title: Peripheral blood sample from patient 1 & 3 before treatment

description:
SampleTag03 = Patient1_pre-treatment
SampleTag02 = Patient3_pre-treatment
Using a mixed sample on the machine, the samples are differentiated according to the sampletag number provided.

value: 1 and 3

value: no treatment


title: Donor1_Treg_HDAC7_WT

status: Public on Oct 17 2022

type: SRA

city: Toulouse

first: Pierre-Paul

last: Axisa

address: 2 avenue Hubert Curien

department: CRCT

country: France

institute: INSERM

library_source: transcriptomic

data_processing:
Sequence reads were aligned to the human genome using STAR
Gene quantitation was performed with RSEM
Gene counts were then used as input for differential expression analysis with DESeq2, using a local fit and normal log fold change shrinkage. Batch and treatment were included as covariates in the model.
Genes with base mean < 10 were filtered out and genes with FDR < 0.1 were considered differentially expressed.
Assembly: GRCh38 release 88
Supplementary files format and content: rsem count matrix generatedby tximport

molecule: total RNA

organism: Homo sapiens

source_name: blood

growth_protocol: Sorted human Tregs (CD4+CD25hiCD127lo/neg) were stimulated with plate-bound anti-CD3 (UCHT1, 1 μg/ml) and soluble anti-CD28 (1 μg/ml).

extract_protocol:
cDNA libraries were generated with the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Takara/Clontech).
Barcoded libraries were generated by the Nextera XT DNA Library Preparation kit (Illumina)
Libraries were sequenced with a 2 × 100 bp paired-end protocol HiSeq 2000 Sequencing System (Illumina)

treatment_protocol: After for 24 h, they were transduced with lentiviral particles by spinfection in the presence of Polybrene (5 μg/ml) in plates coated with Retronectin (50 μg/ml) (Takara/Clontech) and anti-CD3 (1–2 μg/ml). Five days after transduction, cells were sorted on the basis of expression of GFP.

tag: tissue

value: blood

tag: cell type

value: human primary regulatory T cells

tag: genotype

tag: treatment

value: HDAC7 scrambled control shRNA


title: Donor2_Treg_HDAC7_KD

value: HDAC7 KD shRNA


title: Donor2_Treg_HDAC7_WT


title: Peripheral blood sample from patient 2 before treatment

city: Guangzhou

first: Feiye

last: Liu

address: No.13, Shiguagang Road, Haizhu District, Guangzhou

country: China

institute: Department of Oncology, Southern Medical University Hospital of Integrative Medicine

description: SampleTag02 = Patient2_pre-treatment

library_source: transcriptomic single cell

data_processing:
Raw files obtained by sequencing with Illumina high-throughput sequencers.
The original file is an image file, and after base calling and Bcl2Fastq transformation, the original sequenced sequence (sequenced reads) in FASTQ (fq for short) format can be obtained.
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: PBMC

extract_protocol:
Peripheral blood samples from patients before and after treatment were extracted and single cell whole transcriptome sequencing libraries were constructed using the BD platform Rhapsody reverse transcription kit and the BD Rhapsody whole transcriptome amplification kit.
RNA libraries were prepared for sequencing using standard BD RhapsodyTM Single cell 3’ whole transcriptome amplification (WTA) with sample multiplexing kit (SMK) protocol.

tag: diagnosis

value: Hepatocellular carcinoma

tag: patient number

value: PBMC


title: U87_V_H3K9_1

first: liu

last: xincheng

address: zhongshan Road 74 Street

institute: sysu

library_source: genomic

data_processing:
Raw reads were filtered first to remove low-quality or adaptor sequences by SOAPnuke with parameters: filter -l 5 -q 0.5 -n 0.1 -Q 2 -5 1 -c 50.
Cleaned reads were mapped to the reference genome of hg38 using SOAP2 (https://github.com/BGI-flexlab/SOAPnuke), whose parameters was -v 2 -s 3 .
We used MACS2 (https://github.com/macs3-project/MACS) to identify peaks (open chromatin regions), in which '--bw 200 -g XXX -s 50 -p 1e-5 -m 10 30 --broad -B --trackline' was used. The significant regions were picked up if |M| >= 1 and P-value <=10-5.
Also, the gene element annotation of peak or different enrichment peak from different samples was carried out by bedtools (https://bedtools.readthedocs.io/en/latest/) intersect mode with overlap 50%.
Assembly: hg38
Supplementary files format and content: wig

molecule: genomic DNA

growth_protocol: The cells were cultured according to the guideline of ATCC

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: U87 cells/GSC  were treated with bulk control/0.5mM 8-cpt-cAMP/1nM MS275 or a combination for 48 hours. Total RNA was extracted from 1×10^6 cells with TRIzol Reagent (Thermo Fisher Scientific) and was sent for RNA sequencing

tag: cell line

tag: group

value: V

tag: chip antibody


title: U87_CM_H3K14_1

value: CM


title: U87_V_H3K14_1


title: Donor1_Treg_HDAC7_KD


title: U87_CM_H3K9_1


title: GSC_V_1

data_processing:
We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC:RNA concentration, RIN value,28S/18S and the fragment length distribution.
We use internal software SOAPnuke to filter reads
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.
We mapped clean reads to reference using Bowtie2 and then calculate gene expression  level with RSEM
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: GSC

extract_protocol:
Total RNA was isolated from cultured cell lines. Beads containing oligo (dT) were used to isolate poly(A) mRNA from total RNA. Purified mRNA was then fragmented in fragmentation buffer. Using these short fragments as templates, random hexamer-primers ere used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I. Short double-stranded cDNA fragments were purified with a QIAquick PCR extraction kit (vendor) and eluted with EB buffer for end repair and the addition of an ‘A’ base. Next, the short fragments were ligated to Illumina sequencing adaptors. DNA fragments of a selected size were gel-purified and amplified by PCR. The amplified library was sequenced using Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: GSC


title: GSC_CM_3


title: GSC_CM_2


title: GSC_V_3


title: H1975/tet-MUC1shRNA 3

city: Boston

first: Yoshihiro

last: Morimoto

address: 450 Brookline Avenue

department: Medical Oncology

country: USA

institute: Dana Farber Cancer Institute

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Assembly: GRCh38.74
Supplementary files format and content: Gene_TPM

growth_protocol: RKO cells (American Type Culture Collection (ATCC), Manassas, VA, USA) were cultured in EMEM medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS; GEMINI Bio-Products, West Sacramento, CA, USA). COLO 201 and H1975 cells (ATCC) were cultured in RPMI1640 medium supplemented with 10% FBS.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNeasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

treatment_protocol: Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline for inducible model.

tag: disease

value: Lung Cancer

value: puromycin resistance

tag: shRNA

tag: agent

value: treatment (DOX)


title: H1975/tet-MUC1shRNA 5


title: H1975/tet-MUC1shRNA 4


title: H1975/tet-MUC1shRNA 6


title: COLO 201/tet-MUC1shRNA 6

source_name: COLO 201

value: Colon Cancer

value: COLO 201


title: H1975/tet-MUC1shRNA 2


title: Core needle biopsy [M140B]

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

data_processing:
The sequences were aligned to the Homo sapiens hg38 reference genome assembly using STAR. Downstream analysis was performed in R/Rstudio using Bioconductor packages.
The aligned data were counted using feature counts. Next, differentially expressed genes (DEG) were identified for pairwise comparison of CNB vs. surgery (pre- vs. post-treatment) using DESeq2.
Assembly: hg38 reference genome
Supplementary files format and content: tab-delimited text files include the normalized counts for each sample

source_name: breast cancer

extract_protocol:
Frozen samples were pulverized and total RNAs were purified using TRIzol reagent (Life Technologies). RNAs were submitted to Macrogen, Inc (South Korea) for RNA sequencing.
SMART-SeqTM v4 UltraTM Low Input RNA Kit, TruSeq RNA Sample Prep Kit v2

treatment_protocol: Mifepristone tablets (200 mg) were purchased from Pharmaweb Canada (Montreal). Each patient received 1 pill of 200mg/day for 14 days by trained volunteers from La Liga Argentina de Lucha contra el Cáncer (Tigre) at the patient’s home signing forms to corroborate compliance. Surgery was performed on day 15.

value: breast cancer

value: Control

tag: treatment response

value: Response


title: H1975/tet-MUC1shRNA 1


title: Surgical sample [M105S]

value: Mifepristone neoadjuvant treatment

value: Non-response


title: GSC_CM_1


title: COLO 201/tet-MUC1shRNA 5


title: Surgical sample [M140S]


title: U87_CM_3


title: U87_CM_2


title: U87_CM_1


title: COLO 201/tet-MUC1shRNA 4


title: COLO 201/tet-MUC1shRNA 2


title: Core needle biopsy [M094B]


title: GSC_V_2


title: COLO 201/tet-MUC1shRNA 3


title: U87_M_3

value: M


title: COLO 201/tet-MUC1shRNA 1


title: RKO/tet-MUC1shRNA 5

source_name: RKO

value: RKO


title: Surgical sample [M090S]


title: U87_M_1


title: U87_M_2


title: RKO/tet-MUC1shRNA 4


title: Core needle biopsy [M077B]


title: Surgical sample [M077S]


title: RKO/tet-MUC1shRNA 6


title: Core needle biopsy [M090B]


title: U87_C_3

value: C


title: Surgical sample [M073S]


title: U87_C_2


title: Surgical sample [M094S]


title: RKO/tet-MUC1shRNA 3


title: Core needle biopsy [M105B]


title: Core needle biopsy [M073B]


title: RKO/tet-MUC1shRNA 2


title: U87_C_1


title: U87_V_3


title: Surgical sample [M070S]


title: U87_V_2


title: Core needle biopsy [M070B]


title: U87_V_1


title: sgC2rRNA

city: Birmingham

first: Yanfeng

last: Zhang

state: AL

address: Kaul Human Genetics Building 720 20th St S

department: Department of Genetics

institute: University of Alabama at Birmingham

description:
DLD1 colorectal human cells wt (sgC for guide control) or crispr knockout for ZNF692 (sgZ1 for guide 1, and sgZ3 for guide 3). We have each condition in triplicates.
geneMatrixCounts_rRNA.txt.gz

data_processing:
Illumina Casava1.7 software used for basecalling.
The qualities of sequencing reads were evaluated using NGS QC Toolkit (v2.3.3) (Patel and Jain, 2012) and aligned to human reference genome (hg38) using STAR (v2.5.2b) (Dobin et al., 2013). SAMtools (v1.9) was used to sort the alignments, and HTSeq Python package was used to count reads per gene.
DESeq2 R Bioconductor package was used to normalize read counts and identify differentially expressed (DE) genes. The enrichment of DE genes to KEGG pathways and GOs were calculated by Fisher's exact test in R statistical package.
Assembly: grch38
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

growth_protocol: DLD1 cells were cultured in DMEM with 5% Fetal Bovine Serum (FBS) and 100 U/mL Penicillin-Streptomycin.

