title: ATAC_VME_rep2

data_processing:
for bulk RNA-seq data, adapter sequences were trimmed from raw fastq file using TrimGalore (v0.6.4), clean data were mapped to the human reference genome (GRCh38) using STAR (2.7.3a) with --quantMode GeneCounts option to output read count tables, differential gene expression analysis was performed using DESeq2 (v1.24.0)
for single cell RAN-seq data, UMI count matrx was generated using cellranger (v2.0.1) software
for ATAC-seq and ChIP-seq, all of the paired-end raw reads were processed using TrimGalore to trim adaptor and low-quality reads. Adaptor-trimmed paired-end reads from ATAC-seq and ChIP-seq were aligned to hg38 by bowtie2 (version 2.3.5) with the parameters: --t --q --N 1 --L 25. PCR duplicates and multiple mapped reads were removed. The replicate BAM files for each time point were merged and removed reads aligning to blacklisted genomic regions before calling peaks with MACS2 (version 2.2.6) and the enriched TF motifs were analyzed by Homer (version 4.10.4, findMotifsGenome).
Genome_build: GRCh38
Supplementary_files_format_and_content: single cell UMI matrix files generated by cellranger, all three files are needed for downstream analysis
Supplementary_files_format_and_content: tab-delimited text files include read count values for all samples

extract_protocol:
Total RNA was isolated from the fresh tissues with RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions and treated with RNase-free DNase.
For RNA-seq, 100ng total RNA in each sample are used for SMART-seq2 library construction.For ATAC-seq, ATAC-seq library was prepared followed the omini-ATAC-seq protocol. For ChIP-seq, ChIP-seq library was prepared followed the ULI-ChIP protocol.

tag: strain


title: U87-Vec-2

status: Public on May 10 2022

type: SRA

city: Fujian Province, China

first: huiqing

last: Liu

address: State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen ,Fujian Province, China

country: China

institute: Xiamen University

library_source: transcriptomic

data_processing:
Differential expressed genes were identified using DESeq2 with fold change>1.5 and p<0.05.
Supplementary_files_format_and_content: tab-delimited text files include raw gene count for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
U87 cells were collected,and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: human gliobastoma cell line


title: P4

city: Majadahonda

first: Francisco

last: Díez-Fuertes

address: Carretera Majadahonda - Pozuelo Km 2.2

country: Spain

institute: Instituto de Salud Carlos III

description: PBMCs from LGMDD2 patient

data_processing:
fastQC tool to evaluate sequence yield, base quality, GC profile, k-mer distribution, overrepresented sequences, and primer contamination.
The Trimmomatic tool is used to trim the adapter and/or primer sequences from the ends of the fastq generated.
The reference index files required by Bowtie2 mapping program and the transcript- specific reference sequences are generated from the reference fasta file and the corresponding annotation gtf file.
The ‘rsem-calculate-expression’ command from the RSEM expression analysis software is used to map single-end reads to the reference transcripts. The RNA expression values at gene and isoform levels are calculated using the expectation-maximization (EM) algorithm as implemented by the RSEM program. Multiple threads of eight or more are used to generate alignments mapped to genomic coordinates, while tagging reads with nonunique alignments (--tag), calculating 95% credibility intervals (--calc-ci) and posterior mean estimates (--calc-pme) and allowing insertions in the range of 1–500 bases (--fragment-length-min/max).
The number of fragments that are derived from a given isoform or gene using RSEM´s approximate maximum likelihood estimates was employed for differential expression between samples from LGMD1F patients and healthy controls. An R package called EBSeq for differential expression analysis using RNA-Seq data was used
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with TPM values for each library
Supplementary_files_format_and_content: Matrix table with fold changes and p-values of the differential expression between LGMDD2 and controls

source_name: PBMCs

growth_protocol: PBMCs from LGMDD2 patients and healthy controls were isolated by centrifugation using Ficoll-Hypaque gradient (GE Healthcare). PBMCs were cultured in RPMI 1640 medium (Bio Whittaker) supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 100 µg/ml streptomycin, 100 units/ml penicillin (Bio Whittaker).

extract_protocol:
Total RNA from activated PBMCs was isolated from 5x106 cells of each samples using RNeasy Mini Kit (Qiagen)
ScriptSeqTM v2 RNA-Seq Library Preparation Kit (Illumina, San Diego, Ca, USA),

treatment_protocol: PBMCs were then activated with purified antihuman CD3 (clone OKT3), CD28 (clone CD28.2) (Biosciences) and 300 U/ml interleukin-2 (IL-2) (Chiron) for 3 days.

tag: pathology


title: scATAC-seq

city: Beijing

first: Jie

address: Qing Hua Yuan

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

description: cultured cells

library_source: genomic

data_processing:
single cell ATAC-seq processed data was generated using cellranger (v2.0.1) software
Genome_build: GRCh38
Supplementary_files_format_and_content: single cell matrix files generated by cellranger, all files are needed for downstream analysis using seurat (v4.0.1)

molecule: genomic DNA

source_name: cultured cells

growth_protocol: Undifferentiated hPSCs were cultured in E8 medium without feeders.

extract_protocol: For ATAC-seq, ATAC-seq library was prepared followed the omini-ATAC-seq protocol.

value: Embryonic stem cells

tag: age

tag: cell type

value: human embryonic stem cell line H1


title: U87-Vec-1


title: P1

description: PBMCs from LGMDD2 patient


title: U87-input DNA

data_processing:
FASTQ data were processed with Trimmomatic v0.39 to remove low-quality reads
reads of ChIP-seq data were aligned to the hg19 genome using Bowtie v2.3.5.
Peak calling was performed using MACS2 with a p value cutoff of 0.01.
For the differential binding peaks of RNF2 ChIP-seq, MAnorm was used with cutoff P<0.05 and fold change>2.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using deepTools 3.1.3 and visualized by IGV 2.4.16

growth_protocol: U87-SCR and U87-shGPR17 were cultured in DMEM (BasalMedia, Cat# L110KJ) supplemented with 10%FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and RNF2-DNA complexes were isolated with antibody.
The libraries were constructed following NEB’s Chip-seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an ‘A’ base so the adaptors from NEB with a ‘T’ can ligate on the ends. Then 200–400 bp fragments are double-selected and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: U87 cells were transfected with scramble or GPR17 shRNA(pLKO1 vector), and screened by  2ug/ml puromycin treatment until monoclonal cell line was obtained.

tag: chip antibody


title: ATAC_HPC_rep1


title: ATAC_VME_rep1


title: ATAC_hPSC_rep2


title: ATAC_HPC_rep2


title: H3K4me3_VME_rep2

tag: antibody


title: P3

description: PBMCs from LGMDD2 patient


title: ATAC_hPSC_rep1


title: ATAC_EPC_rep1


title: ATAC_EPC_rep2


title: H3K4me3_HPC


title: H3K4me3_EPC_rep1


title: S. glacialis, day 6, 6 h after the switch to dark phase, replicate B

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

data_processing:
The sequencing output (50-bp paired-end) was processed using the FASTQ-mcf suite (https://github.com/ExpressionAnalysis/ea-utils). Low-quality bases (Phred score < 30) and Illumina adapters were clipped.
Reads were mapped to the genome of strain AAP5 using bowtie2 with default parameters for single-end reads. The resulting sam files were converted to an indexed binary format using samtools.
featureCounts was used to count the reads mapping to genes. Quality control of biological replicates and statistical analysis were performed in the R environment using the package edgeR
Genome_build: GCF_004354345.1
Supplementary_files_format_and_content: read counts per gene

organism: Sphingomonas glacialis

source_name: S. glacialis AAP5 cultivated in 0.1 organic medium (Kopejtka et al., 2020)

extract_protocol:
Cells were harvested by centrifugation. Pellets were resuspended in 1 ml PGTX extraction solution (Pinto et al., 2009) and immediately frozen in liquid nitrogen. RNA was extracted and processed as described earlier in  Kopejtka et al. (2020).
Libraries for transcriptomics were generated according to Shishkin et al., 2015 including rRNA removal with the RiboZero Kit (Illumina Inc., San Diego, CA, US).

tag: treatment

value: dark

tag: time

value: 6 hr

tag: replicate

value: B


title: H3K4me3_hPSC


title: H3K4me3_EPC_rep2


title: H3K27me3_VME_rep2


title: S. glacialis, day 6, 1 h after the switch to dark phase, replicate A

value: 1 hr

value: A


title: S. glacialis, day 6, 6 h after the switch to light phase, replicate C

value: light

value: C


title: H3K27me3_HPC_rep2


title: H3K27me3_VME_rep1


title: S. glacialis, day 6, 6 h after the switch to light phase, replicate B


title: H3K4me3_VME_rep1


title: H3K27me3_hPSC_rep2


title: S. glacialis, day 6, 6 h after the switch to dark phase, replicate C


title: S. glacialis, day 6, 6 h after the switch to light phase, replicate A


title: S. glacialis, day 6, 1 h after the switch to dark phase, replicate C


title: S. glacialis, day 6, 1 h after the switch to light phase, replicate C


title: S. glacialis, day 6, 1 h after the switch to light phase, replicate A


title: H3K27me3_EPC_rep2


title: S. glacialis, day 6, 6 h after the switch to dark phase, replicate A


title: RNA_VME_rep2


title: S. glacialis, day 5, 6 h after the switch to dark phase, replicate C


title: scRNA-seq

description: cultured cells


title: RNA_VME_rep1


title: S. glacialis, day 6, 1 h after the switch to dark phase, replicate B


title: RNA_HPC_rep2


title: H3K27me3_HPC_rep1


title: S. glacialis, day 5, 6 h after the switch to dark phase, replicate A


title: RNA_HPC_rep1


title: S. glacialis, day 5, 1 h after the switch to dark phase, replicate C


title: S. glacialis, day 5, 1 h after the switch to dark phase, replicate A


title: H3K27me3_hPSC_rep1


title: S. glacialis, day 5, 1 h after the switch to dark phase, replicate B


title: RNA_EPC_rep2


title: S. glacialis, day 5, 6 h after the switch to light phase, replicate C


title: H3K27me3_EPC_rep1


title: RNA_hPSC_rep1


title: S. glacialis, day 6, 1 h after the switch to light phase, replicate B


title: S. glacialis, day 5, 6 h after the switch to dark phase, replicate B


title: S. glacialis, day 5, 6 h after the switch to light phase, replicate B


title: S. glacialis, day 5, 6 h after the switch to light phase, replicate A


title: scRNA-seq_GP66+_Day10_M2

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

country: USA

institute: Northwestern University

description: scRNA-seq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Spleen

extract_protocol:
Cells were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5′ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol
Libraries for transcriptome sequencing were constructed using 10x Chromium v2 5' reagents using standard protocols. Libraries for TCR sequencing were prepared from the same cDNA used in transcriptome sequencing using nested PCR as described in the associated publication.
scRNA-seq + TCR-seq

treatment_protocol: GP66-specific splenic CD4+ T cells were FACS-sorted from LCMV Cl13-infected C57BL/6 mice on day 10 p.i. and were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5′ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol

value: CD4+ T cells

tag: tissue

value: Spleen

value: C57BL/6 mice

value: 6-8 weeks old


title: RNA_EPC_rep1


title: scTCR-seq_GP66+_Day10_M1

description: scTCR-seq


title: scTCR-seq_GP66+_Day10_M2

description: scTCR-seq


title: S. glacialis, day 5, 1 h after the switch to light phase, replicate A


title: RNA_hPSC_rep2


title: scRNA-seq_GP66+_Day10_M1

description: scRNA-seq


title: ISOS-1_VPA_3

city: Sapporo

first: Keisuke

last: Aoshima

state: Hokkaido

address: Kita 18 Nishi 9

department: Faculty of Veterinary Medicine

country: Japan

institute: Hokkaido University

data_processing:
bcl2fastq ver2.17 (illumina)
STAR
RSEM
edgeR
Assembly: mm39
Supplementary files format and content: An Excel file include TPM values for each Sample

source_name: angiosarcoma cells

growth_protocol: ISOS-1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
NucleoSpin RNA isolation kit (#740955.50, Macherey-Nagel GmbH & Co. Düren, Germany)
QuantSeq 3’mRNA-Seq Library Prep Kit for Illumina (FWD) <015.384> (LEXOGEN)

treatment_protocol: ISOS-1 were treated with 1 µM SAHA for 24 h, 1 µM JQ1 for 36 h, or 2 mM VPA for 36 h in triplicate.

