quality
Assembly: Mus musculus (mm10) and Homo Sapiens (GRCh38/hg38)
Supplementary files format and content: counts_human.csv
Supplementary files format and content: counts_mouse.csv

extract_protocol:
RNA was harvested using Pure Link RNA Mini kit (Invitrogen)
RNA libraries were prepared by Novogene. Messenger RNA was isolated using poly-T oligo-attached magnetic beads, followed by cDNA synthesis using random hexamers. Libraries (including strand-specific options using dUTP) were prepared via end-repair, A-tailing, and adapter ligation, then validated using Qubit, real-time PCR, and Bioanalyzer for precise quantification and size distribution.

tag: cell line

value: skeletal myoblast

value: control


title: HFD_1

description: Library name: Sample4

tag: tissue


title: AK28

description: Tumor


title: MM130863

description:
Library name: MM130863
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

tag: cell type


title: MM130846

description:
Library name: MM130846
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

tag: population

value: African American


title: MM130850

description:
Library name: MM130850
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

tag: Sex


title: OP_3

description: Library name: Sample3

value: OP


title: MM130852

description:
Library name: MM130852
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

value: monocytes

tag: age


title: FA_2

description: Library name: Sample8


title: MM130860

description:
Library name: MM130860
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

tag: bmi


title: maltose, high salt, +small RNAs, rep2

city: Turku

first: Georgiy

middle: A

last: Belogurov

address: Tykistökatu 6

department: Dept. of Life Technologies

country: Finland

institute: University of Turku

description:
Library name: 06VT18
early saturation

data_processing:
The automated transcriptome assembly was conducted using Rockhopper v2.03 that aligned raw reads (FASTQ format) to the annotated S. africana DSM8902 genome, produced coverage traces (WIG format) and a table containing raw read counts and expression values (analogues of FPKM but normalized by the upper quartile of gene expression, excluding genes with zero expression) for annotated genome features.
As an alternative analysis method, raw reads (FASTQ format) were mapped to the S. africana genome using Bowtie2 v2.5.3. The resulting alignment in SAM format was sorted and indexed using SAMtools v1.19. Reads mapping to the genome features (Gene Transfer Format, GTF) were then counted using HTSeq v2.0.3. The HTSeq read counts were normalized using the transcripts per million (TPM) method.
Assembly: NC_017098, genome-build ASM24259v3; NCBI_Assembly GCA_000242595.3; CP003282.1 Spirochaeta africana DSM 8902.
Supplementary files format and content: Strand-specific read coverage of S. africana genome in .wig format. Output from Rockhopper.
Supplementary files format and content: Tab-delimited .txt file listing raw and normalized read counts for annotated genes/features names for two biological replicates (05VT17 and 06VT18). Raw and normalized output from Rockhopper. Expression values normalized using upper quartile of gene expression excluding genes with zero expression.
Supplementary files format and content: Tab-delimited .txt file listing raw and normalized read counts for annotated genes/features names for two biological replicates (05VT17 and 06VT18). Raw and TPM-normalized output from HTSeq.

organism: Spirochaeta africana

growth_protocol: S. africana was cultivated in a modified DSMZ alkaliphilic spirochaete medium #700 (sucrose was replaced with maltose and NaCl was increased to 50 g/l) at 30°C for 3 days (1:130 inoculum) to reach OD600 0.7-0.9 (samples 05VT17, 06VT18).

extract_protocol:
Total cell RNA was isolated using TRIzol® Max™ Bacterial RNA Isolation Kit (Thermofisher). Cells were harvested by centrifugation and resuspended in Max Bacterial Enhancement Reagent. The sample was then dissolved in TRIzol and extracted twice with cold chloroform. RNA was then precipitated from the aqueous phase by the addition of cold isopropanol. The RNA pellet was washed with 75% ethanol and dissolved in RNase-free water. The sample was treated with DNase (TURBO DNA-free™ Kit, Thermofisher), followed by cleanup using Qiagen RNAeasy mini kit. Briefly, the RNA sample was supplemented with 350 µl of high-salt proprietary buffer containing guanidine thiocyanate, 950 µl of ethanol (small RNAs retained) and applied to the silica-based spin column. The column was washed two times with the low-salt proprietary buffer containing 75% ethanol, and RNA was eluted with 50 µl of RNase-free water.
Total RNA was converted into a dual-indexed library using Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit, and sequenced with Illumina NovaSeq 6000 SP v1.5 (2x100 bp).