extract_protocol:
RNA was harvested using Tri-Reagent (sigma). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To generate stable cell lines, 48 h after lentiviral particles addition, media was replaced and puromycin added for selection. 10 µg/ml puromycin was used for DLD1

value: colorectal human cells

value: WT


title: sgC3rRNA


title: RKO/tet-MUC1shRNA 1


title: sgC1rRNA


title: Core needle biopsy [M062B]


title: 3sgZ1rRNA

value: ZNF692 KO


title: 2sgZ3rRNA


title: 1sgZ3rRNA


title: Surgical sample [M062S]


title: 2sgZ1rRNA


title: sgC3

molecule: polyA RNA


title: HT124 cells, Human norovirus-infected, experiment 3

city: Ann Arbor

first: Christiane

last: Wobus

state: MI

address: 1150 West Medical Center Dr

department: Microbiology and Immunology

institute: University of Michigan

data_processing:
Data quality were checked via fastQC
Raw reads were aligned using STAR v2.5.2a
Reads were mapped to the reference genome GRCh38 (ENSEMBL)
Alignment options followed ENCODE standards for RNA-seq
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files of count data for each sample

source_name: intestine, ileum

growth_protocol: Cells were maintained in differentiation media (Advanced DMEM-F12, Noggin, B27, N2, mrEGF, N-acetyl cysteine, Leu15-Gastrin and A-83-01) for 6 days

extract_protocol:
RNA extraction after TRI Reagent lysis with the Zymo Research Direct-Zol RNA miniprep kit (cat nr. R2051)
This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

treatment_protocol: Cells were kept uninfected or were infected with human norovirus-positive stool sample for 2 days in the presence of the bile acid GCDCA (500µM) and Ruxolitinib (2µM)

value: intestine, ileum

value: Intestinal enteroids

value: Ruxolitinib, Human norovirus

tag: time

value: 2 days


title: HT124 cells, Human norovirus-infected, experiment 2


title: 3sgZ3rRNA


title: HT124 cells, Human norovirus-infected, experiment 1


title: HT124 cells, Non-infected, experiment 3

value: Ruxolitinib


title: H3K9me3 ChIPseq, clr4wt, Meiosis 3h, rep1

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
smallRNA-seq:Raw data were demultiplexed and converted to fastq format using bcl2fastq2 (v1.17) Illumina. Qiagen 3' adaptors were trimmed using cutadapt (v1.18) with the parameters --discard-untrimmed -m 18. Fastq files were aligned using Bowtie (v1.2.2) with parameters -f -M 10000 -v 0 -S --best --strata. Bowtie sam output was converted to bam using samtools (v1.9). Bam files were converted to bed using bedtools bamtobed (v2.27.1), bed files were used to calculate strand-specific coverage using bedtools genomeCoverageBed (v2.27.1), resulting bedgraph files were normalized to 1 million genome mapping reads (RPM), and converted to bigWig format using bedGraphToBigWig (v4).
RNA-seq: Raw data were demultiplexed and converted to fastq format using bcl2fastq2 (v1.17) Illumina. Fastq files were aligned using STAR (v2.7.3a) with the parameters --runMode alignReads --outFilterType BySJout --outFilterMultimapNmax 100 --outFilterMismatchNoverLmax 0.05 --outSAMmultNmax 1 --outMultimapperOrder Random --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI NM MD AS nM --outSAMunmapped Within. STAR sam output was converted to bam using samtools (v1.9). Bam files were used to calculate strand-specific coverage using bedtools genomeCoverageBed (v2.27.1), resulting bedgraph files were normalized to 1 million genome mapping reads (RPM), and converted to bigWig format using bedGraphToBigWig (v4).
ChIP-seq: Raw data were demultiplexed and converted to fastq format using bcl2fastq2 (v1.17) and mapped using STAR with the following parameters: –alignIntronMax 1–alignEndsType EndToEnd–outFilterType Normal–seedSearchStartLmax 30–outFilterMultimapNmax 10000–outSAMattributes NH HI NM MD AS nM–outMultimapperOrder Random–outSAMmultNmax 1–outSAMunmapped Within. For bigwig track generation bedtools (version 2.26.0) and bedGraphToBigWig (from UCSC binary utilities) were used and read coverage was normalized to 1 million genome mapping reads (RPM).
Assembly: mm10; Spombe.ASM294v2.24
Supplementary files format and content: bigWig files containing normalized (to 1 mio genome mapping reads per library) genome mapping read counts for visualization in UCSC or IGV. Counts per million (CPM) table for the RNAseq samples as a text file.

organism: Schizosaccharomyces pombe

source_name: S. pombe cell culture

growth_protocol: S. pombe cell cultures were grown exponentially in YES media at 25°C or 30°C, depending on the strain. For more details see Methods section in Kuzdere et al. (2021)

extract_protocol:
ChIP was performed as described in Kuzdere et al. (2021). In brief, exponentially growing or synchronized fission yeast cells were fixed with formaldehyde and lysed by beat-beating. Chromatin was sheared by sonication and the IP was performed for 2h at 4°C. ChIPs were decrosslinked overnight at 65°C and cleaned up using AMPure XP beads.
ChIP-seq libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L) according to the manufacturer's instructions.

tag: strain

value: h-/h- ade6-M210/ade6-M216 pat1::NatR/pat1::NatR pat1-as(L95A)::HygR/pat1-as(L95A)::HygR lys1::MatPc-Bleo


title: HT124 cells, Non-infected, experiment 1


title: C957501-

type: RNA

city: Shanghai

first: WEI

last: Cao

address: Zhizaoju Road 639

institute: Shanghai Ninth People’s Hospital, Shanghai Jiao  Tong University School of Medicine

description: LncRNA expression data from LncRNA expression data from normal tissue

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned by the Affymetrix Scanner 3000(Affymetrix).

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis. Then the gene expression analysis and alternative splice analysis proceeded separately.

label: biotin

source_name: normal tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: tongue


title: 1sgZ1rRNA


title: C958774+

description: LncRNA expression data from OSCC

source_name: OSCC


title: C958630+

description: LncRNA expression data from OSCC


title: C958630-


title: C957501+

description: LncRNA expression data from OSCC


title: sgC2

description:
DLD1 colorectal human cells wt (sgC for guide control) or crispr knockout for ZNF692 (sgZ1 for guide 1, and sgZ3 for guide 3). We have each condition in triplicates.
geneMatrixCounts_mRNAseq.txt.gz


title: C957103-


title: HT124 cells, Non-infected, experiment 2


title: SCCs

city: Kobe

first: Shunsuke

last: Yahiro

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Orthopaedic Surgery

country: Japan

institute: Kobe University Graduate School of Medicine

data_processing:
Raw sequence files (fastq) were aligned to the human genome build 38 (hg38) and mapped to Refseq transcripts by Strand NGS software using default parameters.
All aligned reads were normalized using Transcripts per million (TPM).
TPM values were log2-transformed with an offset value of 1.0. Baseline transformation was not performed.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include gene symbol, gene ID and TPM values (log2-transformed with an offset value of 1.0) for each Sample.

source_name: Bone

extract_protocol:
Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacture's instruction.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

value: Bone

value: Ewing sarcoma


title: 3sgZ3


title: C957079+

description: LncRNA expression data from OSCC


title: sgC1


title: C957103+

description: LncRNA expression data from OSCC


title: 2sgZ1


title: non-SCCs


title: SH-SY5Y cells, MPP, 3D, 3

city: Medford

first: Nicholas

middle: James

last: Fiore

state: MA

address: 200 College Ave

department: Biomedical Engineering

institute: Tufts University

data_processing:
Illumina pipeline CASAVA v1.8.2 was used for base calling.
Raw sequencing reads were uploaded to the Tufts University Galaxy Server to generate quality reports with FastQC (https://www.bioinformatics.babraham.ac.uk/), read alignment with RNA STAR using Genome Reference Consortium Human Build 38 patch release 13 (GRCh38.p13, downloaded from https://www.ncbi.nlm.nih.gov/), and read quantification with featureCounts with default settings.
Data was first transformed using variance stabilization before differential expression analysis using the DESeq2 R package. The normalized read count table was extracted using the DESeq2 R package.
Assembly: Genome Reference Consortium Human Build 38 patch release 13 (GRCh38.p13, downloaded from https://www.ncbi.nlm.nih.gov/)
Supplementary files format and content: .csv file. Normalized read count table with ENTREZID and HGNC official gene symbols. Low expressed genes across all samples were filtered out (<10 counts on average across all samples).

extract_protocol:
Cell pellets were collected from 2D systems using Accutase detachment solution and centrifugation at 300g, while 3D cultures were carefully placed into individual tubes. All samples were immediately stored at -80°C. Frozen 2D cell pellets and 3D scaffolds were thawed on ice and lysed with 350μL RLT lysis buffer from the RNeasy kit (Qiagen, 74106, Hilden, Germany) supplemented with 1% β-mercaptoethanol (v/v). The extraction of RNA from this lysate was performed with the RNeasy kit with the on-column genomic DNA degradation step added, according to the manufacturer’s protocol. RNA concentrations and 260/280 values were measured with a NanoDrop 2000 Spectrophotometer (ThermoFisher, ND-2000). Isolated RNA samples (1μg/sample) were sent to Novogene for RNA quality control tests, library preparation, and sequencing.
Library preparation was achieved using the NEBNext Ultra RNA library prep kit for Illumina systems following manufacturer’s recommendations (New England Biolabs, Ipswich, MA, USA) and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand complementary DNA (cDNA) was synthesized using random hexamer primer and M-MuLV reverse transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptors with a hairpin loop structure were ligated to prepare for hybridization. To select cDNA fragments of 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Brea, CA, USA). Then 3 μL USER Enzyme (New England Biolabs) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 minutes followed by 5 minutes at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system, Beckman Coulter) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on an Illumina Novaseq sequencer according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on the same machine and paired-end reads were generated at a read depth of 20 million reads.

treatment_protocol: Either untreated (CTRL) or treated (MPP) with 1mM 1-methyl-4-phenylpyridinium for 48 hours

value: dopamine-like neurons

value: differentiated for 15 Days

tag: condition

value: 3D culture

value: 1mM 1-methyl-4-phenylpyridinium (MPP) for 48 hours


title: C957202+

description: LncRNA expression data from OSCC


title: 3sgZ1


title: 2sgZ3


title: SH-SY5Y cells, MPP, 3D, 4


title: 1sgZ1


title: 1sgZ3


title: SH-SY5Y cells, MPP, 3D, 2


title: SH-SY5Y cells, MPP, 3D, 1


title: human2, cd45-, scRNAseq

city: New York

first: Haocheng

last: Yu

state: New York

address: 1 Gustave L. Levy Place

department: Precision Immunology Institute

institute: Icahn School of Medicine at Mount Sinai

description:
humanN_2a
10x Genomics

data_processing:
R package Seurat was used to process scRNA-seq data.
Single-cell data were filtered to exclude putative doublet populations, dead or mitochondrial high cells. Numbers of total cells sequenced ranged from 807-1,927 for 10 human samples.
Cells with more than 2500 genes detected were removed from human scRNA-seq samples for concerns of doublet contamination. In addition, cells with percentage of mitochondrial genes higher than 5% were removed.
Assembly: GRCh38
Supplementary files format and content: count_matrix.txt: Read count for each gene in each cell.
Supplementary files format and content: gene_info.txt: Gene symbols.
Supplementary files format and content: cell_info.txt: Cell cluster annotation.