value: angiosarcoma cells

value: endothelial cells

tag: genotype

value: WT

value: VPA


title: ISOS-1_VPA_2


title: ISOS-1_VPA_1


title: S. glacialis, day 4, 6 h after the switch to dark phase, replicates A to C


title: S. glacialis, day 4, 1 h after the switch to dark phase, replicates A to C


title: S. glacialis, day 4, 6 h after the switch to light phase, replicates A to C


title: ISOS-1_SAHA_3

value: SAHA


title: S. glacialis, day 5, 1 h after the switch to light phase, replicate C


title: Panc1-GR2

city: Fuzhou

first: Zu-wei

last: Wang

address: No. 134, East Street, Fuzhou, 350001, Fujian Province, PR China

institute: Fujian provincial hospital

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts. In this step,  clean data (clean reads) were obtained by removing following reads: (1) reads with 5’ adapter; (2) reads  without 3’ adapter or insert sequence; (3) reads with more than 10% N; (4) reads with more than 50%  nucleotides with Qphred<=20; (5) reads with ploy A/T/G/C. Adapter trimming for the removal of adapter  sequences from the 3’ ends of reads was also performed. At the same time, Q20, Q30 and GC content of  the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Clean reads for each sample were first mapped to a reference genome with the software HISAT2. Reads alignment results were transferred to the program StringTie for transcript assembly
Quantification of the transcripts and genes was performed using StringTie software and Reads Per  Kilobase of transcript per Million mapped reads (RPKM) was obtained. Cuffdiff or edgeR was used for  differential expression analysis. The resulting P-values were adjusted using the Benjamini and Hochberg’s  approach for controlling the false discovery rate. Genes with |log2 (Fold Change) | > 0 & padj < 0.05 were  assigned as differentially expressed.

organism: Homo

source_name: pancreatic cancer cell

extract_protocol:
A total amount of 3 µg RNA per sample was used as input material for the RNA  sample preparations. Sequencing libraries were generated using NEBNext® UltraTM  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations and index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic  beads. Fragmentation was carried out using divalent cations under elevated temperature  in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA wassynthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase  H-). Second strand cDNA synthesis was subsequently performed using DNA  Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via  exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments,  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization.  In order to select cDNA fragments of preferentially 150~200 bp in length, the library  fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).  Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated  cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was  performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and  Index (X) Primer. At last, PCR products were purified (AMPure XP system) and  library quality was assessed on the Agilent Bioanalyzer 2100 system
RNA library for lncRNA-seq was prepared as rRNA depletion and stranded method. After library construction, the concentration of library was measured by the Qubit® fluorometer and adjusted to 1ng/uL. Agilent 2100 Bioanalyzer was deployed to examine the insert size of the acquired  library. At last, the accurate concentration of cDNA library was again examined using qPCR. Once the  insert size and concentration of the library was identical, the samples can then be subjected for sequencing

tag: phenotype

value: gemcitabine resistance


title: S. glacialis, day 4, 1 h after the switch to light phase, replicates A to C


title: Panc1-GR1


title: ISOS-1_JQ1_3


title: ISOS-1_SAHA_2


title: S. glacialis, day 5, 1 h after the switch to light phase, replicate B


title: Panc1-GR3


title: ISOS-1_JQ1_2


title: Panc1-WT1

value: wild type


title: ISOS-1_SAHA_1


title: Panc1-WT3


title: Panc1-WT2


title: ISOS-1_JQ1_1


title: Wild type normoxia rep2

city: Warsaw

first: Klaudia

last: Brodaczewska

address: Szaserow 128

country: Poland

institute: Military Institute of Medicine

description:
WT_NO_2
raw_counts_mmu_miRNA.txt

data_processing:
Single-end reads were aligned to Ensembl GRCm38 mouse genome with STAR (v2.7)
Counts were obtained using featureCounts v1.6.3
Genome_build: mmu38
Supplementary_files_format_and_content: tab-delimited text file include table with raw gene counts for every gene and every sample

source_name: renal cell cancer

growth_protocol: Cancer cells were seeded on standard tissue culture treated flasks (VWR Interna-tional, USA) in the right density (7000 cells/cm2 Renca pten/WT pten/KO, 12 000 cells/cm2 Caki-1 and 1000 cells/cm2 786-O) and allowed to adhere to the culture surface for 24h. Media were exchanged with pre-equilibrated normoxic or hypoxic medium and cultured in standard cell culture incubator (21% pO2; 5% CO2) or XVivo X3 workstation (Biospherix, USA) in 1% pO2; 5% CO2, respectively. After 72 hours, cells were harvested using Accutase (Biolegend, USA), cell counts and viability were assessed by Trypan blue exclusion test using a Burker chamber. Collected cells were used for further analysis – RNA isolation. For tumor samples, Renca cells were implanted in BALB/c mice leg as subcutaneous tumors by injec-tion of a plug constituted by 105 cells in 100 μl MatrigelTM (Corning, USA) diluted in 1:3 in PBS. After 22 days of tumor growth, the mice were killed and fragments of tumor tissue were used to isolate RNA

extract_protocol:
Total RNA was extracted from cancer cells cultured in normoxia and hypoxia or tumor tissues using RNeasy Mini Kit (Qiagen, Germany). The samples were freed from DNA using TURBO DNA-free kit (Thermo Fisher Scientific, USA) and RNA quality and concentrations were evaluated using the fluorometer Qubit (Qubit RNA BR Assay Kit, RNA with Qubit RNA IQ Assay Kit, Thermo Fisher Scientific, USA) according to manufacturers’ instructions.
Total RNA from Renca cells and tumors (pten/WT, pten/KO) was used to prepare libraries and perform high-throughput sequencing by an external service Lexogen GmbH (Vienna, Austria) with NextSeq 500 system (Illumina, USA). Briefly, RNA concentration was measured by UV-Vis spectrophotometry (Nanodrop 2000c, Thermo Fisher), and RNA integrity was assessed on a Fragment Analyzer System using the DNF-471 RNA Kit (15 nt) (Agilent, USA). Sequencing-ready libraries were produced using a Small RNA-SeqLibrary Prep Kit by Lexogen (052UG128V0110) per manufacturer instructions. Indexed library preparation was performed to allow for multiplexed sequencing. For library preparation, 100ng of each provided RNA sample was used. All libraries were analyzed for adapter dimers, size distribution and concentration on a Fragment Analyzer System using the DNF-474 HS NGS Fragment kit (1-6,000bp) (Agilent, USA). Libraries were pooled in an  equimolar ratio. After pooling, 1,3x magnetic bead purification and agarose gel size selection was performed to target miRNA fraction. The concentration and the size distribution of the final lane mix was analyzed by Qubit dsDNA HS assay (Thermo Fisher Scientific) and by Fragment Analyzer System using the DNF-474 HS NGS Fragment kit (1-6,000bp) (Agilent, USA). A 2 nM dilution of the lane mix was denatured and diluted to loading  concentration for sequencing on a NextSeq 500 instrument with SR75 High Output Kit (Illumina).

treatment_protocol: Hypoxia exposure described above

value: RenCa

tag: origin

value: monolayer culture


title: ISOS-1_DMSO_3

value: DMSO


title: ISOS-1_DMSO_2


title: PTEN knock-out  rep2

description:
PTEN_KO_2
raw_counts_mmu_miRNA.txt

value: subcoutaneus tumor


title: ISOS-1_DMSO_1


title: Wild type normoxia rep1

description:
WT_NO_1
raw_counts_mmu_miRNA.txt


title: PTEN knock-out hypoxia rep1

description:
PTEN-KO_HO_1
raw_counts_mmu_miRNA.txt


title: PTEN knock-out normoxia rep2

description:
PTEN-KO_NO_2
raw_counts_mmu_miRNA.txt


title: ATAC_HEC_WT_Rep2

description: cultured cells

data_processing:
for ATAC-seq and ChIP-seq, all of the paired-end raw reads were processed using TrimGalore to trim adaptor and low-quality reads. Adaptor-trimmed paired-end reads from ATAC-seq and ChIP-seq were aligned to hg38 by bowtie2 (version 2.3.5) with the parameters: --t --q --N 1 --L 25. PCR duplicates and multiple mapped reads were removed. The replicate BAM files for each time point were merged and removed reads aligning to blacklisted genomic regions before calling peaks with MACS2 (version 2.2.6) and the enriched TF motifs were analyzed by Homer (version 4.10.4, findMotifsGenome).
Genome_build: GRCh38

value: Embryonic stem cells

value: human embryonic stem cell line H1


title: Wild type hypoxia rep2

description:
WT_HO_2
raw_counts_mmu_miRNA.txt


title: PTEN knock-out hypoxia rep2

description:
PTEN-KO_HO_2
raw_counts_mmu_miRNA.txt


title: Wild type rep2

description:
Ctrl_KO_2
raw_counts_mmu_miRNA.txt


title: Wild type hypoxia rep1

description:
WT_HO_1
raw_counts_mmu_miRNA.txt


title: PTEN knock-out normoxia rep1

description:
PTEN-KO_NO_1
raw_counts_mmu_miRNA.txt


title: Wild type rep1

description:
Ctrl_KO_1
raw_counts_mmu_miRNA.txt


title: PTEN knock-out  rep1

description:
PTEN_KO_1
raw_counts_mmu_miRNA.txt


title: RNA_pu1_pbs_rep3

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

description:
processed data file:
pu1_count_matrix.txt
pu1_metadata.txt

data_processing:
bulk RNA-seq: From the paired-end fastq files, the first three nucleotides were trimmed off the second sequencing read using cutadapt version 1.16. TrimGalore version 0.4.5 was used in paired mode to trim adapters and low-quality portions of reads. Reads were aligned using Salmon version 0.12.0 to mouse genome version GRCm38.94 and human genome version GRCh38.94. For downstream analysis, TPM files from Salmon were imported into R version 3.6.1 using tximport version 1.14.0 with the option to generate estimated counts using abundance estimates scaled up to library size, and additionally scaled using the average transcript length over samples and the library size (countsFromAbundance = lengthScaledTPM).
scRNA-seq: We aligned 40-bp paired-end reads to the mm10 genome for each of 1,357 single nuclei from 12 mice (64 cells each for 6 CK controls and an average of 162 cells in each of 6 CKp25 mice) using bwa mem (options: -k 15 -M) and filtered out improperly aligned reads and secondary alignments with samtools (options: -f 3 -F 1280). We ran HTSeq-count10 on each cell’s filtered bam file to compute the cell’s transcriptomic coverage over each gene’s exons in vM25 GENCODE gene annotation.
Genome_build: mm10
Supplementary_files_format_and_content: TPM, raw counts

molecule: nuclear RNA

source_name: cortex

growth_protocol: CK-p25 double transgenic mice were raised and maintained on a doxycycline diet. All mice were induced by removing doxycycline from their diet to drive the expression of p25-GFP in forebrain excitatory neurons. All mice were induced at 3-4 months old.