treatment_protocol: no treatment of cells


title: LHCNM2, day12-1

description: Library name: Sample21


title: HFD_2

description: Library name: Sample5


title: maltose, high salt, +small RNAs, rep1

description:
Library name: 05VT17
early saturation


title: MM130857

description:
Library name: MM130857
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

tag: smoke


title: LHCNM2, day12-3

description: Library name: Sample23


title: FA_1

description: Library name: Sample7


title: MM130854

description:
Library name: MM130854
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

tag: alcohol drinking


title: MM130851

description:
Library name: MM130851
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: MM130830

description:
Library name: MM130830
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: MM130859

description:
Library name: MM130859
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: C2C12, day6-4

description: Library name: Sample12


title: MM130839

description:
Library name: MM130839
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: MM130825

description:
Library name: MM130825
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: MM130818

description:
Library name: MM130818
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: MM130819

description:
Library name: MM130819
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: LHCNM2, day1-1

description: Library name: Sample17


title: C2C12, day6-2

description: Library name: Sample10


title: MM130817

description:
Library name: MM130817
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: LHCNM2, day0-3

description: Library name: Sample15


title: C2C12, day6-3

description: Library name: Sample11


title: MM130838

description:
Library name: MM130838
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: OP_1

description: Library name: Sample1


title: LHCNM2, day12-2

description: Library name: Sample22


title: MM130803

description:
Library name: MM130803
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: MM130808

description:
Library name: MM130808
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: LHCNM2, day0-2

description: Library name: Sample14


title: LHCNM2, day0-1

description: Library name: Sample13


title: MM130827

description:
Library name: MM130827
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: MM130836

description:
Library name: MM130836
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: OP_2

description: Library name: Sample2


title: LHCNM2, day1-3

description: Library name: Sample19


title: MM130802

description:
Library name: MM130802
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: LHCNM2, day1-2

description: Library name: Sample18


title: forebrain NPC differentiation, day 14, replicate 3, input

city: Gent

first: Eva

last: D'haene

address: Corneel Heymanslaan 10

department: Department of Biomolecular Medicine

country: Belgium

institute: Ghent University

description: Library name: fbNPC diff d14 rep3, input

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

source_name: fbNPC

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

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

value: fbNPC


title: LHCNM2, day0-4

description: Library name: Sample16


title: C2C12, day6-1

description: Library name: Sample9


title: MM130837

description:
Library name: MM130837
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: C2C12, day1-1

description: Library name: Sample5


title: LHCNM2, day1-4

description: Library name: Sample20


title: C2C12, day0-4

description: Library name: Sample4


title: variant and barcode mapping reads

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: reads used for associating barcodes with variants

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

organism: Escherichia coli

source_name: Lucigen Endura Electrocompetent Cells (Biosearch Technologies, Catalog No. 60242-2)

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: WT

value: NO


title: forebrain NPC differentiation, day 14, replicate 3, CTCF

description: Library name: fbNPC diff d14 rep3, CTCF


title: MM130815

description:
Library name: MM130815
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: MM130816

description:
Library name: MM130816
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: MM130793

description:
Library name: MM130793
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: MM130812

description:
Library name: MM130812
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: forebrain NPC differentiation, day 14, replicate3, H3K4me1

description: Library name: fbNPC diff d14 rep3, H3K4me1


title: C2C12, day1-3

description: Library name: Sample7


title: MM130791

description:
Library name: MM130791
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: C2C12, day1-4

description: Library name: Sample8


title: MM130814

description:
Library name: MM130814
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: MM130826

description:
Library name: MM130826
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: C2C12, day0-1

description: Library name: Sample1


title: MM130783

description:
Library name: MM130783
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: MM130813

description:
Library name: MM130813
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: C2C12, day1-2

