title: shNC1

city: Jinan

first: Yuxing

state: Shandong

address: 44 Wenhuaxi Rd

institute: Institute of Molecular Medicine and Genetics Shandong University School of Medicine

description: Knock down control

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.

source_name: Breast cancer cells

growth_protocol: Briefly, All cells were culture maintained in DMEM(Gibco, BRL, Grand Island, NY, USA) containing 10% FBS(AusGeneX, Australia), penicillin and streptomycin.

extract_protocol:
Total RNA was extracted with Trizol reagents (Thermo) following the manufacturer's instructions.
A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, NEB 3' SR Adaptor was directly, and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5 ́ SR Adaptor in the subsequent ligation step. 5 ́ends adapter was ligated to 5 ́ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.

treatment_protocol: No treatment

tag: cell line


title: sh4B1

status: Public on Sep 08 2022

type: SRA

last: Wang

country: China

description: Knock down CUL4B

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: genotype


title: CLL_empty vector_H3K27ac  [P2]

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

library_source: genomic

data_processing:
Raw fastq files alignment using bwa 0.7.7, picard & samtools.
Wiggle plots generation using PhantomPeakQualTools.
Narrow peak calling using MACS2 callpeak function with q-value < 0.01 and without input control.
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: *.bed: Bed files describing the location of the peaks.

molecule: genomic DNA

source_name: Primary CLL cells

extract_protocol:
ChIP-seq were generated as described: http://www.blueprint-epigenome.eu/index.cfm?p=7BF8A4B6-F4FE-861A-2AD57A08D63D0B58
Libraries were constructed using the Kapa Hyper Prep Kit as previously described (https://www.blueprint-epigenome.eu/UserFiles/File/Protocols/Blueprint_Kapa_hyper_prep_kit.pdf).
SE, 50bp

treatment_protocol: Cells were crosslinked with 1% formaldehyde, 15 minutes at 4º. Reaction was stopped with 1.25 M glycine for 5 minutes.

tag: patient

tag: diagnosis

value: Chronic lymphocytic leukemia

tag: cell type

value: Primary CLL cells from peripheral blood

tag: genotype/variation

value: Control

tag: chip antibody


title: naive_lox1

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5). Reads were mapped to the mouse genome (UCSC version mm10) with STAR (version 2.5.2a) with default parameters, except filtering out reads mapping to more than 10 genomic locations (outFilterMultimapNmax=10), reporting only one hit in the final alignment for multimappers (outSAMmultNmax=1) and filtering reads without evidence in the spliced junction table (outFilterType="BySJout").
Gene expression data analysis was performed using the R software (version 3.5). Read alignment quality was evaluated using the qQCReport function of the R Bioconductor package QuasR (version 1.18). Gene expression was quantified using the qCount function of QuasR as the number of reads (5'ends) overlapping with the exons of each gene assuming an exon union model (using the UCSC knownGenes annotation downloaded on 2015-12-18).
The R Bioconductor package edgeR (version 3.24.3) was used for differential gene expression analysis. Between samples normalization was done using the TMM method. Only genes with CPM (counts per million reads mapped) values more than 1 in at least 4 samples (the number of biological replicates) were retained. An generalized linear model including a genotype effect, an activation effect, and a replicate effect (nested within genotype) was fitted to the raw counts (function glmFit), and differential expression was tested using likelihood ratio tests (function glmLRT). P-values were adjusted by controlling the false-discovery rate (Benjamini-Hochberg method) and genes with a FDR lower than 1% were considered differentially expressed.
Gene set enrichment analysis was performed with the function camera from the edgeR package (using the default parameter value of 0.01 for the correlations of genes within gene sets) using gene sets from the curated gene set collection of the Molecular Signature Database (MSigDB v6.0). We considered only sets containing more than 10 genes and gene sets with a false discovery rate lower than 1% were considered significant.
Genome_build: mm10
Supplementary_files_format_and_content: gzipped text file with tab-separated counts for each gene; each row contains the annotation and raw counts per gene; columns correspond to: 1. Entrez Gene ID, 2. gene length (exon union model), 3.-40. read counts per gene and sample.

molecule: polyA RNA

organism: Mus musculus

source_name: CD4+ T cells

growth_protocol: Naïve CD4+ T cells were isolated from cell suspensions of pooled lymph nodes and spleen from single mice (male or female). Isolation was performed with StemCell mouse naïve CD4+ T cell isolation kit according to manufacturer’s instructions.

extract_protocol:
2.5*10^5 cells were washed with PBS and resuspend in 200µl TRI Reagent. RNA was extracted from Trizol-samples with a Zymo Direct-zol kit which includes DNAse treatment.
RNA quality was assessed with a Fragment Analyzer (Advanced Analytical) and RNA-seq library preparation was performed using Illumina Truseq stranded kit. Sequencing was performed on an Illumina NexSeq 500 machine to produce single-end 76-mers reads. All steps were performed at the Genomics Facility Basel (ETH Zurich).

treatment_protocol: Cells were cultured for 24 hours on plates coated with a combination of anti-CD3 (0.5µg per ml PBS) and anti-CD28 (0.2µg per ml PBS) mAb to mimic activation and co-activation signals. Plates were washed with PBS before plating the cells in complete T cell medium supplied with 50U IL2/ml.