extract_protocol: For bulk RNA-sequencing of sorted nuclei, samples were treated for 15 minutes with Proteinase K at 50°C and then for 13 minutes at 80°C. RNA was extracted using Direct-zol RNA MicroPrep kit according to manufacturer’s instructions (cat no. R2062, Zymo Research, Irvine CA). Purified RNA samples underwent fragment analysis at the MIT BioMicro Center. Libraries were generated from samples passing quality control (DV200 < 50%). Library generation was performed using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (cat no. 634412, Takara Bio Inc), then submitted to the MIT BioMicro Center for quality control (fragment analysis and qPCR), followed by sequencing. Paired-end sequencing was performed using the Illumina NextSeq500 platform according to standard operating procedures.

treatment_protocol: PHP.eB AAV shRNA or PBS was delivered retro-orbitally to anesthetized CK-p25 mice, 2x10^11. Two weeks after injection, mice were induced by removing doxycycline diet.

value: CK

tag: celltype

value: microglia

tag: timepoint


title: RNA_pu1_pbs_rep2


title: AgRP-/- fasted 2

type: RNA

city: Concord

first: Eirini

last: Vagena

state: CA

address: 2331 Saint George Dr

institute: UCSF

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Utilized R::limma package with the read.ilmn and neqc functions to extract normalized (neqc, log2 transformed) values

label: biotin

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit

extract_protocol: RNA was extracted using the PerfectPure RNA extraction kit with DNase I treatment in accordance to manifacturer's recommendations. Quality control was performed with Agilent Bioanalyser.

tag: strain background

value: mixed

tag: genotype/variation

value: AgRP-/-

value: fasted for 30h

value: hypothalamus


title: AgRP-/- fasted 3


title: AgRP-/- fasted 4


title: AgRP+/- fasted 2

value: AgRP+/-


title: AgRP-/- fed ad lib 4

value: Ad libitum fed


title: AgRP-/- fasted 1


title: AgRP+/- fasted 4


title: RNA_pu1_pbs_rep1

tag: strain


title: AgRP+/- fasted 1


title: AgRP-/- fed ad lib 3


title: AgRP+/- fasted 3


title: AgRP-/- fed ad lib 2


title: CUTnRUN_IgG_shNT_rep1

city: Daejeon

first: Sungwook

last: Han

address: Deahakro 291

department: Biological Science

country: South Korea

institute: KAIST(Korea Advanced Institute of Science and Technology)

data_processing:
Library strategy: CUT&RUN
For CUT&RUN analysis, raw reads were aligned to the mouse genome (mm10) using Bowtie2 (version 2.2.9) with the parameter (--trim3 125 --local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700), as the previous study (GSM2247138).
For ATAC-seq analysis, raw reads were aligned to the mouse genome (mm10) using Bowtie2 (version 2.2.9) with the following parameter; --very-sensitive -X 100 –local.
We used PICARD to remove the duplicates.
We used MACS2 to convert the aligned BAM files into bedGraph files, and normalized the data with respect to the total read counts.
Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files.
The bigWig files were used as input files for bwtool (matrix and aggregate option) to quantify the intensity of the relevant sequencing data.
Assembly: mouse genome mm10
Supplementary files format and content: We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts. Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files (.bw).

source_name: E14Tg2a (mESCs)

growth_protocol: E14Tg2a mouse embryonic stem cells (mESCs) : cultured in feeder-free gelatin-coated plates in Glasgow minimum essential medium (GMEM, Gibco) supplemented with 10% knockout serum replacement (Gibco), 1% Defined fetal bovine serum (FBS, Hyclone), 1% non-essential amino acids (NEAA, Gibco), 1% sodium pyruvate (Gibco), 0.5% antibiotic-antimycotic (penicillin-streptomycin containing, Hyclone), 0.1mM β-mercaptoethanol (Gibco), and 1000 U/ml Leukemia Inhibitory Factor (LIF, Millipore).

extract_protocol:
CUT&RUN assays were performed as previously described (Meers et al., 2019; Skene and Henikoff, 2017), with minor modification. Briefly, 4 million mESCs were harvested and washed with 1.5 ml Wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine) three times. Cells were bound to activated Concanavalin A-coated magnetic beads (at 25°C for 10 min on a nutator), then permeabilized with Antibody buffer (Wash buffer containing 0.05% Digitonin and 4 mM EDTA). The bead-cell slurry was incubated with 3 μl relevant antibody (see below) in a 150 μl volume at 25°C for 2 hours on a nutator. After two washes in 1 ml Dig-wash buffer (Wash buffer containing 0.05% Digitonin), beads were resuspended in 150 μl pAG/MNase and incubated at 4°C for 1 hour on a nutator. After two washes in 1 ml Dig-wash buffer, beads were gently vortexed with 100 μl Dig-wash buffer. Tubes were chilled to 0°C for 5min and ice-cold 2.2 mM CaCl2 was added while gently vortexing. Tubes were immediately placed on ice and incubated at 4°C for 1 hour on a nutator, followed by addition of 100 μl 2xSTOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 0.1 mg/ml RNase A, 50 μg/ml glycogen) and incubated at 37°C for 30min on a nutator. Beads were placed on a magnet stand and the liquid was removed to a fresh tube, followed by addition of 2 μl 10% SDS and 2.5 μl proteinase K (20mg/ml) and incubated at 50°C for 1 hour. DNA was extracted using phenol chloroform as described at https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-zcpf2vn. CUT&RUN libraries were prepared using either a Accel-NGS 2S Plus DNA Library Kit (21024, SWIFT), according to the manufacturer’s guidelines. The libraries were then sequenced using an Illumina Novaseq 6000 platform. The libraries were generated from two sets of biological replicates.
CUT&RUN libraries for genome-wide sequencing were prepared using either a Accel-NGS 2S Plus DNA Library Kit (21024, SWIFT).

treatment_protocol: In general, mESCs were transfected with 50 nM of the indicated siRNA using DharmaFECT I (T-2001-03, Dharmacon) according to the manufacturer’s protocol. Briefly, mESCs were seeded to 6-well plates. One day later, 50 nM of siRNAs and DharmaFECT reagent were diluted in Opti-MEM (Gibco), incubated separately at 25°C for 5 min, and then mixed together. The mixtures were incubated at 25°C for 20 min and added to the mESC cultures. The culture medium was replaced after 24 hours. Transfected mESCs were harvested at 48 hours after transfection.  shRNA targeting Ipmk was purchased from Sigma Aldrich. Lentiviruses were generated in HEK293T cells by transfecting the lentiviral plasmids together with packaging plasmid (psPAX2) and envelope-expressing plasmid (pMD2.G). Lentiviruses were added to mESCs after 48 hours and incubated for 8 hours. After 40 hours, mESCs with stable gene expression were selected by growing cells in mESC medium supplemented with Hygromycin B (Invitrogen).

value: E14Tg2a (mESCs)

value: 3xFLAG-IPMK tagged

value: In-house generated

value: shRNA against NT (a non-target control)


title: CUTnRUN_BRG1_shIpmk2_rep2

value: BRG1 (ab110641, Abcam)

value: shRNA against Ipmk


title: CUTnRUN_IgG_shNT_rep2


title: AgRP-/- fed ad lib 1


title: RNA_pu1_scr_rep2


title: RNA_pu1_scr_rep1


title: RNA_pu1_scr_rep3


title: CUTnRUN_BRG1_shIpmk1_rep2


title: RNA_pu1_p65kd_rep3


title: CUTnRUN_BRG1_shIpmk2_rep1


title: AgRP+/- fed ad lib 1


title: AgRP+/- fed ad lib 2


title: AgRP+/- fed ad lib 3


title: RNA_pu1_p65kd_rep2


title: CUTnRUN_BRG1_shIpmk1_rep1


title: AgRP+/- fed ad lib 4


title: RNA_dmso_rep3

description:
processed data file:
etp_count_matrix.txt
etp_metadata.txt

source_name: primary neurons DIV 12

growth_protocol: Cortices were dissected from E15 Swiss-Webster embryos in ice-cold HBSS (cat no. 14175103, Thermo Fisher Scientific, Waltham MA) and dissociated with papain (cat no. LS003126, Worthington Biochemical Corp., Lakewood NJ) and DNAse I (cat no. 10104159001, Roche, Basel Switzerland). Cells were resuspended in plating media (Neurobasal media (cat no. 21103049, Thermo Fisher Scientific, Waltham MA), 1% Penicillin/Streptomycin Solution (cat no. 400-109, Gemini Bio-Products, Sacramento CA), 10% FBS)) and filtered through a 100 uM cell strainer (cat no. 21008-950, VWR, Radnor PA). Cell density was quantified using a Countess II Automated Cell Counter (cat no. AMQAX1000, Thermo Fisher Scientific, Waltham MA), then plated on poly-D-Lysine-coated 12-well culture dishes, 0.5x10^6. Cultures were maintained in 5% CO2 at 37 °C in a cell culture incubator. After allowing four hours for the cells to adhere to the plate, the media was replaced and maintained with neurobasal media supplemented with B-27 (cat no. 17504-044, Invitrogen, Carlsbad CA), 1% Penicillin/Streptomycin, and 1% GlutaMAX Supplement (cat no. 35050-079, Thermo Fisher Scientific, Waltham MA).

extract_protocol: For bulk RNA sequencing of etoposide-treated primary neurons, cultures were collected in Trizol LS (cat no. 10296028, Thermo Fisher Scientific, Waltham MA). mRNA was purified and extracted using Direct-zol RNA MicroPrep kit according to manufacturer’s instructions. RNA was submitted to the MIT BioMicro Center for library preparation and sequencing. Libraries were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (cat no. E7770, New England Biolabs, Ipswich MA). Single-end sequencing was performed using the Illumina NextSeq500 platform according to standard operating procedures.

treatment_protocol: Primary cortical neuron cultures (DIV11-13) were treated with 50uM etoposide prepared from 20mM stock (cat no. E1383-250MG, Sigma, St. Louis MO) or the equivalent volume of vehicle control (DMSO). Cultures were treated for  6 hours before collection for sequencing.

value: Swiss Webster

value: primary neuron


title: RNA_pu1_p65kd_rep1


title: CUTnRUN_BRG1_shNT_rep1


title: CUTnRUN_BRG1_shNT_rep2


title: RNA_dmso_rep2


title: CUTnRUN_BRG1_IpmkKD_SA_rep1

value: siRNA against Ipmk, followed by catalytically-dead (SA) IPMK transfection


title: RNA_etp_rep2


title: CUTnRUN_BRG1_IpmkKD_WT_rep2

value: siRNA against Ipmk, followed by WT IPMK transfection


title: RNA_dmso_rep1


title: RNA_etp_rep1


title: VDS_6

city: College Station

first: Masako

last: Suzuki

state: TX

address: 498 Olsen Blvd, Norman E. Borlaug Building 202C

department: Nutrition

institute: Texas A&M University

description: Prenatal vitamin D sufficiency exposed

data_processing:
After removing reads that failed the quality check and trimming adapter sequences, the resulting sequences were aligned to the mouse mm10 reference genome, quantifying gene expression by transcript counting (GENECODE release M15, GRCm38) using the STAR aligner
Genome_build: mm10
Supplementary_files_format_and_content: htcount

source_name: Liver

extract_protocol:
Total RNA was extracted from mouse livers at 16 weeks of age using the AllPrep DNA/RNA Micro Kits (QIAGEN).
The RNA-seq libraries were generated using KAPA RNA HyperPrep with RiboErase kit (Roche).

