title: MM130366

description:
Library name: MM130366
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: Normal, replicate2, snATAC-seq

status: Public on Mar 16 2026

type: SRA

city: Guangzhou

last: He

state: Guangdong

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

department: Department of Basic Research

country: China

institute: Guangzhou National Laboratory

description: 10x Genomics

library_source: genomic single cell

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Liver

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

tag: tissue

value: Liver


title: WT Mock 7dpi 5

city: Manhattan

first: Chaitra

last: Sreenivasaiah

state: NY

address: 227 E 30th St

department: Applied Bioinformatics Laboratory

country: USA

institute: NYU Langone Health

description: Library name: TOI 5

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: nasal lavages

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

value: nasal lavages

tag: genotype

value: WT

tag: treatment

value: PBS


title: Normal, replicate1, snATAC-seq

description: 10x Genomics


title: NPC differentiation, day4, replicate 1, H3K4me1

city: Gent

first: Eva

last: D'haene

address: Corneel Heymanslaan 10

department: Department of Biomolecular Medicine

country: Belgium

institute: Ghent University

description: Library name: NPC diff d4 rep1, H3K4me1

library_source: genomic

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

source_name: NPC

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

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

tag: cell type

value: NPC


title: WT Mock 7dpi 4

description: Library name: TOI 4


title: NPC differentiation, day4, replicate 1, H3K4me3

description: Library name: NPC diff d4 rep1, H3K4me3


title: MM130363

city: New Orleans

first: Hong-Wen

last: Deng

state: LA

institute: Tulane University

description:
Library name: MM130363
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

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

source_name: peripheral blood

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

value: peripheral blood

value: monocytes

tag: population

value: European American

tag: Sex

value: male

tag: age

tag: bmi

tag: smoke

tag: alcohol drinking


title: NPC differentiation, day0, replicate 2, input

description: Library name: NPC diff d0 rep2, input

source_name: iPSC

value: iPSC


title: WT Mock 7dpi 3

description: Library name: TOI 3


title: MM130362

description:
Library name: MM130362
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

value: African American


title: MASH, replicate5, snATAC-seq

description: 10x Genomics


title: MM130361

description:
Library name: MM130361
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: WT Mock 7dpi 1

description: Library name: TOI 1


title: MASH, replicate6, snATAC-seq

description: 10x Genomics


title: WT Mock 7dpi 2

description: Library name: TOI 2


title: MASH, replicate3, snATAC-seq

description: 10x Genomics


title: MM130365

description:
Library name: MM130365
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: NPC differentiation, day0, replicate 2, H3K4me1

description: Library name: NPC diff d0 rep2, H3K4me1


title: TPP-DMSN-Fe/Cu3

city: hongkong

first: yuwen

last: wang

address: G10A, G/F, Run Run Shaw Science Building,

department: Biomedical Engineering

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
Library name: SAMPLES12
FPKM.m_Control_3

data_processing:
Sequence and filtering of Clean Reads
A cDNA library constructed by technology from the pooled RNA from <sample deseription>samples of < researchspecies>was sequenced run with Illumina NovasegTM X Plus sequence platform. Using the Illumina paired-end RNA-seq approach,we sequenced the transcriptome, generating a total of millon 2x150 bp paired-end reads, Reads obtainedfrom the sequencing machines includes raw reads containing adapters or low quality bases which will affect thefollowing
assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt(https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;
2) removing reads containing polyA and polyG;
3) removing reads containing more than 5% of unknown nucleotides (N);
4) removing low quality reads containing more than 20% of low quality (Q-value20) bases.
Then sequence quality was verified using FastQC(http://www.bioinformatics.babraham.ac.uk/projects/fastqe/, 0.11.9).
including the Q20, Q30 and GC-content of the clean data.
After that, a total of G bp of cleaned,paired-end reads were produced.
Assembly: Ensembl_v112（GRCm39）
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: Embryonic tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Embryonic tissue

tag: cell line

value: Mesenchymal stem cells


title: MM130360

description:
Library name: MM130360
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: NPC differentiation, day0, replicate 2, H3K4me3

description: Library name: NPC diff d0 rep2, H3K4me3


title: MM130359

description:
Library name: MM130359
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: MM130358

description:
Library name: MM130358
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: TPP-DMSN-Fe/Cu1

description:
Library name: SAMPLES10
FPKM.m_Control_1


title: NPC differentiation, day0, replicate 1, input

description: Library name: NPC diff d0 rep1, input


title: MASH, replicate2, snATAC-seq

description: 10x Genomics


title: NPC differentiation, day0, replicate 1, H3K4me1

description: Library name: NPC diff d0 rep1, H3K4me1


title: DMSN-Fe/Cu3

description:
Library name: SAMPLES9
FPKM.m_DMSN_3


title: NPC differentiation, day0, replicate 1, H3K27ac

description: Library name: NPC diff d0 rep1, H3K27ac


title: TPP-DMSN-Fe/Cu2

description:
Library name: SAMPLES11
FPKM.m_Control_2


title: MM130357

description:
Library name: MM130357
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: NPC differentiation, day0, replicate 1, H3K4me3

description: Library name: NPC diff d0 rep1, H3K4me3


title: MASH, replicate4, snATAC-seq

description: 10x Genomics


title: NPC differentiation, day0, replicate 2, H3K27ac

description: Library name: NPC diff d0 rep2, H3K27ac


title: Lx2 cell, TGFb, MPRA mRNA barcode reads replicate 2

description: MPRA RNA barcode reads used for regulatory activity analysis

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

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

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

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

value: hepatic stellate cell lines

value: Transforming growth factor beta (TGFb)