tag: activation

value: naive

value: CD4+ T cells


title: Breast cancer cells - MCF7 CL

city: Portland

first: Ellen

last: Langer

state: OR

address: 2720 SW Moody Ave

department: DOS (Department of Oncological Sciences)

country: USA

institute: Oregon Health and Science University

description: scRNAseq

data_processing:
Aligning and gene counting with CellRanger version 3.0.2.
Filtering quality cells with Seurat (v 3.1.1).
Demultiplexing cell identity with Seurat (v 3.1.1).
Clustering and Differential Expression with Seurat (v 3.1.1).
Topic Modeling Analysis with TITAN.
Enriched genes were tested for significance of overlap with the cistrome database ChIP-seq human factor binding for T4D, MCF7 and ZR-75-1.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: counts.txt, metadata.txt

source_name: Breast cancer cell line

growth_protocol: MCF-7, T-47D and ZR-75-1 cell lines were obtained from ATCC. MCF-7 cells were maintained in high glucose DMEM with L-glutamine and pyruvate (Gibco) supplemented with 10% FBS (HyClone) and 1% Penicillin-streptomycin (Gibco). T-47D and ZR-75-1 cells were maintained in RPMI 1640 (Gibco) supplemented with 10% FBS and 1% penicillin-streptomycin. Cells were grown at 37oC with 5% CO2.

extract_protocol:
After treatment, cells were detached using phenol-red free TrypLE (Gibco) and collected in 1X DPBS (Gibco). After one wash in 1X DPBS, cells were resuspended in 2% BSA-DPBS at a concentration of 10000 cells/ml. Following incubation with TruStain Fcx blocking solution (BioLegend), Totalseq A Hashtag antibodies were added per treatment group. Cells were washed 3 times with 1 ml 2%BSA-DPBS and resuspended to a volume of ~10000 cells/ml. Equal volumes of each treatment group were pooled and cell pool was assessed for cell concentration and viability.
Single-cell cDNA and HTO libraries were generated using Chromium Single Cell 3′ version 3 and 3.1 reagents (10x Genomics and Biolegend) per manufacturer’s protocols.
Single-end sequencing of libraries was performed per manufacturer’s protocol on a Novaseq 6000 (Illumina) sequencer with HTO libraries constituting 5% of the sample.

treatment_protocol: Three days prior to hormone stimulation, cells were transferred in their respective phenol-red free media supplemented with 5% charcoal-stripped FBS (Gibco). Culture media was refreshed 1 day prior to treatments. 17-b-estradiol (E2, Millipore Sigma), progesterone (PG, Millipore Sigma) or both hormones in combination were added at a final concentration of 100 nmol/l each for given time points.

tag: treatment

value: Separated by clone

tag: timepoint

value: Multiple


title: naive_lox2


title: Spleen mito+

city: Singapore

first: Rui

last: Yokomori

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore, National University of Singapore

data_processing:
Raw reads were aligned to the pre-build mm10 reference genome using cellranger count v6.0.0 (10X Genomics) with default settings.
The molecule information file from mito- and mito+ samples were combined using cell ranger aggr with --normalize=none --nosecondary options.
Cells were removed if the number of UMIs was less than 500, the number of genes detected was less than 100, or ≥ 10% of reads were mapped to mitochondrial genes.
Read counts were normalized for each sample using the Seurat SCTransform function.
The variation due to mitochondrial RNA ratio and cell cycle phase scores were regressed out.
The normalized data from mito- and mito+ samples were integrated based on the 3,000 most highly variable genes using the Seurat integration procedure.
Top 40 principal components were used for Uniform manifold approximation and projection (UMAP) followed by cell clustering.
Marker genes for each cluster was identified using the Seurat FindConservedMarkers function.
Clusters were annotated by comparing the marker genes to known cell type markers from literatures.
Early erythroblast cells were used to identify differential exressed genes between mito- and mito+ samples using the Seurat FindAllMarkers function.
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 file continaing a feature barcode matrix of early erythroblasts. This file can be loaded into R using Seurat.
Supplementary_files_format_and_content: TSV file containig the result of differential gene expression alaysis

source_name: House mouse

growth_protocol: The F4/80+CD106+CD169+ macrophages were isolated from mito-Dendra2 mice and intravenously injected into wildtype mice after PHZ treatment. 5 days later, early erythroblasts (Ter119+Cd44+) were isolated from BM and spleen and separated into mito- and mito+ by flow cytometry based on the presence of mito-Dendra2 signal.

extract_protocol:
Cells were washed, and processed using the 10x Genomics Chromium controller and Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 following manufacturer's instructions.
The library was prepared using 10xGenomics's Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 and dual index kit following manufacturer's instructions.  Illumina P5 and P7 sequences and sample index sequences are added during the Sample Index PCR. The final library fragments contain the P5, P7, Read 1 and Read 2 sequences used in Illumina bridge amplification and sequencing. Additionally, each fragment contains the 10x Barcode, UMI and cDNA insert sequence used in data analysis.  Sequencing was done by DNBseq platform at BGI Genomics.
Single cell RNA-Seq (3'GEM)

tag: cells

value: mito-dendra2+ Spleen cells


title: naive_ko4


title: PBS_rep1

city: Suita

first: Masayuki

last: Nakamori

state: Osaka

address: 2-2, D-4, Yamadaoka

department: Neurology

country: Japan

institute: Osaka University Graduate School of Medicine

data_processing:
The libraries were sequenced on an Illumina Nova Seq 6000 (Illumina),
FastQC evaluated FASTQ files after the trimming process using PRINSEQ v0.19.2 (Schmieder and Edwards, 2011).
The FASTQ files were aligned to the genomic reference sequence using TopHat v.2.0.13 (Kim et al., 2013).
The estimated transcript abundance was calculated, and the count values were normalized to the upper quartile of the fragments per kilobase of transcript per million mapped reads using Cufflinks v2.2.1 (Trapnell et al., 2010).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

extract_protocol:
At 22 weeks of age, mice were sacrificed, and RNA were isolated from the murine brain tissue. RNA was harvested using Trizol reagent. Illumina TruSeq stranded mRNA library prep was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: striatum