description: Library name: Sample6


title: MM130801

description:
Library name: MM130801
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: forebrain NPC differentiation, day 14, replicate 2, CTCF

description: Library name: fbNPC diff d14 rep2, CTCF


title: MM130777

description:
Library name: MM130777
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: MM130797

description:
Library name: MM130797
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: MM130784

description:
Library name: MM130784
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: liver_male_TWD_replicate.3

city: Santa Cruz

first: Carlos

last: Diaz-Castillo

state: California

address: 448 Physical Sciences Building

institute: University of California Santa Cruz

description: Library name: L_M_TWD_688

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

source_name: liver

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

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

value: liver

tag: strain

tag: developmental stage

value: adult

value: TWD

tag: time

value: 12 weeks old

tag: animal id


title: MM130780

description:
Library name: MM130780
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: MM130796

description:
Library name: MM130796
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: liver_male_TWD_replicate.4

description: Library name: L_M_TWD_689

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


title: C2C12, day0-2

description: Library name: Sample2


title: MM130774

description:
Library name: MM130774
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: forebrain NPC differentiation, day 14, replicate 3, H3K27ac

description: Library name: fbNPC diff d14 rep3, H3K27ac


title: forebrain NPC differentiation, day 14, replicate 2, H3K4me1

description: Library name: fbNPC diff d14 rep2, H3K4me1


title: MM130770

description:
Library name: MM130770
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: forebrain NPC differentiation, day 14, replicate 3, H3K4me3

description: Library name: fbNPC diff d14 rep3, H3K4me3


title: MM130776

description:
Library name: MM130776
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: MM130782

description:
Library name: MM130782
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: C2C12, day0-3

description: Library name: Sample3


title: MM130786

description:
Library name: MM130786
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: MM130762

description:
Library name: MM130762
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: liver_male_IAS_replicate.5

description: Library name: L_M_IAS_818

value: IAS


title: MM130766

description:
Library name: MM130766
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: liver_male_TWD_replicate.5

description: Library name: L_M_TWD_808


title: forebrain NPC differentiation, day 14, replicate 1, H3K27ac

description: Library name: fbNPC diff d14 rep1, H3K27ac


title: MM130761

description:
Library name: MM130761
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: MM130779

description:
Library name: MM130779
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: MM130778

description:
Library name: MM130778
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: liver_male_IAS_replicate.4

description: Library name: L_M_IAS_804


title: forebrain NPC differentiation, day 14, replicate 2, H3K27ac

description: Library name: fbNPC diff d14 rep2, H3K27ac


title: MM130785

description:
Library name: MM130785
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: MM130773

description:
Library name: MM130773
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: liver_male_IAS_replicate.2

description: Library name: L_M_IAS_673


title: forebrain NPC differentiation, day 14, replicate 2, input

description: Library name: fbNPC diff d14 rep2, input


title: MM130756

description:
Library name: MM130756
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: liver_male_IAS_replicate.1

description: Library name: L_M_IAS_612


title: MM130769

description:
Library name: MM130769
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: MM130764

description:
Library name: MM130764
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: forebrain NPC differentiation, day 14, replicate 2, H3K4me3

description: Library name: fbNPC diff d14 rep2, H3K4me3


title: MM130771

description:
Library name: MM130771
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: forebrain NPC differentiation, day 14, replicate 1, CTCF

description: Library name: fbNPC diff d14 rep1, CTCF


title: liver_male_TWD_replicate.2

description: Library name: L_M_TWD_683


title: liver_male_DMSO_replicate.4

description: Library name: L_M_DMSO_713

value: DMSO


title: forebrain NPC differentiation, day 14, replicate 1, H3K4me1

description: Library name: fbNPC diff d14 rep1, H3K4me1


title: MM130746

description:
Library name: MM130746
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: liver_male_TWD_replicate.1

description: Library name: L_M_TWD_621


title: MM130768

description:
Library name: MM130768
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: forebrain NPC differentiation, day 14, replicate 1, H3K4me3

description: Library name: fbNPC diff d14 rep1, H3K4me3


title: forebrain NPC differentiation, day 14, replicate 1, input

description: Library name: fbNPC diff d14 rep1, input


title: MM130757

description:
Library name: MM130757
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: liver_male_IAS_replicate.3