value: Liver

tag: prenatal condition

value: Vitamin D sufficiency

tag: age (weeks)


title: VDS_3

description: Prenatal vitamin D sufficiency exposed


title: VDS_4

description: Prenatal vitamin D sufficiency exposed


title: VDS_5

description: Prenatal vitamin D sufficiency exposed


title: Bulk_RNA_CK_Glia_rep2

description:
processed data file:
bulk_RNA_CKp25_all_count_matrix.txt

treatment_protocol: no treatment

value: CK

value: Glia


title: irisin treated-group2

city: Guangzhou

first: Taiqiu

last: Chen

state: Guangdong

address: 33, Yinfeng Road

institute: Sun yat-sen university

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary mesenchymal stem cells

growth_protocol: C3H 10T1/2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

tag: cell type

value: primary mesenchymal stem cells

value: chondrogenic differentiation

value: Day 7


title: CUTnRUN_BRG1_IpmkKD_WT_rep1

value: E14Tg2a (mESCs)

tag: chip antibody


title: VDS_2

description: Prenatal vitamin D sufficiency exposed


title: irisin treated-group3


title: VDS_1

description: Prenatal vitamin D sufficiency exposed


title: Bulk_RNA_CK_Glia_rep1


title: VDD_5

description: Prenatal vitamin D deficiency exposed

value: Vitamin D deficiency


title: CUTnRUN_BRG1_IpmkKD_SA_rep2

value: 3xFLAG-IPMK tagged


title: Bulk_RNA_CK_Baseline_rep2

value: Baseline


title: RNA_etp_rep3


title: VDD_3

description: Prenatal vitamin D deficiency exposed


title: Bulk_RNA_CK_Baseline_rep1


title: control-group3


title: VDD_1

description: Prenatal vitamin D deficiency exposed


title: irisin treated-group1


title: VDD_4

description: Prenatal vitamin D deficiency exposed


title: Bulk_RNA_CKp25_Glia_rep2


title: Bulk_RNA_CKp25_Glia_rep1


title: VDD_6

description: Prenatal vitamin D deficiency exposed


title: 18 month male M4

city: Kingston

first: Madhuri

last: Koti

state: Ontario

address: 10 Stuart Street

department: Department of Biomedical and Molecular Sciences

country: Canada

institute: Queen's University

description: bulk RNA

data_processing:
Remove Illumina adapters with Trimmomatic (0.36) using the following reference adapters; Forward:  AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC – Reverse:  AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Pseudoalign reads to reference transcript sequences (GRCm38.p6) from Gencode Release M25 using Salmon (1.3.0) in mapping based mode with default parameters
Raw and TPM normalized counts from salmon Quant.sf.txt files were then extracted into R (4.1.0) using Tximport to get read coverage tables (available in supplemental files)
Genome_build: mm10
Supplementary_files_format_and_content: Quantification files from Salmon with gene names, gene length, effective length, TPM counts, and raw counts
Supplementary_files_format_and_content: Matrix tables of raw or TPM normalzed counts for all samples (Supplementary tables)

source_name: bladder

extract_protocol:
Bladders were collected and snap frozen in liquid nitrogen, total RNA from fresh-frozen bladders was isolated using the RNeasy Mini Kit (Qiagen Inc, Canada). Qualitative and quantitative assessments of RNA were performed using a spectrophotometer (Nanodrop ND-100) and a bioanalyzer (Agilent). Samples that met the purity requirement (>8.0 RNA integrity number) were subjected to bulk RNA-sequencing (Genome Quebec, Montreal, QC, Canada)
Libraries were prepared using standard illumina protocols after samples were treated with the Ribo-zero rRNA depletion kit (Illumina)

value: bladder

tag: age

value: 18 months old

tag: Sex

value: Male


title: 18 month male M3

description: bulk RNA


title: 18 month male M1

description: bulk RNA


title: 18 month male M2

description: bulk RNA


title: Bulk_RNA_CKp25_Baseline_rep1


title: 18 month female M3

description: bulk RNA

value: Female


title: Bulk_RNA_CKp25_Stage2_rep2

value: Stage 2


title: control-group1

tag: treatment

tag: time


title: HSC_mut_rep2_RNA

city: Tianjin

first: chao

last: tang

state: Tianjin

address: 288 Nanjing Road

institute: Institute of Hematology and Blood Diseases Hospital

data_processing:
Basecalls perfomed using CASAVA2.19
WGBS and RNA-seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS-Seeker2(v2.1.8) and hisat2(v2.2.1) with parameters "-t Y -m 0.04 --bt2--end-to-end" and "--known-splicesite-infile -p 30 -k 10 --dta -t" separately.
Student's T-test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeq(v0.12.4) and differentially expressed genes(DEGs) were determined by DESeq2(v1.30.1)
Genome_build: GRCz11
Supplementary_files_format_and_content: RNA-seq raw count matrix
Supplementary_files_format_and_content: raw_count.txt raw counts
Supplementary_files_format_and_content: EC_sib.bed DMRs of  EC sibling compared with HE sibling and HSC sibling
Supplementary_files_format_and_content: HE_sib.bed DMRs of  HE sibling compared with EC sibling and HSC sibling
Supplementary_files_format_and_content: HSC_sib.bed DMRs of  HSC sibling compared with EC sibling and HE sibling
Supplementary_files_format_and_content: EC_HE_sib.bed DMRs of  EC and HE sibling
Supplementary_files_format_and_content: HE_HSC_sib.bed DMRs of  HE and HSC sibling
Supplementary_files_format_and_content: EC_sib_mut.bed DMRs of  EC sibling and EC mutant
Supplementary_files_format_and_content: HE_sib_mut.bed DMRs of  HE sibling and HE mutant
Supplementary_files_format_and_content: HSC_sib_mut.bed DMRs of  HSC sibling and HSC mutant

molecule: polyA RNA

organism: Danio rerio

source_name: hematopoietic stem cells

extract_protocol:
Zebrafish embryos were harvested and dissected for single-cell suspension. Single-cell was sorted in lysis buffer by fluorescence-activated cell sorting.
The RNA-seq library preparation and sequencing were performed based on the 3′-biased single-cell tagged reverse transcription sequencing (STRT-seq).The DNA libraries conduction were performed according to the scBS-seq with some modification

tag: developmental stage

value: HSC

value: dnmt1 mutant

tag: region

value: AGM


title: 18 month female M1

description: bulk RNA

tag: tissue


title: 18 month female M2

description: bulk RNA


title: 15 month male M4

description: bulk RNA

value: 15 months old


title: HSC_mut_rep3_RNA

tag: genotype


title: control-group2


title: Bulk_RNA_CKp25_Baseline_rep2

tag: celltype


title: HE_mut_rep3_RNA

source_name: hemogenic endothelium cells

value: HE


title: 15 month female M4

description: bulk RNA


title: HSC_sib_rep3_RNA

value: sibling


title: Bulk_RNA_CKp25_Stage1_rep1

value: Stage 1

tag: timepoint


title: VDD_2

description: Prenatal vitamin D deficiency exposed

value: Liver


title: Bulk_RNA_CKp25_Stage2_rep1


title: HDF_Whole_3

city: Kyoto

first: Mio

last: Iwasaki

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

data_processing:
Illumina bcl2fastq (v2.17) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.12) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.5.3a)
"rsem-calculate-expression" in RSEM (v1.3.3) was perfomed for counting reads and calculating TPM with the GENCODE (version 35) annotation gtf file.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: HDF

growth_protocol: Human induced pluripotent stem cells (201B7) were maintained under feeder-free conditions on iMatrix-511 (Nippi) with StemFit AK03N medium (Ajinomoto).  Human dermal fibroblasts (Tig120) were cultured in Dulbecco’s modiﬁed Eagle’s medium (DMEM; Nacalai Tesque) with 10% fetal bovine serum (FBS, Thermo Fisher Scientific) and 0.5% penicillin and streptomycin (gibco).

extract_protocol:
For RNA extraction, an equal volume of TRIZOL LS reagent (Thermo Fisher Scientific) was added to the cytosol fraction. For the nucleus fraction, 400 μL (24-well plate) or 1000 μL (6-well plate) of QIAzol lysis reagent (QIAGEN) was added to solubilize the pellet. The RNA was purified using a miRNeasy Mini Kit (QIAGEN).
Illumina TruSeq Stranded Total RNA Library Prep

treatment_protocol: Subcellular fractionations of cytoplasm and nuclei were performed using the Subcellular Protein Fractionation Kit for Cultured Cells (Thermo Fisher Scientific, #78840).

value: HDF

tag: fraction

value: Whole

tag: molecule

value: Whole total RNA


title: 15 month male M2

description: bulk RNA

tag: strain


title: HE_mut_rep2_RNA


title: 15 month male M3

description: bulk RNA


title: HE_mut_rep1_RNA


title: 12 month male M2

description: bulk RNA

value: 12 months old


title: Bulk_RNA_CKp25_Stage1_rep2


title: 12 month female M4

description: bulk RNA

value: bladder


title: 15 month female M3

description: bulk RNA


title: 12 month male M3

description: bulk RNA


title: 15 month female M1

description: bulk RNA


title: HE_sib_rep2_RNA


title: 15 month female M2

description: bulk RNA


title: 12 month female M3

description: bulk RNA


title: HSC_sib_rep2_RNA


title: HDF_Whole_1


title: HE_sib_rep3_RNA


title: HE_sib_rep1_RNA


title: 12 month male M1

description: bulk RNA


title: 12 month female M1

description: bulk RNA


title: 12 month female M2

description: bulk RNA


title: HDF_Nucleus_2

value: Nucleus

value: Nuclear total RNA


title: 15 month male M1

description: bulk RNA

value: Male


title: EC_mut_rep3_RNA

source_name: endothelial cells

value: EC


title: 9 month male M4

description: bulk RNA

value: 9 months old


title: HDF_Nucleus_1


title: HDF_Whole_2


title: 9 month male M2

description: bulk RNA


title: 9 month male M3

description: bulk RNA


title: HDF_Cytosol_3

value: Cytosol

value: cytoplasmic total RNA


title: EC_mut_rep2_RNA

value: dnmt1 mutant

value: AGM


title: 9 month male M1

description: bulk RNA


title: 9 month female M4

description: bulk RNA

value: Female


title: 9 month female M3

description: bulk RNA


title: HDF_Cytosol_2


title: EC_mut_rep1_RNA


title: HDF_Cytosol_1


title: EC_sib_rep2_RNA

value: sibling


title: EC_sib_rep3_RNA


title: HDF_Nucleus_3


title: iPS_Whole_3

source_name: iPS

value: iPS


title: 6 month male M3

description: bulk RNA

value: 6 months old


title: 9 month female M1

description: bulk RNA


title: 6 month male M2

description: bulk RNA


title: 9 month female M2

description: bulk RNA


title: 6 month male M1

description: bulk RNA


title: EC_sib_rep1_RNA


title: 6 month female M3

description: bulk RNA


title: 6 month female M2

description: bulk RNA


title: HSC_mut_rep3_MET

value: HSC


title: iPS_Whole_1

value: Whole

value: Whole total RNA


title: iPS_Nucleus_3


title: 3 month male M4

description: bulk RNA

value: bladder

value: 3 months old


title: HSC_mut_rep2_MET


title: HSC_mut_rep1_MET


title: 3 month male M3

description: bulk RNA


title: 3 month male M2

description: bulk RNA


title: iPS_Nucleus_2

value: Nucleus

value: Nuclear total RNA


title: 3 month male M1

description: bulk RNA

value: Male


title: 3 month female M3

description: bulk RNA


title: HSC_sib_rep3_MET


title: HSC_sib_rep2_MET


title: 3 month female M2

description: bulk RNA


title: HSC_sib_rep1_MET


title: iPS_Cytosol_3


title: 6 month female M4

description: bulk RNA


title: 3 month female M4

description: bulk RNA


title: iPS_Cytosol_2


title: Sample 26_L53

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

data_processing:
Following sequencing quality control, CellRanger v3.0.2 (10X Genomics) was used to align reads to a custom reference genome which included introns and exons to consider pre-mRNA and mature mRNA present in the nuclei.
Raw counts were further analysed using Seurat v4.0.0. Each sample was filtered for (i) genes expressed in at least 3 nuclei, (ii) nuclei which express at least 100 genes, and (iii) ≤1% mitochondrial genes.
Additional quality control was performed using the scater package (v1.18.6). The DoubletFinder v2.0.3 package excluded putative doublets from subsequent analyses.
Clustering of nuclei was performed using Seurat integration tools at a resolution of 0.1
Genome_build: mm10 release 93
Supplementary_files_format_and_content: Processed data files for individual sample are CellRanger filtered_feature_bc_matrix outputs which includes barcodes (barcodes.tsv.gz),  features (features.tsv.gz), and the matrix (matrix.mtx.gz).
Supplementary_files_format_and_content: RData file represents the full processed Seurat R data object generated using Seurat v4.0.0.
Supplementary_files_format_and_content: Sparse matrices for log normalized (log_norm mtx and tsv files) and SCT (sct mtx and tsv files)