title: Lx2 cell, TGFb, MPRA mRNA barcode reads replicate 3


title: MM130355

description:
Library name: MM130355
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: MM130356

description:
Library name: MM130356
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: NPC differentiation, day12, UMI-4C FOXG1 viewpoint, replicate 2

description: Library name: NPC diff d12 rep2 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: Lx2 cell, TGFb, MPRA mRNA barcode reads replicate 4


title: Lx2 cell, TGFb,  MPRA DNA barcode reads replicate 4

description: MPRA DNA barcode reads used for regulatory activity analysis


title: NPC differentiation, day8, UMI-4C FOXG1 viewpoint, replicate 2

description: Library name: NPC diff d8 rep2 FOXG1


title: DMSN-Fe/Cu1

description:
Library name: SAMPLES7
FPKM.m_DMSN_1


title: DMSN-Fe/Cu2

description:
Library name: SAMPLES8
FPKM.m_DMSN_2


title: NPC differentiation, day8, UMI-4C FOXG1 viewpoint, replicate 1

description: Library name: NPC diff d8 rep1 FOXG1


title: DMSN1

description:
Library name: SAMPLES4
FPKM.m_FeCu_1


title: MASH, replicate1, snATAC-seq

description: 10x Genomics


title: Lx2 cell, TGFb, MPRA mRNA barcode reads replicate 1


title: DMSN2

description:
Library name: SAMPLES5
FPKM.m_FeCu_2


title: MM130353

description:
Library name: MM130353
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: MM130354

description:
Library name: MM130354
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: MM130352

description:
Library name: MM130352
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: NPC differentiation, day4, UMI-4C FOXG1 viewpoint, replicate 1

description: Library name: NPC diff d4 rep1 FOXG1


title: DMSN3

description:
Library name: SAMPLES6
FPKM.m_FeCu_3


title: Lx2 cell, TGFb,  MPRA DNA barcode reads replicate 3


title: Lx2 cell, control, MPRA mRNA barcode reads replicate 4

value: Control


title: Lx2 cell, control, MPRA mRNA barcode reads replicate 2


title: NPC differentiation, day12, UMI-4C FOXG1 viewpoint, replicate 1

description: Library name: NPC diff d12 rep1 FOXG1


title: MM130347

description:
Library name: MM130347
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: Lx2 cell, TGFb,  MPRA DNA barcode reads replicate 1


title: NPC differentiation, day6, UMI-4C FOXG1 viewpoint, replicate 2

description: Library name: NPC diff d6 rep2 FOXG1


title: MM130350

description:
Library name: MM130350
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: Lx2 cell, TGFb,  MPRA DNA barcode reads replicate 2


title: Control1

description:
Library name: SAMPLES1
FPKM.m_TPP_1


title: Lx2 cell, control, MPRA mRNA barcode reads replicate 3


title: Control3

description:
Library name: SAMPLES3
FPKM.m_TPP_3


title: NPC differentiation, day4, UMI-4C FOXG1 viewpoint, replicate 2

description: Library name: NPC diff d4 rep2 FOXG1


title: MM130348

description:
Library name: MM130348
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: NPC differentiation, day6, UMI-4C FOXG1 viewpoint, replicate 1

description: Library name: NPC diff d6 rep1 FOXG1


title: NPC differentiation, day0, UMI-4C FOXG1 viewpoint, replicate 3

description: Library name: NPC diff d0 rep3 FOXG1


title: NPC differentiation, day0, UMI-4C FOXG1 viewpoint, replicate 2

description: Library name: NPC diff d0 rep2 FOXG1


title: Cad-MD_Cko 4

city: Madison

first: Fei

last: Zhao

state: WI

address: 2015 Linden Drive, Room 4206/4210

department: CBS

institute: School of Veterinary Medicine, University of Wisconsin Madison

description:
Library name: UK11
Novogene

data_processing:
Raw read quality was assessed using fastQC (v0.12.1).
Low-quality, high-N, and short reads were filtered with fastp (v0.23.4) under default settings.
Gene counts were generated using featureCounts (v2.0.6) with default parameters.
Differential expression gene analysis was performed with DESeq2 (v1.42.0) under R program (v4.3.2).
Cutoff for DEGs: |log₂(FoldChange)| > 1 and padj < 0.05 (Gata2cKO vs. Control).
Assembly: Filtered reads were aligned to the mouse mm39 genome using STAR (v2.7.11b).
Supplementary files format and content: Processed DEG's are in an Excel sheet titled, "Cranial MD_DEGs_cKO vs Control.xlsx".
Supplementary files format and content: Processed DEG's are in an Excel sheet titled, "Caudal MD_DEGs_cKO vs Control.xlsx".
Supplementary files format and content: C8, C9, C10, C12 are controls and KO7, KO8, KO9, KO10 are all knockouts for cranial MD.
Supplementary files format and content: UC2, UC3, UC6, UC11 are controls and UK6, UK7, UK8 and UK11 are all knockouts for caudal MD.