source_name: bladder tumor

extract_protocol:
Resected tumor sample were examined by a genitourinary pathologist who confirmed the pathological staging and tumor content. Human tumors were then resected and dissociated to the single cell level in a solution of RPMI-10% FBS (Gibco) + 1% type 1 collagenase (Gibco). The dissociate is subject to mechanical dissociation through a 16G needle and syringe (5-10 passes) and then a 21.5G needle (5-10 passes). Single cell dissociates were then sorted for live CD45 positive cells and sorted using a BD Aria after cell staining using a BV510-CD45 antibody (Biolegend) and DAPI stain. Single cell suspensions of all sorted samples were then resuspended in BSA (0.2 % in PBS) at a concentration of 2x10^6 cells/ml followed by barcoding with a 10x Chromium Controller (10x Genomics).
To prepare tissues for scRNA-seq, human tissues were enzymatically and mechanically digested to the single-cell level, flow cytometry sorted for CD45-positive and CD45-negative cells followed by processing using the 10x Chromium platform. Sequencing was done on a Nextseq 500 platform and analyzed using Cell Ranger V2.

value: bladder tumor

tag: specimen

value: TURBT

tag: gender

value: Male

tag: smoking history

value: Yes (80 pack per year, quit 2016)

tag: brp

tag: experiment

tag: patient id


title: human2, cd45+, scRNAseq

description:
humanP_2b
10x Genomics

tag: tissue

tag: cell type


title: human1, cd45+, scRNAseq

description:
humanP_1b
10x Genomics

value: Female

value: Yes (unknown packs, quit 1982)


title: SH-SY5Y cells, MPP, 2D, 3

tag: cell line

value: 2D culture

tag: treatment


title: SH-SY5Y cells, MPP, 2D, 4


title: GSC_V_H3K14

value: GSC

tag: group

value: V

tag: chip antibody


title: SH-SY5Y cells, MPP, 2D, 1


title: SH-SY5Y cells, MPP, 2D, 2


title: human171, cd45-, scRNAseq

description:
humanN_171
10x Genomics

value: Cystectomy

value: No (never smoker)


title: SH-SY5Y cells, CTRL, 3D, 4

value: Negative Control


title: imb_roignant_2019_12_Mkrn1_2

city: Mainz

first: Annabelle

last: Dold

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology, IMB

data_processing:
Sequencing qualities were checked for all reads using FastQC (version 0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Afterwards, reads were filtered based on sequencing qualities (Phred score) of the barcode region. Reads with more than one position with a Phred score < 20 in the experimental barcode (positions 6 to 11 of the reads) or any position with a Phred score < 10 in the random barcode (positions 1 to 5 and 12 to 15 ) were excluded from subsequent analysis. Remaining reads were de-multiplexed based on the experimental barcode (positions 6 to 11) using Flexbar (version 3.0.0, Dodt et al., 2012) without allowing any mismatch.
All following steps of the analysis were performed on the individual samples after de-multiplexing. Remaining adapter sequences were removed from the read ends using Flexbar (version 3.0.0) with a maximal error rate of 0.1 and a minimal overlap of 1 nt between the beginning of the adapter and the end of the read. Following adapter trimming, the first 15 nt of each read containing the experimental and random barodes were trimmed off and added to the read name in the fastq files in order to keep this information for downstream analysis. Reads shorter than 15 nt were removed from further analysis.
Trimmed and filtered reads were mapped to the Drosophila melanogaster genome (Ensembl genome assembly version BDGP6) and its annotation (Ensembl release 90, Bronwen et al., 2017) using STAR (version 2.5.2b, Dobin et al., 2013). When running STAR, up to two mismatches were allowed, soft-clipping was prohibited at the 5' end of reads and only uniquely mapping reads were kept for further analysis. For further analysis, only unspliced reads were kept and analyzed.
Following mapping, duplicate reads were marked using the dedup function of bamUtil (version 1.0.13), which defines duplicates as reads whose 5' ends map to the same position in the genome (https://github.com/statgen/bamUtil). Subsequently, marked duplicates with identical random barcodes were removed since they are considered technical duplicates, while biological duplicates showing unequal random barcodes were kept.
Genome_build: Ensembl BDGP6
Supplementary_files_format_and_content: Resulting bam files were sorted and indexed using SAMtools (version 1.3.1, Li et al., 2009). Afterwards, bedgraph files were created based on bam files, using bamToBed of the BEDTools suite (version 2.25.0, Quinlan and Hall, 2010), considering only the position upstream of the 5' mapping position of the read, since this nucleotide is considered as the crosslinked nucleotide. Using bedGraphToBigWig of the UCSC tool suite (Kent et al., 2010), all bedgraph files were converted into bigWig files.

organism: Drosophila melanogaster

source_name: ovaries

extract_protocol:
The iCLIP protocol was from (Sutandy et al., 2016) with the following adaptations. FLAG-Mkrn1 was overexpressed in Mkrn1N ovaries using a nos>Gal4 driver. To crosslink the RNA-protein complexes, ovaries were hand-dissected and crosslinked using 2x 100 mJ/cm2 of UV light. Cells were lysed in urea cracking buffer (50 mM Tris pH 7.5, 6 M urea, 1% SDS, 25% PBS) and sonicated using 2 cycles with 30 sec “ON”/“OFF” at low setting. Remaining cell debris was removed by centrifugation at 21,000 x g for 10 min at 4°C. Lysate was diluted 1:5 in IP buffer (150 mM NaCl, 50 mM Tris pH 7.5, 0.5% Tween-20, 0.1 mM EDTA) and incubated with 4 µg of anti-FLAG M2® antibody (Sigma-Aldrich) pre-coupled to 100 µl of protein G Dynabeads® (ThermoFisher Scientific) for 2 h at 4°C. After IP, the pulled-down RNA-protein complexes were washed 3x with high salt buffer (1 M NaCl, 50 mM Tris pH 7.4, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.5% Na-DOC) and 3x with PNK buffer (10 mM MgCl2, 20 mM Tris pH 7.6, 0.2% Tween-20). To trim the length of the crosslinked RNA, on-bead digestion using Turbo DNase (Ambion) and RNase I (Ambion) was performed. Subsequently, the beads were washed again 3x with high salt buffer and 3x with PNK buffer.
For high-throughput sequencing, libraries of 4 technical replicates for FLAG-Mkrn1 and 1 replicate for nos>Gal4 (Neg) were prepared with an optimized protocol (iCLIP2) to increase protocol efficiency as well as library complexity (Buchbender et al., 2019). Compared to the iCLIP protocol used for S2R+ cells, the library preparation includes separate ligation of used adapters, two rounds of cDNA amplification and size selection via beads [68]. For the iCLIP2 library preparation, 4 technical replicates and one negative control (Neg_1) were used. Barcodes contain the following sequences: Mkrn1_1 (NNNNNATTGGCNNNN), Mkrn1_2 (NNNNNAAGCTANNNN), Mkrn1_3 (NNNNNGCTCATNNNN), Mkrn1_4 (NNNNNTACAAGNNNN), Neg_1 (NNNNNCGTGATNNNN)

value: ovaries

value: female

tag: technique

value: iCLIP


title: imb_roignant_2019_12_Mkrn1_3


title: imb_roignant_2019_12_Mkrn1_1


title: SH-SY5Y cells, CTRL, 3D, 3

value: dopamine-like neurons

value: differentiated for 15 Days

value: 3D culture


title: human171, cd45+, scRNAseq

description:
humanP_171
10x Genomics

value: bladder tumor


title: imb_roignant_2019_12_Neg_1


title: C956566+

description: LncRNA expression data from OSCC

value: tongue


title: C952494+

description: LncRNA expression data from OSCC


title: SH-SY5Y cells, CTRL, 3D, 2


title: human1, cd45-, scRNAseq

description:
humanN_1a
10x Genomics

value: TURBT


title: C956244+

description: LncRNA expression data from OSCC


title: C956566-


title: C951554+

description: LncRNA expression data from OSCC


title: human170, cd45+, scRNAseq

description:
humanP_170
10x Genomics

value: Male

value: Yes (20 pack per year, quit 1970)


title: KI_CNS_infiltrating_Tcells_mouse4

data_processing:
Alignement and quantitation were performed with the “cellranger count” command for each emulsion, to generate unique molecular identifier (UMI) count matrices.
filtered count matrices were merged
Assembly: 2020-A 10x genomics mouse reference
Supplementary files format and content: cellranger count output matrix of filtered droplets

organism: Mus musculus

source_name: Central Nervous System

growth_protocol: At day 14 post-immunization, mice were injected with 2ug of CD45 flow antibody (Biolegend) via intravenous injection (CD45iv) at least 5 minutes prior to sacrifice and perfusion. Following anesthesia induction with isoflurane, mice were transcardially perfused with 15-20 ml of PBS supplemented with 2 mM EDTA before sacrifice.

extract_protocol:
Live CD45iv—CD11b—CD45+CD3+ cells were sorted on a FACSAria (BD Biosciences). Cells were resuspended in PBS 2% FBS and counted on a hemocytometer, before being loaded on the 10x genomics instrument using the Chromium Single Cell 5’ kit v2 (10x genomics).
Single-cell libraries were generated according to the manufacturer’s protocol (10× Genomics).  Single-cell library size and quality were confirmed on the Fragment Analyzer (Agilent). KAPA Quantification Kit for Illumina platforms (KAPA Biosystems, Roche) was used to quantify libraries.
The libraries were sequenced on a NovaSeq (Illumina) in pair-end sequencing 150bp

treatment_protocol: Resected brains were homogenized and digested by a 30 minute incubation at 37 °C with 1mg/mL of collagenase IV (Worthington) and 100ug/mL DNase (Roche). Mononuclear cells were isolated with a triple Percoll gradient (90, 60, 40%) after centrifugation at 1700 RPM for 20 minutes at 4°C, and stained with flow cytometry antibodies for 30 minutes at 4°C, followed by DAPI staining (Thermofisher) to exclude dead cells.