extract_protocol:
Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle.
Libraries were prepared using the 10X Genomics Chromium Single Cell 3’ v3.1 kit (10X Genomics)

treatment_protocol: Mice were orally gavaged with sesame oil vehicle control, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 µg/kg TCDD every 4 days for 28 days.

value: day

value: degree celsius

value: percent

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

tag: vendor

value: Accustandard

value: sesame oil

value: oral gavage

tag: dose

value: microgram per kilogram

value: 10X Genomics Chromium Single Cell 3’ v3 kit


title: Sample 27_L54


title: 3 month female M1

description: bulk RNA

value: bladder

tag: age

value: 3 months old

value: Female


title: iPS_Whole_2

tag: cell type

value: iPS

value: Whole

value: Whole total RNA


title: 6 month female M1

description: bulk RNA

value: 6 months old

tag: Sex


title: iPS_Cytosol_1

value: Cytosol

value: cytoplasmic total RNA


title: HE_mut_rep2_MET

value: HE

value: dnmt1 mutant

value: AGM


title: Sample 23_L50

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Accustandard


title: Sample 24_L51

value: sesame oil

value: oral gavage

value: microgram per kilogram

value: 10X Genomics Chromium Single Cell 3’ v3 kit


title: Lib_rep4

city: Taipei

first: Chien-Ling

last: Lin

address: 128 Academia Road, Section 2

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

data_processing:
0-3 random nucleotides were attached at the end of the amplicons to ensure the balanced fluorescence detection on the NextSeq platform.
Single-end reads are aligned to our synthetic “reference genome” by hisat2.
High-quality (q60) reads selected by SAMtools.
Spliced reads crossing barcode position with GT-AG splice junctions annotation by RegTools are preserved. Reads without junctions spanning the most used splice site position are preserved as unspliced reads.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with every spliced (including canonical and noncanonical) and unspliced reads for every wildtype and mutant sample

source_name: Human embryonic kidney cells

growth_protocol: HEK293T cells were grown in 6-well plates in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum

extract_protocol:
Harvested 24 hours post-transfection and processed according to the instruction of Direct-zol™ RNA MiniPrep Plus kit (Zymo Research) for RNA extraction. cDNA was prepared from 2 μg total RNA using SuperScript®IV reverse transcriptase (Thermo Fisher Scientific) with random hexamer, following the manufacturer’s protocol.
Standard Illumina library construction protocol
Amplicon sequencing; The PCR amplicons were subject to Illumina NextSeq 150 single-end sequencing

treatment_protocol: Cells cultured in 6-well plate were transfected with 1 μg of MaPSy-library DNA templates.

tag: cell line

value: kidney


title: Sample 22_L49


title: HE_mut_rep1_MET

tag: developmental stage

value: HE

value: dnmt1 mutant


title: HE_sib_rep3_MET

value: sibling

tag: region

value: AGM


title: HE_mut_rep3_MET


title: iPS_Nucleus_1

value: iPS

value: Nucleus

value: Nuclear total RNA


title: Sample 17_L44

value: Male

value: day

value: degree celsius

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)


title: Sample 25_L52

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Accustandard

value: sesame oil

value: oral gavage


title: Sample 19_L46

value: microgram per kilogram

value: 10X Genomics Chromium Single Cell 3’ v3 kit


title: Lib_rep1

tag: tissue

value: kidney


title: Sample 21_L48


title: Sample 13_L40


title: EC_mut_rep3_MET

value: EC

tag: genotype

value: dnmt1 mutant

value: AGM


title: Sample 14_L41

value: Male

value: day


title: Lib_rep2


title: Sample 12_L39

value: degree celsius

value: percent


title: Lib_rep3


title: Sample 18_L45

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)


title: Sample 15_L42

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940


title: Control neurons_rep2

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

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
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
Genome_build: mm10
Supplementary_files_format_and_content: Count Tables (.txt), BigWigs (.bw)

growth_protocol: Primary cultures of hippocampal neurons were established from P0-P2 old pups of CD1 mice and cultured in the Neurobasal medium supplemented with 2% B-27 supplement, 2 mmol/L glutamine, 50 mg/mL of streptomycin, and 100 U/mL penicillin.  One-third of the medium volume was replaced every third day. On the third day in vitro (DIV) primary hippocampal neurons were treated with 5 mmol/L cytosine-β-D-arabinoside to prevent growth of non-neuronal cells.

extract_protocol:
Neuronal RNA was isolated using RNeasy Mini Kit, following manufacturer provided protocol, which  included in column DNA digestion with 2 U of DNAse I.
Libraries were generated with Illumina Truseq kit with an input of 200ng of RNA and 10 cycles

treatment_protocol: Neurons were treated on the 10 DIV and again on the 13 DIV apoE-enriched, 10-fold concentrated astrocytic conditioned media in Neurobasal medium (1:10 vol/vol). The experiment was concluded at 17 DIV.

value: Primary hippocampal neurons

value: Wild type

tag: treatment

value: Control Media


title: Control neurons_rep4


title: HE_sib_rep1_MET

value: HE

value: sibling


title: Control neurons_rep3


title: Sample 16_L43

value: Harlan Teklad

value: Accustandard

value: sesame oil

value: oral gavage

value: microgram per kilogram

value: 10X Genomics Chromium Single Cell 3’ v3 kit


title: Sample 11_L38

value: Male

value: day

value: degree celsius


title: EC_mut_rep2_MET

value: EC

value: dnmt1 mutant

value: AGM


title: Sample 9_L36

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940


title: Sample 10_L37

value: Harlan Teklad


title: EC_sib_rep2_MET

value: sibling


title: ApoE4 treated neurons_rep4

value: Primary hippocampal neurons

value: Wild type

value: apoE4 lipoproteins


title: ApoE4 treated neurons_rep3


title: 4T1_ApoA1_2

city: Nanjing

first: Jie

last: Dong

address: Hankou road 22

institute: Nanjing University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol. 1.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: breast cancer

value: ApoA1 over-expression

value: culture


title: Control neurons_rep1

value: Control Media


title: EC_sib_rep3_MET

value: EC


title: Sample 5_L32

value: Male

value: day

value: degree celsius

value: Accustandard

value: sesame oil

value: oral gavage

value: microgram per kilogram

value: 10X Genomics Chromium Single Cell 3’ v3 kit


title: 4T1_ApoA1_1


title: AAV_ApoA1

source_name: Primary tumor

growth_protocol: Feamle BALB/c mice were orthotopically injected with 4T1 cells.

treatment_protocol: Mice were treated twice with PBS, 5 x 108 PFU of ADV-CON, or ADV-ApoA1. Tumors were collected 48h after the last injection. For the AAV treatment,tumor burden mice were injected with 1 x 10E11 v.g. of AAV-CON or AAV-ApoA1.  Tumors were collected 10 days after the injection.

value: Primary tumor

value: WT


title: HE_sib_rep2_MET

value: HE

value: sibling

value: AGM


title: EC_sib_rep1_MET


title: 4T1_CON_2

value: breast cancer


title: Sample 6_L33

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad


title: ApoE4 treated neurons_rep2

value: Primary hippocampal neurons

value: Wild type

value: apoE4 lipoproteins


title: AAV_CON

value: AAV-CON


title: Sample 3_L30

value: Male

value: day

value: degree celsius

value: Accustandard

value: sesame oil

value: oral gavage

value: microgram per kilogram

value: 10X Genomics Chromium Single Cell 3’ v3 kit


title: ApoE3 treated neurons_rep4

value: apoE3 lipoproteins


title: ApoE4 treated neurons_rep1


title: HiC_Chd4KD_rep1

description:
Chd4KD_20kb_abs.bed
Chd4KD_20kb_ICE.matrix
Chd4KD_40kb_abs.bed
Chd4KD_40kb_ICE.matrix

data_processing:
For Hi-C analysis, we analyzed our in situ Hi-C data using HiC-Pro (Servant et al., 2015). This includes alignment to the mouse genome (UCSC mm10), extracting valid Hi-C interactions, merging replicates, building Hi-C matrix, and performing ICE normalization.  We applied reciprocal insulation scores to identify TADs (topologically associating domains) by using CaTCH (Zhan et al., 2017).   For most of Hi-C related analysis including RCP (relative contact probability), ATA (aggregate TAD analysis), or APA (aggregate peak analysis), we used GENOVA (Van der Weide et al., 2021).
Genome_build: mouse genome : mm10
Supplementary_files_format_and_content: Using HiC-Pro, we generated ICE-normalized Hi-C matrix (.matrix file) for 20kb and 40kb resolution and annotation file that indicates the genomic bins (abs.bed).
For Mnase-seq, ATAC-seq, ChIP-seq, CUT&RUN, and GRO-seq analysis, raw reads were aligned to the mouse genome (UCSC mm10) using Bowtie2 (version 2.2.9) with default parameters.  We used MACS2 to convert the aligned BAM files into bedGraph files, and normalized the data with respect to the total read counts.  Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files.  The bigWig files were used as input files for bwtool (matrix and aggregate option) to quantify the intensity of the relevant sequencing data.
Genome_build: mouse genome : mm10
Supplementary_files_format_and_content: We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts. Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files (.bw).
For TotalRNA-seq and mRNA-seq analysis, raw reads were aligned to the mouse genome (UCSC mm10) using STAR (version 2.5.2a) with default parameters.  We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts.  Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files.  The bigWig files were used as input files for bwtool (matrix and aggregate option) to quantify the intensity of the relevant sequencing data.  Finally, we used Cufflinks (Cuffdiff option, fr-firststrand) to assess the gene expression.
Genome_build: mouse genome : mm10
Supplementary_files_format_and_content: We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts. Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files (.bw).