source_name: E16.5 XX Caudal Mesonephros

extract_protocol:
RNA was harvested using PicoPure RNA Isolation Kit from ThermoFisher Scientific cat#KIT0204
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: E16.5 XX Caudal Mesonephros

value: Osr2Cre/+;Gata2 f/f


title: Control2

description:
Library name: SAMPLES2
FPKM.m_TPP_2


title: Lx2 cell, control, MPRA mRNA barcode reads replicate 1


title: Cad-MD_Cko 2

description:
Library name: UK7
Novogene


title: MM130349

description:
Library name: MM130349
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: MM130341

description:
Library name: MM130341
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: MM130346

description:
Library name: MM130346
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: Lx2 cell, control, MPRA DNA barcode reads replicate 4


title: MM130343

description:
Library name: MM130343
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: Cad-MD_Cko 3

description:
Library name: UK8
Novogene


title: MM130342

description:
Library name: MM130342
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: MM130340

description:
Library name: MM130340
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: NPC differentiation, day0, UMI-4C FOXG1 viewpoint, replicate 1

description: Library name: NPC diff d0 rep1 FOXG1


title: Cad-MD_Cko 1

description:
Library name: UK6
Novogene


title: Lx2 cell, control, MPRA DNA barcode reads replicate 2


title: neuron, UMI-4C FOXG1 viewpoint, replicate 3

description: Library name: iN rep3 FOXG1

source_name: neuron

value: neuron


title: Lx2 cell, control, MPRA DNA barcode reads replicate 3

value: WT


title: Cad-MD_Ctrl 4

description:
Library name: UC11
Novogene

value: Osr2Cre/+;Gata2 f/+


title: MM130336

description:
Library name: MM130336
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: Cad-MD_Ctrl 2

description:
Library name: UC3
Novogene


title: neuron, UMI-4C FOXG1 viewpoint, replicate 2

description: Library name: iN rep2 FOXG1


title: HepG2 cell, PAOA, MPRA DNA barcode reads replicate 4

value: hepatocyte cell line

value: Palmitic acid and oleic acid (PAOA)


title: MM130339

description:
Library name: MM130339
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: peripheral blood

value: monocytes


title: HepG2 cell, PAOA, MPRA mRNA barcode reads replicate 4

description: MPRA RNA barcode reads used for regulatory activity analysis


title: neuron, UMI-4C FOXG1 viewpoint, replicate 1

description: Library name: iN rep1 FOXG1


title: MM130335

description:
Library name: MM130335
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

value: male


title: Cra-MD_Cko 4

description:
Library name: KO10
Novogene

source_name: E16.5 XX Cranial Mesonephros

value: E16.5 XX Cranial Mesonephros


title: Lx2 cell, control, MPRA DNA barcode reads replicate 1

description: MPRA DNA barcode reads used for regulatory activity analysis


title: scRNA-seq part 5

description:
scRNA-seq
features.tsv.gz
matrix.mtx.gz
barcodes.tsv.gz

library_source: transcriptomic single cell

data_processing:
Map sgRNA together with other genomic gene transcripts to a custom reference, which builted by add each sgRNA as ‘pseudo-genes’ to human GRCh38 version genome. cell barcode were assigned to sgRNA by get_barcodes.py, and only when dominant sgRNA was three times abundant than sum of all other sgRNAs in same cells it will assigned to this cells.
6 lane of scRNA-seq data were mapped to custom reference genome by cellranger separately, and then aggregated. Aggregated scRNA-seq data were processed by Seurat, filtered with parameter nFeature_RNA > 200 & nFeature_RNA < 10000 & percent.mt < 10. DEGs between sgRNA targeting cells and other cells were detected by FindMarkers function with t test method, SCT assay and scale.data slot.
Assembly: GRCh38
Supplementary files format and content: CROP-seq assignment of cell barcode to sgRNA target regions.
Supplementary files format and content: Aggregated scRNA-seq expression matrix

molecule: polyA RNA

growth_protocol: CRISPRi_hepG2 (dCas9-KRAB/MeCP2_Knock-in) 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:
Firstly, we created the CROPi-DAVs plasmid library, and co-transfected into HEK-293T cells. Lentivirus was collected at 48h post-transfection.  For library infection, CRISPRi_HepG2 cells were infected with CROPi-DAVs lentivirus library. Puromycin screening was performed at 48h post-infection and following by maintaining for another 7 days .
After puromycin selection and expansion, cells were captured by the 10X Chromium Controller using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10X Genomics, PN-1000268). The sgRNA-enrichment library were constructed by multiple-PCR using using 2x KAPA HiFi HotStart ReadyMix.

treatment_protocol: CRISPRi_hepG2 cells were infected with CROPi-DAVs lentivirus library at a low MOI level (~0.1) to minimize double infection, followed by Puromycin selection (6 μg/ml) for 7 days.

value: NO


title: MM130337

description:
Library name: MM130337
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

value: African American


title: Cad-MD_Ctrl 1

description:
Library name: UC2
Novogene


title: Cad-MD_Ctrl 3

description:
Library name: UC6
Novogene


title: NPC, UMI-4C FOXG1 viewpoint, replicate 2

description: Library name: NPC rep2 FOXG1

value: NPC


title: scRNA-seq part 6


title: NPC, UMI-4C FOXG1 viewpoint, replicate 3

description: Library name: NPC rep3 FOXG1


title: Cra-MD_Cko 3

description:
Library name: KO9
Novogene


title: Cra-MD_Ctrl 4

description:
Library name: C12
Novogene


title: NPC, UMI-4C PRKD1 viewpoint, replicate 2

description: Library name: NPC rep2 PRKD1


title: NPC, UMI-4C PRKD1 viewpoint, replicate 1

description: Library name: NPC rep1 PRKD1


title: MM130324

description:
Library name: MM130324
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: European American


title: scRNA-seq part 2


title: NSC, UMI-4C FOXG1 viewpoint, replicate 2

description: Library name: NSC rep2 FOXG1

source_name: NSC

value: NSC


title: NSC, UMI-4C FOXG1 viewpoint, replicate 1

description: Library name: NSC rep1 FOXG1


title: MM130334

description:
Library name: MM130334
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: NPC, UMI-4C FOXG1 viewpoint, replicate 1

description: Library name: NPC rep1 FOXG1


title: MM130333

description:
Library name: MM130333
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: Cra-MD_Cko 2

