title: iPSC-MSC-2_XAV

city: Zhunan

first: B. LINJU

last: Yen

address: 35 Keyan Road

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: Samples were hybridized with [HTA-2_0] Affymetrix Human Transcriptome Array 2.0 [transcript (gene) version] and scanned at the NHRI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: The data were analyzed using Affymetrix Expression Console™ Software (version 1.4) default analysis settings and RMA (Robust Multi-Array) summarization and normalization options.

source_name: iPSC-MSC-2, XAV, 72 h

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Human MSCs were cultured in DMEM with 10% FBS, 2mM L-glutamine, 100 units/ml penicillin, 100 μg/ml streptomycin and sub-cultured at the dilution of 1:3 to 1:4 at 80-90% conﬂuence.

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. Inclusion of 1 U/ µL of the RiboLock RNase Inhibitor (Thermo) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with RQ1 RNase-Free DNasee (Peomega) to remove trace amounts of genomic DNA.

treatment_protocol: 2×10^5 trypsinized MSCs were centrifuged 450×g for 10 minutes to form a pellet in expansion medium. After 16 hours, the medium was changed to chondrogenic basal medium consisting of low-glucose DMEM supplemented with 100 units/ml penicillin, 100 μg/ml streptomycin, 1% Insulin-transferrin-sodium selenite media supplement, 2 mM L-glutamine, 10 μM L-Ascorbic acid 2-phosphate, 100 nM dexamethasone. Addition of TGFβ3 (10 ng/mL), XAV939 (XAV; 10 μM) to ChBM was performed as indicated.

value: Mesenchymal stem cell

value: Lab-generated, HUVECs reprogrammed by 2-factor-Lentivirus (OCT4 and SOX2)  then differentiated into MSCs


title: sarcoma sample 6

status: Public on Jan 04 2023

type: SRA

city: Linhai

first: BINXIANG

last: CHU

address: XINMEN street

country: China

library_source: transcriptomic

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: mRNA_Expression_Summary.xlsx files include RPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Tumor tissue

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.

tag: tissue

value: Tumor tissue

tag: gender

value: Female

tag: age

tag: genotype

value: WT

tag: grade

value: i


title: HSV-202_Day0

city: Bethesda

first: Foo

last: Cheung

address: Bethesda

country: USA

institute: NIH

description: RNAseq data from PBMC extracted from individual HSV-202

data_processing:
Illumina Casava1.7 software used for basecalling.
The Spliced Transcripts Alignment to a Reference (STAR) software was used for RNA-seq alignment
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample
Supplementary_files_format_and_content: titre.txt includes titre and demographics information. 'serology' column provides serostatus group association for each sample.

source_name: PBMC

extract_protocol:
PBMCs were isolated with Ficoll-Hypaque reagent and lysed in QIAzol (Qiagen, Hilden, Germany) and stored at -80°C until use. Their total RNA was extracted and purified with the miRNeasy kit (Qiagen). RNA quality and quantity were estimated using Nanodrop (Thermo Scientific, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Stranded cDNA sequencing libraries were generated with TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA) following the manufacturerâs instructions. Briefly 500 ng of total RNA was used for mRNA selection. After the reverse transcription to 1st strand cDNA, strand info was reserved with dUTPs during 2nd strand synthesis. The dsDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched with PCR to create the final cDNA library. The library was qualified with Agilent Bioanalyzer and quantified with Qubit 2.0 fluorometer. The cluster generation and pair-end (2x75 bp) sequencing was run on Illumina HiSeq 3000 at NHLBI Sequencing Core. Up to 96 barcoded samples were pooled for one single run, which yielded at least 30M passed filter paired reads per sample.

tag: individual

tag: cell type

value: PBMC

tag: day after vaccination


title: LNPPS overexpressing 5637 cells-1

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

institute: The Second Hospital of Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
We aligned clean reads of samples to the reference genome using HISAT2 package.
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Genome_build: ftp://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: bladder cancer cells

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 5637 cells were transfete with LNPPS plasmid or its control plasmid to construct LNPPS-overexpressing 5637 cells or control 5637 cells

tag: genotype/variation

value: LNPPS-overexpressing


title: iPSC-MSC-2_TGFβ

type: RNA

label: biotin

source_name: iPSC-MSC-2, TGFβ3, 72 h

tag: cell line


title: URB1_iCLIP_rep2

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

data_processing:
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Raw read quality was evaluated by FastQC (v0.11.9). Deep sequencing datasets were mapped with Bowtie2 (Bowtie2 v2.3.5, parameters: -q --sensitive -a -p 8 --no-mixed --reorder --no-unal) and aligned to 45SrRNA sequence in human reference genome, then we removed reads introduced by PCR duplicates via a custom script. We got the read-coverage on 45SrRNA using genomeCoverageBed (genomeCoverageBed v2.29.0, parameters: -split), and calculated the fraction of reads overlapping each position in 45S rDNA.
Genome_build: 45SrRNA reference sequence for human samples
Supplementary_files_format_and_content: bedgraph files for RNA sequencing

source_name: HeLa cells

growth_protocol: HeLa cells with Flag-tag knock-in at the N-terminal of URB1 were maintained in DMEM, which was supplemented with 10% Fetal Bovine Serum (FBS).

extract_protocol:
HeLa cells expressing Flag-tagged URB1 were UV-crosslinked, resuspended in lysis buffer and sonicated for 20 s x 6 times on 25% duty. Supernatants were incubated with anti-Flag antibodies (Shanghai Genomics) or control IgG-conjugated beads for 2h at 4°C. Beads with protein-RNA complexes were treated with 5 Kunz U/ml of micrococcal nuclease in the presence of 5 μg yeast tRNAs for 5 min at 37°C, followed by dephosphorylation of RNA 3’ ′ ends with PNK. Then pre-adenylated linker L3 (3′ modification with biotin) was linked to 3′ end of RNA using T4 RNA ligase 1 at 16°C overnight. The 5′ end of RNA was labeled with [γ- 32P] ATP using PNK. Protein-RNA complexes were eluted with 1x Nupage loading buffer (Invitrogen) at 70°C for 10 min, resolved on 4%–12% NuPAGE Bis-Tris gel (Invitrogen), transferred to a nitrocellulose membrane and exposed to a Fuji film at −80°C. Bands corresponding to specific protein-RNA complexes were excised and then digested with proteinase K. RNAs were purified and cDNAs were made using Superscript III (Invitrogen) with Rclip primers. cDNAs were separated on 6% denaturing urea polyacrylamide gel, then three bands at 120-200 nt (high), 85-120 nt (medium) and 70-85 nt (low) were excised, purified and circularized by Circligase II (Epicenter). Single-stranded cDNAs were hybridized with Cut-Oligo and then digested by BamH I. Linearized cDNAs were PCR amplified and purified. The obtained iCLIP libraries were subjected to high throughput deep sequencing.
Linearized cDNAs were PCR amplified and purified on PAGEs to obtain iCLIP libraries, which were subjected to Illumina HiSeq X ten at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

value: HeLa

tag: type

value: HeLa cells expressing Flag-tagged URB1

tag: antibody

value: anti-Flag

tag: barcode sequence

value: NNNAACCNN


title: HSV-202_Day30


title: HSV-120_Day180

description: RNAseq data from PBMC extracted from individual HSV-120


title: sarcoma sample 5

value: ii


title: HSV-202_Day37


title: HSV-120_Day37


title: sarcoma sample 3


title: sarcoma sample 2

value: Male


title: HSV-202_Day1


title: sarcoma sample 1

value: iii


title: iPSC-MSC-1_TGFβ

source_name: iPSC-MSC-1, TGFβ3, 72 h

value: Lab-generated, PBMCs reprogrammed by 4-factor-Sendai virus (OCT4, SOX2, KLF4, and c-MYC) then differentiated into MSCs


title: HSV-120_Day30


title: iPSC-MSC-1_XAV

source_name: iPSC-MSC-1, XAV, 72 h


title: BMMSC_XAV

source_name: BMMSC, XAV, 72 h

value: Commercial source (Promocell, Germany)


title: HSV-120_Day0


title: HSV-120_Day1


title: HSV-120_Day7


title: sarcoma sample 8


title: NIID4

city: Houston

first: Ziyi

last: Li

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

description:
hNPC_NIID4
HsNPC_NIIDvCTL.txt

data_processing:
All total reads were mapped to hg38/mm9 by TopHat2 with default parameter followed by gene expression quantification and differential expression analysis using Cuffdiff.
The alternative splicing events, including SE, IR, MXE, A3SS and A5SS, were reported by rMATS.
Genome_build: hg38 (GRCh38), mm9 (MGSCv37)
Supplementary_files_format_and_content: txt and csv files include FPKM.

molecule: polyA RNA

source_name: neural progenitor cells

growth_protocol: Human neural progenitor cells were cultured in neural progenitor media from Stem cell (Cat.05833).

extract_protocol:
Samples for RNA-seq were extracted with Trizol and quick RNA kit.
An amount of 1ug total RNA per sample was processed for library preparation using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Libraries were sequenced on a HiSeq with a read length configuration of 150 PE, targeting 100M total reads per sample.

treatment_protocol: No treatment.

value: Neural progenitor cells

tag: disease/model

value: NIID


title: HSV-119_Day187

description: RNAseq data from PBMC extracted from individual HSV-119


title: HSV-202_Day180


title: HSV-120_Day187


title: HSV-119_Day180


title: NIID3

description:
hNPC_NIID3
HsNPC_NIIDvCTL.txt


title: HSV-119_Day1


title: NIID1

description:
hNPC_NIID1
HsNPC_NIIDvCTL.txt


title: HSV-117_Day187

description: RNAseq data from PBMC extracted from individual HSV-117


title: HSV-117_Day180


title: HSV-119_Day0


title: HSV-119_Day7


title: HSV-117_Day7


title: HSV-117_Day1


title: HSV-117_Day0


title: HSV-117_Day30


title: HSV-117_Day37


title: HSV-116_Day187

description: RNAseq data from PBMC extracted from individual HSV-116


title: Intestinal metaplasia_28_IM

city: Daejeon

first: Byoung-Ha

last: Yoon

address: Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea

country: South Korea

institute: KRIBB

library_source: genomic

data_processing:
perfored trim-galore for trim off the adapter sequences or low-quality reads
Aligned to the mouse reference genome (hg19) using Bismark
Duplicated reads were removed using Bismark command "deduplicate_bismark"
methylation level calculated by Bismark command "bismark_methylation_extractor --no_overlap --comprehensive --cutoff 5 --bedgraph"
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, methylation value

molecule: genomic DNA

source_name: stomach

growth_protocol: Human tissues

extract_protocol:
QIAmp DNA mini kit was used for gDNA extraction
Library was constructed using the Illumina TruSeq DNA methylation kit according to the manufactures instruction

treatment_protocol: For bisulfite conversion, we used EZ DNA methylation Gold kit

tag: source

value: gastric tissue

tag: disease state

value: Intestinal metaplasia


title: Ctrl1

description:
hNPC_Ctrl1
HsNPC_NIIDvCTL.txt

value: Control


title: HSV-116_Day180


title: WT_RNA_rep4

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

institute: Yonsei University College of Medicine

data_processing:
sequenced using Illumina Hiseq platform
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using STAR v2.6.0c with parameters --sjdbOverhang 100 --twopassMode Basic --chimSegmentMin 20 --quantMode TranscriptomeSAM
Fragments Per Kilobase Million (FPKM), Transcripts Per Kilobase Million(TPM) and raw counts were calculated using RSEM
bigwig files were generated using homer
Assembly: mm10
Supplementary files format and content: RSEM output files including raw counts, FPKM, TPM values
Supplementary files format and content: normalized bigwig

organism: Mus musculus

source_name: BMDC

growth_protocol: Bone marrow cells prepared from CreER mice were culutred under the presence of murine GM-CSF for 6 days with chaning medium every 2 days.

extract_protocol:
Cells were PBS washed, and RNA was harvested and isolated using Hybrid-R Total RNA kits (Gene All Biotechnology) and rRNAs were depleted by using the NEBNext rRNA Depletion Kit (NEB #E6350).
TruSeq RNA sample prep kit (illumina #FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Bone marrow-derived dendritic cells (BMDCs) were stimulated with 100ng/ml of LPS for 3 hours, following the 100μM of JSH23 for 3 hours.