value: Central Nervous System

value: T cell

tag: genotype

value: HDAC7 R150H


title: C956244-


title: SH-SY5Y cells, CTRL, 3D, 1

tag: time


title: C952359+

description: LncRNA expression data from OSCC


title: imb_roignant_2019_12_Mkrn1_4


title: C952494-

description: LncRNA expression data from normal tissue


title: human168, cd45+, scRNAseq

description:
humanP_168
10x Genomics

value: Cystectomy

value: Yes (60 pack per year, quit unknown)


title: SH-SY5Y cells, CTRL, 2D, 4

value: 2D culture

value: Negative Control


title: C944512+

description: LncRNA expression data from OSCC


title: KI_CNS_infiltrating_Tcells_mouse2


title: WT_CNS_infiltrating_Tcells_mouse4

value: HDAC7 WT


title: KI_CNS_infiltrating_Tcells_mouse1

description: KI


title: WT_CNS_infiltrating_Tcells_mouse3


title: SH-SY5Y cells, CTRL, 2D, 3


title: KI_CNS_infiltrating_Tcells_mouse3


title: human166, cd45+, scRNAseq

description:
humanP_166
10x Genomics

value: Female

value: Yes (30 pack per year, quit 1993)


title: human158, cd45+, scRNAseq

description:
humanP_158
10x Genomics

value: Yes (20 pack per year, quit 2017)


title: SH-SY5Y cells, CTRL, 2D, 1

value: dopamine-like neurons

value: differentiated for 15 Days


title: SH-SY5Y cells, CTRL, 2D, 2


title: human170, cd45-, scRNAseq

description:
humanN_170
10x Genomics

value: bladder tumor


title: human157, cd45+, scRNAseq

description:
humanP_157
10x Genomics

value: TURBT

value: Yes (28 pack per year, quit 1994)


title: WT_CNS_infiltrating_Tcells_mouse1

description: WT


title: SLEbiao1117

city: changsha

first: zheng

last: meiling

state: Hunan

address: jiefang middle street

institute: central south university

data_processing:
The Cell Ranger software pipeline(V3.0.0) provided by 10x Genomics was used to demultiplex cellular barcodes, map reads to the human genomics
The Seurat packages(v3) was used as the mainly tools for downstream bioinformatics analysis.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: skin

extract_protocol:
The skin biopsies were firstly incubated in diapase enzyme for 8-10h. Then we used enzyme isolation method to make single cell suspension according to the operation manual of miltenyi biotechology.
RNA library were prepared according to the manufacturer's protocol of chromium single cell 3' reagent V3 Kits.

tag: subject status

value: SLE

value: skin


title: human167, cd45+, scRNAseq

description:
humanP_167
10x Genomics

value: Male

value: Yes (1 pack per year, quit 1994)


title: SLE1218E


title: human155, cd45+, scRNAseq

description:
humanP_155
10x Genomics

value: Yes (30 pack per year)


title: Input DNA SY5YtetCASZ1b_Input_Ctrl

city: Bethesda

first: Zhihui

state: Maryland

address: 9000 rockville pike

institute: National Cancer Institute

description: Input DNA

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome using bwa and then use the MACS2 for peak calling
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using deeptools. The coverage is calculated as the number of reads per bin.

source_name: SY5Y cells

growth_protocol: SY5Y cells are cultured in RPMI 1640 containing 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody following the Active Motif's instructions of the ChIP-IT High Sensitivity Kit.
Libraries were prepared according to Illumina's TruSeq ChIP Sample Preparation Guide.

treatment_protocol: ChIP experiment was performed using SY5YtetCASZ1b cells being cultured with or without Tet for 48 hr.

value: Neuroblastoma


title: HC1119E

value: HC


title: HC11118D


title: River, L, PR8

city: Chapel Hill

first: Alex

last: McCumber

state: NC

address: 426 Hickory Drive

institute: Duke University

data_processing:
The RNA-Seq fastq files were quality filtered with fastq-mcf, then mapped to the Genome Reference Consortium Mouse Build 38 using STAR. DESeq2 was then used to identify differentially expressed genes.
Supplementary files format and content: Genome Reference Consortium Mouse Build 38
Supplementary files format and content: GeneCountMatrix.csv

source_name: lung

extract_protocol:
Qiagen Rneasy
cDNA

value: lung

tag: cage

tag: ear

value: L

tag: cohort

value: B

tag: virus

value: River

tag: strain

value: BALB/c

tag: Sex

value: male

tag: age


title: HC1120E

tag: tissue


title: RNAPolII_ChIPSeq SY5YtetCASZ1b_RNAPolII_Tet

tag: cell type

value: RNA Pol II (Active Motif, 39097)


title: River, R, PR8

value: R


title: River, O, PR8

value: O


title: H3K27ac_ChIPSeq SY5YtetCASZ1b_H3K27Ac_Tet

value: H3K27ac (Abcam, ab4729)


title: H3K27ac_ChIPSeq SY5YtetCASZ1b_H3K27Ac_Ctrl


title: Input DNA SY5YtetCASZ1b_Input_Tet

description: Input DNA


title: River, L, HI

value: HI


title: SLE1116E

value: SLE

value: skin


title: HC1119D


title: WT_CNS_infiltrating_Tcells_mouse2

value: Central Nervous System

value: T cell

value: HDAC7 WT


title: HC1zhenpi

value: HC


title: HC2zhenpi1117


title: River, R, HI

value: lung


title: Road, L, PR8

value: L

value: Road


title: River, O, HI

value: B

value: River


title: Road, R, PR8

value: BALB/c

value: male


title: CASZ1_ChIPSeq SY5YtetCASZ1b_CASZ1_Tet

value: Neuroblastoma

value: Home-made Cas-ab8540 in collaboration with  Rockland


title: CASZ1_ChIPSeq SY5YtetCASZ1b_CASZ1_Ctrl


title: HCBIAO1117


title: RNAPolII_ChIPSeq SY5YtetCASZ1b_RNAPolII_Ctrl

value: RNA Pol II (Active Motif, 39097)


title: Road, O, PR8

value: O


title: DLE1204E

value: DLE


title: Road, L, HI

value: HI


title: Road, R, HI

value: R


title: HC1118E

value: skin


title: DLE1203


title: Road, O, HI


title: Pine, L, PR8

value: Pine


title: DLE1113E


title: PT_Myc_PTEN_MGT_b9

city: Portland

first: Zinab

last: Doha

state: OR

address: 2730 S MOODY AVE

institute: Oregon Health & Science University

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

source_name: mammary 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.

value: mammary tissue

value: no


title: PT_Myc_PTEN_MGT_b11


title: PT_Myc_PTEN_MGT_b8


title: PT_Myc_PTEN_MGT_b13


title: PT_Myc_PTEN_MGT_b12


title: PT_Myc_PTEN_MGT_b10


title: RING1A_ChIP_in_MESP1-KO_CPC (re-sequenced)

city: Philadelphia

first: Siqing

last: Wang

state: PENNSYLVANIA

address: 3401 Civic Center Blvd

department: Department of Pediatrics, Division of Hematology

institute: Children’s Hospital of Philadelphia

description:
Sample 37
78-RING1_D4_MESP1-KO_20.09.08+21.11.16-black.narrowPeak

data_processing:
The FASTQ data were trimmed adaptor by trim_galore (bioinformatics.babraham.ac.uk)
ChIP-seq data mapped to human genome hg19 with Bowtie2  in pair-end mode.
bam files were merged with previously mapped bam files by 'samtools merge', filtered out low quality reads by 'samtools view -q 30',  de-duplicated by 'samtools rmdup', and sorted by 'samtools sort'.
ChIP-seq peaks were called by MACS2 .
Genome_build: hg19
Supplementary_files_format_and_content: ".narrowPeak" files are tab-delimited text files for ChIP-seq peaks in Sample 36-37, which were called by MACS2 using corresponding ChIP-seq data and input data. In these narrowPeaks files, "merge1kb"  implies merging the peaks within the distance of 1 kb, since MACS2 sometimes splits long peaks, which is verified in UCSC tracks.

source_name: MESP1 knockout human cardiac progenitor cells (day 4 post differentiation from ESCs)

growth_protocol: Human ESC lines H7 were maintained on Matrigel-coated plates (Growth Factor Reduced, BD Biosciences) in mTeSR Medium (STEMCELL Technologies). The medium was changed every day.

extract_protocol:
Chromatin immunoprecipitation (ChIP) and ChIP-seq were performed as described previously (Lan et al., 2007; Niu et al., 2021). Cells were cross-linked with 1% formaldehyde for 10 minutes, quenched with 0.125 M glycine for 10 minutes; then, the cell pellets were wash twice by cold PBS, and then resuspended in high salt Lysis buffer (50 mM HEPES/KOH, pH 7.5, 500 mM NaCl, 1% Trixon-X 100, 0.05% SDS, 10 mM EDTA, and proteinase inhibitors), and sonicated with Qsonica (Misonix) to shear the chromatin into 200- to 400-bp lengths. Chromatin was immunoprecipitated with the indicated antibodies overnight and MagPoly protein A/G magnetic beads (Smart, Changzhou, China) for 2 hours. Then the beads were washed 3 times of high salt lysis buffer, 3 times of low salt buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40, 0.5% Na-Deoxycholate), once of 50mM HEPES/KOH, pH 7.5, and DNA was eluted in elution buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) with Proteinase K (Invitrogen-Thermo Fisher, Waltham, MA) in 72℃ for 3 hours. DNA was isolated by MinElute PCR Purification Kit (QIAGEN 28006). RNA-seq: Total RNA was isolated using TRIzol (Life Technologies). Non-ribosomal RNA was isolated from 1 μg total RNA by using a TrueLib Poly (A) mRNA Magnetic Isolation Module (Excell Bio, Shanghai, China), and sequencing libraries were prepared with the TrueLib mRNA Library Prep Kit for Illumina (ExCell Bio, Shanghai, China). Hi-C: 1,000,000 Cells were cross-linked with 1% formaldehyde for 10 minutes, quenched with 0.2 M glycine for 5 minutes; then, the cell pellets were wash twice by ice cold PBS, and then resuspended in 300 μl of ice cold Hi-C lysis buffer (10 mM Tris-HCl 8.0, 10 mM NaCl, 0.2% NP40, cOmplete Ultra protease inhibitors) and incubated on ice for 15 min. Samples were then centrifuged and washed once with 500 μl of ice cold Hi-C lysis buffer. Nuclei were centrifuged (2,500 g for 5 min at 4℃) and permeabilized by resuspending them in 20 μl of 0.5% SDS and incubating at 62℃ for 10 min with shaking (1,000 rpm). SDS was quenched by adding 58 μl of nuclease-free water and 10 μl of 10% Triton X-100 and incubated at 37℃ for 15 min with shaking (1,000 rpm). Chromatin was digested by adding 100 U of DpnII and 10 μl of 10x DpnII buffer for 2 hours at 37℃ with rotation. DpnII was heat-inactivated at 62℃ for 20 min. The overhangs generated by the restriction enzyme were filled-in by adding a mix of  0.4 mM biotin-dATP (10 μl; PicoHeliex), 10 mM dCTP/dGTP/dTTP (0.5 μl of each dinucleotide), and 5 U/μl DNA polymerase I，Large（Klenow）Fragment (8 μl; New England Biolabs), and incubated for 90 min at 37℃ with rotation. DNA fragments were ligated in 10X T4 DNA ligase buffer (5 μl), 10mM dATP(10 μl), 10 mg/mL BSA (1.5 μl) and 400 U/μl T4 DNA ligase (1.5 μl; NEB) by incubating 8 hours at 20℃. Protein and RNA were digested by adding 5 μl of 20 mg/mL Proteinase K (Thermo Scientific), 10 mg/ml RNase A (2 μl ; Thermo Scientific), 20 μl of 10% SDS and 25 μl of nuclease-free water and incubated at 65℃ with shaking (1,000 rpm) for 8 hours. Phenol-Chloroform-Isoamyl alcohol (25:24:1; Solarbio) extracted DNA was resuspended in 110 μl of 10mM Tris pH 8.0 and incubated for 15 min at 37℃. Samples were sheared using a Qsonica sonicator (6 cycles, each 30 s, 80% duty). DNA size was selected with VAHTS DNA Clean Beads (Vazyme Biotech, Nanjing, China) to get 250 – 500 bp length of DNA fragments dissolved in 300 μl of 10mM Tris pH 8.0. Biotinylated DNA fragments were pulled down using Streptavidin MagPoly Beads (30 μl; Smart Lifesciences, Changzhou, China) supplemented with 300μl of 2X binding buffer (10mM Tris pH 7.5, 1mM EDTA, 2M NaCl) and incubated in 25℃ with rotation for 15 min. The biotinylated DNA fragments on streptavidin beads were washed twice with 600 μl of Tween Wash buffer (5mM Tris pH 7.5, 0.5mM EDTA, 1M NaCl, 0.05% Tween 20) incubated in 55℃ with shaking (800 rpm) for 2min. The Hi-C DNA libraries were prepared as directed by the protocol of VAHTS Universal DNA Library Prep Kit for Illumina (Vazyme Biotech, Nanjing, China).
ChIP DNA libraries, input DNA libraries and HiC DNA libraries were prepared as directed by protocol of VAHTS Universal DNA Library Prep Kit for Illumina (Vazyme Biotech, Nanjing, China).