description:
Library name: KO8
Novogene


title: scRNA-seq part 4


title: Cra-MD_Ctrl 3

description:
Library name: C10
Novogene


title: scRNA-seq part 3


title: Cra-MD_Cko 1

description:
Library name: KO7
Novogene


title: MM130321

description:
Library name: MM130321
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: MM130326

description:
Library name: MM130326
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: Cra-MD_Ctrl 2

description:
Library name: C9
Novogene


title: Cra-MD_Ctrl 1

description:
Library name: C8
Novogene


title: MM130320

description:
Library name: MM130320
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: NSC, UMI-4C PRKD1 viewpoint, replicate 2

description: Library name: NSC rep2 PRKD1


title: MM130314

description:
Library name: MM130314
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: MM130323

description:
Library name: MM130323
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: MM130318

description:
Library name: MM130318
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: 6h_TPA_Yr2_Ctrl_Rep1

city: New York

first: Luis

middle: F

last: Soto-Ugaldi

institute: The Rockefeller University

description:
Library name: Sample 1
250,000 EpdSCs per condition were FACS-sorted directly into room temperature buffer RLT (QIAGEN) and immediately flash frozen. Two biological replicates were used per condition, with 2-3 mice pooled per biological replicate. Total RNA was isolated with RNeasy Mini Kit (QIAGEN) as per manufacturer’s instructions. Libraries were then prepared using Illumina TruSeq standard mRNA library kit and sequenced on Illumina NextSeq using 40-bp paired-end reads. Reads were aligned to the mouse exons using the mm10 reference genome (GENCODE v.30), exon positions from TxDb.Mmusculus.UCSC.mm10.knownGene and Rsubread for alignment, Aligned reads were counted using the summarizeOverlaps() function of the GenomicAlignments R package (v. 1.38.2). Raw counts were used as input into DESeq2 (v1.42.1) (Love et al., 2014) for differential gene expression testing with default parameters.
y2_tpa_geneCounts.rds

data_processing:
Reads were aligned to the mouse exons using the mm10 reference genome (GENCODE v.30), exon positions from TxDb.Mmusculus.UCSC.mm10.knownGene and Rsubread for alignment, Aligned reads were counted using the summarizeOverlaps() function of the GenomicAlignments R package (v. 1.38.2). Raw counts were used as input into DESeq2 (v1.42.1) (Love et al., 2014) for differential gene expression testing with default parameters.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Raw counts RDS file

source_name: Skin

extract_protocol:
250,000 EpdSCs per condition were FACS-sorted directly into room temperature buffer RLT (QIAGEN) and immediately flash frozen. Two biological replicates were used per condition, with 2-3 mice pooled per biological replicate. Total RNA was isolated with RNeasy Mini Kit (QIAGEN) as per manufacturer’s instructions. Libraries were then prepared using Illumina TruSeq standard mRNA library kit and sequenced on Illumina NextSeq using 40-bp paired-end reads.
PCR amplified library from genomic DNA

value: Skin

value: Epidermal Stem Cell

value: wildtype

value: non-treated


title: iPSC, UMI-4C PRKD1 viewpoint, replicate 2

description: Library name: iPSC rep2 PRKD1

value: iPSC


title: scRNA-seq part 1

value: WT


title: A375_CTC_8

city: Portland

first: Rosalyn

middle: M

last: Fey

state: OR

address: 3181 S.W. Sam Jackson Park Road

institute: Oregon Health & Science University

description: Library name: A375_CTC_8

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

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

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

value: melanoma


title: A375_CTC_9

description: Library name: A375_CTC_9


title: 051923_ENSGut

city: New Haven

first: I-Uen

last: Hsu

state: Connecticut

address: 100 College Street

department: Neuroscience

institute: Yale University School of Medicine

description:
Library name: ENS_intestine_biol rep 3
10x Genomics

data_processing:
Raw sequencing data were aligned to the mm10-2020-A mouse genome reference using Cell Ranger software v.7.1.0 (10x Genomics).
Assembly: mm10-2020-A mouse genome reference
Supplementary files format and content: Filtered gene expression matrix

source_name: Intestine

growth_protocol: For co-culture experiments, cardiac atria and intestines were dissected from E13.5 Phox2b-Flpo;frt-tdTomato embryos and dissociated into single cell suspensions. Neuronal and non-neuronal cells were separated and collected by FACS. Cells were centrifuged at 200 x g for 10 minutes at 4 ˚C and plated for co-culture. Per well, 3,000 tdTomato+ enteric neuronal cells and 6,000 tdTomato-negative cardiac or intestinal cells were mixed and plated into 24-well plates pre-coated with a thin layer of Collagen I/Matrigel (Corning 356237) mixture that contains 0.5 mg /mL of Matrigel and 33 µg/mL Collagen I (Enzo Life Sciences ALX-522-440-0050). Cultures were maintained in Neurobasal Plus Medium (Gibco A3582901) supplemented with 1% FBS (Thermo Scientific 10082147), 2 mM L-Glutamine (Thermo Scientific 25030149), B-27 Plus Supplement (Gibco A3582801), 100 U/mL penicillin, 100 µg/mL streptomycin (Thermo Scientific 15140122), and 100 µg/mL Gentamicin (Thermo Scientific 15710064) at 37 ˚C in 5% CO2 for 4-5 days before harvesting for single-cell RNA sequencing.