value: dentritic cells

tag: strain

value: CreER


title: WTLPS_RNA_rep6


title: WTLPS_RNA_rep4


title: WT_RNA_rep6


title: WTLPS_RNA_rep5


title: BMMSC_TGFβ

source_name: BMMSC, TGFβ3, 72 h

value: Mesenchymal stem cell


title: WTJSH_RNA_rep3


title: NIID2

description:
hNPC_NIID2
HsNPC_NIIDvCTL.txt

tag: tissue


title: HSV-119_Day30

value: PBMC


title: WT_RNA_rep5


title: HSV-116_Day37


title: HSV-119_Day37


title: Ctrl3

description:
hNPC_Ctrl3
HsNPC_NIIDvCTL.txt


title: Gastric mucosa_28_GM

value: Normal


title: HSV-116_Day7


title: WTJSH_RNA_rep2


title: Ctrl2

description:
hNPC_Ctrl2
HsNPC_NIIDvCTL.txt


title: HSV-116_Day30


title: HSV-116_Day1


title: WTJSH_RNA_rep1


title: Adenoma_28_AD

value: Adenoma


title: WTJSHLPS_RNA_rep3


title: Intestinal metaplasia_08_IM


title: HSV-115_Day187

description: RNAseq data from PBMC extracted from individual HSV-115


title: HSV-115_Day37


title: HSV-115_Day180


title: Gastric_tumor_08_GT

value: Tumor


title: WTJSHLPS_RNA_rep2


title: HSV-115_Day1


title: WTJSHLPS_RNA_rep1


title: HSV-115_Day0


title: HSV-115_Day30


title: Gastric mucosa_08_GM


title: HSV-115_Day7


title: Intestinal metaplasia_06_IM


title: WTLPS_H3K27ac_rep3

data_processing:
sequenced using Illumina Hiseq2500 platform
Raw ChIP-seq reads were trimmed for adaptor sequence, and aligned to the mm10 genome assembly using bwa mem v0.7.12 with default parameters
aligned files were filtered for MAPQ > 5 and sorting, deduplication were processed using PICARD  v2.18.23
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.4.3
Assembly: mm10
Supplementary files format and content: CPM normalized bigwig

extract_protocol:
Fixed cells were sonicated and immunoprecipitated with antibody recognizing specific protein. Antibody-chromatin complexed were captured with protein A&G beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Reverse-crosslinked DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina HiSeq2500 platform.

tag: passages

value: 8 weeks old

tag: chip antibody

value: H3K27ac (Abcam #ab4729)


title: HSV-114_Day37

description: RNAseq data from PBMC extracted from individual HSV-114


title: HSV-114_Day180


title: WTLPS_H3K27ac_rep2

tag: genotype


title: Gastric mucosa_06_GM


title: Adenoma_06_AD


title: HSV-116_Day0


title: HSV-114_Day187


title: HSV-114_Day30


title: HSV-114_Day0


title: 17AB

city: Baltimore

first: JP

last: Courneya

state: United States of America

address: 685 W Baltimore St., HSF2 Room 480

institute: University of Maryland, Baltimore

data_processing:
gene alignment: Salmon
transcript abundance: tximport
differential gene expression: DESeq2
Genome_build: gencodev29 / GRCh38.p12
Supplementary_files_format_and_content: normalized counts from DESeq2 per condition

source_name: Normal Human Lung Fibroblasts 2

extract_protocol:
Following treatments cells were flash-frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Library preparation for RNA-Seq was performed using the TruSeq Stranded Total Library Preparation workflow with Ribo-Zero Gold rRNA removal mix (Illumina, Catalog# 20020598), which depletes samples of both cytoplasmic and mitochondrial rRNA.

value: lung fibroblasts

value: NULL control

tag: activation

tag: activation time


title: 17ABT

value: TGF-B


title: WTJSHLPS_H3K27ac_rep2

tag: cell type


title: HSV-112_Day187

description: RNAseq data from PBMC extracted from individual HSV-112

tag: individual

tag: day after vaccination


title: 17ART

tag: genotype/variation

value: RGCC overexpression


title: HSV-112_Day37


title: HSV-112_Day180


title: HSV-114_Day1


title: WTJSH_H3K27ac_rep1


title: HSV-112_Day30


title: HSV-114_Day7


title: WTJSHLPS_H3K27ac_rep1


title: 21ABT

source_name: Normal Human Lung Fibroblasts 1


title: HSV-112_Day1


title: HSV-112_Day7


title: HSV-112_Day0


title: WT_H3K27ac_rep3


title: HSV-111_Day187

description: RNAseq data from PBMC extracted from individual HSV-111


title: HSV-111_Day180


title: T cell sufficient lymphoma_1_batch2

city: Melbourne

first: Zhoujie

last: Ding

state: VIC

address: 89 Commercial Road

country: Australia

institute: Monash University

data_processing:
Reads were aligned  with  package rnasik 1.5.4 and used iGenomes, UCSC mm10 as reference
Gene read counts were converted to log 2 counts per million, quantile normalized and precision weighted with the Voom function of the Limma package through Degust
Genes were filtered from downstream analysis if they failed to achieve a counts-per-million mapped reads (CPM) value of at least 1 in at least 7 sample libraries.
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: Matrix table (CSV) with raw gene counts and normalised counts for every gene and every sample

source_name: B lymphoma cells from spleen

extract_protocol:
RNA was isolated from 1-2x10^6 purified B lymphoma cells with Qiagen Rneasy Mini Kits following manufacturer's instructions
TruSeq RNA Library Prep Kit

value: spleen

tag: batch

value: batch 2


title: 21ART


title: HSV-111_Day37


title: 21AB


title: HSV-111_Day30


title: U-WN2

data_processing:
gene alignment: Salmon
transcript abundance: tximport
differential gene expression: DESeq2
Genome_build: gencodevM24/ GRCm38.p6
Supplementary_files_format_and_content: normalized counts from DESeq2 per condition

source_name: unseparated lung cells

extract_protocol: To be updated.

value: unseparated lung cells

tag: infection

value: AdV-NULL

value: wild-type


title: HSV-111_Day7


title: 21AR


title: WTJSH_H3K27ac_rep2

value: dentritic cells

value: CreER


title: HSV-109_Day187

description: RNAseq data from PBMC extracted from individual HSV-109

value: PBMC


title: U-WM


title: HSV-109_Day37


title: HSV-109_Day180


title: U-WF


title: HSV-109_Day30


title: WT_H3K27ac_rep2


title: RAW 264.7 WT Replicate 2

city: Heidelberg

first: F. Nina

last: Papavasiliou

address: Im Neuenheimer Feld 280

department: Tumor Immunology Unit

country: Germany

institute: German Cancer Research Center (DKFZ)

data_processing:
Adapters were trimmed using the Trim Galore software (https://github.com/FelixKrueger/TrimGalore).
Before and after trimming we evaluated the RNAseq quality with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Quality control, including per-base quality, duplication levels, and over-representative sequences, passed all the checkpoints.
The RNA-seq reads were then aligned to mm10 reference genome (publicly available by the UCSC genome browser) using the STAR aligner (v. 2.6.0a, https://github.com/alexdobin/STAR(Dobin et al. 2013), with default settings.
Potential PCR duplicates were removed using the MarkDuplicates function from Picard tools (http://broadinstitute.github.io/picard).
The aligned RNAseq (.bam files) were sorted and indexed with SAMtools (https://github.com/samtools/samtools).
The sorted bam files were used as an input for the REDItoolsDnaRna.py script, part of the REDItools suite (v. 1.0.4(Picardi et al. 2015; Picardi and Pesole 2013).
Genome_build: mm10
Supplementary_files_format_and_content: RAW_WT_A1KO_cpms.txt: tab-delimited text file includes  read-counts per million for all samples

source_name: RAW 264.7 macrophages

growth_protocol: RAW 264.7 cells (ATCC® TIB-71™) were subcultured at 37°C, 5% CO2, in high glucose DMEM (Sigma-Aldrich), supplemented with 5% endotoxin low fetal bovine serum (Sera Pro FBS, PAN Biotech), 1% Glutamine and 1% Penicillin/Streptomycin (Sigma).

extract_protocol:
RNA was extracted using RNeasy Mini kit (Qiagen), and treated with DNase (Turbo DNA-free kit, Invitrogen) following manufacturers' instructions.
Total RNA was extracted from 10,000,000 cells in triplicate (RAW 264.7 and RAW 264.7 APOBEC1 knockout each from separate plates). RNA was extracted using RNeasy mini kit (Qiagen) and then treated with turbo DNase (Life technologies). RNA concentration and integrity was determined by a Qubit 4 (Thermo Fischer scientific) using the Qubit RNA BR assay kit or Qubit XR assay kit and the Qubit RNA IQ kit (Thermo Fischer scientific). 1μg of RNA was processed with Kapa mRNA hyperprep Kit for illumine platforms (Kapa Biosystems, Roche) and KAPA Single-Indexed Adapter Kit for Illumina® Platforms (Kapa Biosystems, Roche). Libraries were sequenced with the Illumina HiSeq 2000 v4 technology, generating 125-nucleotide, paired-end reads.

tag: cell line

value: macrophage

value: WT


title: U-KN1

value: ST2 KO


title: RAW 264.7 WT Replicate 3


title: HSV-109_Day7


title: HSV-109_Day1


title: Inf_Ctrl_Fe_R2

city: Bellaterra

first: Blanca

last: San Segundo

address: Edifici CRAG. Campus UAB. Carrer de la Vall Moronta s/n

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic. The minimum length was set to 35 bp and the quality score to 25.
Trimmed sequence reads were mapped to Oryza sativa Japonica (IRGSP-1.0 Ensembl release 41) using STAR mapper
Read counts were obtained with featureCounts. Data normalization and differential expression analysis was done in R using edgeR and NOISeq
Assembly: IRGSP-1.0
Supplementary files format and content: Excel files including FPKM values for each sample

organism: Oryza sativa

source_name: Leaf

growth_protocol: Rice plants were grown at 28 °C with a 14 h/10 h light/ dark cycle. For Fe treatment, plants were grown in soil (turface:vermiculite:quartz sand [2:1:3]), and watered  with a half-strength Hoagland solution for 14 days  (2.5 mM KNO3, 2.5 mM Ca(NO3)2·4H2O, 1 mM MgSO4·7H2O, 0.5 mM NH4NO3, 25 μM KH2PO4, 23.15 μM H3BO3, 4.55 μM MnCl2·4H2O, 0.38 μM ZnSO4·7H2O, 0.1 μM CuSO4·5H2O, 0.14 μM Na2MoO4·2H2O, 50 μM Fe-EDDHA, pH 5.5).