value: PBS

tag: strain

value: Q113 DRPLA transgenic mice


title: Spleen mito-

value: mito-dendra2- Spleen cells


title: PBS_rep2


title: NA_rep3


title: naive_ko3


title: BM mito+

value: mito-dendra2+ BM cells


title: Breast cancer cells - MCF7 PD

description: scRNAseq

value: Progesterone and combination treatment


title: BM mito-

value: mito-dendra2- BM cells


title: Breast cancer cells - MCF7 E2

description: scRNAseq

value: Estrogen treatment


title: NA_rep2


title: Breast cancer cells - ZR

description: scRNAseq

value: ALL


title: NA_rep1


title: CLL_empty vector_H3K27ac  [P1]

value: Chronic lymphocytic leukemia


title: naive_ko1


title: naive_ko2


title: Breast cancer cells - T47D

description: scRNAseq


title: ATTX-POSTCX.92-RNA

status: Public on Sep 07 2022

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

data_processing:
Quality control of the raw reads was performed using FastQC (v.0.11.9).
Raw sequencing reads were trimmed for quality control using TrimGalore (v.0.6.5).
Trimmed sequence reads were mapped to a chimeric human+mouse genome and transcriptome using the STAR (v.2.7.2b) aligner.
Read quantification was performed using RSEM (v.1.3.3).
Assembly: Human: GRCh38 primary assembly / hg38 / Gencode.v.33 (Ensembl.v.99), Mouse: GRCm38 primary assembly / mm10 / Gencode.v.M24 (Ensembl.v.99)
Supplementary files format and content: Tab separated TXT file with TPM values for human genes for each sample as generated by RSEM, gene symbol duplicates were collapsed by calculating their means.

source_name: prostate cancer cell line xenograft

extract_protocol:
Total cellular RNA was extracted using the Norgen RNA Purification PLUS kit (#48400, Norgen Biotek Corp) as per manufacturer's instructions. RNA quality (RIN>8) and quantity were determined on an Agilent 2100 Bioanalyzer (Agilent Technologies) and Qubit®. 2.0 Fluorometer (Thermo Fisher Scientific).
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit (strand-specific, polyA enrichment), including ERCC controls.
Paired-end sequencing on Illumina HiSeq 2500 (Kinghorn Centre for Clinical Genomics, Sydney, Australia) with a read length of 125 bp, yielding about 40 M read pairs per sample.

treatment_protocol: For the in vivo tumour progression study, xenografts were established by subcutaneous injection of one million LNCaP cells (CVCL_0395, ATCC #CRL-1740 clone FGC) into the flank of NOD-SCID mice (54 mice in total). At a tumour size of ~200 cubic mm (mm3), mice were either surgically castrated (45 mice) or received mock surgery for the PRE-CX group (pre-castration, 9 mice). Tumours from the PRE-CX group (9 mice) were harvested when the ethical tumour size endpoint of 1000 mm3 was reached. Tumours from the POST-CX (post-castration, 8 mice) group were harvested one-week post-castration at primary serum PSA (Prostate-Specific Antigen) nadir. CRPC (Castrate-Resistant Prostate Cancer, 10 mice) tumours were harvested when PSA levels recurred to pre-castration levels or when tumour burden reached 1000 mm3 post-castration. For the enzalutamide (ENZ) groups, treatment with 10 mg/kg ENZ (oral gavage, 5 days/week) commenced as serum PSA began to rise post-castration. Tumours were harvested either at secondary PSA nadir (ENZS, 12 mice) while on ENZ treatment, with the remaining tumours collected when PSA had recurred to pre-ENZ treatment levels or when tumour volume reached ethical endpoint of 1000 mm3 despite ENZ treatment (ENZR, 15 mice). Xenografts were rapidly dissected, snap frozen in liquid nitrogen and stored at −80°C; until being homogenised in a pre-cooled TissueLyser (Qiagen) for RNA extraction.