extract_protocol:
For scRNA-seq of OINS cells, the heart, lungs, pancreas and intestines were dissected from Wnt1-Cre;lox-tdTomato, Phox2b-Flpo;frt-tdTomato, or Baf53b-Cre;lox-L10GFP mice as indicated at E12.5, E14.5, E16.5, E18.5 and P56 in ice-cold Leibovitz's L-15 Medium (Gibco). For the hearts and lungs, fluorescently labelled OINS regions were isolated by microdissection under a Leica M205FCA fluorescence stereomicroscope. For experiments comparing heart-near and heart-far regions, atrial areas containing Wnt1-Cre;lox-L10GFP labelled ICNS cells were dissected to separate from the atrial areas lacking ICNS. Dissected tissues were cut into 1-3 mm2 pieces and incubated in 0.25% trypsin-EDTA (Gibco) at 37 ˚C for 10 minutes (E12.5, E14.5), 20 minutes (E16.5, E18.5), or 25 minutes (P56) with shaking. After washing with L-15 media containing 10% fetal bovine serum (L15/FBS), tissues were incubated in 2 mg/mL Collagenase A (Sigma-Aldrich) and 2 mg/mL of Dispase II (Sigma-Aldrich) in 1 x HBSS at 37°C for 30 minutes (E12.5, E14.5) or 40 minutes (E16.5, E18.5, P56) with shaking. After washing with L15/FBS, cells were separated into single cells by trituration using three fire-polished Pasteur pipettes of decreasing diameter. Mature ICNS-neurons isolated from Baf53b-Cre;lox-L10GFP hearts at E18.5 and P56 were further purified using 30% and 60% Percoll density gradients. The cell suspension was filtered through a 40 μm cell strainer (Corning). All centrifugation steps were performed at 200 x g at 4°C. After the final centrifugation, the cell pellet was resuspended in 1x HBSS containing 0.04% BSA. Fluorescently labelled cells were sorted on a BD FACS Aria cell sorter at Yale Flow Cytometry Facility and collected in ice-cold 1x HBSS containing 0.04% BSA.  For co-culture experiments, after 4-5 days of culture, media were removed and cells were incubated with 2 mg/mL Collagenase A (Sigma-Aldrich) and 2 mg/mL of Dispase II (Sigma-Aldrich) solutions at 37 ˚C for 10 minutes. The digested cells were collected into ice-cold 10% FBS L-15 media (L15/FBS). This digestion was repeated 3-6 times until the coating layer was completely dissociated. Cells pooled from multiple wells were centrifuged at 200 x g at 4 ˚C for 10 minutes, washed three times with L15/FBS, and treated with Corning Cell Recovery solution (#354253) on ice for 20 minutes to dissolve residual Matrigel. After two additional washes with L15/FBS, cells were gently triturated with a Pasteur pipet, filtered through a 40 μm cell strainer, washed three times, and resuspended in 1x HBSS, 0.04% BSA for scRNA-seq using the 10x Genomics platform.
Single-cell libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Reagent Kit v3 chemistry according to the manufacturer’s instructions and sequenced using an Illumina NovaSeq 6000 S4 sequencer at 300 million reads to achieve a sequencing depth of 20,000–300,000 reads per cell.

value: Intestine

value: Intestinal cells and enteric neurons

value: Phox2b-Flpo; frt-tdTomato


title: D6_Naive_highH2AZ_Rep2

description:
Library name: Sample 19
MINT-ChIP was performed as described (van Galen et al., 2016), using 50,000 FACS-purified EpdSCs per target histone mark for each biological replicate, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Briefly, purified samples were split in two (25,000 cells each), then lysed for 20 minutes on ice in the presence of either low (60 units) or high (120 units) concentration of micrococcal nuclease (NEB). Sample/MNase concentration-specific T7 adapters were then ligated to each sample. Following ligation, samples for each MNase concentration were pooled together, then split evenly for overnight incubation with ChIP antibodies in 4°C (H2A.Z: rabbit, AbCam; H3K4me1: rabbit, Cell Signaling; H3K27ac: rabbit, Active Motif). Antibody-bound DNA was isolated the following day through 4h incubation with protein G beads in 4°C, after which samples were washed twice with ice-cold RIPA, then once each with high salt RIPA, LiCL wash buffer, and TE buffer. Eluted DNA was then cleaned and subjected to overnight in vitro transcription in 4°C. Resulting RNA was isolated and reverse transcribed, then final library PCR was performed with sample-specific barcodes for pooled sequencing. Finally, libraries were cleaned, pooled, then sequenced for 50bp paired-end reads on an Illumina NextSeq P2000. MINT-ChIP reads were processed as described (van Galen et al., 2016). Reads were first demultiplexed into FASTQ files specific for each target histone mark and MNase digest condition using Illumina’s bcl2fastq2, and further demultiplexed into sample-specific FASTQ files using the T7 adapter barcode from read2. Demultiplexed reads were trimmed for adapters using Skewer and aligned to the mm10 genome using Bowtie2. Duplicated reads were marked and removed using Picard, then replicates per condition and MNase digest conditions (high/low) merged using Samtools. For visualization, bigWig files were generated using the bamCoverage function in deeptools (version 3.5.5) with RPKM normalization, and summary counts of bigWigs over ATAC-seq peaks generated using deeptools computeMatrix. All plots were created using the profileplyr R package (version 1.4.3).
D6_Ctrl_rep2_H2AZ_MERGE_sorted_RPKM.bw