extract_protocol:
Total RNAs were obtained using Maxwell(R) RSC Plant RNA Kit (Promega). For RNA-Seq, two biological replicates for each condition were examined, each biological replicate consisting of leaves from five individual plants (youngest totally expanded leaf).
Truseq mRNA strand specific libraries were generated according to manifacturer's instructions

treatment_protocol:
To assess the effect of Fe supply, the same nutrient solution was used but with a higher Fe concentration (1 mM Fe-EDDHA). Treatment with high Fe was carried out for 5 days.
Soil-grown plants at the 3–4 leaf stage were spray-inoculated with M. oryzae spores (5x105 spores/ml; 0.3 ml/plant) using an aerograph at 2 atm of pressure. Plants were maintained overnight in the dark under high humidity

value: Leaf

tag: cultivar

value: Nipponbare

tag: treatment

value: control Fe, infected

tag: time

value: day 21


title: U-WN1

tag: strain


title: HSV-111_Day1

source_name: PBMC


title: RAW 264.7 WT Replicate 1


title: Inf_Ctrl_Fe_R1

tag: tissue


title: U-KN2


title: Mock_High_Fe_R2

value: high Fe, non infected


title: RAW 264.7 APOBEC1 KO Replicate 3

value: APOBEC1 KO


title: HSV-111_Day0


title: Inf_High_Fe_R1

value: high Fe, infected


title: HSV-109_Day0


title: U-KM


title: Mock_High_Fe_R1


title: Inf_High_Fe_R2


title: U-KF


title: RAW 264.7 APOBEC1 KO Replicate 2


title: Mock_Ctrl_Fe_R2

value: control Fe, non infected


title: HSV-108_Day187

description: RNAseq data from PBMC extracted from individual HSV-108


title: WN2

source_name: primary lung fibroblasts

value: primary lung fibroblasts


title: HSV-108_Day180


title: WN1

value: AdV-NULL


title: HSV-108_Day37


title: hdc_wt_ventral_striatum_3a_TGAGGTT

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

data_processing:
5’ and 3’ adapter sequences were trimmed from each read using Trimmomatic (v0.32), and all reads shorter than 20 bases after adapter clipping were discarded
rRNA reads were identified by mapping to a mouse rRNA reference sequence using Bowtie2 (v2.2.3) and were discarded
The remaining reads were aligned to the mouse genome (Ensembl GRCm38 annotation 75) using STAR (v2.3.1z8)
SAMtools (v0.1.19) was used to convert SAM format to BAM format, then to create sorted and indexed BAM files for visualization
Default union mode in HTSeq-count (v0.6.1p1) was used to compute read counts for reads uniquely mapping to exons in the mouse genome
Genome_build: Ensembl 75 (mouse) genome
Supplementary_files_format_and_content: txt files with counts of certain gene for each sample

extract_protocol:
Mouse brains rapidly dissected on ice.  Dissected tissues were ventral and dorsal striatum, hypothalamus, and motor cortex.  Tissue was rapidly frozen and stored at -80° until processing using the RNeasy MinElute columns (Qiagen, Valencia, CA).
RNA quality and quantity were confirmed with a Bioanalyzer (Agilent Technologies, Santa Clara, CA).  We generated double-stranded complementary DNA using the Ovation RNA-Seq system V2 (NuGEN Technologies, Inc., San Carlos, CA), starting from 5 ng of RNA.  Standard sequencing libraries (Illumina, Inc., San Diego, CA) were generated from 1-2 µg of cDNA, sheared to ~200 bp.  Sequencing was performed at the Genome Technology Access Center (GTAC) at Washington University in St. Louis.
Fastq files containing demultiplexed, single-end 50 base-pair reads were used as the basis for exploratory analysis.

value: Hdc wt

tag: age

value: 2-3 months


title: SpermRNA500T

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Dr.

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

description:
individually sequenced
RawGeneCounts_ramF2.txt

data_processing:
WGBS
Fastq files were generated and demultiplexed with the bcl2fastq Conversion Software (version 2.20, Illumina)
TrimGalore version was used to remove adapter sequences, and low-quality reads and bases
Alignment to the sheep reference genome (Oar_rambouillet_v1.0) was performed using bowtie2 of the Bismark software, followed by deduplication to remove reads aligned to the same region of the genome
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: Matrix tables (CG, CHG, an CHH contexts) with methylation counts for every cytosine and every sample
RNA-Seq
The bcl2fastq Conversion Software (version 2.20, Illumina) was used to generate and demultiplexe the Fastq files
Trimmomatic was used to remove adapter sequences, and low-quality reads and bases
STAR was used to align the trimmed reads to the sheep reference genome (Oar_rambouillet_v1.0) using the “--quantMode GeneCounts” option to estimate gene counts
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

organism: Ovis aries

source_name: Sperm

extract_protocol:
Total RNA was then extracted using 1 ml of TRIzol Reagent (Life Technologies, CA, USA), according to manufacturer instructions, followed by DNase I treatment (Lucigen, Middleton, WI).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The RNAlater-preserved samples (200 ul) were centrifuged for four minutes at 4000 RPM. After supernatant removal, cells were suspended with 1 ml of somatic cell lysis buffer for four minutes on ice. Samples were centrifuged for four minutes at 4000 RPM and lysis supernatant was removed.

value: Sperm

value: F0 methionine treated grand-progeny group


title: hdc_wt_ventral_striatum_2a_GTCTGAT


title: WF

value: wild-type


title: hdc_wt_ventral_striatum_1a_GAGGCGT


title: HSV-108_Day30

value: PBMC


title: KN2

value: ST2 KO


title: HSV-108_Day1


title: hdc_wt_motor_cortex_2d_GCAGGGG


title: SpermRNA485C

value: F0 control grand-progeny group


title: KM


title: SpermRNA468C


title: SpermRNA475C


title: SpermRNA453C


title: hdc_wt_hypothalamus_3f_TTTAACT

source_name: hypothalamus

value: hypothalamus


title: SpermRNA480T


title: KN1


title: HSV-108_Day0


title: HSV-107_Day187

description: RNAseq data from PBMC extracted from individual HSV-107


title: Mock_Ctrl_Fe_R1

value: Leaf

value: Nipponbare


title: KF


title: hdc_wt_hypothalamus_2f_ACGTCTG


title: WM


title: SpermRNA449C


title: HSV-108_Day7


title: T cell deficient lymphoma_11

value: spleen

value: batch 1


title: RAW 264.7 APOBEC1 KO Replicate 1

value: macrophage

value: APOBEC1 KO


title: HSV-107_Day37


title: SpermRNA426T


title: T cell deficient lymphoma_10


title: hdc_wt_dorsal_striatum_2b_CAAGCCG


title: HSV-107_Day30


title: SpermRNA413C


title: hdc_ko_ventral_striatum_8a_CGGTGGC

value: Hdc ko


title: HSV-107_Day7


title: T cell deficient lymphoma_8


title: hdc_wt_dorsal_striatum_1b_CGTCGCT


title: SpermRNA409C


title: SpermRNA382T


title: hdc_ko_ventral_striatum_7a_GCAACGC


title: T cell deficient lymphoma_7


title: T cell deficient lymphoma_9


title: HSV-107_Day1


title: HSV-107_Day0


title: hdc_wt_hypothalamus_1f_TTTTGTC


title: T cell deficient lymphoma_6

value: batch 2


title: hdc_ko_motor_cortex_8d_GTACGGC


title: HSV-107_Day180


title: HSV-105_Day187

description: RNAseq data from PBMC extracted from individual HSV-105


title: T cell deficient lymphoma_5


title: SpermRNA372T


title: hdc_ko_hypothalamus_8f_GCCGTTT


title: 17AR

value: lung fibroblasts

value: RGCC overexpression


title: SpermRNA366C

value: Sperm


title: T cell deficient lymphoma_4


title: HSV-105_Day180


title: hdc_ko_hypothalamus_7f_ATGACAG

value: 2-3 months


title: SpermRNA359T

value: F0 methionine treated grand-progeny group


title: HSV-105_Day37

value: PBMC


title: SpermRNA400C


title: T cell deficient lymphoma_3


title: T cell deficient lymphoma_2


title: HSV-105_Day30


title: SpermRNA350C


title: hdc_ko_dorsal_striatum_8b_TACATGG


title: SpermRNA340T


title: hdc_ko_dorsal_striatum_7b_TCCCAGC


title: T cell sufficient lymphoma_12


title: HSV-105_Day7


title: hdc_ko_motor_cortex_7d_TACAGAC


title: hdc_het_ventral_striatum_5a_GGGTCAA

value: Hdc het


title: HSV-105_Day1


title: HSV-105_Day0


title: hdc_het_ventral_striatum_6a_GGTCCTC


title: T cell sufficient lymphoma_11


title: T cell deficient lymphoma_1


title: SpermRNA323T


title: SpermRNA320T


title: hdc_het_ventral_striatum_4a_TCAACTG


title: SpermRNA329T


title: T cell sufficient lymphoma_10


title: HSV-103_Day187

description: RNAseq data from PBMC extracted from individual HSV-103


title: hdc_het_motor_cortex_6d_CCGGACC


title: ramF2_409.24C

description:
individually sequenced
MethyLevelCG_ramF2.txt
MethyLevelCHG_ramF2.txt
MethyLevelCHH_ramF2.txt

extract_protocol:
Genomic DNA from semen samples was extracted using the Quick-DNA Miniprep Plus (Zymo Research, Irvine, CA, USA) and then bisulfite treated with the EZ DNA Methylation-Lightning kit from Zymo Research.
WGBS libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Five male twin pairs (10 sheep in total) were divided into two groups, in which one animal from each pair was fed a control diet, and the other twin received the control diet plus an additional, top-dressed encapsulated methionine supplement (0.22% addition, 1.5g; RPM Smartamine®, Adisseo, Alpharetta, GA, USA), from weaning until puberty. The 10 F0 rams (five from each group) were housed in individual pens with a group of eight to nine untreated Polypay female sheep each, for two breeding cycles to produce F1 generation. To produce the F2 generation, ten F1 rams (one each from the five F0 sires from the control group and from the five F0 sires from the treatment group) were individually housed with a group of ten untreated Polypay ewes each, for two breeding cycles. All F1 and F2 animals were fed control diets for the remainder of the trial.

value: F0 control grand-progeny group (F2)


title: HSV-103_Day180


title: hdc_het_motor_cortex_5d_GTCGATA


title: T cell sufficient lymphoma_9


title: ramF2_400.24C


title: HSV-103_Day37


title: T cell sufficient lymphoma_8


title: hdc_het_hypothalamus_6f_CTCCCGA

value: hypothalamus


title: ramF2_413.12C


title: hdc_het_hypothalamus_5f_GCTTAGA


title: T cell sufficient lymphoma_7


title: ramF2_366.12C


title: HSV-103_Day7


title: HSV-103_Day1


title: T cell sufficient lymphoma_5


title: T cell sufficient lymphoma_6


title: ramF2_468.10C


title: ramF2_475.10C


title: hdc_het_dorsal_striatum_6b_TGTTTGT


title: HSV-103_Day0


title: T cell sufficient lymphoma_4


title: ramF2_485.6C


title: T cell sufficient lymphoma_3


title: hdc_het_hypothalamus_4f_CAATATC


title: hdc_het_dorsal_striatum_5b_AGATACT


title: HSV-102_Day180

description: RNAseq data from PBMC extracted from individual HSV-102


title: HSV-102_Day187


title: T cell sufficient lymphoma_2


title: ramF2_453.4C


title: T cell sufficient lymphoma_1


title: model cortex after BHD intervention Replicate 3

city: Changsha

first: Bo-wei

last: CHEN

address: No. 95 Shaoshan Middle Road

institute: Hunan University of Chinese Medicine

description:
Biological replicate 3 of 3. erebral ischemia-reperfusion model rat cortex after BHD intervention.7days.
C3

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Rat mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing:
Data was extracted using Agilent Feature Extraction software. The probe signals passing "P" or "M" QC flags in a certain proportion were retained for further analysis.
processed data includes normalized signal for IP and Sup.

organism: Rattus norvegicus

source_name: IP cortex,BHD intervention 7days

label_protocol: "IP" and "Sup" RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

growth_protocol: Drink and eat freely

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: After harvesting on ice, snap frozen in liquid nitrogen, and stored at - 80 ° C

value: cortex

tag: disease state

value: cerebral ischemia-reperfusion injury with BHD

tag: gender

value: male

source_name: Sup cortex,BHD intervention 7days


title: HSV-103_Day30


title: ramF2_449.4C


title: HSV-102_Day30


title: HSV-102_Day37


title: model cortex after BHD intervention Replicate 2

description:
Biological replicate 2 of 3. erebral ischemia-reperfusion model rat cortex after BHD intervention.7days.
C2


title: ramF2_329.23T

value: F0 methionine treated grand-progeny group (F2)


title: WT_rep3_rnaseq

data_processing:
sequnced using Illumina Hiseq platform
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using STAR v2.5.1 with parameters --sjdbOverhang 100 --twopassMode Basic --chimSegmentMin 20 --quantMode TranscriptomeSAM
Fragments Per Kilobase Million (FPKM), Transcripts Per Kilobase Million(TPM) and raw counts were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: RSEM output files including raw counts, FPKM, TPM values

growth_protocol: Bone marrow cells prepared from CreER or CreER;CTCFfl/fl mice were culutred under the presence of murine GM-CSF for 6 days with chaning medium every 2 days. For the deletion of Ctcf allele, 4-OH tamoxifen is added only on the first day of culture.

treatment_protocol: Bone marrow-derived dendritic cells were stimulated with LPS at the concentreation of 100ng/ml for 3 hours.