description: Library name: L_M_IAS_779


title: liver_male_DMSO_replicate.1

description: Library name: L_M_DMSO_573


title: MM130759

description:
Library name: MM130759
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: MM130747

description:
Library name: MM130747
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: MM130735

description:
Library name: MM130735
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: liver_male_DMSO_replicate.5

description: Library name: L_M_DMSO_788


title: liver_male_DMSO_replicate.3

description: Library name: L_M_DMSO_703


title: MM130751

description:
Library name: MM130751
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: forebrain NPC TAD boundary deletion, UMI-4C FOXG1 viewpoint, replicate 1

description: Library name: fbNPC TADdel rep1 FOXG1

data_processing:
Reads were first filtered based on the presence of the downstream primer sequence (20% mismatch allowed). The resulting fastq files were used as input to the UMI-4C R package (https://github.com/tanaylab/umi4cpackage) to generate genomic interaction tracks representing UMI counts (i.e. unique interactions) per genomic restriction fragment. The package was then used to generate smoothed, viewpoint-specific interaction profiles for the region of interest. For each profile, interaction counts were normalized to the total UMI count within the profile.
Assembly: hg19
Supplementary files format and content: bedgraph files containing normalized (to total UMI count) and smoothed (using winCov parameter) interaction frequencies
Library strategy: 4C-Seq

growth_protocol: Induced pluripotent stem cells (iPSCs) Human iPSC cells (Axol Bioscience, lot #30270222072019) were cultured in feeder-free conditions on Geltrex® LDEV-Free hESC-Qualified Reduced Growth Factor Basement Membrane Matrix (Fisher Scientific #12063569)-coated 6-well plates in mTeSR Plus medium (Stemcell Technologies #100-0276) that was changed every other day. Cells were dissociated with ReLeSR (Stemcell Technologies #100-0483) after reaching 80% confluency.  Neural stem cells (NSCs) & Induced neurons (iNs) To minimize technical artifacts, hiPSCs were plated as single cells at 80% confluence on a Matrigel-coated 6-well plate with Y-27632 dihydrochloride (1 mg/mL). Polybrene was added at 8 mg/mL 1 h after re-plating. Cells were incubated with polybrene for 10–15 min prior to the addition of lentivirus. Lentiviral constructs for directed differentiation of hiPSCs into iNs were made as described previously. hiPSC lines were differentiated into NSCs with the protocol detailed by Thermo Fisher (MAN0008031).  Neural progenitor cells (NPCs) iPSCs were differentiated towards NPCs using the STEMdiff™ SMADi Neural Induction Kit following the monolayer protocol provided by the manufacturer (Catalog #08581), which directs differentiation by blocking TGF-β/BMP-dependent SMAD signalling. NPCs were seeded at a density of 4 × 105 cells per well in a Geltrex coated 12-well plate in STEMdiff™ SMADi Neural Induction medium over 8 or 12 days, with media changes each day. For the 12 day protocol the cells were split at day 6, for the 8 day protocol no split was performed.