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

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


title: D6_IMQ_ETS1_rep1

description:
Library name: Sample 3
using 500,000 FACS-purified EpdSCs per biological replicate per target antibody, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Cells were lightly fixed in crosslinking buffer (10mM HEPES-NaOH pH 7.5, 100mM NaCl, 1mM EGTA, 1mM EDTA, 1% formaldehyde) and rotated at room temperature for 10 min. Crosslinking was quenched with glycine (0.125M final concentration) and rotated at room temperature for 5 min. Cells were washed with cold PBS and nuclei isolated by resuspending in NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM MgCl2, 1mM DTT, 0.1% Triton X-100, with Roche complete EDTA-free protease inhibitor) and rotated at 4°C for 10 min. Nuclei were washed twice with wash buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5% BSA, 0.5mM spermidine, with protease inhibitor) then incubated with concanavalin-A (ConA) beads previously washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2), for 10 min at 4°C. ConA-bead-bound nuclei were incubated overnight at 4°C in antibody buffer (Wash buffer supplemented with 0.1% Triton X-100 and 2nM EDTA) and antibody (c-FOS: Cell Signaling 1:50; c-JUN: Cell Signaling 1:50; deltaNP63: BioLegend 1:10). ConA-bound nuclei were washed once with triton wash buffer (wash buffer supplemented with 0.1% Triton X-100) then resuspended in antibody wash buffer with 2.5uL pAG-MNase (EpiCypher) and incubated at 4°C for 1 hr. ConA-bound nuclei were washed twice with triton wash buffer and resuspended in 100uL of lysis buffer (50mM Tris-HCl, 150mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5mM CaCl2) and incubated iced metal block (0°C) for 30min. MNase reaction was stopped with addition of 100uL 2x stop buffer (30mM EGTA) and incubated at 37°C for 10min. After incubation, ConA-bound nuclei were captured using a magnetic tube holder and supernatant containing CUT&RUN DNA fragments was collected. Supernatant was incubated with 2uL 10% SDS and 2.5uL 20mg/mL proteinase K at 70°C for 2hrs. DNA was purified using PCI and overnight ethanol precipitation with glycogen at -20°C. DNA was spun down and washed once with 100% ethanol before being resuspended in 15uL of buffer EB. Sequencing libraries were generated using NEBNext Ultra II DNA library Prep Kit for Illumina (Index Primer set 2). PCR-amplified libraries were purified using 1.2x ratio of AMPure XP beads and eluted in 15uL 0.1x TE buffer. Libraries were pooled and sequenced on Illumina NextSeq using 40-bp paired-end reads.40 bp paired-end reads raw reads were aligned to the mouse reference genome (mm10, GENCODE v30 annotation) using BWA-MEM in paired-end mode with the -M and -T 10 parameters to mark split alignments and increase mapping stringency. Alignment quality was confirmed for all samples, with mapping rates exceeding 80%. Resulting BAM files were processed using a standardized filtering pipeline. Reads were filtered with SAMtools (-F 1804 -f 2 -q 30) to retain only properly paired reads with a mapping quality score ≥30, while excluding unmapped reads, secondary alignments, optical duplicates, and reads failing vendor or platform quality control. PCR duplicates were marked using Picard and subsequently removed with SAMtools. To focus the analysis on canonical autosomes and the X chromosome, only alignments mapping to chromosomes 1–19 and X were retained; reads aligning to non-standard scaffolds or blacklisted regions were removed using BEDTools intersect with ENCODE blacklist annotations. Signal tracks were generated by computing genome-wide coverage using the coverage function from the rtracklayer package. Coverage values were normalized to counts per million (CPM) to account for differences in sequencing depth across samples. The resulting bigWig files were used as input for DeepTools. Specifically, computeMatrix was run in reference-point mode, centered on regions of interest with a 1,000 bp window upstream and downstream. Aggregated signal profiles were visualized using the plotProfile function, enabling direct comparison across conditions and genomic features.

data_processing:
40 bp paired-end reads raw reads were aligned to the mouse reference genome (mm10, GENCODE v30 annotation) using BWA-MEM in paired-end mode with the -M and -T 10 parameters to mark split alignments and increase mapping stringency. Alignment quality was confirmed for all samples, with mapping rates exceeding 80%. Resulting BAM files were processed using a standardized filtering pipeline. Reads were filtered with SAMtools (-F 1804 -f 2 -q 30) to retain only properly paired reads with a mapping quality score ≥30, while excluding unmapped reads, secondary alignments, optical duplicates, and reads failing vendor or platform quality control. PCR duplicates were marked using Picard and subsequently removed with SAMtools. To focus the analysis on canonical autosomes and the X chromosome, only alignments mapping to chromosomes 1–19 and X were retained; reads aligning to non-standard scaffolds or blacklisted regions were removed using BEDTools intersect with ENCODE blacklist annotations. Signal tracks were generated by computing genome-wide coverage using the coverage function from the rtracklayer package. Coverage values were normalized to counts per million (CPM) to account for differences in sequencing depth across samples. The resulting bigWig files were used as input for DeepTools. Specifically, computeMatrix was run in reference-point mode, centered on regions of interest with a 1,000 bp window upstream and downstream. Aggregated signal profiles were visualized using the plotProfile function, enabling direct comparison across conditions and genomic features.
Assembly: mm10
Supplementary files format and content: Bigwig files include CPM normalized counts
Library strategy: CUT&Run