value: dentritic cells

tag: genotype

value: CreER


title: HSV-102_Day7


title: model cortex Replicate 3

description:
Biological replicate 3 of 3. erebral ischemia-reperfusion model rat cortex.7days.
B3

source_name: IP cortex,model 7days

value: cerebral ischemia-reperfusion injury

source_name: Sup cortex,model 7days


title: model cortex Replicate 2

description:
Biological replicate 2 of 3. erebral ischemia-reperfusion model rat cortex.7days.
B2


title: HSV-102_Day0


title: ramF2_340.11T


title: HSV-102_Day1


title: ramF2_323.23T


title: WT_rep1_rnaseq


title: ramF2_350.6C


title: WTLPS_rep3_rnaseq

value: LPS


title: Control cortex Replicate 3

description:
Biological replicate 3 of 3. Control rat cortex.
A3

source_name: IP cortex,normal

value: normal

source_name: Sup cortex,normal


title: HSV-101_Day187

description: RNAseq data from PBMC extracted from individual HSV-101


title: HSV-101_Day180


title: ramF2_426.11T


title: ramF2_382.9T


title: WTLPS_rep2_rnaseq

source_name: BMDC


title: WTLPS_rep1_rnaseq


title: HSV-101_Day37


title: ramF2_372.9T


title: KO_rep3_rnaseq

value: CreER;CTCF fl/fl


title: model cortex after BHD intervention Replicate 1

description:
Biological replicate 1 of 3. erebral ischemia-reperfusion model rat cortex after BHD intervention.7days.
C1


title: Control cortex Replicate 2

description:
Biological replicate 2 of 3. Control ratcortex.
A2


title: Control cortex Replicate 1

description:
Biological replicate 1 of 4. Control rat cortex.
A1


title: ramF2_359.5T

value: Sperm


title: HSV-101_Day30


title: WT_rep2_rnaseq


title: model cortex Replicate 1

description:
Biological replicate 1 of 3. erebral ischemia-reperfusion model rat cortex.7days.
B1


title: ramF2_320.5T


title: HSV-101_Day7


title: SGC7901 cells, CEP120-overexpressed, rep 3

city: wuhan

first: Chenggang

last: Zhang

state: hubei

address: No. 1277 Jiefang Avenue

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturers instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150bp paired-end reads were generated.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to hg38 whole genome using STAR (2.7.4a) with parameters
HISAT2 2.2.1 was used to count the reads numbers mapped to each genes.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: cell line

extract_protocol:
RNA was harvested using TRIzol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1ug of total RNA for the construction
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cell line

value: gastric cancer cells

value: Lentivirus infection


title: SGC7901 cells, vector, rep 3


title: HSV-101_Day1

data_processing:
Illumina Casava1.7 software used for basecalling.
The Spliced Transcripts Alignment to a Reference (STAR) software was used for RNA-seq alignment
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample
Supplementary_files_format_and_content: titre.txt includes titre and demographics information. 'serology' column provides serostatus group association for each sample.

extract_protocol:
PBMCs were isolated with Ficoll-Hypaque reagent and lysed in QIAzol (Qiagen, Hilden, Germany) and stored at -80°C until use. Their total RNA was extracted and purified with the miRNeasy kit (Qiagen). RNA quality and quantity were estimated using Nanodrop (Thermo Scientific, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Stranded cDNA sequencing libraries were generated with TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA) following the manufacturerâs instructions. Briefly 500 ng of total RNA was used for mRNA selection. After the reverse transcription to 1st strand cDNA, strand info was reserved with dUTPs during 2nd strand synthesis. The dsDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched with PCR to create the final cDNA library. The library was qualified with Agilent Bioanalyzer and quantified with Qubit 2.0 fluorometer. The cluster generation and pair-end (2x75 bp) sequencing was run on Illumina HiSeq 3000 at NHLBI Sequencing Core. Up to 96 barcoded samples were pooled for one single run, which yielded at least 30M passed filter paired reads per sample.

value: PBMC


title: KOLPS_rep3_rnaseq


title: ramF2_500.3T


title: KO_rep1_rnaseq


title: SGC7901 cells, CEP120-overexpressed, rep 2


title: HSV-101_Day0


title: ramF2_480.3T


title: SGC7901 cells, CEP120-overexpressed, rep 1


title: morula_siTardbp_rep3

city: Shinjuku

first: Haruhiko

last: Siomi

state: Tokyo

address: 35 Shinanomachi

department: Department of Molecular Biology

country: Japan

institute: Keio University School of Medicine

description: rRNA-depleted total RNA

data_processing:
Base calling was performed using bcl2fastq v2.20 to generate raw reads.
Quality control and adapter trimming was done using fastp (Chen et al., 2018) v0.23.2.
Quality controlled reads were aligned to GRCm38.p6 reference genome using STAR (Dobin et al., 2013) v2.7.9a with default arguments.
Reads were counted against GRCm38.p6 comprehensive gene annotation (Frankish et al., 2020) and mm10 repeats from UCSC RepeatMasker using FeatureCounts (Liao et al., 2014) v2.0.1 with multi mapping reads discard for non-TE features and count fractionally for TEs.
Assembly: mm10
Supplementary files format and content: count matrix (.csv)

source_name: morula

growth_protocol: Eight-weeks old female and male B6D2F1 (BDF1) mice were purchased from the Japan SLC, Inc. All animal experiments were reviewed and approved by the Institutional Animal Care and Use Committee (protocol no. 09105-(10) and 11045-(6)) at Keio University, where mice were maintained and fed ad libitum with standard diet and water in a temperature- and light-controlled room (23℃±3℃, 14/10 hour light/dark cycle).

extract_protocol:
Preparation of total RNA-seq library was performed using SMART-Seq Stranded Kit (Clontech), according to manufacturers’ instruction. In brief, 19 of siScramble injected or 23 of siTardbp injected ZP-free embryos were lysed in 1× Lysis Buffer containing RNase inhibitor (0.2 IU/µl, from SMART-Seq Stranded Kit, Clontech), directly. RNAs were sheared by heating at 85℃ for 8 minutes and used for reverse transcription with random hexamers and PCR amplification.
Ribosomal fragments were depleted from each cDNA sample with scZapR and scR-Probes. Indexed total RNA-seq libraries were enriched by second PCR amplification then sequenced using HiSeq Ⅹ sequencer (Illumina, paired-end, 150 bp). Three biological replicates were generated for each sample.

treatment_protocol: 8-weeks-old BDF1 female mice were injected with 150µL CARD HyperOva (Kyudo Co., Ltd.). After 48 hours, the female mice were injected with 5IU hCG (ASKA Animal Health Co., Ltd.) and mated with BDF1 male mice. After 22 hours, PN3 zygotes were collected. Cumulus cells were removed by briefly culture the zygotes in KSOM medium (Merck, MR-101-D) supplemented with 0.3µg/µL hyaluronidase (Merck, H4272). Embryos were cultured in KSOM medium drops covered with liquid paraffin (Nacalai Tesque, 26137-85) under 5% CO2 at 37°C. After 4 hours, PBS containing either 40µM scramble ASO, 20µM anti-Dux ASO, 20µM anti-Obox4 ASO, 40µM equal molar anti-Dux/anti-Obox4 ASO mixture, or 40µM equal molar anti-Dux/anti-Obox4 ASO mixture with 100ng/μL codon-optimized Obox4 mRNA were microinjected into male pronuclei of zygotes using FemtoJet 4i microinjector (Eppendorf, 5252000013).

tag: background strain

value: embryo

tag: developmental stage

value: morula


title: SGC7901 cells, vector, rep 2

tag: cell type


title: KOLPS_rep2_rnaseq


title: morula_siTardbp_rep2

description: rRNA-depleted total RNA


title: KO_STAT5

data_processing:
sequnced using Illumina Hiseq2500 platform
Raw ChIP-seq reads were trimmed for adaptor sequence, and aligned to the mm10 genome assembly using bwa mem v0.7.12 with default parameters
aligned files were filtered for MAPQ > 5 and sorting, deduplication were processed using PICARD  v1.77
peaks were called using macs2 v2.1.2 with the following setting: -f BAMPE -g mm (--broad-cutoff 0.1 --broad for H3K27ac,H3K27me3 ChIP-seq peak calling)
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.1.3
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak, broadPeak, CPM normalized bigwig

treatment_protocol: Bone marrow-derived dendritic cells (BMDCs) were stimulated with LPS at the concentration of 100ng/ml for 3 hours. In case of STAT5 ChIP-seq, BMDCs were re-stimulated with GM-CSF for 15 minutes.

tag: passages

value: 8 weeks old

tag: chip antibody


title: SGC7901 cells, vector, rep 1


title: KOLPS_rep1_rnaseq


title: KO_rep2_rnaseq


title: morula_siTardbp_rep1

description: rRNA-depleted total RNA


title: morula_siScramble_rep3

description: rRNA-depleted total RNA


title: pool_6C

description:
poolled sequenced
MethyLevelCG_pool.txt
MethyLevelCHG_pool.txt
MethyLevelCHH_pool.txt

value: F0 control progeny group (F1)


title: pool_10C


title: SUBQ03

city: Durham

first: Matthew

last: Waitkus

state: NC

address: 203 Research Drive, Medical Science Research Building 1, Room 181A

institute: Duke University

description: Column 8

data_processing:
mRNA seqeuncing data was aligned to Human hg38 by HISAT2
Bam files was counted by featureCounts packages to generate gene expression data.
DESeq2 was used to analyze differentially expressed features and normalized counts.
Assembly: Human hg38
Supplementary files format and content: tabular, data matrix

source_name: glioblastoma

growth_protocol: D06MG cell line was grown in stem cell media supplemented with  heparin, human EGF, human basic FDF

extract_protocol:
Three samples for each condition were harvested and RNA extractions were done using Maxwell RSC simplyRNA Cells Kit (Promega #AS1390).
mRNA library preparation (poly A enrichment) performed by novogene
NovaSeq PE150 (6 G raw data per sample ) performed by novogene

value: glioblastoma

value: cancer cell line

value: no


title: KOLPS_SMC1

value: dentritic cells

value: SMC1 (Bethyl lab #A300-055A)


title: SUBQ02

description: Column 8


title: pool_4C


title: hdc_het_dorsal_striatum_4b_ACCCACT

value: Hdc het

value: 2-3 months


title: SUBQ01

description: Column 8


title: KO_SMC1

value: CreER;CTCF fl/fl


title: pool_23T

value: Sperm

value: F0 methionine treated progeny group (F1)


title: morula_siScramble_rep2

description: rRNA-depleted total RNA


title: pool_24C


title: pool_12C


title: NSC03

description: Column 4


title: WTLPS_SMC1

value: CreER


title: pool_11T


title: WT_SMC1


title: NSC02

description: Column 3


title: KO_p65


title: KOLPS_p65


title: WT_STAT5


title: pool_9T


title: IC03

description: Column 7


title: scRNA_vivo_Day7_rep2

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (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

source_name: Spleen

extract_protocol:
The scRNA-seq samples of Th2 at day7 and day11 in vivo that were freshly prepared from KJ1+CD4+ T cells sorted using a BD FACS Aria III (10,000 cells each, cell viability >98%).
Libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3.1 according to manufacturer’s protocol (10X Genomics). The generated scRNA-seq libraries were sequenced using a 128 cycle (paired-end reads) with a NovaSeq 6000 (Illumina).

treatment_protocol: Splenic naïve CD4+ T cells (CD44loCD62Lhi) from DO11.10 OVA-specific TCR transgenic mice were purified with a magnetic cell sorter (autoMACS; Miltenyi Biotec, Tokyo, Japan), yielding a purity exceeding 90%. Purified naïve CD4+ T cells were stimulated by irradiated (3500 rad) Thy-1.2 depleted splenic cells (i.e. APCs) with OVA peptides (Loh15, 0.3 μM) in the presence of IL-2 (25 U/mL) for  IL-2 (25 U/mL), IL-4 (100 U/mL) (PeproTech, New Jersey, USA), and anti-IFN-γ mAb (R46A2, 2.5% [v/v]) for Th2 cell differentiation.

value: Spleen

tag: assay

value: scRNA-seq

value: CD4+CD44high T cells

tag: tranferred

tag: vivo


title: pool_5T


title: scRNA_vivo_Day11_rep2

description: 10x Genomics


title: scRNA_vivo_Day7_rep1

description: 10x Genomics


title: IC02

description: Column 6

tag: cell line


title: pool_3T

tag: treatment


title: WT_p65


title: WTLPS_p65


title: morula_siScramble_rep1

description: rRNA-depleted total RNA

value: embryo

value: morula


title: IC01

description: Column 5


title: ram_12C

description:
individually sequenced
MethyLevelCG_ram.txt
MethyLevelCHG_ram.txt
MethyLevelCHH_ram.txt

value: F0 control group


title: ram_10C


title: scRNA_vivo_Day11_rep1

description: 10x Genomics


title: NSC01

description: Column 2

value: glioblastoma


title: scRNA_TxnipWT_transferred_Th2_48h_rep1

description: 10x Genomics

value: KJ1+CD4+ T cells


title: LNCaP:C42 shMETTL3 guide 1 vehicle #2

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

description: METTL3 depleted

data_processing:
Contaminating adapters and low quality reads with phred scores <30 were removed using the Trimgalore wrapper for Cutadapt and Fastqc.
The resultant quality controlled fastq files were aligned to the Ensembl annotated Human genome (GRCh38.83) using STAR.
Gene expression was quantified using FeatureCounts.
Assembly: GRCh38.83
Supplementary files format and content: *.sortedByCoord.out.bam.counts.txt: Tab-delimited text files contain gene expression in counts.

growth_protocol: Cells were maintained at 37C and 5% CO2 in phenol red containing RPMI-1640 medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin-glutamine, 2 mM L-Glutamine and 1 mM sodium pyruvate.