value: prostate cancer cell line xenograft

value: LNCAP

tag: host

value: NOD-SCID mouse

tag: mouseid

tag: sample group

value: POST-CX


title: ATTX-POSTCX.86-RNA


title: ATTX-POSTCX.99-RNA


title: ATTX-POSTCX.91-RNA


title: ATTX-POSTCX.44-RNA


title: ATTX-POSTCX.48-RNA


title: ATTX-INTACT.67-RNA

value: PRE-CX


title: ATTX-INTACT.9-RNA


title: ATTX-INTACT.58-RNA


title: ATTX-INTACT.112-RNA


title: ATTX-INTACT.5-RNA


title: ATTX-INTACT.4-RNA


title: ATTX-INTACT.62-RNA


title: ATTX-INTACT.111-RNA


title: ATTX-ENZ.95-RNA

value: ENZR


title: ATTX-ENZ.98-RNA


title: ATTX-ENZ.80-RNA

value: ENZS


title: ATTX-ENZ.75-RNA


title: ATTX-ENZ.79-RNA


title: ATTX-ENZ.76-RNA


title: ATTX-ENZ.6-RNA


title: ATTX-ENZ.72-RNA


title: ATTX-ENZ.65-RNA


title: ATTX-POSTCX.66-RNA


title: ATTX-POSTCX.18-RNA


title: ATTX-ENZ.57-RNA


title: ATTX-ENZ.64-RNA


title: ATTX-ENZ.56-RNA


title: ATTX-ENZ.49-RNA


title: ATTX-ENZ.45-RNA


title: ATTX-INTACT.53-RNA


title: ATTX-ENZ.33-RNA


title: ATTX-ENZ.28-RNA


title: ATTX-ENZ.23-RNA


title: ATTX-ENZ.21-RNA


title: ATTX-ENZ.94-RNA


title: ATTX-ENZ.106-RNA


title: ATTX-ENZ.104-RNA


title: ATTX-ENZ.101-RNA


title: ATTX-ENZ.105-RNA


title: ATTX-ENZ.103-RNA


title: ATTX-ENZ.87-RNA


title: ATTX-CRPC.89-RNA

value: CRPC


title: ATTX-ENZ.17-RNA


title: ATTX-CRPC.78-RNA


title: ATTX-CRPC.81-RNA


title: ATTX-CRPC.47-RNA


title: ATTX-CRPC.35-RNA


title: ATTX-CRPC.29-RNA


title: ATTX-CRPC.36-RNA


title: ATTX-CRPC.102-RNA


title: ATTX-CRPC.107-RNA


title: ATT-BIC.VEH-RNA.7, biol rep 2

data_processing:
Quality control of the raw reads was performed using FastQC (v.0.11.9).
Raw sequencing reads were trimmed for quality control using TrimGalore (v.0.6.5).
Trimmed sequence reads were mapped to the human genome and transcriptome using the STAR (v.2.7.2b) aligner.
Read quantification was performed using RSEM (v.1.3.3).
Assembly: GRCh38 primary assembly / hg38 / Gencode.v.33 (Ensembl.v.99)
Supplementary files format and content: Tab separated TXT file with TPM values for each sample as generated by RSEM, gene symbol duplicates were collapsed by calculating their means.

source_name: prostate cancer

growth_protocol: LNCaP cells were seeded and cultured for 72 hr in RPMI media with 5% FBS in a humidified incubator at 37°C and 5% CO2. This was followed by a 48 hr incubation in androgen-depleted conditions using media + 5% charcoal-stripped serum (CSS).

treatment_protocol: Treatment with the androgen receptor targeting drugs enzalutamide (10uM, ENZ), bicalutamide (10uM, BIC) and apalutamide (10uM, ARN) was performed for 48 hr, either in the absence or presence of 10 nM dihydrotestosterone (DHT). DHT was dissolved in Ethanol, all other drugs in DMSO - control treated cells (VEH) received both solvents.

value: prostate cancer

value: VEH+Bicalutamide


title: ATT-ENZ.DHT-RNA.3, biol rep 1

value: DHT+Enzalutamide


title: ATT-BIC.VEH-RNA.3A, biol rep 1


title: ATT-DHT-RNA.3C, biol rep 1

value: DHT+VEH


title: ATT-DHT-RNA.7B, biol rep 2


title: ATT-ENZ.VEH-RNA.7, biol rep 2

value: VEH+Enzalutamide


title: ATT-VEH-RNA.3A, biol rep 1

value: VEH


title: ATT-VEH-RNA.7B, biol rep 2


title: ATTX-ENZ.100-RNA


title: ATT-BIC.DHT-RNA.7, biol rep 2

value: DHT+Bicalutamide


title: ATT-ENZ.DHT-RNA.7, biol rep 2


title: FBS-VCAP.1-RNA/biol rep 1

data_processing:
Paired-end sequencing on Illumina HiSeq 2500 (Kinghorn Centre for Clinical Genomics, Sydney, Australia) with a read length of 125 bp, yielding about 30 M read pairs per sample.
Quality control of the raw reads was performed using FastQC (v.0.11.9).
Raw sequencing reads were trimmed for quality control using TrimGalore (v.0.6.5).
Trimmed sequence reads were mapped to the human genome and transcriptome using the STAR (v.2.7.2b) aligner.
Read quantification was performed using RSEM (v.1.3.3).
Assembly: GRCh38 primary assembly / hg38 / Gencode.v.33 (Ensembl.v.99)
Supplementary files format and content: Tab separated TXT file with TPM values for each sample as generated by RSEM, gene symbol duplicates were collapsed by calculating their means.

source_name: prostate cancer cell line

growth_protocol: The human prostate cancer cell lines LNCaP, VCaP, DU-145, PC-3 and DuCaP were cultured in Phenol-red free RPMI media supplemented with 5-10% fetal bovine serum (FBS) in a humidified incubator at 37°C and 5% CO2 and were harvested for RNA extraction during their exponential growth phase.

extract_protocol:
Total cellular RNA was extracted using the Norgen RNA Purification PLUS kit (#48400, Norgen Biotek Corp) as per manufacturer's instructions. RNA quality (RIN>8) and quantity were determined on an Agilent 2100 Bioanalyzer (Agilent Technologies) and Qubit®. 2.0 Fluorometer (Thermo Fisher Scientific).
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit (strand-specific, polyA enrichment), including ERCC controls.