treatment_protocol: hESCs were differentiated into beating cardiomyocytes using a small-molecule-based monolayer method that has been described previously (Lian et al., 2012). Briefly, hESCs at ~90% confluence were incubated with differentiation basal medium comprising RPMI 1640 medium (Corning Cellgro) and B27 supplement minus insulin (Invitrogen). 6 μM GSK-3β inhibitor CHIR99021 (Selleck Chem) was added into differentiation basal medium for 2 days. After 2 days, the medium was changed to differentiation basal medium minus CHIR99021 for 24 h, followed by differentiation basal medium supplemented with 5 μM Wnt inhibitor IWR-1 (Selleck Chem) for 2 days, then differentiation basal medium for another 2 days, and finally changed to CDM3 medium containing RPMI 1640 supplemented with BSA and ascorbic acid (Figure S1B). Beating cells should be observed at around day 8 after differentiation. Monolayers of CMs derived from hESCs (hESC-CMs) were cultured for defined days and subsequently dissociated for experimental use using TrypLE Express (Life Technologies). Specific day time point of five selected stages are day 0 (hESC), day 2 (mesoderm, MES), day 4 (cardiac progenitor, CP), day12 (cardiomyocyte, CM), and day 35 (mature CM).

value: MESP1 -/-

value: Rabbit Polyclonal anti-RING1A, Cell Signaling Technology, 2820; RRID:AB_2177962


title: PT_Myc_PTEN_MGT_b6


title: Pine, R, HI

value: lung

value: B


title: Pine, R, PR8

value: BALB/c


title: PT_Myc_PTEN_MGT_b7


title: Pine, L, HI

value: L

value: male


title: PT_Myc_PTEN_MGT_b5


title: Pine, O, HI


title: PT_Myc_PTEN_MGT_b2


title: PT_Myc_PTEN_MGT_b4


title: PT_Myc_PTEN_MGT_b1


title: PT_Myc_PTEN_MGT_b3


title: Pine, O, PR8


title: Control, O, PR8

value: Control


title: Control, R, HI


title: Control, L, HI


title: PT_Normal_MG_b2

value: WT


title: PT_Normal_MG_b1


title: Control, O, HI

value: O


title: db15_gWAT_vehicle_RNAseq

city: La Jolla

first: Matthew

last: Wortham

state: CA

address: 2880 Torrey Pines Scenic Drive, Sanford Consortium for Regenerative Medicine, Room 3102

institute: University of California, San Diego

data_processing:
mRNA-seq reads were mapped to the NCBI37/mm9 (mouse) genome by STAR (STAR-STAR_2.4.0f1, --outSAMstrandField intronMotif --outFilterMultimapNmax 1 --runThreadN 5), excluding reads mapping to multiple loci. Reads with exact matches were used to determine RPKM by Cufflinks (cufflinks v2.2.1,-p 6 -G $gtf_file --max-bundle-frags 1000000000).
mRNA-seq: Cuffdiff was used to assess expression differences for all pairwise comparisons, with P < 0.01 considered significant. Genes with mean RPKM > 1 in at least one experimental group were considered to be expressed, and all non-expressed genes were excluded from downstream analyses.
Assembly: mm9

source_name: gWAT

extract_protocol:
Total RNA was isolated in Trizol from homogenized tissue and purified using RNeasy columns and Rnase free Dnase digestion according to the manufacturer’s instructions (QIAGEN).
For mRNA-seq library preparation, total RNA was assessed for quality using an Agilent Tapestation 4200, and samples with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries using the Illumina® Stranded mRNA Prep (Illumina, San Diego, CA). For each sample, 500 ng of RNA was processed following manufacturer’s instructions.

treatment_protocol: Mice homozygous for the leptin receptor (BKS.Cg-Dock7m +/+ Leprdb/J, JAX #000642 thereafter referred to as db/db) and the respective lean control animals (db/+) were  treated starting at 4 weeks of age with either GSK-LSD1 (500 ug/kg/mouse, Sigma SML1072) or vehicle (0.9% NaCl) daily via intraperitoneal injections. Gonadial WAT was harvested after 6 weeks of treatment.

value: gWAT

value: db/db

value: vehicle (0.9% NaCl) daily for 6 weeks


title: Lung, E13.5, Cxcl12+ sort

city: Nashville

first: Jennifer

last: Sucre

state: TN

address: 2215 B Garland Ave, 1125 Light Hall

department: Division of Neonatology, Department of Pediatrics

institute: Vanderbilt University Medical Center

description: 10x Genomics

data_processing:
CellRanger Count v3.1 (10X Genomics) was used to demultiplex align reads onto the mm10 reference genome.
For the E18.5 Cxcl12 homozygous null and Cxcl12 heterozygous control datasets only, ambient background RNA were cleaned from the scRNA-seq data with “SoupX” (version 1.2.2). For all datasets, quality filtering was then used to remove cells with > 10% or < 0.5% mitochondrial mRNA, and to remove cells with < 700 detected genes.
Dimensionality reduction, clustering, and visualization was performed using Seurat v3.2.2 and SCTransform. SCTransform (version 0.3.2.9008) was used with glmGamPoi (version 1.2.0) to normalize the data prior to PCA, UMAP embedding, and cell clustering.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files from Cellranger count, and SoupX adjusted counts (when computed).

source_name: Lung

extract_protocol:
Lungs were removed, minced and processed into a single cell suspension in a Collagenase I (8 mg/5ml) /Dispase (1:10)/RNase-free DNase (1:500) solution for 20 min at 37˚C. CD31+TdTomato+ cells underwent FACS-based isolation from single cell suspension using a MoFlo Astrios EQ (Beckman Coulter) flow cytometer with antibody staining for CD31-PECy7, CD45-APC, and EpCAM- FITC. Following negative selection for CD45 and EpCAM, CD31+/TdTomato+ ECs and CD31-/TdTomato+ mesenchymal-enriched cells were collected in FACS buffer without EDTA.
Cells were resuspended as per the 10X Genomics recommended protocol, and 16,500 cells were loaded onto the 10X Chromium platform, to target a recovery of 10000 cells. The libraries were prepared according to the manufacturer’s protocol using 10x Single cell 3’ v3 chemistry.

value: Lung

value: Embryonic day 13.5


title: db12_gWAT_GSK-LSD1i_RNAseq_1


title: Lung, E18.5, Cxcl12 homozygous null

description: 10x Genomics

value: Embryonic day 18.5


title: db25_gWAT_GSK-LSD1i_RNAseq

value: GSK-LSD1 (500 ug/kg/mouse) daily for 6 weeks


title: Lung, E18.5, Cxcl12+ sort

description: 10x Genomics


title: SEK00_74290 (sham, 3 days, Rep. 4)

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq v2.20.0.422.
The RNA sequencing reads were aligned to the mouse  reference genome (GRCm38 with the Ensembl genome annotation release 99) using STAR 2.7.2b (parameters: --alignIntronMax 100000, --outSJfilterReads Unique, --outSAMmultNmax 1, --outFilterMismatchNoverLmax 0.04) (PMID: 23104886)
For each gene, all reads that map uniquely to one genomic position were counted with FeatureCounts 1.6.5 (multi-mapping or multi-overlapping reads were discarded, stranded mode was set to “–s 2”) (PMID: 24227677)
Assembly: GRCm38
Supplementary files format and content: csv file containing raw read counts per gene over all samples

source_name: isolated brain CD11b cells

growth_protocol: Animals were housed under controlled/standardized day-night conditions (12h/12h) at room temperature (23±1°C, 30%–60% environmental humidity) and received a standard diet (AIN) and water ad libitum. Polymicrobial sepsis was induced by injection of fecal slurry into the peritoneum.

extract_protocol:
CD11b positive cells were isolated according to MACS cell separation protocol (Miltenyi Biotec). Total RNA extraction was carried out using QIAzol lysis reagent and RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer's instructions.
Libraries were prepared from 150 ng total RNA using NEBNext Ultra II Directional RNA Library Preparation Kit in combination with NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1/2/3/4) following the manufacturer's instructions (New England Biolabs).

treatment_protocol: Sepsis was induced by peritoneal contamination and infection model (PCI). Mice were treated with meropenem beginning 6 hours following sepsis induction.