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit with on-column DNase treatment.
Library constructions protocol: Illumina

treatment_protocol: The phenotypic and transcriptomic effect of shRNA-mediated METTL3 knockdown was assessed in the enzalutamide-sensitive CRPC cell line, LNCaP:C4-2. shRNA-mediated functional depletion of METTL3 was performed in LNCaP:C42 grown in phenol red-free RPMI-1640 medium supplemented with 1% penicillin-streptomycin, 2mM L-Glutamine and 1 mM sodium pyruvate and 10% charcoal-stripped FBS. The shRNA-target regions were identified using RNAi Consortium tools (www.broad.mit.edu/genome_bio/trc/rnai.html) and were located in exon 5 for shRNA:METTL3 guide 1 (5’- CGTCAGTATCTTGGGCAAGTT-3’) and spanning exon 4 and 5 for shRNA:METTL3 guide 2 (5’- GCTGCACTTCAGACGAATTAT-3’ located ). The shRNA:METTL3 guide 1 duplex (5’-CCGGCGTCAGTATCTTGGGCAAGTTCTCGAGAACTTGCCCAAGATACTGACGTTTTTG-3’) and shRNA:METTL3 guide2 duplex (5’-CCGGGCTGCACTTCAGACGAATTATCTCGAGATAATTCGTCTGAAGTGCAGCTTTTTG-3’) was expressed using a doxycycline inducible pLKO.1-puro construct. A scramble, non-gene targeting shRNA (5’-CCGGGCGCGATAGCGCTAATAATTTCTCGAGAAATTATTAGCGCTATCGCGCTTTTTG-3’) in pLKO.1-puro was used as control. Lentiviral particles were generated in HEK293T cells using the pVSV-G envelope vector and pDR8.91 packaging vector using standard protocols and were used to transduce LNCaP:C42 cells. Puromycin (1ug/mL) was used for three weeks to select for cells with stable lentiviral integration and knockdown induced by doxycycline (1ug/mL) treatment for 6 days.

value: Prostate cancer cells

tag: shRNA


title: scRNA_TxnipKOtransferred_Th2_48h_rep1

description: 10x Genomics


title: scRNA_TxnipWT_transferred_Th2_48h_rep2

description: 10x Genomics


title: ram_4C


title: WT_H3K4me3

value: dentritic cells

value: 8 weeks old

tag: strain

value: H3K4me3 (Abcam #ab8580)


title: scRNA_TxnipKO_effector_Th2_rep2

description: 10x Genomics

tag: tissue


title: LNCaP:C42 shMETTL3 guide 1 vehicle #1

description: METTL3 depleted


title: WTLPS_H3K4me3


title: ram_23T

value: F0 methionine treated group


title: scRNA_TxnipKO_effector_Th2_rep1

description: 10x Genomics


title: LNCaP:C42 shMETTL3 guide 2 vehicle #2

description: METTL3 depleted


title: ram_11T


title: scRNA_TxnipWT_effector_Th2_rep2

description: 10x Genomics


title: KOLPS_H3K4me1

value: H3K4me1 (Abcam #ab8895)

value: CreER;CTCF fl/fl


title: scRNA_TxnipKOtransferred_Th2_48h_rep2

description: 10x Genomics


title: KO_H3K4me1


title: scRNA_TxnipWT_effector_Th2_rep1

description: 10x Genomics


title: LNCaP:C42 shMETTL3 guide 1 vehicle #3

description: METTL3 depleted


title: ram_9T

value: Sperm


title: KOLPS_H3K4me3


title: LNCaP:C42 shMETTL3 guide 2 vehicle #1

description: METTL3 depleted


title: KO_H3K4me3


title: WTLPS_H3K4me1

value: CreER


title: ram_5T


title: ram_6C


title: LNCaP:C42 shScramble non-gene targetting Vehicle #3

description: Non-gene targeting control

value: shScramble


title: ram_24C


title: scRNA_transferred_Th2_48h_rep2

description: 10x Genomics

value: Spleen

value: scRNA-seq


title: WT_H3K4me1


title: LNCaP:C42 shScramble non-gene targetting Vehicle #2

description: Non-gene targeting control


title: LNCaP:C42 shMETTL3 guide 2 vehicle #3

description: METTL3 depleted


title: scRNA_transferred_Th2_48h_rep1

description: 10x Genomics


title: ram_3T


title: KOLPS_H3K27me3

value: H3K27me3 (Abcam #ab6002)


title: KO_H3K27me3


title: Shoot_NoDMS_OsNRT2.3B

city: Nanjing

first: Xiaorong

last: Fan

address: Nanjing city Wei Tong Road 6

department: 1State Key Laboratory of Crop Genetics and Germplasm Enhancement

institute: Nanjing Agricultural University

data_processing:
For filtering the raw fastq files, Trimmomatic was used to remove adapter sequences. A sliding window trimming approach was used to filter the reads with quality scores lower than 20. Next, 2 nt from the 5′ end of each read were trimmed, and the reads over 200 bp were kept for further analysis.
Reads were aligned to the reference sequence using TopHat with parameter setting: --library-type fr-unstranded --no-novel-juncs -N 25 --read-gap-length 7 --read-edit-dist 25 --max-insertion-length 5 --max-deletion-length 5 -g 3 --no-mixed.
Mismatch count and coverage in each nuclotide were called, and mismatches located within 3nt of an insertions or deletion were masked for future analysis.
Assembly: MSU Rice Genome Annotation Project Release 7
Supplementary files format and content: text files include mutation ratio in each nucleotide for each Sample.

organism: Oryza sativa Japonica Group

source_name: rice shoots

growth_protocol: Two-week-old rice (Oryza sativa ssp.Nipponbare) seedlings grown in hydroponic nutrient solution

extract_protocol:
DMS-treated or DMS-Untreated samples were pelleted and resuspended in 1 mL Trizol, RNA was extracted by phenol-chloroform extraction and isopropanol precipitation.
For target-specific DMS-MaPseq, 3 µg of DMS-treated sample was mixed with gene-specific RT primers. The reverse transcription was proceeded with TGIRT-III (Ingex). Then specific gene cDNA were amplified using KOD hot start DNA polymerase with gene-specific primers.The mixture was incubated under vacuum for 5 min at room temperature. The samples were then washed three times with 50 mL of DEPC-treated water each, frozen in liquid nitrogen, and ground to fine powder.

treatment_protocol: Two-week-old rice seedlings were collected and immersed in 20ml of 1X DMS reaction buffer (40mM HEPES pH7.5, 100mM KCl and 0.5mM MgCl2).  200µl of DMS was added to the reaction buffer to give a final concentration of 1%.The same volume of DEPC-treated water was added into the reaction buffer for the mock treatment. DMS treatment was performed for 15 min at 30°C with shaking at 250rpm.

value: Shoot

tag: age

value: Two-week-old

tag: target


title: Shoot_1%DMS_OsNRT2.3B


title: scRNA_effector_Th2_rep2

description: 10x Genomics


title: Batch 3 PBMC 10x Lane 16 (Batch3P16) CSP

city: Bethesda

first: William

middle: W

last: Lau

state: MD

address: 4 Memorial Drive

department: Laboratory of Immune System Biology

institute: National Institute of Allergy and Infectious Diseases

description: Cell Surface Protein Tag reads from multimodal scRNAseq

library_source: other

data_processing:
fastq generation: CellRanger 6.0.1 (10x Genomics)
mapping, CellRanger 6.0.1 (10x Genomics)
sample demultiplexing: popscle demuxlet (https://github.com/statgen/popscle)
secondary analysis: Seurat 4.0.3 (R package)
Multiple donor samples are combined within each lane. A demultiplexed dataset of all cells that passed QC is provided as an R Seurat object.
Assembly: hg19 (cellranger version 1.2.0, https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build#hg19_1.2.0)
Supplementary files format and content: R Seurat object with count matrices
Library strategy: CITE-seq

molecule: protein

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Frozen PBMC samples were thawed, recovered and washed using RPMI media with 10% FBS and 10mg/mL DNase I (STEMCELL 07470). Samples from different donors were pooled evenly before staining; single cells can be demultiplexed in silico using individual specific single nucleotide polymorphism (SNP) information during data analysis (see below; demultiplexing for each lane is provided in the *demux.best supplemental files). Multiple cell pools were prepared, such that cells from the same individual but different timepoints would be in different pools. PBMC pools were Fc blocked (Human TruStain FcX, BioLegend 422302) and stained with Totalseq-C human ‘hashtag’ antibodies (BioLegend), washed with staining buffer (2% BSA in PBS). This round of hashtag staining allows the different pools to be identified in the analysis, which when combined with the SNP-based demultiplexing, allows full identification of each sample. Hashtagged PBMC pools were combined and cells were stained with a cocktail of TotalSeq-C human lyophilized panel (BioLegend) of 137 surface proteins and SARS-CoV-2 S1 protein probe. Then, cells were washed three times, resuspended in PBS, and counted before proceeding immediately to the single cell partition step.
PBMC samples were partitioned into single cell Gel-Bead in Emulsion (GEM) mixed together with the reverse transcription (RT) mix using 10x 5’ Chromium Single Cell Immune Profiling Next GEM v2 chemistry (10x Genomics, Pleasanton, CA), as previously described (PMID: 33713619). The RT step was conducted in the Veriti Thermo Cycler (ThermoFisher Scientific, Waltham, MA). Single cell gene expression and cell surface protein libraries were prepared as instructed by 10x Genomics user guides (https://www.10xgenomics.com/resources/user-guides/). All libraries were quality controlled using Bioanalyzer (Agilent, Santa Clara, CA) and quantified using Qubit Fluorometric (ThermoFisher). 10x Genomics 5’ Single cell gene expression, cell surface protein tag, TCR and BCR libraries were pooled and sequenced on Illumina NovaSeq platform (Illumina, San Diego, CA) using the following sequencing parameters: read1-100-cycle, i7-10-, i5-10, read2-100.
single cell RNAseq (10x Genomics 5' v2)

tag: unsorted or sorted

value: UnSorted

value: blood

value: PBMC


title: Batch 3 PBMC 10x Lane 16 (Batch3P16) GEX

description: mRNA (cDNA) reads from multimodal scRNAseq


title: scRNA_effector_Th2_rep1

description: 10x Genomics

value: KJ1+CD4+ T cells


title: WTLPS_H3K27me3

extract_protocol:
Fixed cells were sonicated and immunoprecipitated with antibody recognizing specific protein. Antibody-chromatin complexed were captured with protein A&G beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Reverse-crosslinked DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina HiSeq2500 platform.