value: prostate cancer cell line

value: VCAP

value: untreated


title: ATT-ARN.DHT-RNA.7, biol rep 2

value: LNCAP

value: DHT+Apalutamide


title: FBS-DUCAP.2-RNA/biol rep 2

value: DUCAP


title: ATT-BIC.DHT-RNA.3A, biol rep 1


title: ATT-ARN.VEH-RNA.3C, biol rep 1

value: VEH+Apalutamide


title: ATT-ARN.DHT-RNA.3, biol rep 1


title: FBS-VCAP.2-RNA/biol rep 2


title: ATTX-CRPC.43-RNA

value: prostate cancer cell line xenograft

value: NOD-SCID mouse


title: FBS-PC3.2-RNA/biol rep 1


title: FBS-LNCAP.2-RNA/biol rep 2


title: FBS-DU145.1-RNA/ biol rep 1


title: FBS-LNCAP.1-RNA/biol rep 1


title: FBS-DU145.3-RNA/biol rep 2


title: FBS-DUCAP.1-RNA/biol rep 1


title: ATT-ENZ.VEH-RNA.3, biol rep 1


title: Capture Hi-C, NA07056-batch-2, biological replicate B

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

data_processing:
The capture Hi-C paired-end sequencing reads were mapped to the SNP-masked hg19 human genome using HiC-Pro software (version 2.6.0; Servant et al., 2015: PMID: 26619908) as follows. First, we obtained phased genotype VCF files for NA07000 and NA07056 cell lines from 1000 Genomes Project (version v5a.20130502), and generated two SNP-masked (i.e. alternative/reference and alternative/alternative SNP genotype loci were masked with N) hg19 genomes files for these two cell lines.  The individual reads in each mapped paired-end read are evaluated for the presence of heterozygous SNPs and labeled as one of the following using phased genotype data from 1000 Genomes Project: parent-1 allele (M), parent-2 allele (P), or allele unassigned (UA). The M-M, M-UA and UA-M paired-end reads were grouped as ‘parent-1’ and P-P, P-UA and UA-P paired-end reads were grouped as ‘parent-2’ to compute chromatin interaction frequencies on two homologous chromosomes (G1 is SLE non-risk haplotype and G2 is SLE risk haplotype) at 5kb resolution for each replicate library. Raw interaction frequency count sparse matrices G1 (non-risk) and G2 (risk) were generated. The IDs of two 5kb regions from the first two columns in the matrix files are decoded in the dictionary file hg19_HiC_region_Ids_chr8.bed.
To identify differences in cis-interaction frequencies of homologous chromosomes 8 harboring risk and non-risk haplotypes, we determined haplotype-specific (G1 and G2) interaction frequency matrices in 5kb bins for each replicate library. For n replicate libraries from each cell line, we computed n matrices for G1 haplotype and n matrices for G2 haplotype. For NA07000, we used n = 5 (p1, p2, p3, p4 and p5). For NA07056, we used n = 4 (p1_a, p1_b, p2_a and p2_b). Treating the entries of these matrices as sequence count data with the study design (G1, G1, G1, G1, G1, G2, G2, G2, G2, G2) for NA07000  and the study design (G1, G1, G1, G1, G2, G2, G2, G2) for NA07056, we determined differential chromatin interactions using multiHiCcompare (version 1.10.0) method (Stansfield et al., 2019: PMID: 30668639) with the following parameters: make_hicexp(zero.p=0.8, A.min=5), cyclic_loess(span = 0.2), logfc_cutoff = 0.5, logcpm_cutoff = 0.5,  p.method = ‘fdr’ and p.adj_cutoff = 0.05. The differential interactions are reported in the supplementary files *FDR5.csv. The interactions with positive log2FC (base-2 log fold-change) values are stronger on the risk haplotype than on the non-risk haplotype, and those with negative log2FC are weaker on the risk haplotype than on the non-risk haplotype.
Assembly: hg19
Supplementary files format and content: HiC-Pro output raw cis-interactions count matrices (*.matrix) in sparse 3-column format. Columns 1 and 2 contain IDs of pairs of 5kb regions on chromosome 8; third column contains the raw cis-interaction frequency of the two regions.
Supplementary files format and content: hg19_HiC_region_IDs_chr8.bed file contains IDs of 5kb regions on chromosome 8

source_name: Epstein-Barr Virus- (EBV-) Immortalized Lymphoblastoid Cell Line (LCL)

growth_protocol: LCLs were maintained in RPMI medium supplemented with 10% FBS and 1% penicillin-streptomycin, and were grown at 37C in 5% CO2.

extract_protocol:
Capture Hi-C libraries were prepared according to the protocol described in (Jäger et al., 2015: PMID: 25695508). The protocol consists of two parts: Hi-C library preparation and target enrichment (Figure 1A). A SureSelect Custom Target Enrichment Library covering a 3Mb region in the 8p23.1 (hg19 coordinates: chr8:8190000-11838000) was designed using eArray software (Agilent). Hi-C library preparation, comprising chromatin fixation, HindIII digestion, biotin labelling, ligation and crosslink reversal was performed as described in (Rao et al., 2014: PMID: 25497547) with minor modifications described in (Jäger et al., 2015). Target enrichment was performed according to the SureSelect protocol (Agilent) with minor modifications described in (Jäger et al., 2015: PMID: 25695508). We have prepared 10 capture Hi-C libraries from 5 independent batches of NA07000 cells and 4 capture Hi-C libraries from 2 independent batches of NA07056 cells (2 biological replicates per cell batch).
Capture Hi-C

value: NA07056 LCL

value: B-cell derived LCL


title: Capture Hi-C, NA07056-batch-2, biological replicate A

value: Epstein-Barr Virus- (EBV-) Immortalized Lymphoblastoid Cell Line (LCL)


title: Capture Hi-C, NA07056-batch-1, biological replicate B


title: ATT-ARN.VEH-RNA.7, biol rep 2

value: prostate cancer


title: Capture Hi-C, NA07000-batch-5, biological replicate A

value: NA07000 LCL


title: FBS-PC3.3-RNA/biol rep 2


title: Capture Hi-C, NA07000-batch-4, biological replicate B


title: Capture Hi-C, NA07056-batch-1, biological replicate A


title: GM10253A_IgG_ChIP_chip_rep1

type: genomic

city: Edinburgh

first: Catherine

last: Naughton

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

description: Chinese hamster/human hybrid retaining human chromosome #3

hyb_protocol: Labeled DNA was diluted in hybridization buffer (Agilent) and hybridized to arrays for 24 h at 65°C. Slides were washed according to the manufacturer’s instructions. Agilent-053809  (7MB human chr3) and Agilent -077398 (22MB human chr3) arrays were used.

scan_protocol: Arrays were scanned on a Nimblegen Microarray scanner at 2 μm resolution generating a TIFF file.

data_processing:
Spot signal intensity was extracted from the TIFF files using Agilent Feature Extraction software and were pre-processed in R using the RINGO bioconductor package to give the raw Cy5 and Cy3 signal intensities for each spot. Individual Cy5 and Cy3 channels were normalized to each other and between arrays and then normalised and scaled using the standard Bioconductor LIMMA package. Normalisation was as follows: loess normalisation for H3K27ac, H3K4me2, H3K9me2, H3K9me3, H4K20me1, H3K27me3 and H3K36me3 ChIps, vsn normalisation for RNA pol II and CTCF ChIps and nimblegen normalisation for CENPA and CENPC ChIPs.
ChIP_chip_normalized_matrix: Normalized Log2 (ChIP/Input) for the 7MB region common between both Agilent array types used (all ChIP's except RNA polymerase where normalisation was of a 3MB region surrounding the neocentromere).