extract_protocol:
500,000 FACS-purified EpdSCs per biological replicate per target antibody, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Cells were lightly fixed in crosslinking buffer (10mM HEPES-NaOH pH 7.5, 100mM NaCl, 1mM EGTA, 1mM EDTA, 1% formaldehyde) and rotated at room temperature for 10 min. Crosslinking was quenched with glycine (0.125M final concentration) and rotated at room temperature for 5 min. Cells were washed with cold PBS and nuclei isolated by resuspending in NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM MgCl2, 1mM DTT, 0.1% Triton X-100, with Roche complete EDTA-free protease inhibitor) and rotated at 4°C for 10 min. Nuclei were washed twice with wash buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5% BSA, 0.5mM spermidine, with protease inhibitor) then incubated with concanavalin-A (ConA) beads previously washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2), for 10 min at 4°C. ConA-bead-bound nuclei were incubated overnight at 4°C in antibody buffer (Wash buffer supplemented with 0.1% Triton X-100 and 2nM EDTA) and antibody (c-FOS: Cell Signaling 1:50; c-JUN: Cell Signaling 1:50; deltaNP63: BioLegend 1:10). ConA-bound nuclei were washed once with triton wash buffer (wash buffer supplemented with 0.1% Triton X-100) then resuspended in antibody wash buffer with 2.5uL pAG-MNase (EpiCypher) and incubated at 4°C for 1 hr. ConA-bound nuclei were washed twice with triton wash buffer and resuspended in 100uL of lysis buffer (50mM Tris-HCl, 150mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5mM CaCl2) and incubated iced metal block (0°C) for 30min. MNase reaction was stopped with addition of 100uL 2x stop buffer (30mM EGTA) and incubated at 37°C for 10min. After incubation, ConA-bound nuclei were captured using a magnetic tube holder and supernatant containing CUT&RUN DNA fragments was collected. Supernatant was incubated with 2uL 10% SDS and 2.5uL 20mg/mL proteinase K at 70°C for 2hrs. DNA was purified using PCI and overnight ethanol precipitation with glycogen at -20°C. DNA was spun down and washed once with 100% ethanol before being resuspended in 15uL of buffer EB. Sequencing libraries were generated using NEBNext Ultra II DNA library Prep Kit for Illumina (Index Primer set 2). PCR-amplified libraries were purified using 1.2x ratio of AMPure XP beads and eluted in 15uL 0.1x TE buffer. Libraries were pooled and sequenced on Illumina NextSeq using 40-bp paired-end reads.
NEBNext Ultra II DNA Library Prep Kit for Illumina

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


title: 051923_ENSHeart

description:
Library name: ENS_heart_biol rep 2
10x Genomics

source_name: Intestine and heart

value: Intestine and heart

value: Cardiac cells and enteric neurons


title: CROP-seq Enrichment

description: CROPseq Enrichment

value: hepatocyte cell line

value: NO


title: 6h_TPA_Yr2_Ctrl_Rep2

description:
Library name: Sample 2
250,000 EpdSCs per condition were FACS-sorted directly into room temperature buffer RLT (QIAGEN) and immediately flash frozen. Two biological replicates were used per condition, with 2-3 mice pooled per biological replicate. Total RNA was isolated with RNeasy Mini Kit (QIAGEN) as per manufacturer’s instructions. Libraries were then prepared using Illumina TruSeq standard mRNA library kit and sequenced on Illumina NextSeq using 40-bp paired-end reads. Reads were aligned to the mouse exons using the mm10 reference genome (GENCODE v.30), exon positions from TxDb.Mmusculus.UCSC.mm10.knownGene and Rsubread for alignment, Aligned reads were counted using the summarizeOverlaps() function of the GenomicAlignments R package (v. 1.38.2). Raw counts were used as input into DESeq2 (v1.42.1) (Love et al., 2014) for differential gene expression testing with default parameters.
y2_tpa_geneCounts.rds


title: A375_CTC_11

description: Library name: A375_CTC_11


title: NSC, UMI-4C PRKD1 viewpoint, replicate 1

description: Library name: NSC rep1 PRKD1


title: A3_E14F_V1_MMT

description:
Library name: E14_5_ICNS_Visium
10x Genomics Visium

data_processing:
The raw sequencing data was processed using the 10x Genomics Space Ranger pipeline to produce FASTQ files.
The sequences were mapped to the mm10-2020-A genome for gene expression counting using spaceranger-2.0.0 default parameters.
We pre-processed the 10x Visium dataset using log-normalization. Gene expression values for each spot were normalized to the total number of transcripts and multiplied by a scaling factor of 10,000. The normalized dataset was then transformed to log scale using log1p. The log-normalization process was performed using the Python package Scanpy 1.8.2.
Assembly: mm10-2020-A
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: RoiSet.zip: ICNS ROIs
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image_rois.png: hi-res image of tissue with ICNS ROIs
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Heart

extract_protocol:
Hearts from E14.5 Wnt1-Cre;lox-Sun1-GFP mice were acutely dissected and freshly frozen in OCT. Cryosections (10 μm) were cut using a cryostat (Thermo Fisher Scientific) and mounted onto the 10x Visium Spatial Gene Expression Slide.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

value: Heart

value: Intrinsic cardiac neurons and cardiac cells


title: iPSC, UMI-4C PRKD1 viewpoint, replicate 1

description: Library name: iPSC rep1 PRKD1


title: 6h_TPA_Yr2_PIMQ_Rep1

description:
Library name: Sample 3
250,000 EpdSCs per condition were FACS-sorted directly into room temperature buffer RLT (QIAGEN) and immediately flash frozen. Two biological replicates were used per condition, with 2-3 mice pooled per biological replicate. Total RNA was isolated with RNeasy Mini Kit (QIAGEN) as per manufacturer’s instructions. Libraries were then prepared using Illumina TruSeq standard mRNA library kit and sequenced on Illumina NextSeq using 40-bp paired-end reads. Reads were aligned to the mouse exons using the mm10 reference genome (GENCODE v.30), exon positions from TxDb.Mmusculus.UCSC.mm10.knownGene and Rsubread for alignment, Aligned reads were counted using the summarizeOverlaps() function of the GenomicAlignments R package (v. 1.38.2). Raw counts were used as input into DESeq2 (v1.42.1) (Love et al., 2014) for differential gene expression testing with default parameters.
y2_tpa_geneCounts.rds

value: Skin


title: MM130309

description:
Library name: MM130309
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