extract_protocol:
in situ Hi-C :    For Control and Chd4KD cells : in situ Hi-C was performed as previously described (Rao et al., 2014). Briefly: 1.5 million mESCs were crosslinked with 1% formaldehyde; nuclei were isolated; chromatin was digested with MboI (R0147, NEB); 5’ ends were filled by incorporation of biotinylated-dCTP (19524-016, Life Technologies); proximity ligation, reverse-crosslinking, and DNA shearing were performed; biotinylated junctions were isolated with streptavidin beads (65601, Life Technologies); and DNA libraries were prepared. Each Hi-C library was amplified for six cycles and then subjected to deep sequencing on a Hiseq4000 Illumina platform.    For Aux and +Aux cells : in situ HiC was performed using the Arima Hi-C kit following the manufacturer’s protocols. Breifly, 1.5 million mESCs were crosslinked with 2% formaldehyde and 150ng of sheared DNA was used for biotin enrichment. Hi-C libraries were prepared using the Kapa Library Prep Kit with a modified protocol provided by Arima. Each Hi-C library was amplified for seven cycles and then subjected to deep sequencing on a Novaseq6000 Illumina platform.
Mnase-seq : Cells cultured in 60Ф culture dishes were washed with PBS and incubated with modified PBS (150 mM NaCl, 0.02% Tween-20, 0.02% Triton X-100) at 25°C for 5 min. The cells were then fixed with 1% formaldehyde at 25°C for 10 min, quenched with 125 mM glycine at 25°C for 5 min, washed, and suspended with lysis buffer (18% Ficoll-400, 10 mM KH2PO4, 10 mM K2HPO4, 1 mM MgCl2, 250 nM EGTA). The lysates were centrifuged at 12,000 rpm for 40 min at 4°C, and the pelleted chromatin was resuspended in A buffer (10 mM Tris-Cl, pH 7.4, 150 mM NaCl, 5 mM KCl, 1 mM EDTA). CaCl2 (5 mM) was added to the samples, which were immediately digested with MNase (M0247S, NEB) at 37°C for 60 min. The reaction was inactivated with 1% SDS and 500 mM EDTA, and reverse-crosslinking was performed overnight at 68°C. Proteinase K and RNase were added sequentially to the samples, and DNAs were recovered using phenol-chloroform-isoamyl alcohol extraction. The MNase-digested DNAs were separated on a 1.5% agarose gel, and mono-nucleosomal DNAs were extracted using a QIAEX II gel extraction kit (20021, Qiagen) according to the manufacturer’s manual. The purified mono-nucleosomal DNAs were subjected to sequencing using a TruSeq DNA library prep kit (FC-121-2001, Illumina).
The purified mono-nucleosomal DNAs were subjected to sequencing using a TruSeq DNA library prep kit (FC-121-2001, Illumina).
ATAC-seq : ATAC-seq libraries were prepared as previously described (Buenrostro et al., 2013; Buenrostro et al., 2015), with minor modification. Briefly, 50,000 mESCs were harvested, washed with cold PBS, lysed with cold lysis buffer, and immediately centrifuged. The nuclear pellets were resuspended in 25 μl of 2X tagmentation reaction buffer (10 mM Tris, pH 8.0, 5 mM MgCl2, 10% dimethylformamide), 23 μl of nuclease-free water, and 2 μl of Tn5 transposase (in-house generated), and incubated at 37°C for 30 min. The samples were then immediately purified using a QIAquick PCR purification kit (28106, Qiagen). The libraries were pre-enriched for five cycles using the KAPA HiFi Hotstart ready mix (KK2601, Kapa Biosystems), and the threshold cycle (Ct) was monitored using qPCR to determine the additional enrichment cycles, which were then applied. The final libraries were purified again with a QIAquick PCR purification kit, and sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates.
ChIP : E14Tg2a mESCs (1x10^6cells/well) were seeded to 100-mm dish. After treatment (siRNA transfection or auxin treatment), cells were cross-linked using fresh 1% formaldehyde solution at 25°C for 10 min. This crosslinking was quenched with 125 mM glycine at 25°C for 5 minutes, and the cells were harvested with cold PBS and suspended in SDS lysis buffer (50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA). The chromatin was sheared to mono- or dinucleosome sizes using a focused ultrasonicator (Covaris S220). Immunoprecipitated DNA and input DNA were purified by treatment with proteinase K (40 µg, at 55°C for 3 hours), RNase A (20 µg, at 37°C for 1 hour), and phenol:chloroform:isoamyl alcohol extractions.
ChIP-seq libraries for genome-wide sequencing were prepared using either a NEXTflex™ Illumina ChIP-Seq Library Prep kit (5143-02, BIOO) or Accel-NGS 2S Plus DNA Library Kit (21024, SWIFT).
CUT&RUN assays were performed as previously described (Meers et al., 2019; Skene and Henikoff, 2017), with minor modification. Briefly, 4 million mESCs were harvested and washed with 1.5 ml Wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine) three times. Cells were bound to activated Concanavalin A-coated magnetic beads (at 25°C for 10 min on a nutator), then permeabilized with Antibody buffer (Wash buffer containing 0.05% Digitonin and 4 mM EDTA). The bead-cell slurry was incubated with 3 μl relevant antibody (see below) in a 150 μl volume at 25°C for 2 hours on a nutator. After two washes in 1 ml Dig-wash buffer (Wash buffer containing 0.05% Digitonin), beads were resuspended in 150 μl pAG/MNase and incubated at 4°C for 1 hour on a nutator. After two washes in 1 ml Dig-wash buffer, beads were gently vortexed with 100 μl Dig-wash buffer. Tubes were chilled to 0°C for 5min and ice-cold 2.2 mM CaCl2 was added while gently vortexing. Tubes were immediately placed on ice and incubated at 4°C for 1 hour on a nutator, followed by addition of 100 μl 2xSTOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 0.1 mg/ml RNase A, 50 μg/ml glycogen) and incubated at 37°C for 30min on a nutator. Beads were placed on a magnet stand and the liquid was removed to a fresh tube, followed by addition of 2 μl 10% SDS and 2.5 μl proteinase K (20mg/ml) and incubated at 50°C for 1 hour. DNA was extracted using phenol chloroform as described at https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-zcpf2vn. CUT&RUN libraries were prepared using either a Accel-NGS 2S Plus DNA Library Kit (21024, SWIFT), according to the manufacturer’s guidelines. The libraries were then sequenced using an Illumina Novaseq 6000 platform. The libraries were generated from two sets of biological replicates.
CUT&RUN libraries for genome-wide sequencing were prepared using either a Accel-NGS 2S Plus DNA Library Kit (21024, SWIFT).
Total RNA-seq : total RNAs were purified from mESCs using the TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Briefly, mESCs were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform (200 μL/sample) was added, and the samples were mixed vigorously by hand for 15 seconds and incubated at 25 °C for 2 minutes. The mixtures were centrifuged at 12,000 rpm for 15 minutes at 4 °C, and 500 μL of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25 °C for 10 minutes to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 minutes at 4 °C, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 minutes at 4°C. The RNA pellets were dried and dissolved in RNase-free water.
Total RNA-seq libraries were prepared using a TruSeq stranded RNA kit (RS-122-2301, Illumina) according to the manufacturer’s manual.
mRNA-seq : To isolate mRNA, total RNAs were purified from mESCs using the TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Briefly, mESCs were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform (200 μL/sample) was added, and the samples were mixed vigorously by hand for 15 seconds and incubated at 25 °C for 2 minutes. The mixtures were centrifuged at 12,000 rpm for 15 minutes at 4 °C, and 500 μL of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The

treatment_protocol: In genral, mESCs were transfected with 50 nM of the indicated siRNA using DharmaFECT I (T-2001-03, Dharmacon) according to the manufacturer’s protocol. Briefly, mESCs were seeded to 6-well plates. One day later, 50 nM of siRNAs and DharmaFECT reagent were diluted in Opti-MEM (Gibco), incubated separately at 25°C for 5 min, and then mixed together. The mixtures were incubated at 25°C for 20 min and added to the mESC cultures. The culture medium was replaced after 24 hours. Transfected mESCs were harvested at 48 hours after transfection.    For auxin treatment and temporal aspect siRNA / auxin withdrawal / RNA binding ChIP-seq experiments, we treated siRNA or auxin as indicated.

value: Wild-type Chd4KD

value: siRNA against Chd4


title: EC_mut_rep1_MET

value: EC

value: dnmt1 mutant

value: AGM


title: HiC_Chd4KD_rep2


title: Sample 8_L35

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad


title: HiC_Control_rep2

description:
Control_20kb_abs.bed
Control_20kb_ICE.matrix
Control_40kb_abs.bed
Control_40kb_ICE.matrix

value: Wild-type Control

value: siRNA against EGFP


title: ADV_ApoA1

value: Primary tumor

value: breast cancer

value: WT


title: Sample 2_L29

value: Male

value: day

value: degree celsius

value: Accustandard

value: sesame oil

value: oral gavage

value: microgram per kilogram

value: 10X Genomics Chromium Single Cell 3’ v3 kit


title: ApoE3 treated neurons_rep3

value: Primary hippocampal neurons

value: Wild type

value: apoE3 lipoproteins


title: Sample 1_L28

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad


title: ApoE3 treated neurons_rep2


title: 4T1_CON_1

value: breast cancer

value: WT

value: culture


title: HiC_Control_rep1

value: Wild-type Control

value: siRNA against EGFP


title: CUTnRUN_IgG_rabbit_rep2

data_processing:
Library strategy: CUT&RUN
For CUT&RUN analysis, raw reads were aligned to the mouse genome (mm10) using Bowtie2 (version 2.2.9) with the parameter (--trim3 125 --local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700), as the previous study (GSM2247138).
For ATAC-seq analysis, raw reads were aligned to the mouse genome (mm10) using Bowtie2 (version 2.2.9) with the following parameter; --very-sensitive -X 100 –local.
We used PICARD to remove the duplicates.
We used MACS2 to convert the aligned BAM files into bedGraph files, and normalized the data with respect to the total read counts.
Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files.
The bigWig files were used as input files for bwtool (matrix and aggregate option) to quantify the intensity of the relevant sequencing data.
Genome_build: mouse genome: mm10
Supplementary_files_format_and_content: We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts. Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files (.bw).

treatment_protocol:
In general, mESCs were transfected with 50 nM of the indicated siRNA using DharmaFECT I (T-2001-03, Dharmacon) according to the manufacturer’s protocol. Briefly, mESCs were seeded to 6-well plates. One day later, 50 nM of siRNAs and DharmaFECT reagent were diluted in Opti-MEM (Gibco), incubated separately at 25°C for 5 min, and then mixed together. The mixtures were incubated at 25°C for 20 min and added to the mESC cultures. The culture medium was replaced after 24 hours. Transfected mESCs were harvested at 48 hours after transfection.
shRNA targeting Ipmk was purchased from Sigma Aldrich. Lentiviruses were generated in HEK293T cells by transfecting the lentiviral plasmids together with packaging plasmid (psPAX2) and envelope-expressing plasmid (pMD2.G). Lentiviruses were added to mESCs after 48 hours and incubated for 8 hours. After 40 hours, mESCs with stable gene expression were selected by growing cells in mESC medium supplemented with Hygromycin B (Invitrogen).