organism:
Homo sapiens
Cricetulus griseus

source_name: IgG IP from GM10253A cells

label_protocol: For microarray hybridization, immunoprecipitated DNA was amplified using whole-genome amplification (Sigma) and 500 ng DNA was random prime labeled (ENZO) with Cy3 (Sample DNA) or Cy5 (Input DNA) and purified on a MinElute PCR purification column (Qiagen).

growth_protocol: Human/Hamster hybrid cell lines GM10253A and HybNeo3 were grown in RPMI 1640 with L-Glutamine, 10% FCS and penicillin and streptomycin. Human parenral lymphoblastoid cell line was grown in RPMI 1640 with L-Glutamine, 20% FCS and penicillin and streptomycin.

extract_protocol: ChIP was done as described in Kimura et al. (2008) Cell Structure and function, except that a Soniprep 150 (Sanyo) was used for sonication. In brief, cells (5-6 x 106 in 10 cm dishes) were cross-linked with 10 ml 1% formaldehyde (Sigma) in medium for 5 min at room temperature and then incubated in 10 ml 200mM glycine in medium for 5 min. Cells were rinsed twice with PBS and incubated with 7 ml lysis buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl and 0.5% NP-40) for 10 min at room temperature with mild rotation. This lysis buffer was then aspirated off and cells were scraped into 1 ml lysis buffer and centrifuged at 3000 rpm for 3 min at 4°C. Cell pellet was resuspended in 100 μl SDS lysis buffer (50 mM Tris-HCl (pH 7.5), 10 mM EDTA and 1% SDS) and mixed by pipetting. 400 μl ChIP dilution buffer (50 mM Tris-HCl (pH 7.5), 167 mM NaCl, 1.1% Triton X-100, 0.11% sodium deoxycholate and protease inhibitor cocktail (complete EDTA-free; Roche)) was added before sonication (fifteen times for 20 seconds at 2 μm). After centrifugation at 13,000 rpm for 15 min at 4°C to remove the insoluble material the supernatant was removed to a new 1.5 ml tube and the volume made up to 500 μl with ChIP dilution buffer. 50 μl was removed as input for ChIP and the rest of the sample was incubated with antibody-bound Dynabeads overnight at 4°C with rotation. Dynabeads were prepared in advance by taking 50 μl of beads and washing three times with 500 μl cold RIPA-150 mM NaCl buffer (50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.11% sodium deoxycholate and protease inhibitor cocktail). Beads were then incubated with 500 μl cold RIPA-150 mM NaCl buffer plus antibody for 2 hr at 4°C with rotation. Beads were then washed three times with 500 μl cold RIPA-150 mM NaCl buffer and were then ready for overnight incubation with the ChIP sample. Beads were washed sequentially with 1 ml cold RIPA- 500 mM NaCl (50 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.11% sodium deoxycholate and protease inhibitor cocktail) and twice with 1 ml TE (10 mM Tris-HCl (pH 8.0) and 1 mM EDTA). DNA was eluted by the addition of 200 μl ChIP direct elution buffer (10mM Tris-HCl (pH8.0), 300 mM NaCl, 5mM EDTA and 0.5% SDS) and incubated overnight at 65°C. Samples were then treated with DNase-free RNase (Roche; 5 μg.ml-1; 37°C; 30 min) and proteinase K (250 μg.ml-1; 55°C; 1 hr). DNA was extracted with phenol-chloroform-isoamyl alcohol (25:24:1) and ethanol precipitated with carrier (1μl glycogen, Invitrogen) on dry ice for 30 min. Following 70% ethanol wash the DNA pellet was resuspended in 20 μl water and quantified using a NanoDrop.

treatment_protocol: Normally growing cells

value: GM10253A cells

value: Untreated

source_name: Input from GM10253A cells


title: Parental_Neo6_CENPA_ChIP_chip_rep1

description: Parental Human Lymphoblastoid cells with one canonical chromosome 6 (HSA6) and one chromosome 6 with a neocentromere (Neo6)

hyb_protocol: Labeled DNA was diluted in hybridization buffer (Agilent) and hybridized to arrays for 24 h at 65°C. Slides were washed according to the manufacturer’s instructions. Agilent-053809 (7MB human chr3) and Agilent -077398 (22MB human chr3) arrays were used.

data_processing: Spot signal intensity was extracted from the TIFF files using Agilent Feature Extraction software and were pre-processed in R using the RINGO bioconductor package to give the raw Cy5 and Cy3 signal intensities for each spot. Individual Cy5 and Cy3 channels were normalized to each other and between arrays and then normalised and scaled using the standard Bioconductor LIMMA package. Normalisation was as follows: loess normalisation for H3K27ac, H3K4me2, H3K9me2, H3K9me3, H4K20me1, H3K27me3 and H3K36me3 ChIps, vsn normalisation for RNA pol II and CTCF ChIps and nimblegen normalisation for CENPA and CENPC ChIPs.

source_name: CENPA IP from Parental Neo6 cells

growth_protocol: Human/Hamster hybrid cell lines GM10253A and HybNeo3 were grown in RPMI 1640 with L-Glutamine, 10% FCS and penicillin and streptomycin. Human parental lymphoblastoid cell line was grown in RPMI 1640 with L-Glutamine, 20% FCS and penicillin and streptomycin.