value: peripheral blood

value: monocytes

value: African American

value: male


title: D6_Ctrl_ETS1_rep2

description:
Library name: Sample 2
using 500,000 FACS-purified EpdSCs per biological replicate per target antibody, with two biological replicates per condition and 2-3 mice pooled per biological replicate. Cells were lightly fixed in crosslinking buffer (10mM HEPES-NaOH pH 7.5, 100mM NaCl, 1mM EGTA, 1mM EDTA, 1% formaldehyde) and rotated at room temperature for 10 min. Crosslinking was quenched with glycine (0.125M final concentration) and rotated at room temperature for 5 min. Cells were washed with cold PBS and nuclei isolated by resuspending in NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM MgCl2, 1mM DTT, 0.1% Triton X-100, with Roche complete EDTA-free protease inhibitor) and rotated at 4°C for 10 min. Nuclei were washed twice with wash buffer (20mM HEPES pH7.5, 150mM NaCl, 0.5% BSA, 0.5mM spermidine, with protease inhibitor) then incubated with concanavalin-A (ConA) beads previously washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2), for 10 min at 4°C. ConA-bead-bound nuclei were incubated overnight at 4°C in antibody buffer (Wash buffer supplemented with 0.1% Triton X-100 and 2nM EDTA) and antibody (c-FOS: Cell Signaling 1:50; c-JUN: Cell Signaling 1:50; deltaNP63: BioLegend 1:10). ConA-bound nuclei were washed once with triton wash buffer (wash buffer supplemented with 0.1% Triton X-100) then resuspended in antibody wash buffer with 2.5uL pAG-MNase (EpiCypher) and incubated at 4°C for 1 hr. ConA-bound nuclei were washed twice with triton wash buffer and resuspended in 100uL of lysis buffer (50mM Tris-HCl, 150mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 5mM CaCl2) and incubated iced metal block (0°C) for 30min. MNase reaction was stopped with addition of 100uL 2x stop buffer (30mM EGTA) and incubated at 37°C for 10min. After incubation, ConA-bound nuclei were captured using a magnetic tube holder and supernatant containing CUT&RUN DNA fragments was collected. Supernatant was incubated with 2uL 10% SDS and 2.5uL 20mg/mL proteinase K at 70°C for 2hrs. DNA was purified using PCI and overnight ethanol precipitation with glycogen at -20°C. DNA was spun down and washed once with 100% ethanol before being resuspended in 15uL of buffer EB. Sequencing libraries were generated using NEBNext Ultra II DNA library Prep Kit for Illumina (Index Primer set 2). PCR-amplified libraries were purified using 1.2x ratio of AMPure XP beads and eluted in 15uL 0.1x TE buffer. Libraries were pooled and sequenced on Illumina NextSeq using 40-bp paired-end reads.40 bp paired-end reads raw reads were aligned to the mouse reference genome (mm10, GENCODE v30 annotation) using BWA-MEM in paired-end mode with the -M and -T 10 parameters to mark split alignments and increase mapping stringency. Alignment quality was confirmed for all samples, with mapping rates exceeding 80%. Resulting BAM files were processed using a standardized filtering pipeline. Reads were filtered with SAMtools (-F 1804 -f 2 -q 30) to retain only properly paired reads with a mapping quality score ≥30, while excluding unmapped reads, secondary alignments, optical duplicates, and reads failing vendor or platform quality control. PCR duplicates were marked using Picard and subsequently removed with SAMtools. To focus the analysis on canonical autosomes and the X chromosome, only alignments mapping to chromosomes 1–19 and X were retained; reads aligning to non-standard scaffolds or blacklisted regions were removed using BEDTools intersect with ENCODE blacklist annotations. Signal tracks were generated by computing genome-wide coverage using the coverage function from the rtracklayer package. Coverage values were normalized to counts per million (CPM) to account for differences in sequencing depth across samples. The resulting bigWig files were used as input for DeepTools. Specifically, computeMatrix was run in reference-point mode, centered on regions of interest with a 1,000 bp window upstream and downstream. Aggregated signal profiles were visualized using the plotProfile function, enabling direct comparison across conditions and genomic features.

value: Epidermal Stem Cell

value: wildtype

value: non-treated


title: 6h_TPA_Yr2_PIMQ_Rep2

description:
Library name: Sample 4
250,000 EpdSCs per condition were FACS-sorted directly into room temperature buffer RLT (QIAGEN) and immediately flash frozen. Two biological replicates were used per condition, with 2-3 mice pooled per biological replicate. Total RNA was isolated with RNeasy Mini Kit (QIAGEN) as per manufacturer’s instructions. Libraries were then prepared using Illumina TruSeq standard mRNA library kit and sequenced on Illumina NextSeq using 40-bp paired-end reads. Reads were aligned to the mouse exons using the mm10 reference genome (GENCODE v.30), exon positions from TxDb.Mmusculus.UCSC.mm10.knownGene and Rsubread for alignment, Aligned reads were counted using the summarizeOverlaps() function of the GenomicAlignments R package (v. 1.38.2). Raw counts were used as input into DESeq2 (v1.42.1) (Love et al., 2014) for differential gene expression testing with default parameters.
y2_tpa_geneCounts.rds


title: 090523_ENSGut

description:
Library name: ENS_intestine_biol rep 1
10x Genomics

value: Intestine

value: Intestinal cells and enteric neurons


title: 090523_ENSHeart

description:
Library name: ENS_heart_biol rep 1
10x Genomics

value: Phox2b-Flpo; frt-tdTomato


title: A375_CTC_10

description: Library name: A375_CTC_10

value: melanoma


title: 042023_ENSGut

description:
Library name: ENS_intestine_biol rep 4
10x Genomics