value: E14Tg2a (mESCs)

value: 3xFLAG-IPMK tagged

tag: chip antibody

value: In-house generated


title: CUTnRUN_IgG_rabbit_rep1


title: TGFb_D2_2

city: Tsukuba, Ibaraki

first: Ken

last: Nishimura

address: 1-1-1 Tennodai

institute: University of Tsukuba

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using STAR aligner
Read counts were calculated by featureCounts (v2.0.0) with the gene model from Ensemble (Mus_musculus GRCm38.75.gtf) at gene level to obtain TPM
Gene count data was normalized by variance stabilizing transformations (VST) using DESeq2 (v1.26.0)
Genome_build: mm10
Supplementary_files_format_and_content: TPM in Excel format

source_name: NMuMG+TGFb; day2

growth_protocol: NMuMG cells were cultured in DMEM+10%FBS+10 µg/mL Insulin

extract_protocol:
RNA was extracted by ISOGEN (NipponGene)
RNA-seq library was constructed by Illumina platform

treatment_protocol: Infected with retroviral vector expressing Osr2 or Kusabira Orange, or treated with 5 ng/mL TGFb1

tag: cell

value: NMuMG

value: TGFb

tag: time point

value: 2 days


title: ATF4 KO, biological rep 3

city: Athens

first: Evdokia

last: Karagouni

state: Attica

address: 127 Vas. Sofias Avenue

department: Department of Microbiology

country: Greece

institute: Hellenic Pasteur Institute

description:
84855
scRNA-Seq

data_processing:
Alignment of raw sequencing reads, pre-processing and generation of feature-barcode matrices was conducted using Cell Ranger v3.1.0 with default parameters.
Quality control, pre-processing, filtering, clustering, differential expression analysis and visualizations were performed using Seurat v3.2.1 and ggplot2 v3.2.2.
Trajectory analysis was conducted using Slingshot.
Genome_build: GRCm38
Supplementary_files_format_and_content: barcodes_*.tsv, features_*.tsv, matrix_*.mtx. Filtered feature-barcode count matrix.

source_name: B16F10 tumor

extract_protocol:
Tumors were dissociated to single cell suspension following the 10X Genomics protocol. Cells were loaded into a 10X Genomics Chromium Single-Cell controller following manufacturer's instructions using the 10X 3' RNA-Seq V3 kit.
Illumina sequencing libraries were prepared then sequenced on three lanes of a HiSeq 4000 (28bp x 98bp).

value: B16F10 tumor

tag: tumor size

value: large

tag: host genotype

tag: gender

value: Male

value: 12 weeks


title: CUTnRUN_IPMK_rep2

value: FLAG (F7425, Sigma Aldrich)


title: ATF4 KO, biological rep 4

description:
84856
scRNA-Seq


title: TGFb_D2_1


title: PBS

value: Primary tumor

value: PBS


title: ATF4 KO, biological rep 2

description:
84854
scRNA-Seq


title: Osr2_D9_1

source_name: NMuMG+Osr2; day9

value: 9 days


title: ApoE2 treated neurons_rep2

tag: strain

value: Primary hippocampal neurons

value: Wild type

value: apoE2 lipoproteins


title: Osr2_D9_2


title: ADV_CON

value: breast cancer

value: WT

value: ADV-CON


title: CUTnRUN_IPMK_rep1

value: E14Tg2a (mESCs)

value: 3xFLAG-IPMK tagged


title: ApoE2 treated neurons_rep3


title: CUTnRUN_BRG1_IpmkKD_rep2

value: BRG1 (ab110641, Abcam)

value: siRNA against Ipmk


title: ATF4 WT, biological rep 4

description:
84852
scRNA-Seq

value: B16F10 tumor

value: large

value: Female


title: CUTnRUN_BRG1_EgfpKD_rep2

value: siRNA against EGFP


title: ATF4 KO, biological rep 1

description:
84853
scRNA-Seq

value: 12 weeks


title: CUTnRUN_BRG1_IpmkKD_rep1


title: ATF4 WT, biological rep 3

description:
84851
scRNA-Seq

value: Male


title: ApoE2 treated neurons_rep1


title: Osr2_D3_1

source_name: NMuMG+Osr2; day3

value: NMuMG

value: 3 days


title: ApoE3 treated neurons_rep1

value: Primary hippocampal neurons

value: Wild type

value: apoE3 lipoproteins


title: ApoE2 treated neurons_rep4

value: apoE2 lipoproteins


title: GRO_seq_Chd4KD_rep2

description:
nascent RNA
GRO_seq_Chd4KD.bw

data_processing:
Library strategy: GRO-seq
For Hi-C analysis, we analyzed our in situ Hi-C data using HiC-Pro (Servant et al., 2015). This includes alignment to the mouse genome (UCSC mm10), extracting valid Hi-C interactions, merging replicates, building Hi-C matrix, and performing ICE normalization.  We applied reciprocal insulation scores to identify TADs (topologically associating domains) by using CaTCH (Zhan et al., 2017).   For most of Hi-C related analysis including RCP (relative contact probability), ATA (aggregate TAD analysis), or APA (aggregate peak analysis), we used GENOVA (Van der Weide et al., 2021).
Genome_build: mouse genome : mm10
Supplementary_files_format_and_content: Using HiC-Pro, we generated ICE-normalized Hi-C matrix (.matrix file) for 20kb and 40kb resolution and annotation file that indicates the genomic bins (abs.bed).
For Mnase-seq, ATAC-seq, ChIP-seq, CUT&RUN, and GRO-seq analysis, raw reads were aligned to the mouse genome (UCSC mm10) using Bowtie2 (version 2.2.9) with default parameters.  We used MACS2 to convert the aligned BAM files into bedGraph files, and normalized the data with respect to the total read counts.  Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files.  The bigWig files were used as input files for bwtool (matrix and aggregate option) to quantify the intensity of the relevant sequencing data.
Genome_build: mouse genome : mm10
Supplementary_files_format_and_content: We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts. Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files (.bw).
For TotalRNA-seq and mRNA-seq analysis, raw reads were aligned to the mouse genome (UCSC mm10) using STAR (version 2.5.2a) with default parameters.  We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts.  Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files.  The bigWig files were used as input files for bwtool (matrix and aggregate option) to quantify the intensity of the relevant sequencing data.  Finally, we used Cufflinks (Cuffdiff option, fr-firststrand) to assess the gene expression.
Genome_build: mouse genome : mm10
Supplementary_files_format_and_content: We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts. Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files (.bw).

value: Wild-type Chd4KD

value: siRNA against Chd4


title: ATF4 WT, biological rep 2

description:
84850
scRNA-Seq


title: CUTnRUN_BRG1_EgfpKD_rep1

value: E14Tg2a (mESCs)

value: 3xFLAG-IPMK tagged


title: GRO_seq_Chd4KD_rep1

description:
nascent RNA
GRO_seq_Chd4KD.bw


title: control_D9_2

source_name: NMuMG+hKO; day9

value: Kusabira Orange

value: 9 days


title: GRO_seq_Control_rep2

description:
nascent RNA
GRO_seq_Control.bw

source_name: E14Tg2a (mESCs)

value: Wild-type Control


title: control_D9_1


title: ATAC_seq_IpmkKD_rep1

data_processing:
For CUT&RUN analysis, raw reads were aligned to the mouse genome (mm10) using Bowtie2 (version 2.2.9) with the parameter (--trim3 125 --local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700), as the previous study (GSM2247138).
For ATAC-seq analysis, raw reads were aligned to the mouse genome (mm10) using Bowtie2 (version 2.2.9) with the following parameter; --very-sensitive -X 100 –local.
We used PICARD to remove the duplicates.
We used MACS2 to convert the aligned BAM files into bedGraph files, and normalized the data with respect to the total read counts.
Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files.
The bigWig files were used as input files for bwtool (matrix and aggregate option) to quantify the intensity of the relevant sequencing data.
Genome_build: mouse genome: mm10
Supplementary_files_format_and_content: We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts. Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files (.bw).

extract_protocol: ATAC-seq : ATAC-seq libraries were prepared as previously described (Buenrostro et al., 2013; Buenrostro et al., 2015), with minor modification. Briefly, 50,000 mESCs were harvested, washed with cold PBS, lysed with cold lysis buffer, and immediately centrifuged. The nuclear pellets were resuspended in 25 μl of 2X tagmentation reaction buffer (10 mM Tris, pH 8.0, 5 mM MgCl2, 10% dimethylformamide), 23 μl of nuclease-free water, and 2 μl of Tn5 transposase (in-house generated), and incubated at 37°C for 30 min. The samples were then immediately purified using a QIAquick PCR purification kit (28106, Qiagen). The libraries were pre-enriched for five cycles using the KAPA HiFi Hotstart ready mix (KK2601, Kapa Biosystems), and the threshold cycle (Ct) was monitored using qPCR to determine the additional enrichment cycles, which were then applied. The final libraries were purified again with a QIAquick PCR purification kit, and sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates.

value: siRNA against Ipmk


title: Control_Early [xz3-3MLL]

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

data_processing:
Base calling and quality scoreing were performed in Illumina HiSeq
The reads were mapped to the mouse genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to Gencode M15 genes using featureCounts (from subread v1.5.3) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) < 0.5 in more than 4 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: mm10
Supplementary_files_format_and_content: Raw count

source_name: Quadriceps muscle

extract_protocol:
RNA extraction and purification from tissue snap frozen in liquid nitrogen was done via homogenization in Trizol and the Qiagen miRNeasy Mini Kit.
The Illumina TruSeq Standed mRNA standard methods were used for RNA sequencing (RNAseq). Total RNA extracted from the mouse quadriceps skeletal muscles was first evaluated for its quantity, and quality, using Agilent Bioanalyzer 2100. For RNA quality, a RIN number (RNA Integrity Number) of 7 or higher is desired. Five hundred nanograms of total RNA was used for library preparation. Briefly, cDNA library preparation included mRNA enrichment/purification, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification, following the TruSeq Stranded mRNA Sample Preparation Guide, RS-122-9004DOC, Part# 15031047 Rev. E (Illumina, Inc.). Each resulting indexed library with average insert size of 150-200b was quantified and its quality accessed by Qubit and Agilent Bioanalyzer, and multiple libraries pooled in equal molarity. Five microliters of 2 nM pooled libraries per lane were then denatured, neutralized and applied to the cBot for flow cell deposition and cluster amplification, before loading to HiSeq 4000 for 75b paired-end read sequencing (Illumina, Inc.). Approximately 30M reads per library were generated. A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy).

treatment_protocol: RNA isolation, sequencing for all quadriceps samples were done at one time.