extract_protocol: ChIP was done as described in Kimura et al. (2008) Cell Structure and function, except that a Soniprep 150 (Sanyo) was used for sonication. In brief, cells (5-6 x 10^6 in 10 cm dishes) were cross-linked with 10 ml 1% formaldehyde (Sigma) in medium for 5 min at room temperature and then incubated in 10 ml 200mM glycine in medium for 5 min. Cells were rinsed twice with PBS and incubated with 7 ml lysis buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl and 0.5% NP-40) for 10 min at room temperature with mild rotation. This lysis buffer was then aspirated off and cells were scraped into 1 ml lysis buffer and centrifuged at 3000 rpm for 3 min at 4°C. Cell pellet was resuspended in 100 μl SDS lysis buffer (50 mM Tris-HCl (pH 7.5), 10 mM EDTA and 1% SDS) and mixed by pipetting. 400 μl ChIP dilution buffer (50 mM Tris-HCl (pH 7.5), 167 mM NaCl, 1.1% Triton X-100, 0.11% sodium deoxycholate and protease inhibitor cocktail (complete EDTA-free; Roche)) was added before sonication (fifteen times for 20 seconds at 2 μm). After centrifugation at 13,000 rpm for 15 min at 4°C to remove the insoluble material the supernatant was removed to a new 1.5 ml tube and the volume made up to 500 μl with ChIP dilution buffer. 50 μl was removed as input for ChIP and the rest of the sample was incubated with antibody-bound Dynabeads overnight at 4°C with rotation. Dynabeads were prepared in advance by taking 50 μl of beads and washing three times with 500 μl cold RIPA-150 mM NaCl buffer (50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.11% sodium deoxycholate and protease inhibitor cocktail). Beads were then incubated with 500 μl cold RIPA-150 mM NaCl buffer plus antibody for 2 hr at 4°C with rotation. Beads were then washed three times with 500 μl cold RIPA-150 mM NaCl buffer and were then ready for overnight incubation with the ChIP sample. Beads were washed sequentially with 1 ml cold RIPA- 500 mM NaCl (50 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.11% sodium deoxycholate and protease inhibitor cocktail) and twice with 1 ml TE (10 mM Tris-HCl (pH 8.0) and 1 mM EDTA). DNA was eluted by the addition of 200 μl ChIP direct elution buffer (10mM Tris-HCl (pH8.0), 300 mM NaCl, 5mM EDTA and 0.5% SDS) and incubated overnight at 65°C. Samples were then treated with DNase-free RNase (Roche; 5 μg.ml-1; 37°C; 30 min) and proteinase K (250 μg.ml-1; 55°C; 1 hr). DNA was extracted with phenol-chloroform-isoamyl alcohol (25:24:1) and ethanol precipitated with carrier (1μl glycogen, Invitrogen) on dry ice for 30 min. Following 70% ethanol wash the DNA pellet was resuspended in 20 μl water and quantified using a NanoDrop.

value: Parental Human Lymphoblastoid cells

source_name: Input from Parental cells


title: HybNeo3_IgG_ChIP_chip_rep1

description: Chinese hamster/human hybrid retaining the following human chromosomes ; 4, 6, 8, 11, 13, 18 ,X and a 3 carrying a neocentromere (Neo3).

source_name: IgG IP from HybNeo3 cells

value: HybNeo3 cells

source_name: Input from HybNeo3 cells


title: Parental_Neo6_CENPC_ChIP_chip_rep1

source_name: CENPC IP from Parental Neo6 cells


title: Capture Hi-C, NA07000-batch-5, biological replicate B


title: Capture Hi-C, NA07000-batch-3, biological replicate B


title: Capture Hi-C, NA07000-batch-3, biological replicate A


title: Parental_CENPA_ChIP_chip_rep1

description: Parental Human Lymphoblastoid cells with one canonical chromosome 3 (HSA3) and one chromosome 3 with a neocentromere (Neo3)

source_name: CENPA IP from parental cells


title: Capture Hi-C, NA07000-batch-4, biological replicate A


title: Capture Hi-C, NA07000-batch-2, biological replicate A


title: HybNeo3_CENPC_ChIP_chip_rep1

source_name: CENPC IP from HybNeo3 cells


title: Parental_CENPC_ChIP_chip_rep1

source_name: CENPC IP from Parental cells


title: Capture Hi-C, NA07000-batch-2, biological replicate B


title: HybNeo3_H3K27me3_ChIP_chip_rep2

source_name: H3K27me3 IP from HybNeo3 cells


title: HybNeo3_H3K27me3_ChIP_chip_rep1


title: GM10253A_H3K27me3_ChIP_chip_rep2

source_name: H3K27me3 IP from GM10253A cells


title: HybNeo3_H4K20me1_ChIP_chip_rep2

source_name: H4K20me1 IP from HybNeo3 cells


title: HybNeo3_H4K20me1_ChIP_chip_rep1


title: GM10253A_CENPC_ChIP_chip_rep1

source_name: CENPC IP from GM10253A cells


title: GM10253A_H4K20me1_ChIP_chip_rep1

source_name: H4K20me1 IP from GM10253A cells


title: HybNeo3_H3K4me2_ChIP_chip_rep1

source_name: H3K4me2 IP from HybNeo3 cells


title: GM10253A_H3K4me2_ChIP_chip_rep1

source_name: H3K4me2 IP from GM10253A cells


title: Capture Hi-C, NA07000-batch-1, biological replicate A

source_name: Epstein-Barr Virus- (EBV-) Immortalized Lymphoblastoid Cell Line (LCL)


title: Capture Hi-C, NA07000-batch-1, biological replicate B


title: GM10253A_H3K27me3_ChIP_chip_rep1

source_name: Input from GM10253A cells


title: HybNeo3_H3K27ac_ChIP_chip_rep1

source_name: H3K27ac IP from HybNeo3 cells


title: GM10253A_H3K7ac_ChIP_chip_rep1

source_name: H3K27ac IP from GM10253A cells


title: HybNeo3_bTMP_chip_rep2

hyb_protocol: Labeled DNA was diluted in hybridization buffer (Agilent) and hybridized to arrays for 24 h at 65°C. Slides were washed according to the manufacturer’s instructions. Agilent-053809  (7MB human chr3) arrays were used.