value: isolated brain CD11b cells

value: sham

value: 3 days

value: 10-13 weeks


title: PT_Normal_MG_b3

value: mammary tissue

value: no


title: Lung, E15.5, Cxcl12+ sort

description: 10x Genomics

value: Embryonic day 15.5


title: Lung, E18.5, Cxcl12 heterozygous control

description: 10x Genomics


title: db26_gWAT_GSK-LSD1i_RNAseq


title: Control, L, PR8

value: lung

value: L

value: B

value: Control

value: BALB/c

value: male


title: db29_gWAT_vehicle_RNAseq

value: gWAT

value: db/db

value: vehicle (0.9% NaCl) daily for 6 weeks


title: db24_gWAT_vehicle_RNAseq


title: db3_gWAT_lean_vehicle_RNAseq

value: db/+


title: SEK00_74275 (PCI, 3 days, Rep. 2)

value: isolated brain CD11b cells

value: PCI


title: db11_gWAT_vehicle_RNAseq


title: db2_gWAT_lean_vehicle_RNAseq


title: Control, R, PR8

value: R


title: SEK00_74281 (PCI, 3 days, Rep. 3)

value: 3 days

value: 10-13 weeks


title: HiC_in_RING1A-KO_CPC_rep2

description:
Sample 17
merge_62.72_R1-KO_HiC-pro.hic

data_processing:
The FASTQ data were trimmed adaptor by trim_galore (bioinformatics.babraham.ac.uk)
ChIP-seq data mapped to human genome hg19 with Bowtie2  in pair-end mode.
ChIP-seq peaks were called by MACS2 .
RNA-seq data were mapped to human genome hg19 using hisat2 and assembled by homer to get couts by million (CPM).
Differentially expressed genes were generated by DEseq2 with fold change > or = 2 and p <0.05.
Reads were aligned and quality-controlled through HiC-Pro 2.11.1 . Next, 2 replicates of WT samples were merged, and 2 replicates of RING1A-KO samples were merged. Finally, the merged allValidPairs files were converted to .hic files. Hi-C loops were called by Homer and cLoops2 and merged together. Differential enriched loops for WT and RING1A-KO samples were identified by cLoops2 callDiffLoops.
Genome_build: hg19
Supplementary_files_format_and_content: ".narrowPeak" files are tab-delimited text files for ChIP-seq peaks in Sample 1-13, which were called by MACS2 using corresponding ChIP-seq data and input data. In these narrowPeaks files, "merge1kb" and "merge500bp" imply merging the peaks within the distance of 1 kb and 500 bp, since MACS2 sometimes splits long peaks, verified in UCSC tracks.  ".hic" files are HiC-Pro mapped and hicpro2juicebox.sh conveted Hi-C results for Sample 14-17. "diffExp_log2CPM_D4_WT-RING1-KO-MESP1-KO_20210217_GEO.xlsx" and "diffExp_log2CPM_D6_WT_MESP1-KO_RING1A-KO_201222_GEO.xlsx" files are RNA-seq gene expression data (log2CPM) and differentially expressed in WT, MESP1-KO and RING1-KO CPCs for Sample 18-35.

source_name: RING1A knockout human cardiac progenitor cells (day 4 post differentiation from ESCs)

value: RING1A -/-


title: HiC_in_WT_CPC_rep1

description:
Sample 14
merge_61.71_WT_D4_0420_HiC-pro.hic

source_name: Human cardiac progenitor cells (day 4 post differentiation from ESCs)

value: Wild type


title: SEK00_74272 (PCI, 3 days, Rep. 1)


title: db4_gWAT_lean_vehicle_RNAseq


title: HiC_in_RING1A-KO_CPC_rep1

description:
Sample 15
merge_62.72_R1-KO_HiC-pro.hic

data_processing:
The FASTQ data were trimmed adaptor by trim_galore (bioinformatics.babraham.ac.uk)
ChIP-seq data mapped to human genome hg19 with Bowtie2  in pair-end mode.
ChIP-seq peaks were called by MACS2 .
RNA-seq data were mapped to human genome hg19 using hisat2 and assembled by homer to get couts by million (CPM).
Differentially expressed genes were generated by DEseq2 with fold change > or = 2 and p <0.05.
Reads were aligned and quality-controlled through HiC-Pro 2.11.1 . Next, 2 replicates of WT samples were merged, and 2 replicates of RING1A-KO samples were merged. Finally, the merged allValidPairs files were converted to .hic files. Hi-C loops were called by Homer and cLoops2 and merged together. Differential enriched loops for WT and RING1A-KO samples were identified by cLoops2 callDiffLoops.
Genome_build: hg19
Supplementary_files_format_and_content: ".narrowPeak" files are tab-delimited text files for ChIP-seq peaks in Sample 1-13, which were called by MACS2 using corresponding ChIP-seq data and input data. In these narrowPeaks files, "merge1kb" and "merge500bp" imply merging the peaks within the distance of 1 kb and 500 bp, since MACS2 sometimes splits long peaks, verified in UCSC tracks.  ".hic" files are HiC-Pro mapped and hicpro2juicebox.sh conveted Hi-C results for Sample 14-17. "diffExp_log2CPM_D4_WT-RING1-KO-MESP1-KO_20210217_GEO.xlsx" and "diffExp_log2CPM_D6_WT_MESP1-KO_RING1A-KO_201222_GEO.xlsx" files are RNA-seq gene expression data (log2CPM) and differentially expressed in WT, MESP1-KO and RING1A-KO CPCs for Sample 18-35.

value: RING1A knockout human cardiac progenitor cells (day 4 post differentiation from ESCs)


title: HiC_in_WT_CPC_rep2

description:
Sample 16
merge_61.71_WT_D4_0420_HiC-pro.hic

value: Human cardiac progenitor cells (day 4 post differentiation from ESCs)


title: H3K27ac_ChIP_in_WT_CPC

description:
Sample 10
61_K27ac_D4_210327_peaks-black.narrowPeak

data_processing:
The FASTQ data were trimmed adaptor by trim_galore (bioinformatics.babraham.ac.uk)
ChIP-seq data mapped to human genome hg19 with Bowtie2  in pair-end mode.
ChIP-seq peaks were called by MACS2 .
RNA-seq data were mapped to human genome hg19 using hisat2 and assembled by homer to get couts by million (CPM).
Differentially expressed genes were generated by DEseq2 with fold change > or = 2 and p <0.05.
Reads were aligned and quality-controlled through HiC-Pro 2.11.1 . Next, 2 replicates of WT samples were merged, and 2 replicates of MESP1-KO samples were merged. Finally, the merged allValidPairs files were converted to .hic files. Hi-C loops were called by Homer and cLoops2 and merged together. Differential enriched loops for WT and MESP1-KO samples were identified by cLoops2 callDiffLoops.
Genome_build: hg19
Supplementary_files_format_and_content: ".narrowPeak" files are tab-delimited text files for ChIP-seq peaks in Sample 1-13, which were called by MACS2 using corresponding ChIP-seq data and input data. In these narrowPeaks files, "merge1kb" and "merge500bp" imply merging the peaks within the distance of 1 kb and 500 bp, since MACS2 sometimes splits long peaks, verified in UCSC tracks.  ".hic" files are HiC-Pro mapped and hicpro2juicebox.sh conveted Hi-C results for Sample 14-17. "diffExp_log2CPM_D4_WT-RING1-KO-MESP1-KO_20210217_GEO.xlsx" and "diffExp_log2CPM_D6_WT_MESP1-KO_RING1A-KO_201222_GEO.xlsx" files are RNA-seq gene expression data (log2CPM) and differentially expressed in WT, MESP1-KO and RING1-KO CPCs for Sample 18-35.

value: Rabbit polyclonal anti-H3K27ac (Millipore, Cat# 07-360)


title: db21_gWAT_GSK-LSD1i_RNAseq

value: GSK-LSD1 (500 ug/kg/mouse) daily for 6 weeks


title: SEK00_74274 (sham, 3 days, Rep. 3)

value: sham


title: SEK00_74271 (sham, 3 days, Rep. 2)


title: 73519 (PCI, 20 days, Rep. 3)

value: 20 days


title: Left Gastrocnemius, Sed + pH 7.2, 24hr, male rep4

city: Iowa City

first: Michael

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

data_processing:
Samples were processed with 'bcbio-nextgen.py' (v 1.2.4) running on Argon HPC at the University of Iowa. Bcbio-nextgen.py includes read quality control, read alignment, and quantitation.
The pipeline was run in "RNA-seq" mode with "mm10" selected for the genome build (referencing GRCm38.p6 v94 and transcriptome GENCODE M19).
Reads were aligned with hisat2 (2.1.0) and quantified with salmon (0.9.1). Qualimap (2.2.2) was used to examine hisat2 BAM files for quality control.  BAM alignments were quantified with featureCounts.
Salmon-derived transcript quantifications were imported and summarized to gene counts using tximport (1.12.3) in RStudio. DESeq2 (1.24.0) was used for DE analysis in RStudio.
Assembly: GRCm38.p6 v94; transcriptome GENCODE M19
Supplementary files format and content: counts

source_name: Left gastrocnemius muscle

extract_protocol:
RNA was harvested using RNeasy Fibrous tissue mini kit (Qiagen) and further cleaned with a clean and concetratate kit (Zymo). 0.5 µg of total RNA was used for the construction of sequencing libraries.
Samples were prepared according to Illumina TruSeq stranded NovaSeq SP 200 cycles (100PE).

treatment_protocol:
Animals were grouped as either sedentary or physically active. Physically active animals were given access to running wheels for 8 weeks prior to induction of the pain model. Pain model was induced with 2 stimuli spaced 5 days apart. On day one, animals received a 20μl injection of pH 5.0±0.1 into the left gastrocnemius muscle. On day 5, animals received 6 minutes of electrically stimulated muscle contractions in the left gastrocnemius muscle followed immediately by a second pH 5.0 injection into the left gastrocnemius muscle.
To create pain free controls, animals received two 20μl injections of pH 7.2±0.1 saline into the left gastrocnemius muscle spaced 5 days apart.

value: WT

value: Left gastrocnemius muscle

value: male

value: Sed + ph 7.2


title: Lung, P8, Cxcl12+ sort

description: 10x Genomics

value: Lung

value: Postnatal day 8


title: AStetCASZ1b_Tet-Rep3

last: Liu

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg19 whole genome using STAR 2.5.1
Counts per million (CPM) were quantified using the Partek E/M model
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each Sample.

source_name: SK-N-AS cells

growth_protocol: The CASZ1b stably transfected SK-N-AS cells (AStetCASZ1b)  are cultured in RPMI 1640 containing 10% FBS. CASZ1b expression is induced by Tetracycline (Tet) treatment.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA was isolated from AStetCASZ1b cells that treated with or without Tet for 72 hr

value: Neuroblastoma


title: db1_gWAT_lean_vehicle_RNAseq

value: gWAT

value: db/+

value: vehicle (0.9% NaCl) daily for 6 weeks


title: SEK00_74286 (PCI, 3 days, Rep. 4)

value: isolated brain CD11b cells

value: PCI

value: 3 days

value: 10-13 weeks


title: 73511 (sham, 20 days, Rep. 3)


title: 73510 (sham, 20 days, Rep. 2)


title: 73497 (PCI, 20 days, Rep. 2)


title: Left Gastrocnemius, Sed + pH 7.2, 24hr, male rep2


title: 73496 (PCI, 20 days, Rep. 1)


title: GM2131 (sham, PLX, 10 days, Rep. 4)

source_name: hippocampus

growth_protocol: Animals were housed under controlled/standardized day-night conditions (12h/12h) at room temperature (23±1°C, 30%–60% environmental humidity) and received a standard diet (AIN) and water ad libitum. Three days following sepsis induction (injection of fecal slurry into the peritoneum) PLX5622 diet was started until the end of experiment.

extract_protocol:
Total RNA extraction was carried out using QIAzol lysis reagent and RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer's instructions.
Libraries were prepared from 500 ng (total RNA using NEBNext Ultra II Directional RNA Library Preparation Kit in combination with NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1/2/3/4) following the manufacturer's instructions (New England Biolabs).

treatment_protocol: Sepsis was induced by peritoneal contamination and infection model (PCI). Mice were treated with meropenem beginning 6 hours following sepsis induction. PLX5622 diet was implemented 3 days following sepsis induction.