tag: agent

value: Control

value: Early

value: Muscle


title: Osr2_D3_2

value: NMuMG


title: ATAC_seq_EgfpKD_rep2

value: siRNA against EGFP


title: KPC_Early [143]

value: Female

value: KPC


title: Control_Early [142]


title: mRNA_seq_Control_rep2

description:
mRNA-seq
mRNA_seq_Control.bw


title: Osr2+SB_D5

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using STAR aligner
Read counts were calculated by featureCounts (v2.0.0) with the gene model from Ensemble (Mus_musculus GRCm38.75.gtf) at gene level to obtain TPM
Genome_build: mm10
Supplementary_files_format_and_content: TPM in Excel format

source_name: MEF+Osr2+SeVdp(KOSMaB)+SB431542; day5

growth_protocol: MEFs were reprogrammed by SeVdp(KOSMaB)

extract_protocol:
RNA was extracted by ISOGEN (NipponGene)
RNA-seq library was prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra Directional RNA Library Prep Kit

treatment_protocol: Reprogrammed cells were selected by 2 µg/mL Blasticidin S and treated with or without 10 µM Sb431542

tag: strain background

value: mouse embryonic fibroblast

tag: transgene

tag: date

value: 5 days


title: mRNA_seq_Chd4KD_rep2

description:
mRNA-seq
mRNA_seq_Chd4KD.bw

value: Wild-type Chd4KD


title: KPC_Early [136]

tag: Sex


title: ATAC_seq_EgfpKD_rep1

tag: cell type


title: GRO_seq_Control_rep1

description:
nascent RNA
GRO_seq_Control.bw


title: ATF4 WT, biological rep 1

description:
84849
scRNA-Seq

value: B16F10 tumor

value: large

value: Male

tag: age

value: 12 weeks


title: Control_Early [134]

tag: tissue


title: Control_Early [119]


title: control-SB_D5

source_name: MEF+hKO+SeVdp(KOSMaB); day5

value: Kusabira Orange


title: Osr2-SB_D5

source_name: MEF+Osr2+SeVdp(KOSMaB); day5


title: ATAC_seq_IpmkKD_rep2

value: E14Tg2a (mESCs)

tag: genotype

value: 3xFLAG-IPMK tagged


title: SHR-SHAM_rep3

city: nanjing

first: mingyan

last: lin

address: 101Longmian Avenue, Jiangning District, Nanjing

institute: nanjing medical university

data_processing:
Illumina 1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to Rn6 whole genome using STAR v2.7.3a with parameters --outSAMtype BAM   SortedByCoordinate      --outSAMstrandField intronMotif   --outSAMattribute  s NH   HI   AS   NM   MD      --outSAMunmapped Within      --outFilterType BySJout   --outFilterMultimapNmax 20   --outFilterMismatchNmax 999   --outFilterM  ismatchNoverReadLmax 0.04   --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJoverhangMin 8   --alignSJDBoverhangMin 1    --sjdbScore 1   --quantMode TranscriptomeSAM
Abundance estimates of genes calculated using RSEM and differential expression was performed using DESeq2
Genome_build: Rn6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: DRG

extract_protocol:
Total RNA was extracted from DRG neurons using TRIzol (Invitrogen, USA) according to manufacturer’s instructions, followed by DNase I treatment to remove DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Spontaneously Hypertensive Rats

value: DRG

value: 6-8 week

value: wild type

tag: treatment

value: Sham-operation


title: mRNA_seq_Control_rep1

description:
mRNA-seq
mRNA_seq_Control.bw

value: Wild-type Control

value: siRNA against EGFP


title: TotalRNA_seq_Chd4KD_rep2

description:
Total RNA-seq
TotalRNA_seq_Chd4KD.bw

value: siRNA against Chd4


title: KPC_Early [118]

value: Female

value: KPC

value: Early

value: Muscle


title: SHR-SHAM_rep2


title: control+SB_D5

source_name: MEF+hKO+SeVdp(KOSMaB)+SB431542; day5

value: mouse embryonic fibroblast

value: 5 days


title: KPC_Early [135]


title: SHR-SHAM_rep1


title: KPC_Early [117]

value: Male


title: KPC_Early [111]


title: TotalRNA_seq_Chd4KD_rep1

description:
Total RNA-seq
TotalRNA_seq_Chd4KD.bw

value: Wild-type Chd4KD


title: TotalRNA_seq_Control_rep2

description:
Total RNA-seq
TotalRNA_seq_Control.bw


title: RNA_Binding_ChIP_seq_Input_forCTCF_ppAux_FLAG-CHD4-CD2_rep1

description: RNA_Binding_ChIP_seq_Input_forCTCF_ppAux_FLAG-CHD4-CD2.bw

value: ++Aux transfected with FLAG-CHD4-CD2


title: TotalRNA_seq_Control_rep1

description:
Total RNA-seq
TotalRNA_seq_Control.bw


title: ChIP_seq_Input_forH3K9me3_Chd4KD_rep2


title: SHR-PRATA_rep2

value: Spontaneously Hypertensive Rats

value: Perirenal adipose ablation


title: RNA_Binding_ChIP_seq_Input_forCTCF_ppAux_FLAG-CHD4-CD1_rep2

description: RNA_Binding_ChIP_seq_Input_forCTCF_ppAux_FLAG-CHD4-CD1.bw

value: ++Aux transfected with FLAG-CHD4-CD1


title: RNA_Binding_ChIP_seq_Input_forCTCF_ppAux_FLAG-CHD4-CD1_rep1


title: RNA_Binding_ChIP_seq_Input_forCTCF_ppAux_FLAG-CHD4-CD2_rep2


title: KPC_Early [107]


title: SHR-PRATA_rep3

value: DRG

value: 6-8 week

value: wild type


title: mRNA_seq_Chd4KD_rep1

description:
mRNA-seq
mRNA_seq_Chd4KD.bw


title: Control_Early [110]

value: Control


title: SHR-PRATA_rep1


title: ChIP_seq_Input_forH3K9me3_Chd4KD_rep1

value: siRNA against Chd4


title: RNA_Binding_ChIP_seq_Input_forCTCF_ppAux_FLAG-CHD4-WT_rep1

description: RNA_Binding_ChIP_seq_Input_forCTCF_ppAux_FLAG-CHD4-WT.bw

value: ++Aux transfected with FLAG-CHD4-WT


title: ChIP_seq_Input_forH3K9me3_Control_rep2_2

value: Wild-type Control

value: siRNA against EGFP


title: RNA_Binding_ChIP_seq_Input_forCTCF_ppAux_FLAG-CHD4-WT_rep2


title: N2_GONH3

city: Cologne

first: Bjoern

last: Schumacher

state: NRW

address: Joseph-Stelzmann-Strasse 26

department: Institute for Genome Stability in Ageing and Disease

country: Germany

institute: CECAD Cologne

data_processing:
Reads were mapped to the Caenorhabditis elegans
Differential gene expression was analyzed using the DESeq2
Results were uploaded into the QuickNGS database
Genome_build: Caenorhabditis elegans (Ensembl Version 87)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

organism: Caenorhabditis elegans

growth_protocol: growth in liquid culture for 12 hours

extract_protocol:
500 animals in trizol, homogenizer with beads, phenol-chlorform extraction, RNA isolation via RNeasy Mini Kit (Qiagen)
RNA-seq libraries were prepared using the Illumina® TruSeq stranded® RNA sample preparation Kit.  The pool was sequenced by using an Illumina HiSeq 4000 sequencer with a paired-end protocol

treatment_protocol: treatment with either GO or GONH2 or mock

tag: genotype/variation

value: amino-functionalized GO (GONH2)

value: whole animal


title: ChIP_seq_Input_forH3K9me3_Control_rep2_3


title: KPC_ACVR2B/Fc_Late [93]

value: Female

value: Late

value: Muscle


title: ChIP_seq_Input_forH3K9me3_Control_rep1


title: KPC_ACVR2B/Fc_Late [96]


title: KPC_ACVR2B/Fc_Late [90]


title: RNA_Binding_ChIP_seq_Input_forCTCF_ppAux_rep1

description: RNA_Binding_ChIP_seq_Input_forCTCF_ppAux.bw

value: ++Aux (auxin treated for 48 hours)


title: ChIP_seq_Input_forH3K9me3_Control_rep2_1


title: RNA_Binding_ChIP_seq_Input_forCTCF_mAux_rep1

description: RNA_Binding_ChIP_seq_Input_forCTCF_mAux.bw

value: -Aux


title: RNA_Binding_ChIP_seq_Input_forCTCF_ppAux_rep2

value: ++Aux


title: ChIP_seq_H3K9me3_Chd4KD_rep2

value: Wild-type Chd4KD

tag: chip antibody

value: H3K9me3 (ab8898, Abcam)


title: Control_Early [106]

value: Male

tag: time point

value: Early


title: RNA_Binding_ChIP_seq_Input_forCTCF_mAux_rep2


title: Control_Late [94]

value: Control


title: ChIP_seq_H3K9me3_Chd4KD_rep1

value: siRNA against Chd4


title: KPC_Vehicle_Late [87]


title: N2_GONH1

value: wild type


title: RNA_Binding_ChIP_seq_CTCF_ppAux_FLAG-CHD4-CD2_rep2

description: RNA_Binding_ChIP_seq_CTCF_ppAux_FLAG-CHD4-CD2.bw

value: CTCF (07-729, Millipore)

value: ++Aux transfected with FLAG-CHD4-CD2


title: N2_GONH2

value: amino-functionalized GO (GONH2)


title: N2_Go3

value: Graphene oxide (GO)

value: whole animal


title: N2_Go2


title: ChIP_seq_H3K9me3_Control_rep2_3

value: Wild-type Control

value: siRNA against EGFP


title: RNA_Binding_ChIP_seq_CTCF_ppAux_FLAG-CHD4-CD2_rep1


title: N2_Go1


title: Control_Late [86]

value: Female

value: Late

value: Muscle


title: N2_noGo3

value: none (control)


title: Control_Early [82]


title: RNA_Binding_ChIP_seq_CTCF_ppAux_FLAG-CHD4-CD1_rep2

description: RNA_Binding_ChIP_seq_CTCF_ppAux_FLAG-CHD4-CD1.bw

value: ++Aux transfected with FLAG-CHD4-CD1


title: KPC_Early [84]

value: Male

value: KPC


title: RNA_Binding_ChIP_seq_CTCF_ppAux_FLAG-CHD4-CD1_rep1


title: N2_noGo2


title: ChIP_seq_H3K9me3_Control_rep2_1

value: H3K9me3 (ab8898, Abcam)


title: ChIP_seq_H3K9me3_Control_rep2_2


title: ChIP_seq_H3K9me3_Control_rep1


title: ChIP_seq_Input_forH3K4me1me3_Control_rep2

description:
ChIP_seq_Input_forH3K4me1_Control.bw
ChIP_seq_Input_forH3K4me3_Control.bw


title: Control_Late [80]

value: Control


title: RNA_Binding_ChIP_seq_CTCF_ppAux_FLAG-CHD4-WT_rep1

description: RNA_Binding_ChIP_seq_CTCF_ppAux_FLAG-CHD4-WT.bw

value: ++Aux transfected with FLAG-CHD4-WT


title: RNA_Binding_ChIP_seq_CTCF_ppAux_FLAG-CHD4-WT_rep2

value: CTCF (07-729, Millipore)


title: ChIP_seq_Input_forH3K27ac_Control_rep1


title: SPRI: S1 Treatment

city: Los Angeles

first: Jordan

last: Cheng

institute: UCLA

data_processing:
Demultiplexed using SRSLYumi:SRSLYumi (0.4 version), Claret Bioscience
Fastq trimmed with fastp:fastp (0.23.1 version)
Align with bwa mem:BWA-mem (0.7.17)
sam to bam and indexing with Samtools:Samtools (1.9 version)
Quality Cotrol using Qualimap:Qualimap (2.2.2c version)
Move UMI tags with SRSLYumi (srslyumi-bamtag):SRSLYumi (0.4 version), Claret Bioscience
Mark UMI with umi-tools:umi-tools (11.2 version)
Remove duplicates with Picard:Picard (2.27.0 version)
Files split by alignmentsieve (uscfDNA 25-100 and mncfDNA 101-250) with alignmentsieve in deep tools:DeepTools (3.31 version).
Functional peaks called with macs2 :Macs2 (2.2.7.1 version)
Assembly: GRC38
Assembly: LambdaPhage
Supplementary files format and content: Functional Elements called with HOMERannotatePeaks:HOMERannotatePeaks (version 4.11.1).

source_name: Plasma

extract_protocol:
QiaM extracted cfDNA
SRSLYTM PicoPlus DNA NGS Library Preparation  CBS-K250B-24

treatment_protocol: No treatment

tag: organism

value: Human + Lambda Genome


title: SPRI: NEB Nick Repair Treatment


title: ChIP_seq_Input_forH3K4me1me3_Control_rep1


title: RNA_Binding_ChIP_seq_CTCF_ppAux_rep2

value: ++Aux


title: KPC_Vehicle_Late [81]


title: SPRI: P1 Treatment


title: Control_Late [78]