value: dentritic cells

value: 8 weeks old

tag: genotype


title: Root_1%DMS_OsNRT2.3A

source_name: rice roots

value: Root


title: Root_NoDMS_OsNRT2.3A


title: WT_H3K27me3


title: OC_IC_2

city: Hangzhou

first: Lai

last: Pan

state: Zhejiang

address: Jiefang Road 88

institute: The second affiliated hospital of Zhejiang University

data_processing:
Experimental procedures were performed according to standard procedures provided by Illumina, including library preparation and sequencing experiments. Small RNA sequencing libraries were prepared using TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA). After library preparation, the constructed libraries were sequenced using Illumina Hiseq2000/2500 with single-end 1X50bp reads.
The miRNA data analysis software ACGT101-mir (LC Sciences, USA), developed independently by Lianchuan Bio-Technology, was used. This software performs the analysis as follows: (1) data cleaning: by removing 3' connections and garbage sequences; (2) the length screening should be performed on sequences whose bases range between 18 and 26 nucleotides; (3) comparison and analysis of various RNA databases conducted using the remaining sequences (excluding miRNA) and filtering against the mRNA, RFam, and Repbase databases; (4) identification of miRNA: miRNA is identified by comparing the precursor and genome data; (5) miRNA difference analysis.

growth_protocol: RAW264.7  cells were procured from the National Collection of Authenticated Cell Cultures (Shanghai, China).  Osteoblasts were enzymatically isolated from the skull bones of 1-day-old C57BL/6 mice.  RAW264.7 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) (Sigma, USA) supplemented with 100 U/μL penicillin, streptomycin (TBD Science, China), and 10% foetal bovine serum (FBS) (Bovogen, AUS).   The cells were incubated under 5% carbon dioxide (CO2) at 37°C until 70-80% convergence was reached.

extract_protocol:
After 5 days of RANKL (50 ng/mL) induction, osteoclasts were cultured with a medium comprising exosome-free FBS. After a 48-h culture, dead cells and debris from cellular supernatants were discarded by centrifuging at 3000 ×g for 10 min. A 70-min ultracentrifugation at 110,000 ×g at 4°C was performed on the supernatants. After resuspension in phosphate-buffered saline (PBS), the precipitate was further centrifuged for 70 min at 110,000 ×g. The precipitate was dissolved in 100 μL of PBS to form a final precipitate (exosomes), which was stored at -80°C.
The experimental procedures, including the preparation of the libraries and sequencing, were performed according to the instructions provided by Illumina (Illumina, USA). A small RNA library preparation kit (TruSeq Small RNA Library Prep Kit, Illumina, USA) was used to create the sequencing libraries. The purified library products were sequenced at LC-Bio Co., Ltd. (Hangzhou, China) using Illumina Hiseq 2000/2500 (the 1 × 50 bp mode).The miRNA data analysis software ACGT101-mir (LC Sciences, USA), developed independently by Lianchuan Bio-Technology, was used. This software performs the analysis as follows: (1) data cleaning: by removing 3' connections and garbage sequences; (2) the length screening should be performed on sequences whose bases range between 18 and 26 nucleotides; (3) comparison and analysis of various RNA databases conducted using the remaining sequences (excluding miRNA) and filtering against the mRNA, RFam, and Repbase databases; (4) identification of miRNA: miRNA is identified by comparing the precursor and genome data; (5) miRNA difference analysis.

value: Murine monocyte-macrophage leukemia cells

value: Mature osteoclasts were induced with 50ng/ml Rankl


title: KOLPS_H3K27ac

value: H3K27ac (Abcam #ab4729)

value: CreER;CTCF fl/fl


title: OC_IC_3


title: Batch 3 PBMC 10x Lane 13 (Batch3P13) GEX


title: Shoot_1%DMS_OsNRT1.1B


title: NC_3

value: control


title: Batch 3 PBMC 10x Lane 11 (Batch3P11) GEX


title: KO_H3K27ac


title: Batch 3 PBMC 10x Lane 13 (Batch3P13) CSP


title: Shoot_NoDMS_OsNRT1.1B


title: WTLPS_H3K27ac

value: CreER


title: Root_1%DMS_OsNRT1.1B


title: LNCaP:C42 shScramble non-gene targetting Vehicle #1

description: Non-gene targeting control

value: Prostate cancer cells

value: shScramble


title: Batch 3 PBMC 10x Lane 11 (Batch3P11) CSP


title: Batch 3 PBMC 10x Lane 10 (Batch3P10) GEX


title: NC_2


title: WT_H3K27ac


title: Root_NoDMS_OsNRT1.1B


title: NC_1


title: KOLPS_CTCF

value: CTCF (CST #2899)


title: Batch 3 PBMC 10x Lane 10 (Batch3P10) CSP


title: dEFP_60

first: Allen

middle: R

last: Buskirk

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

data_processing:
The 3'-linker CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCA was removed with Skewer. Reads were aligned with Bowtie allowing for two mismatches. Reads mapping to tRNA or rRNA were discarded. Reads mapping uniquely to the genome were then mapped to B. subtilis 168 annotation version 3.
Assembly: NC_000964.3
Supplementary files format and content: WIG files of ribosome density, assigned to the 3'-end of reads, normalized by the total number of reads in the library
Library strategy: ribosome profiling

organism: Bacillus subtilis subsp. subtilis str. 168

growth_protocol: 30 mL starter cultures were grown overnight in CH media at 30 C with shaking (220 rpm). The next day, a starter culture in mid-log phase was used to inoculate 225 mL of CH media to a starting OD of 0.025 in a baffled flask. These cultures were grown at 37 C with shaking (220 rpm) for about 3 hours until they reached an OD of 0.4-0.6. Cells were pelleted at 3200 rcf for 10 minutes at room temperature and then resuspended in pre-warmed Sterlini-Madelstam resuspension media at 37 C. Cultures were harvested at 15 minutes or 60 post-resuspension.

extract_protocol: 50 mL of culture was directly flash-frozen in liquid nitrogen and cryogenically pulverized in a Spex 6870 freezer mill using 10 cycles of 1 min at 10 Hz with 1 min cooling. The lysis buffer contained 150 mM MgCl2 to arrest translation. Ribosomes were pelleted over a sucrose cushion prior to digestion of mRNA with MNase. After digestion, 70S monosomes were purified over a sucrose gradient. Ribosome footprints and total RNA fragments 15-45 nt in length were PAGE purified, ligated to a linker using RNA ligase T2, converted to DNA using RT, circularized, and PCR amplified.

value: sporulation by resuspension

tag: time

value: 60 min

value: efp deletion mutant


title: KO_CTCF

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

institute: Yonsei University College of Medicine


title: WT_60

value: WT


title: OC_IC_1


title: WTLPS_CTCF


title: Gene Expression Library 4 Run 1

city: Chicago

first: Alexander

last: Chervonsky

state: IL

department: Pathology

institute: University of Chicago

description: 10X Genomics scRNA-Seq

data_processing:
GE.mtx, Filtered_contig_annotation.csv, and clonotypes.csv files were generated using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) cellranger multi command, combining GEX, VDJ, and antibody capture hashtag libraries. The command was run using Cell Ranger’s supplied VDJ and GEX reference files, refdata-cellranger-vdj-GRCm38-alts-ensembl-4.0.0 and refdata-gex-mm10-2020-A.  Gene expression matrix, features, and barcode files were combined to make a complete gene_expression.csv file in R for each library.
Data from both rounds of sequencing were imported using the scanpy package. Any cell whose second-largest hashtag read count was at least 75% of the cell's largest hashtag read count was filtered out of the dataset as a doublet.
Assembly: mm10
Supplementary files format and content: Comma-separated values files

source_name: Pancreatic Islets of Langerhans

extract_protocol:
Mice were killed by cervical dislocation and the pancreata were perfused with 5 mL of collagenase P solution [0.5 mg/ml, (Roche) in HBSS (Gibco) supplemented with 0.1 M HEPES, 1 mM MgCl2, 5 mM D- glucose, 1.25 mM CaCl2, and 0.02% BSA] via the common bile duct. Perfused pancreata were then dissected away from the surrounding tissue and incubated for 10 minutes at 37°C. Digestion was halted by washing the tissue twice with supplemented HBSS. The tissue was then applied to a Histopaque-1119 (Sigma) gradient, and the interface was collected, washed in supplemented HBSS, and then placed in Click’s medium with 5% FBS. Islets were handpicked using an inverted microscope. Handpicked islets were dissociated by incubation in Enzyme Free Cell Dissociation Buffer (Gibco) at 37° C for 2 minutes followed by washing in Click’s media containing 10% FBS. Islet cells from each animal were then resuspended in 1x PBS supplemented with 1% FBS and 0.05% sodium-azide (FACS buffer) and incubated on ice for 10 minutes with purified anti-mouse CD16/32 Fc block antibodies (BD) at a 1:200 final concentration. Total-Seq-C antibodies (Biolegend) were then added to each sample at a concentration of 1:200 and the samples were incubated on ice for 25 minutes. Finally, all of the samples were washed 2 times with 1 ml of FACS buffer and then pooled together into 1 tube for sequencing.
Pooled cells were split four ways (libraries 1-4). All samples were mixed with the reverse transcription (RT) mix and partitioned into single cell Gel-Bead in Emulsion (GEM) using 10x 5’ Chromium Single Cell Immune Profiling kit (10x Genomics). Single cell gene expression, cell surface protein, and T cell receptor (TCR) libraries were prepared as instructed by 10x Genomics user guides (https://www.10xgenomics.com/resources/user-guides/). All libraries were quality controlled using Bioanalyzer (Agilent, Santa Clara, CA).  Each library was sequenced twice on an Illumina NovaSeq 6000 instrument (runs 1 and 2).

value: Pancreatic Islets of Langerhans

value: NOD/ShiLtJ

value: 15 Weeks old


title: WT_CTCF

city: Seoul

value: dentritic cells

value: 8 weeks old


title: Batch 3 PBMC 10x Lane 8 (Batch3P08) GEX

value: UnSorted

value: blood

value: PBMC


title: Batch 3 PBMC 10x Lane 9 (Batch3P09) CSP


title: Gene Expression Library 4 Run 2

description: 10X Genomics scRNA-Seq


title: Gene Expression Library 3 Run 1

description: 10X Genomics scRNA-Seq


title: Batch 3 PBMC 10x Lane 8 (Batch3P08) CSP


title: dEFP_15

city: Baltimore

value: 15 min


title: KO_input

value: input

value: CreER;CTCF fl/fl


title: Gene Expression Library 2 Run 2

description: 10X Genomics scRNA-Seq


title: Gene Expression Library 3 Run 2

description: 10X Genomics scRNA-Seq


title: WT_15


title: ChIPseq for H3K4me1 in WT_Rep2

city: Vienna

first: Ramesh

last: Yelagandula

address: Dr.-Bohr-Gasse 3

country: Austria

institute: IMBA

data_processing:
ChIP-seq reads were trimmed using trim-galore v0.4.4 and thereafter aligned to the mm10 reference genome using bwa mem v0.7.17. A
A mapping quality filter with cutoff 1 was applied using samtools v1.10.
Duplicated reads were marked and excluded with picard MarkDuplicates v2.23.4 and the obtained bam files were used to generated bigwig files using deeptools bamCoverage v3.5.0 with the parameter -normalizeUsing RPKM.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: ESCs

extract_protocol:
Lysates were clarified from sonicated nuclei and chromatin complexes were isolated either with antibody or Dynabeads M-280 Streptavidin
Libraries were prepared using a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®

value: ESCs

value: Wild type

value: Rabbit anti-H3K4me1/ab8895/abcam


title: KOLPS_input


title: Gene Expression Library 2 Run 1

description: 10X Genomics scRNA-Seq


title: ChIPseq for H3K4me3 in WT_Rep1

value: Rabbit anti-H3K4me3/ab8580/abcam


title: ChIPseq for H3K4me3 in WT_Rep2


title: WTLPS_input

value: CreER


title: Batch 3 PBMC 10x Lane 7 (Batch3P07) GEX


title: Batch 3 PBMC 10x Lane 7 (Batch3P07) CSP


title: Gene Expression Library 1 Run 2

description: 10X Genomics scRNA-Seq


title: Batch 3 PBMC 10x Lane 9 (Batch3P09) GEX


title: ChIPseq for H3K4me1 in WT_Rep1


title: Batch 3 PBMC 10x Lane 6 (Batch3P06) GEX


title: NIID3 cortex

city: Houston

first: Ziyi

last: Li

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

description:
NIID_Ctx3
MmCtx_NIIDvCTL.txt

data_processing:
All total reads were mapped to hg38/mm9 by TopHat2 with default parameter followed by gene expression quantification and differential expression analysis using Cuffdiff.
The alternative splicing events, including SE, IR, MXE, A3SS and A5SS, were reported by rMATS.
Genome_build: hg38 (GRCh38), mm9 (MGSCv37)
Supplementary_files_format_and_content: txt and csv files include FPKM.