value: hippocampus

tag: diet

value: 10 days


title: Left Gastrocnemius, Sed + pH 7.2, 24hr, male rep3

tag: treatment


title: Left Gastrocnemius, Sed + pH 7.2, 24hr, male rep1


title: Left Gastrocnemius, Sed + pH 7.2, 24hr, female rep3

value: female


title: Left Gastrocnemius, Sed + pH 7.2, 24hr, female rep4

value: WT


title: Left Gastrocnemius, Sed + pH 7.2, 24hr, female rep1

value: Left gastrocnemius muscle


title: AStetCASZ1b_Tet-Rep1


title: GM2129 (PCI, AIN, 10 days, Rep. 4)

value: AIN


title: GM2130 (sham, PLX, 10 days, Rep. 3)

value: sham


title: AStetCASZ1b_Ctrl-Rep2


title: AStetCASZ1b_Ctrl-Rep3


title: 73494 (sham, 20 days, Rep. 1)

value: 20 days


title: SEK00_74250 (sham, 3 days, Rep. 1)


title: GM2127 (sham, AIN, 10 days, Rep. 4)


title: Left Gastrocnemius, Sed + pH 5.0, 24hr, male rep4

value: male

value: Sed + pH 5.0


title: SLE_7.E

data_processing:
The Cell Ranger software pipeline(V3.0.0) provided by 10x Genomics was used to demultiplex cellular barcodes, map reads to the human genomics
The Seurat packages(v3) was used as the mainly tools for downstream bioinformatics analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: skin biopsy_SLE

value: SLE

value: skin


title: Left Gastrocnemius, Sed + pH 5.0, 24hr, male rep3


title: SLE_7.D


title: GM2123 (PCI, PLX, 10 days, Rep. 4)


title: Left Gastrocnemius, Sed + pH 5.0, 24hr, male rep2


title: Left Gastrocnemius, Sed + pH 5.0, 24hr, male rep1


title: GM2126 (sham, AIN, 10 days, Rep. 3)


title: GM2122 (PCI, PLX, 10 days, Rep. 3)


title: AStetCASZ1b_Tet-Rep2

value: Neuroblastoma


title: AStetCASZ1b_Ctrl-Rep1


title: SLE_6.D


title: GM2121 (sham, PLX, 10 days, Rep. 2)


title: SLE_6.E


title: GM2119 (PCI, AIN, 10 days, Rep. 3)


title: SLE_5.D


title: Left Gastrocnemius, Sed + pH 5.0, 24hr, female rep4


title: Left Gastrocnemius, Sed + pH 5.0, 24hr, female rep3


title: Left Gastrocnemius, Sed + pH 5.0, 24hr, female rep2


title: Left Gastrocnemius, Sed + pH 7.2, 24hr, female rep2

value: Sed + ph 7.2


title: SLE_4.D


title: SLE_3.D


title: GM2115 (sham, PLX, 10 days, Rep. 1)


title: Left Gastrocnemius, Sed + pH 5.0, 24hr, female rep1


title: Left Gastrocnemius, Ex + pH 5.0, 24hr, male rep4

value: Ex + pH 5.0


title: SLE_2.D


title: GM2118 (PCI, AIN, 10 days, Rep. 2)

value: PCI


title: GM2114 (PCI, PLX, 10 days, Rep. 2)

value: 10-13 weeks


title: Left Gastrocnemius, Ex + pH 5.0, 24hr, male rep3


title: GM2113 (PCI, PLX, 10 days, Rep. 1)

value: hippocampus


title: Left Gastrocnemius, Ex + pH 5.0, 24hr, male rep2


title: GM2111 (sham, AIN, 10 days, Rep. 1)

value: 10 days


title: SLE_1.D


title: DLE_5.D

source_name: skin biopsy_DLE

value: DLE


title: DLE_4.D


title: Left Gastrocnemius, Ex + pH 5.0, 24hr, male rep1

value: WT


title: GM2120 (sham, AIN, 10 days, Rep. 2)


title: GM2110 (PCI, AIN, 10 days, Rep. 1)


title: Left Gastrocnemius, Ex + pH 5.0, 24hr, female rep3

value: Left gastrocnemius muscle

value: female


title: GM2097 (sham, AIN, 3 days, Rep. 3)

value: sham

value: AIN

value: 3 days


title: Left Gastrocnemius, Ex + pH 5.0, 24hr, female rep4


title: DLE_5.E


title: Left Gastrocnemius, Ex + pH 5.0, 24hr, female rep2


title: DLE_2.D


title: DLE_3.D


title: Left Gastrocnemius, Ex + pH 5.0, 24hr, female rep1


title: DLE_1.D


title: GM2096 (sham, AIN, 3 days, Rep. 2)


title: GM2095 (sham, AIN, 3 days, Rep. 1)


title: DLE_1.E


title: RNAseq_Chd8cKO_1

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA-Seq
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Tophat with default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
Genome_build: mm10
Supplementary_files_format_and_content: format:fpkm_matrix ; Contain the estimated expression values produced by Cufflinks.
ATAC-Seq
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Bowtie2 with default options
Peak calling was performed using MACS1.4 with a default p value cut off.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated by MACS14

source_name: mouse E14.5 cortex

extract_protocol:
RNA-seq: Total RNA from control and Chd8 cKO cortices were extracted using Trizol (Life Technologies) protocol followed by purification using an RNeasy Mini Kit (Qiagen).
RNA-seq: RNA-seq libraries from control and Chd8 cKO cortices were prepared using Illumina RNA-Seq Preparation Kit.

treatment_protocol: RNA-seq: For mouse cortical cells, E14.5 control and Eed cKO mouse cortices microdisected and processed to RNA extraction.

tag: group

value: Chd8 cKO

tag: genotype/variation

value: Chd8 c/c, Emx1-cre

value: Cortical cells


title: RNAseq_Chd8cKO_2


title: GM2093 (PCI, AIN, 3 days, Rep. 3)


title: RNAseq_control_3

value: Control

value: Chd8 c/c


title: EG

city: Ikoma

first: Shosuke

last: Yoshida

state: Nara

address: 8916-5 Takayama-cho

institute: Nara Institute of Science and Technology

data_processing:
CLC Genomics Workbench v 20.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to ASM129352v1 using CLC genomic workbench (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: ASM129352v1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Piscinibacter sakaiensis

source_name: bacterial cell

growth_protocol: Cells were cultured in a test tube containing YSV medium with a PET film, TPA·2Na, or EG as the primary carbon source for 20 h.

extract_protocol:
Total RNA was extracted and purified using the RNeasy Mini Kit (Qiagen) with on-column DNA digestion using RNase-Free DNase Set (Qiagen).
Bacterial 16S and 23S ribosomal RNAs were removed from total RNA with the Ribo-Zero rRNA removal kit for gram-negative bacteria (Illumina, San Diego, CA). The enriched mRNA fraction was converted to an RNA-Seq library with multiplexing adaptors.

value: bacterial cell

value: wild-type


title: GM2100 (sham, AIN, 3 days, Rep. 4)

value: 10-13 weeks


title: GM2092 (PCI, AIN, 3 days, Rep. 2)

value: hippocampus

value: PCI


title: PET


title: RNAseq_control_1

value: Chd8 c/+


title: TPA·2Na


title: RNAseq_control_2


title: GM2091 (PCI, AIN, 3 days, Rep. 1)


title: Enamel knot in gerbil tooth germ 2

status: Public on Oct 16 2022

city: Seoul

first: Han-Sung

last: Jung

address: 50, Yonsei-ro, Seodaemun-gu

department: Dental School

country: South Korea

institute: Yonsei University

data_processing:
TotalOmics Transcriptome (Reference-based, Quant): STAR-RSEM-TCC method
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt v.2.8 (parameter- Quality limit: Phred quality score 20, reads shorter than 50 bp were removed)
Trimmed sequence reads were mapped to GrCM38/mm10 and ASM813125v1 using aligner STAR v.2.7.1a (ENCODE standard options with “-quantMode TranscriptomeSAM”)
RPKM/FPKM and TPM values were performed using RSEM v.1.3.1
Assembly: mm10, ASM813125v1
Supplementary files format and content: tab-delimited text files include RPKM/FPKM values for each Sample

organism: Meriones unguiculatus

source_name: epithelial cells

extract_protocol:
Tooth germ were dissected from the mandibles of mouse and gerbil. Tooth germs were fixed with 4% PFA, then frozen-sectioned with cryostat. Then, enamel knot region from mouse and gerbil tooth germs were seperated with laser microdissection. RNA was extracted using TRIzol.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: epithelial cells

value: WT

tag: developmental stage

value: embryonic day 15


title: Enamel knot in gerbil tooth germ 1

tag: genotype


title: GM2094 (PCI, AIN, 3 days, Rep. 4)

tag: time


title: DNase-seq from HCT116 (ENCLB565NVZ)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR799GSS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR799GSS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-04-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB565NVZ

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7

tag: line

value: cell line

tag: biosample encode accession

value: male

tag: health state

value: colorectal carcinoma

tag: dev stage

value: adult

value: 48 year

tag: lab

value: Erez Aiden, Baylor

tag: source

value: Dr. Masato Kanemaki

tag: link

value: ENCBS785ZQK at ENCODE; https://www.encodeproject.org/ENCBS785ZQK/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: DNase-seq from HCT116 (ENCLB804BTQ)

description:
https://www.encodeproject.org/experiments/ENCSR795ZKB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR795ZKB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB804BTQ

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: Sex

tag: age

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS036VAP at ENCODE; https://www.encodeproject.org/ENCBS036VAP/


title: DNase-seq from naive B cell (ENCLB899VLX)

description:
https://www.encodeproject.org/experiments/ENCSR796PIM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR796PIM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB899VLX

source_name: Homo sapiens female adult (39 years) naive B primary cell

value: naive B cell

value: primary cell

value: female

value: 39 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS589EXJ at ENCODE; https://www.encodeproject.org/ENCBS589EXJ/

value: Derived from ENCODE donor ENCDO352FHC; https://www.encodeproject.org/ENCDO352FHC/


title: DNase-seq from PC-9 (ENCLB582INS)

description:
https://www.encodeproject.org/experiments/ENCSR781TYE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR781TYE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-08-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB582INS

source_name: Homo sapiens PC-9 cell line

value: cell line

value: not collected

value: Mats Ljungman, UMichigan

value: Sigma

value: ENCBS747GJP at ENCODE; https://www.encodeproject.org/ENCBS747GJP/

value: Derived from ENCODE donor ENCDO647UHQ; https://www.encodeproject.org/ENCDO647UHQ/


title: ATAC-seq from heart right ventricle (ENCLB336NVC)

description:
https://www.encodeproject.org/experiments/ENCSR374ZRW/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR374ZRW
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB336NVC
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (56 years) heart right ventricle tissue

value: heart right ventricle

value: tissue

value: PGD

value: adult

value: 56 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS963ZRX at ENCODE; https://www.encodeproject.org/ENCBS963ZRX/

value: Derived from ENCODE donor ENCDO907YUG; https://www.encodeproject.org/ENCDO907YUG/


title: DNase-seq from HCT116 (ENCLB477NMY)

description:
https://www.encodeproject.org/experiments/ENCSR795ZKB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR795ZKB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB477NMY