extract_protocol:
UMI-4C was performed according to the protocol by Schwartzman et al. In brief, 1 (iNs), 5 (iPSCs, NSCs, NPCs) or 10 (LCLs) million cells per sample were detached, resuspended in a PBS/10% FBS solution and crosslinked using formaldehyde (final concentration 2%) (Sigma-Aldrich, F1635-500ML) for 10 min. The reaction was quenched on ice using glycine (final concentration 0.125M). Cells were then centrifuged, washed and resuspended in cold lysis buffer (50mM Tris-HCl, 150mM NaCl, 5mM EDTA, 0.5% NP-40, 1% Triton X-100 and 1 tablet protease inhibitor per 10mL (cOmplete, Mini, Sigma-Aldrich, 11836153001)) and incubated for 10 min. After centrifugation, pellets were washed, snap-frozen in liquid nitrogen and stored at -80°C until further processing. Frozen pellets were resuspended in 500µL pre-diluted DpnII buffer and 15µL pre-heated 10% SDS and incubated on a thermomixer for 1h at 37°C, shaking at 900 RPM. We halved these volumes and those mentioned below for smaller cell pellets (from 1 million cells). After adding 150µL 10% Triton X-100, the solution was incubated again (1h, 37°C, 900 RPM). We digested the chromatin using 600U DpnII (NEB, R0543L) in three stages (200U for 2h, 200U overnight, 200U for 2h) at 37°C and 900 RPM. The solution was incubated at 65°C for 20 min to inactivate the restriction enzyme and put on ice. Next, the chromatin was ligated by adding 4000U of T4 DNA ligase (NEB, M0202M) and 10x T4 DNA ligase buffer to a total volume of 1300µL and incubating the solution overnight at 16°C and 300 RPM. Ligated chromatin was de-crosslinked by incubation with 8µL proteinase K (20mg/mL, Qiagen, 19131) (overnight, 65°C, 300 RPM). A 3C template was then purified using 1x Ampure XP beads (Beckman Coulter, A63881).
Up to 4µg 3C template per sample was sheared using microTUBE snap-cap tubes (Covaris, 520045) in a Covaris M220 sonicator to an average fragment length of 300bp. UMI-4C sequencing libraries were generated using the NEBNext Ultra II library prep kit (NEB, E7645L). For each sample, library prep was performed in four parallel reactions with a maximum input of 1000ng per reaction, including an AmpureXP beads size selection targeting fragments with a length of 300-400bp (unless input was <100ng) and 4-8 cycles of PCR enrichment depending on the input. Next, two nested PCR reactions were performed to enrich for fragments captured by the viewpoint of interest, both using 2µL 10mM Illumina enrichment primer 2 and either a viewpoint-specific “upstream” (reaction 1, 2µL 10mM) or “downstream” (reaction 2, 2µL 10mM) primer. For each sample, we performed up to 8 nested PCR reactions in parallel with an input of 100-200ng per reaction using the KAPA2G Robust ready mix (Sigma-Aldrich, KK5702) in a volume of 50µL. PCR program: 3 min 95°C, 20 cycles (18 cycles for reaction 2) of 15 sec 95°C, 15 sec 55°C, 60 sec 72°C and final elongation of 5 min 72°C. Between PCR reactions the product was cleaned up using 1x AmpureXP beads and eluted in 21µL. The final PCR product was cleaned up using 0.7x AmpureXP beads and eluted in 25µL. Reactions per sample were pooled and library concentration was quantified via qPCR using the KAPA SYBR FAST qPCR Master Mix (Sigma-Aldrich, KK4602). UMI-4C libraries were pooled and sequenced on an Illumina HiSeq or NovaSeq (paired-end, 2x150 cycles).


title: MM130745

description:
Library name: MM130745
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: iPSC TAD boundary deletion, UMI-4C FOXG1 viewpoint, replicate 2

description: Library name: iPSC TADdel rep2 FOXG1

source_name: iPSC

value: iPSC


title: MM130740

description:
Library name: MM130740
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: forebrain NPC Enhancer Cluster deletion, UMI-4C FOXG1 viewpoint, replicate 1

description: Library name: fbNPC ECdel rep1 FOXG1


title: forebrain NPC TAD boundary deletion, UMI-4C PRKD1 viewpoint, replicate 2

description: Library name: fbNPC TADdel rep2 PRKD1


title: MM130758

description:
Library name: MM130758
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: forebrain NPC TAD boundary deletion, UMI-4C FOXG1 viewpoint, replicate 2

description: Library name: fbNPC TADdel rep2 FOXG1


title: MM130754

description:
Library name: MM130754
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: iPSC TAD boundary deletion, UMI-4C FOXG1 viewpoint, replicate 1

description: Library name: iPSC TADdel rep1 FOXG1


title: MM130742

description:
Library name: MM130742
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: liver_male_DMSO_replicate.2

description: Library name: L_M_DMSO_627


title: forebrain NPC TAD boundary deletion, UMI-4C PRKD1 viewpoint, replicate 1

description: Library name: fbNPC TADdel rep1 PRKD1