source_name: Cerebral Cortex

extract_protocol:
Samples for RNA-seq were extracted with Trizol and quick RNA kit.
An amount of 1ug total RNA per sample was processed for library preparation using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Libraries were sequenced on a HiSeq with a read length configuration of 150 PE, targeting 100M total reads per sample.

value: Cerebral Cortex

tag: disease/model

value: NIID


title: ChIPseq for ESRRB in Zfp462KO_Rep2

tag: cell type

value: Zfp462 knock out


title: Batch 3 PBMC 10x Lane 6 (Batch3P06) CSP


title: Gene Expression Library 1 Run 1

description: 10X Genomics scRNA-Seq

value: Pancreatic Islets of Langerhans

value: NOD/ShiLtJ

value: 15 Weeks old


title: HT Library 4 Run 2

description: 10X Genomics Hashtag Sequencing. Hashtag antibody information available in supplementary file TCRSeq_mouse_metadata_2022.csv

data_processing:
GE.mtx, Filtered_contig_annotation.csv, and clonotypes.csv files were generated using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) cellranger multi command, combining GEX, VDJ, and antibody capture hashtag libraries. The command was run using Cell Ranger’s supplied VDJ and GEX reference files, refdata-cellranger-vdj-GRCm38-alts-ensembl-4.0.0 and refdata-gex-mm10-2020-A.  Gene expression matrix, features, and barcode files were combined to make a complete gene_expression.csv file in R for each library.
Data from both rounds of sequencing were imported using the scanpy package. Any cell whose second-largest hashtag read count was at least 75% of the cell's largest hashtag read count was filtered out of the dataset as a doublet.
Assembly: mm10
Supplementary files format and content: Comma-separated values files
Library strategy: Hashtag library

molecule: other


title: NIID2 cortex

description:
NIID_Ctx2
MmCtx_NIIDvCTL.txt


title: HT Library 4 Run 1


title: ChIPseq for ESRRB in Zfp462KO_Rep1


title: Batch 3 PBMC 10x Lane 5 (Batch3P05) GEX

value: UnSorted


title: ChIPseq for ESRRB in WT_Rep2


title: NIID1 cortex

description:
NIID_Ctx1
MmCtx_NIIDvCTL.txt


title: Batch 3 PBMC 10x Lane 4 (Batch3P04) GEX

value: blood


title: ChIPseq for ESRRB in WT_Rep1


title: Batch 3 PBMC 10x Lane 5 (Batch3P05) CSP

value: PBMC


title: Ctrl3 cortex

description:
NIID_Ctrl_Ctx3
MmCtx_NIIDvCTL.txt

value: Control


title: HT Library 3 Run 2


title: WT_input

value: dentritic cells

tag: passages

value: 8 weeks old

value: input


title: HT Library 2 Run 2


title: ChIPseq for NR5A2 in Zfp462KO_Rep1

value: ESCs

tag: chip antibody

value: Rabbit anti-NR5A2/ABE2867/SIGMA


title: HT Library 3 Run 1


title: Ctrl1 cortex

description:
NIID_Ctrl_Ctx1
MmCtx_NIIDvCTL.txt


title: NIID3 Hippocampus

description:
NIID_Hip3
MmHip_NIIDvCTL.txt

source_name: Hippocampus

value: Hippocampus


title: HT Library 2 Run 1


title: Ctrl2 cortex

description:
NIID_Ctrl_Ctx2
MmCtx_NIIDvCTL.txt


title: Batch 3 PBMC 10x Lane 3 (Batch3P03) GEX


title: Batch 3 PBMC 10x Lane 4 (Batch3P04) CSP


title: ChIPseq for NR5A2 in WT_Rep2

value: Wild type


title: Batch 3 PBMC 10x Lane 3 (Batch3P03) CSP


title: HT Library 1 Run 2


title: NIID1 Hippocampus

description:
NIID_Hip1
MmHip_NIIDvCTL.txt


title: Batch 3 PBMC 10x Lane 2 (Batch3P02) GEX


title: HT Library 1 Run 1


title: Batch 3 PBMC 10x Lane 2 (Batch3P02) CSP


title: Ctrl3 Hippocampus

description:
NIID_Ctrl_Hip3
MmHip_NIIDvCTL.txt


title: VDJ Library 4 Run 2

description: 10X Genomics TCR Sequencing

data_processing:
GE.mtx, Filtered_contig_annotation.csv, and clonotypes.csv files were generated using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) cellranger multi command, combining GEX, VDJ, and antibody capture hashtag libraries. The command was run using Cell Ranger’s supplied VDJ and GEX reference files, refdata-cellranger-vdj-GRCm38-alts-ensembl-4.0.0 and refdata-gex-mm10-2020-A.  Gene expression matrix, features, and barcode files were combined to make a complete gene_expression.csv file in R for each library.
Data from both rounds of sequencing were imported using the scanpy package. Any cell whose second-largest hashtag read count was at least 75% of the cell's largest hashtag read count was filtered out of the dataset as a doublet.
Assembly: mm10
Supplementary files format and content: Comma-separated values files
Library strategy: VDJ-seq


title: ChIPseq for NR5A2 in Zfp462KO_Rep2


title: VDJ Library 4 Run 1

description: 10X Genomics TCR Sequencing


title: Batch 3 PBMC 10x Lane 1 (Batch3P01) GEX


title: Batch 3 PBMC 10x Lane 1 (Batch3P01) CSP


title: Ctrl2 Hippocampus

description:
NIID_Ctrl_Hip2
MmHip_NIIDvCTL.txt


title: ChIPseq for OCT4 in Zfp462KO_Rep1

value: Goat anti-OCT4/AF1759/R&D Systems


title: ChIPseq for OCT4 in WT_Rep2


title: VDJ Library 3 Run 2

description: 10X Genomics TCR Sequencing


title: Ctrl1 Hippocampus

description:
NIID_Ctrl_Hip1
MmHip_NIIDvCTL.txt


title: ESC_Zfp462+/R1257*_4dayRA_Rep2

data_processing:
RNA-seq reads were trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20) and reads mapping to abundant sequences included in the iGenomes Ensembl GRCm38 bundle (mouse rDNA, mouse mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and gene annotation for the GRCm38/mm10 assembly obtained from Mus musculus Ensembl release 94. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting for QuantSeq experiments (-s 1).
Genome_build: mm10

source_name: Mouse cells from a differentiation assay

extract_protocol:
RNA was extracted using RNAeasy Qiagen kit
Libraries were prepared using a QuantSeq 3' mRNA kit from Lexogen
QuantSeq

tag: mutants

tag: growth protocol

value: Cells were grown at 37º C, 5% CO2

value: 4day retinoic acid


title: Batch 2 PBMC 10x Lane 16 (Batch2P16) GEX


title: ChIPseq for OCT4 in WT_Rep1


title: ESC_Zfp462+/R1257*_4dayRA_Rep1


title: NIID2 Hippocampus

description:
NIID_Hip2
MmHip_NIIDvCTL.txt

value: NIID


title: Batch 2 PBMC 10x Lane 15 (Batch2P15) GEX


title: VDJ Library 3 Run 1

description: 10X Genomics TCR Sequencing

value: Pancreatic Islets of Langerhans

value: NOD/ShiLtJ


title: NIID3 Cerebellum

description:
NIID_Cb3
MmCb_NIIDvCTL.txt

source_name: Cerebellum

value: Cerebellum


title: VDJ Library 2 Run 1

description: 10X Genomics TCR Sequencing

value: 15 Weeks old


title: Batch 2 PBMC 10x Lane 16 (Batch2P16) CSP

value: UnSorted

value: blood

value: PBMC


title: Batch 2 PBMC 10x Lane 15 (Batch2P15) CSP


title: ESC_Zfp462+/R1257*_2dayRA_Rep2

value: 2day retinoic acid


title: ChIPseq for OCT4 in Zfp462KO_Rep2

value: Zfp462 knock out


title: Ctrl3 Cerebellum

description:
NIID_Ctrl_Cb3
MmCb_NIIDvCTL.txt

value: Control


title: ChIPseq for NR5A2 in WT_Rep1

value: ESCs

value: Rabbit anti-NR5A2/ABE2867/SIGMA


title: VDJ Library 2 Run 2

description: 10X Genomics TCR Sequencing


title: Batch 2 PBMC 10x Lane 14 (Batch2P14) GEX


title: ESC_Zfp462+/R1257*_2dayRA_Rep1


title: Ctrl1 Cerebellum

description:
NIID_Ctrl_Cb1
MmCb_NIIDvCTL.txt


title: ESC_Zfp462+/R1257*_4dayEB_Rep2

value: after 4 days of LIF withdrawal


title: VDJ Library 1 Run 1

description: 10X Genomics TCR Sequencing


title: Batch 2 PBMC 10x Lane 14 (Batch2P14) CSP


title: WTLPS_K27Ac_HiChIP_rep4

data_processing:
Sequenced using Illumina NovaSeq6000 platform
Raw reads were processed using HiC-Pro pipeline v2.11.4 with MboI restriction sites
Assembly: mm10
Supplementary files format and content: hic contaning validpairs

extract_protocol:
Fixed chromatin was digested using MboⅠ enzyme, followed by biotin incorporation with Biotin-14-dATP. After DNA ligation, the DNA was sonicated and immunoprecipitated with antibody recognizing specific protein. Antibody-chromatin complexed were captured with protein A&G beads. Reverse-crosslinked DNA was captured with Streptavidin C-1 beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Purified DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina NovaSeq6000 platform.

value: dentritic cells

value: 8 weeks old

value: H3K27ac (Abcam #ab4729)

value: CreER


title: VDJ Library 1 Run 2

description: 10X Genomics TCR Sequencing

value: Pancreatic Islets of Langerhans


title: NIID2 Cerebellum

description:
NIID_Cb2
MmCb_NIIDvCTL.txt

value: NIID


title: Batch 2 PBMC 10x Lane 13 (Batch2P13) GEX


title: ESC_Zfp462+/R1257*_4dayEB_Rep1

value: Cells were grown at 37º C, 5% CO2


title: Ctrl2 Cerebellum

description:
NIID_Ctrl_Cb2
MmCb_NIIDvCTL.txt

value: Cerebellum


title: Batch 2 PBMC 10x Lane 13 (Batch2P13) CSP

value: UnSorted


title: WT_K27Ac_HiChIP_rep4


title: NIID1 Cerebellum

description:
NIID_Cb1
MmCb_NIIDvCTL.txt


title: Batch 2 PBMC 10x Lane 12 (Batch2P12) GEX

value: blood


title: WTLPS_K27Ac_HiChIP_rep3


title: ESC_Zfp462+/R1257*_Serum_LIF_Rep1

value: Serum/LIF


title: DMS-KD4_2-F4R4

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

institute: Fudan University

data_processing:
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Raw read was evaluated quality by FastQC (v0.11.9) and removed PCR primmers by cutadaptor(v1.18). Trimmed data for ${treatment}_F1R1_F3R3.fq.gz and ${treatment}_F4R4.fq.gz were combined together. The combined data was mapped with ShapeMapper2 (v 2.1.3, parameters: --verbose --serial --nproc 16 --min-depth 1000). The RNA secondary structure was predicted by RNAfold (v 2.4.14, parameters: -p -d2 --shapeMethod=D).
Assembly: Target RNA sequence
Supplementary files format and content: TXT files include the read depths, standard errors and SHAPE reactivity of each base. Column "Norm_profile" is the SHAPE reactivity.

source_name: HeLa cells

growth_protocol: HeLa cells expressing scramble tet-on shRNA or URB1-targetting  tet-on shRNA were maintained in DMEM, which was supplemented with 10% Fetal Bovine Serum (FBS).