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS918YSB at ENCODE; https://www.encodeproject.org/ENCBS918YSB/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: DNase-seq from activated T-helper 2 cell (ENCLB190KZM)

description:
https://www.encodeproject.org/experiments/ENCSR780ABS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR780ABS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-11-04
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB190KZM

source_name: Homo sapiens male adult (35 years) activated T-helper 2 primary cell treated with 5 ug/mL Interferon-gamma antibody, 100 ng/mL Interleukin-4, anti-CD3 and anti-CD28 coated beads

value: activated T-helper 2 cell

value: primary cell

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:Interferon-gamma antibody; treatment_type:antibody; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS679QAH at ENCODE; https://www.encodeproject.org/ENCBS679QAH/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: DNase-seq from natural killer cell (ENCLB094IAR)

description:
https://www.encodeproject.org/experiments/ENCSR794TLA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR794TLA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB094IAR

source_name: Homo sapiens female adult (41 years) natural killer primary cell treated with 100 ng/mL Interleukin-12 subunit alpha, 100 ng/mL Interleukin-15, 100 ng/mL Interleukin-12 subunit beta, 100 ng/mL Interleukin-18

value: natural killer cell

value: female

value: adult

value: 41 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:Q14116; treatment_term_name:Interleukin-18; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS829JSB at ENCODE; https://www.encodeproject.org/ENCBS829JSB/

value: Derived from ENCODE donor ENCDO911LCI; https://www.encodeproject.org/ENCDO911LCI/


title: DNase-seq from PC-9 (ENCLB473PBP)

description:
https://www.encodeproject.org/experiments/ENCSR781TYE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR781TYE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-08-09
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB473PBP

value: cell line

value: not collected

value: Mats Ljungman, UMichigan

value: Sigma

value: ENCBS502HXO at ENCODE; https://www.encodeproject.org/ENCBS502HXO/

value: Derived from ENCODE donor ENCDO647UHQ; https://www.encodeproject.org/ENCDO647UHQ/


title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB455JPN)

description:
https://www.encodeproject.org/experiments/ENCSR794KUS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR794KUS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-02-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB455JPN

source_name: Homo sapiens with multiple sclerosis; naive thymus-derived CD4-positive, alpha-beta T primary cell, preserved by cryopreservation

value: primary cell

tag: description

value: CD4+ naive CD3+ CD4+ CD8- CD45RA+ CD45RO- nonTreg

value: multiple sclerosis

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS030NVK at ENCODE; https://www.encodeproject.org/ENCBS030NVK/

value: Derived from ENCODE donor ENCDO157PKH; https://www.encodeproject.org/ENCDO157PKH/


title: ATAC-seq from heart left ventricle (ENCLB370TAF)

description:
https://www.encodeproject.org/experiments/ENCSR769DGC/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR769DGC
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB370TAF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (73 years) heart left ventricle tissue

value: heart left ventricle

value: tissue

value: male

value: ischemic (EF 35%, LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: adult

value: 73 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS733NEA at ENCODE; https://www.encodeproject.org/ENCBS733NEA/

value: Derived from ENCODE donor ENCDO804CLC; https://www.encodeproject.org/ENCDO804CLC/


title: WGBS from motor neuron (ENCLB433QRA)

description:
https://www.encodeproject.org/experiments/ENCSR778ACS/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: Control PGP - iNPC
experiment encode accession: ENCSR778ACS
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB433QRA
fragmentation methods: shearing (Covaris generic)
size range: 450-650

source_name: Homo sapiens male adult (55 years) motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: Healthy donor

value: 55 year

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS393BHK at ENCODE; https://www.encodeproject.org/ENCBS393BHK/

value: Derived from ENCODE donor ENCDO371BAE; https://www.encodeproject.org/ENCDO371BAE/


title: ATAC-seq from heart left ventricle (ENCLB033VNN)

description:
https://www.encodeproject.org/experiments/ENCSR769DGC/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR769DGC
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB033VNN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: heart left ventricle


title: DNase-seq from Calu3 (ENCLB474PXM)

description:
https://www.encodeproject.org/experiments/ENCSR366NBE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR366NBE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB474PXM

source_name: Homo sapiens Calu3 cell line

value: cell line

value: Lung adenocarcinoma

value: 25 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS582MNI at ENCODE; https://www.encodeproject.org/ENCBS582MNI/

value: Derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: DNase-seq from Calu3 (ENCLB348MDY)

description:
https://www.encodeproject.org/experiments/ENCSR366NBE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR366NBE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB348MDY

value: male

value: adult

value: ENCBS821RDX at ENCODE; https://www.encodeproject.org/ENCBS821RDX/


title: ATAC-seq from heart left ventricle (ENCLB539SLN)

description:
https://www.encodeproject.org/experiments/ENCSR745CGG/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR745CGG
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB539SLN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (54 years) heart left ventricle tissue

value: tissue

value: ischemic (EF 13 %, LVEDD 7.1; RV severe dilation, severe dysfunction)

value: 54 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS368XDZ at ENCODE; https://www.encodeproject.org/ENCBS368XDZ/

value: Derived from ENCODE donor ENCDO039RUH; https://www.encodeproject.org/ENCDO039RUH/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB966WRR)

description:
https://www.encodeproject.org/experiments/ENCSR365CUB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR365CUB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-03-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB966WRR

source_name: Homo sapiens male adult (35 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: primary cell

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS971PFL at ENCODE; https://www.encodeproject.org/ENCBS971PFL/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: ATAC-seq from heart left ventricle (ENCLB466BJI)

description:
https://www.encodeproject.org/experiments/ENCSR745CGG/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR745CGG
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB466BJI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: heart left ventricle

value: male


title: ExpB-st10.5

city: Freiburg

first: Peter

last: Walentek

state: BW

address: Breisacherstr. 113

department: Internal Medicine IV & IMITATE

institute: University Freiburg Medical Center

data_processing:
Quality control was done using FastQC v0.11.5
paired-end reads were mapped to Xenopus laevis genome assembly v9.2 using RNA STAR v2.6.0b-1
featureCounts v1.6.3 was used to count uniquely mapped reads per gene
statistical analysis of differential gene expression was conducted in DEseq2 v1.22.1
Assembly: X. laevis v9.2 genome assembly
Supplementary files format and content: tabular results files dervied from DESeq2
DESeq2_result_*.tabular files with GeneID, Base mean, log2(FC), StdErr, Wald-Stats, P-value, P-adj columns

organism: Xenopus laevis

source_name: epidermis, animal cap explant

growth_protocol: Explants were cut from the animal portion of stage 8 Xenopus laevis embryos in 1x Modified Barth's Saline (MBS), then they were maintained in the medium for at least 1 hour to heal. After healing of explants, they were transferred to 0.5x MBS containing 0.1% of Gentamycin and cultured in that medium until they reached the indicated stage.

extract_protocol:
Total RNA was extracted using the standard Trizol protocol.
500 ng total RNA per sample was used, poly-A selection and RNA-sequencing library preparation was done using non strand massively-parallel cDNA sequencing (mRNA-Seq) protocol from Illumina, the TruSeq RNA Library Preparation Kit v2, Set A (Illumina #RS-122-2301) according to manufacturer’s recommendation. Quality and integrity of RNA was assessed with the Fragment Analyzer from Advanced Analytical by using the standard sensitivity RNA Analysis Kit (Advanced Analytical #DNF-471). All samples selected for sequencing exhibited an RNA integrity number over 8. For accurate quantitation of cDNA libraries, the QuantiFluor™dsDNA System from Promega was used. The size of final cDNA libraries was determined using the dsDNA 905 Reagent Kit (Advanced Bioanalytical #DNF-905) exhibiting a sizing of 300 bp on average. Libraries were pooled and paired-end 100bp sequencing on a HiSeq4000 was conducted at the Vincent J. Coates Genomics Sequencing Lab, University of California at Berkeley.

treatment_protocol: Control embryos remained untreated.

tag: tissue

value: epidermis, animal cap explant

value: embryonic stages 10.5

value: wt

tag: treatment

value: control


title: ExpB-st11.5

value: embryonic stages 11.5


title: ExpB-st12.5

value: embryonic stages 12.5


title: ATAC-seq from left cardiac atrium (ENCLB263LTF)

description:
https://www.encodeproject.org/experiments/ENCSR736CIN/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human left cardiac atrium
experiment encode accession: ENCSR736CIN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB263LTF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (66 years) left cardiac atrium tissue, preserved by cryopreservation

value: left cardiac atrium

value: tissue

value: female

value: Chemo-induced cardiomyopathy

value: adult

value: 66 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS265GFY at ENCODE; https://www.encodeproject.org/ENCBS265GFY/

value: Derived from ENCODE donor ENCDO255XON; https://www.encodeproject.org/ENCDO255XON/


title: DNase-seq from memory B cell (ENCLB820SUK)

description:
https://www.encodeproject.org/experiments/ENCSR736VVP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR736VVP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB820SUK

source_name: Homo sapiens female adult (39 years) memory B primary cell

value: memory B cell

value: primary cell

value: 39 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS531EDO at ENCODE; https://www.encodeproject.org/ENCBS531EDO/

value: Derived from ENCODE donor ENCDO352FHC; https://www.encodeproject.org/ENCDO352FHC/


title: DNase-seq from type B pancreatic cell (ENCLB871NFD)

description:
https://www.encodeproject.org/experiments/ENCSR362ZFC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR362ZFC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-11-04
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB871NFD

source_name: Homo sapiens female embryo (5 days) type B pancreatic in vitro differentiated cells

value: type B pancreatic cell

value: in vitro differentiated cells

value: healthy

value: embryonic

value: 5 day

value: SESCC

value: ENCBS024CHQ at ENCODE; https://www.encodeproject.org/ENCBS024CHQ/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: ExpA-st12.5

value: epidermis, animal cap explant

value: embryonic stages 12.5

value: wt

value: control


title: WGBS from motor neuron (ENCLB183KKE)

description:
https://www.encodeproject.org/experiments/ENCSR778ACS/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: Control PGP - iNPC
experiment encode accession: ENCSR778ACS
assay title: WGBS
assembly: GRCh38
encode release date: 2022-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB183KKE
fragmentation methods: shearing (Covaris generic)
size range: 450-650

value: motor neuron

value: male

value: Healthy donor

value: adult

value: 55 year

value: Michael Snyder, Stanford

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS827RRR at ENCODE; https://www.encodeproject.org/ENCBS827RRR/

value: Derived from ENCODE donor ENCDO371BAE; https://www.encodeproject.org/ENCDO371BAE/


title: ExpA-st11.5

value: embryonic stages 11.5


title: ATAC-seq from left cardiac atrium (ENCLB137SRL)

description:
https://www.encodeproject.org/experiments/ENCSR736CIN/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human left cardiac atrium
experiment encode accession: ENCSR736CIN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2022-06-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB137SRL
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: left cardiac atrium

value: tissue

value: female

value: Chemo-induced cardiomyopathy

value: 66 year

value: Shin Lin

value: ENCBS265GFY at ENCODE; https://www.encodeproject.org/ENCBS265GFY/

value: Derived from ENCODE donor ENCDO255XON; https://www.encodeproject.org/ENCDO255XON/