extract_protocol:
The Tet inducible stable URB1-KD HeLa cell lines were seeded and induced with 1μg/mL doxycycline on 6 cm dishes for 6 days. After washed with DPBS, cells were incubated with 270 μL of cell culture medium and 30 μL of 10x SHAPE Chemical in DMSO with the final concentration of NAI (EMD Millipore) at 100 mM for 10 minutes at 37 °C. After removed reaction medium, RNAs were isolated by 1 mL Trizol reagent (Invitrogen) according to the manufacturer’s protocol. The same procedure was also performed in parallel for the untreated control samples, but with the addition of only DMSO. In the denaturing control (DC) reaction, RNAs were suspended in a denaturing buffer containing 50% formamide and were incubated at 95 °C before modification with SHAPE reagents. For DMS samples, after washed with DPBS, cells were treated with the addition of 15uL DMS and incubation at 37°C for 5min. Cell culture media with DMS was slowly decanted. Then cells were washed twice in 30% v/v BME (diluted in DPBS) and collected into a 15ml centrifuge tube using a scraper. Centrifuge cells at 1000 × g at 4°C for 3min and decant the BME solution. Wash the cells with 1ml DPBS twice and centrifuge the cells again. Isolated RNAs were treated with DNase I (Ambion, DNA-freeTM kit) to remove possible DNA contamination. About 50-100 ng of RNAs were obtained under each treatment and were then used for SHAPE-MaP reverse transcription by adding 1 mL (200 U/mL) of SuperScript II (Invitrogen), 6 mM Mn2+ and gene-specific primers for 3' ETS. Second-strand synthesis was performed with TAQ DNA polymerase. The resulting PCR products were further isolated. Primers for SHAPE-MaP reverse transcription and second-strand synthesis (1st round PCR and nested PCR reactions) were listed in Supplementary Table S1. SHAPE-MaP libraries were prepared from 1 ng of DNAs, and size-selected with AmpureXP beads (Agencourt) with a 1:1 (bead to sample) ratio to obtain library DNA products spanning 100-400 bp in length. Final libraries were quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Deep sequencing was performed by Illumina NextSeq 500 at Shanghai Institute Nutrition and Health, Big Data Center Omics Core, Shanghai, China. About 15-25 million mapped sequencing reads were obtained for each sample, with 88% of bases at or above Q30.
Isolated RNAs were treated with DNase I (Ambion, DNA-freeTM kit) to remove possible DNA contamination. About 50-100 ng of RNAs were obtained under each treatment and were then used for SHAPE-MaP reverse transcription by adding 1 mL (200 U/mL) of SuperScript II (Invitrogen), 6 mM Mn2+ and gene-specific primers for 3' ETS. Second-strand synthesis was performed with TAQ DNA polymerase. The resulting PCR products were further isolated. Primers for SHAPE-MaP reverse transcription and second-strand synthesis (1st round PCR and nested PCR reactions) were listed in Supplementary Table S1.
SHAPE-MaP libraries were prepared from 1 ng of DNAs, and size-selected with AmpureXP beads (Agencourt) with a 1:1 (bead to sample) ratio to obtain library DNA products spanning 100-400 bp in length. Final libraries were quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Deep sequencing was performed by Illumina NextSeq 500 at Shanghai Institute Nutrition and Health, Big Data Center Omics Core, Shanghai, China. About 15-25 million mapped sequencing reads were obtained for each sample, with 88% of bases at or above Q30.

treatment_protocol: Scramble and URB1-targetting shRNA expressing HeLa cells were were seeded and induced with 1 μg/ml doxycycline for 6 days.

value: HeLa

value: DMS sampels modified by DMS


title: DMS-KD4_1-F4R4


title: Batch 2 PBMC 10x Lane 12 (Batch2P12) CSP

value: PBMC


title: DMS-KD1_2-F4R4


title: ESC_Zfp462+/R1257*_Serum_LIF_2i_Rep2


title: WTJSHLPS_K27Ac_HiChIP_rep2


title: WT_K27Ac_HiChIP_rep3


title: ESC_Zfp462+/R1257*_Serum_LIF_2i_Rep1


title: DMS-KD1_1-F4R4


title: WTJSHLPS_K27Ac_HiChIP_rep1


title: Batch 2 PBMC 10x Lane 11 (Batch2P11) GEX


title: DMS-SCR_2-F4R4

value: shScr.


title: Batch 2 PBMC 10x Lane 9 (Batch2P09) GEX


title: WTJSH_K27Ac_HiChIP_rep2


title: ESC_Zfp462+/Y1195*_4dayRA_Rep1

value: 4day retinoic acid


title: ESC_Zfp462+/R1257*_Serum_LIF_Rep2


title: WTJSH_K27Ac_HiChIP_rep1


title: ESC_Zfp462+/Y1195*_4dayRA_Rep2


title: DMS-SCR_1-F4R4


title: NAI-KD4_2-F1R1_F3R3

value: NAI samples modified by NAI in DMSO


title: NAI-KD1_2-F1R1_F3R3


title: ESC_Zfp462+/Y1195*_2dayRA_Rep2

value: 2day retinoic acid


title: Batch 2 PBMC 10x Lane 9 (Batch2P09) CSP


title: ESC_Zfp462+/Y1195*_2dayRA_Rep1


title: WT-3

first: Zhenzhen

last: Zhan

address: Jimo Road 150

department: Research Center for Translational Medicine

institute: Shanghai East Hospital, Tongji University School of Medicine,

data_processing:
For each sample, RNA-seq clean reads were obtained that mapped to mm10  using HISAT2 (hierarchical indexing for spliced alignment of transcripts) v2.0.477.
Sequencing read counts were calculated using Stringtie78,79 (v.1.3.0).
Then expression levels from different samples were normalized by the Trimmed Mean of M values (TMM) method79.
The normalized expression levels of different samples were converted to FPKM (Fragments Per Kilobase of transcript per Million mapped fragments). The edgeR package of R was used to analyze the difference between intergroup gene expression, the P-values were calculated, and the multiple hypothesis test was performed.
Differentially expressed genes (DEGs) were defined as transcripts with a fold change in expression level (according to the FPKM value) greater than 2.0 and a q-value less than 0.05.
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: an excel file include RPKM values for total 6 Sample

source_name: heart

extract_protocol:
Cardiac fibroblasts isolated fromKDM5B KO mice and their corresponding WT mice following day 7 of myocardial infarction. Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina, USA) following the manufacturer’s instructions.
Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina, USA) following the manufacturer’s instructions.mRNA was enriched with oligo(dT) beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers.This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).

value: heart

value: 8-10 weeks old

value: cardiac fibroblast

value: wild type

value: myocardial infarction


title: WT-2


title: Batch 2 PBMC 10x Lane 8 (Batch2P08) GEX


title: NAI-SCR_2-F1R1_F3R3


title: WT-1


title: ESC_Zfp462+/Y1195*_4dayEB_Rep2

value: Cells were grown at 37º C, 5% CO2

value: after 4 days of LIF withdrawal


title: NAI-KD1_1-F1R1_F3R3


title: ESC_Zfp462+/Y1195*_4dayEB_Rep1


title: Batch 2 PBMC 10x Lane 8 (Batch2P08) CSP

value: UnSorted


title: Batch 2 PBMC 10x Lane 7 (Batch2P07) CSP

value: blood


title: KO-3

value: KDM5B knockout


title: Batch 2 PBMC 10x Lane 11 (Batch2P11) CSP


title: ESC_Zfp462+/Y1195*_Serum_LIF_Rep2

value: Serum/LIF


title: Batch 2 PBMC 10x Lane 7 (Batch2P07) GEX


title: KO-2


title: NAI-SCR_1-F1R1_F3R3

value: HeLa


title: ESC_Zfp462+/Y1195*_Serum_LIF_Rep1


title: Batch 2 PBMC 10x Lane 6 (Batch2P06) GEX

value: PBMC


title: KO-1


title: ESC_Zfp462+/Y1195*_Serum_LIF_2i_Rep2


title: Division 1, Clone13, Spleen

city: La Jolla

first: Gene

last: Yeo

address: 9500 Gilman Dr

department: Cellular and Molecular Medicine

institute: University of California, San Diego

description: 10x Genomics

data_processing:
Alignment, cell barcode processing, umis processing, abundance measurements: Cellranger ATAC  (version 1.2.0)
QC, cell filtering, dimension reduction: Signac (version 1.5.0)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol: 10X Chromium Single Cell ATAC v1.1 Chemistry

value: CD8 T cells

value: Spleen

value: 7-10 weeks old


title: Batch 2 PBMC 10x Lane 5 (Batch2P05) GEX


title: Batch 2 PBMC 10x Lane 6 (Batch2P06) CSP


title: DMSO-KD4-F1R1_F3R3

description:
NAI-KD4_1-F1R1_F3R3_F4R4_profile.txt
NAI-KD4_2-F1R1_F3R3_F4R4_profile.txt

value: shScr.

value: DMSO samples only treated with DMSO


title: DMSO-KD1-F1R1_F3R3

description:
NAI-KD1_1-F1R1_F3R3_F4R4_profile.txt
NAI-KD1_2-F1R1_F3R3_F4R4_profile.txt


title: ESC_Zfp462+/Y1195*_Serum_LIF_2i_Rep1


title: DMSO-SCR-F1R1_F3R3

description:
NAI-SCR_1-F1R1_F3R3_F4R4_profile.txt
NAI-SCR_2-F1R1_F3R3_F4R4_profile.txt


title: Division 1, Armstrong, Spleen

description: 10x Genomics


title: Batch 2 PBMC 10x Lane 5 (Batch2P05) CSP


title: IgG, Clone13

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.38, discarding reads left with < 25 bp
Reads were aligned to the mouse genome (mm10) using Bowtie version 1.1.2. Parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Reads were aligned to the yeast genome (sacCer3) using Bowtie version 1.1.2. Parameters: --local --very-sensitive-local --no-overlap --no-dovetail --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 70
Spike-in normalization. The genomic coverage were then normalized by applying the scaling factor that is calculated from the number of mapped reads to mouse genome and yeast genome
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01, using Callpeak, and compared the sample to corresponding IgG samples using bdgcmp in FE (fold-enrichment) mode.
bigWig files were generated using bdg2bw from the bedgraph output from last step. Score represents the FE values at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for IgG sample)

source_name: spleen

extract_protocol:
DNA extraction, digestion and purification was performed with the CUT&RUN Assay Kit by CST, #86652
ChIP-seq libraries were prepared using the SimpleChIp ChIp-Seq DNA Library Prep Kit (CST, #567945)  input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: spleen

value: CD8 T Cell

value: Rabbit IgG XP (CST, #66362)


title: ChIPseq for SOX2 in Zfp462KO_Rep2

data_processing:
ChIP-seq reads were trimmed using trim-galore v0.4.4 and thereafter aligned to the mm10 reference genome using bwa mem v0.7.17. A
A mapping quality filter with cutoff 1 was applied using samtools v1.10.
Duplicated reads were marked and excluded with picard MarkDuplicates v2.23.4 and the obtained bam files were used to generated bigwig files using deeptools bamCoverage v3.5.0 with the parameter -normalizeUsing RPKM.
Genome_build: mm10

growth_protocol: Cells were grown at 37º C, 5% CO2

value: Zfp462knock out

value: goat anti-SOX2/AF2018/R&D systems


title: DC-KD4-F1R1_F3R3

value: DC samples denatured by formamide at 95℃


title: Batch 2 PBMC 10x Lane 4 (Batch2P04) GEX

value: UnSorted


title: IgG, Armstrong


title: NAI-KD4_1-F1R1_F3R3

value: NAI samples modified by NAI in DMSO


title: ChIPseq for SOX2 in Zfp462KO_Rep1


title: ChIPseq for SOX2 in WT_Rep2

value: Wild type


title: Batch 2 PBMC 10x Lane 4 (Batch2P04) CSP

value: blood


title: DC-KD1-F1R1_F3R3

value: HeLa


title: H3K4me3, Clone13


title: DC-SCR-F1R1_F3R3


title: Batch 2 PBMC 10x Lane 3 (Batch2P03) GEX

value: PBMC


title: ChIPseq for SOX2 in WT_Rep1