data_processing:
Spot signal intensity was extracted from the TIFF files using Agilent Feature Extraction software and were pre-processed in R using the RINGO bioconductor package to give the raw Cy5 and Cy3 signal intensities for each spot. Individual Cy5 and Cy3 channels were normalized to each other and between arrays and then nimblegen normalised and scaled using the standard Bioconductor LIMMA package.
bTMP_normlized_matrix: Normalized Log2 (bTMP/Input)

source_name: bTMP-IP from HybNeo3 cells

extract_protocol: Cells were treated with 500 μg.ml-1 of bTMP in PBS for 20 min at room temperature in the dark. bTMP was UV cross-linked to DNA at 360 nm for 10 min. DNA was purified from cells using SDS and proteinase K digestion and extracted using phenol-chloroform-isoamyl alcohol (25:24:1). DNA was fragmented by sonication (thirteen times for 30s at 2 μm). Biotin incorporation into DNA was detected by dot blotting using alkaline phosphatase−conjugated avidin as a probe. The bTMP−DNA complex in TE was immunoprecipitated using avidin conjugated to magnetic beads (Dynabeads MyOne Streptavidin Invitrogen, 65001) for 2 h at room temperature and then overnight at 4°C. Beads were washed sequentially for 5 min each at room temperature with TSE I (20 mM Tris-HCl, pH 8.1, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100 and 0.1% SDS), TSE II (20 mM Tris-HCl, pH 8.1, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100 and 0.1% SDS) and buffer III (10 mM Tris-HCl, pH 8.1, 0.25 M LiCl, 1 mM EDTA, 1% NP40 and 1% deoxycholate). Beads were then washed twice with TE buffer for 5 min. To extract DNA and to release psoralen adducts, the samples were boiled for 10 min at 90°C in 50 μl of 95% formamide with 10 mM EDTA. Samples were then made up to 200 μl with water, and the DNA was purified using a Qiagen MinElute PCR purification kit. bTMP bound DNA was amplified using whole-genome amplification (Sigma) prior to microarray hybridization.

treatment_protocol: Cells were untreated or treated with alpha-amanitin (5h)


title: HybNeo3_bTMP_chip_amanitin_rep1

value: 5h alpha-amanitin treatment

source_name: Input from HybNeo3 cells


title: HybNeo3_bTMP_chip_amanitin_rep2


title: HybNeo3_bTMP_chip_rep1


title: GM10253A_H4K20me1_ChIP_chip_rep2


title: GM10253A_bTMP_chip_amanitin_rep1

source_name: bTMP-IP from GM10253A cells


title: 44-2

type: RNA

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

country: Denmark

institute: National Genome Center

hyb_protocol: RNA was hybridized to Affymetrix GeneChip HT HG-U219 arrays, and processed in a Gene Titan Platform (Affymetrix, Santa Clara, USA).

data_processing: The resulting CEL files were pre-processed using the RMA algorithm as implemented in Affymetrix Power Tools, including a log2 transformation step (version 1.16.1) [cite 12925520]. The probes were summarized using custom CDF files remapped to Ensembl genes (Brain array) [PMID 16284200].

label: biotin

source_name: sigmoideum

growth_protocol: Human samples, no growth protocol

extract_protocol: All intestinal biopsies were placed immediately in RNAlater (Qiagen) stored in a refrigerator and later transferred to a -80ºC freezer for long time storage until RNA extraction. The biopsy tissue was transferred into a tube and homogenized with Ultra Turrax (IKA, Staufen, Germany), together with 700µl Qiazol reagent (company ref). The quality and concentration of the purified total RNA was investigated on a Bioanalyzer 2100  (Agilent) using the RNA 6000 Nano Labchip kit (Agilent technologies, Santa Clara, CA), and all RNA sample concentrations were measured on a ND-8000 NanoDrop (Thermo Fisher Scientific, Waltham, MA).  RNA quality was evaluated based on the 28S/18S ratio RIN (RNA integrity number. The RIN value from the human biopsy materials varied but all values above 7 were used for Array. RNA was stored at -80°C until use.

treatment_protocol: Mucosal biopsies were obtained from patients with chronic inflammatory bowel disease (IBD), ulcerative colitis (UC) or Crohn’s disease (CD) diagnosed according to generally accepted standard (Lennard-Jones PMID 2617184). Consecutively included were IBD patients followed at the IBD clinic Northsealand Hospital and referred to colonoscopy or sigmoidoscopy due to clinical activity of at least 14 days duration. As control patients were included persons referred to endoscopy for reasons other than IBD revealing normal endoscopy. Exclusion criteria were for IBD patients and controls: age below 18 years, any gastrointestinal disease other than IBD, malignant disease, or known autoimmune disease not associated to IBD. Totally 109 biopsy donors were included, 53 UC, 25 CD, and 28 controls.

tag: biopsy

tag: age

value: UC

tag: gastroscopy

value: FALSE

tag: inflammation

value: yes

value: sigmoideum


title: 80-6

scan_protocol: RNA was hybridized to Affymetrix GeneChip HT HG-U219 arrays, and processed in a Gene Titan Platform (Affymetrix, Santa Clara, USA).

source_name: rectum

tag: patient

tag: diagnosis

value: CD

value: non

value: rectum


title: 80-4

source_name: descendens

label_protocol: RNA was hybridized to Affymetrix GeneChip HT HG-U219 arrays, and processed in a Gene Titan Platform (Affymetrix, Santa Clara, USA).

value: descendens


title: 80-5


title: 15-3

source_name: ascendens

value: ascendens


title: GM10253A_bTMP_chip_rep2

tag: cell type


title: GM10253A_bTMP_chip_rep1


title: 80-3

source_name: transversum

value: transversum


title: 15-5


title: 35-3


title: 121-5

value: Control


title: 120-2


title: 15-2

source_name: coecum

value: coecum


title: 115-2


title: HybNeo3_amanitin_open_chromatin_rep2

data_processing:
Spot signal intensity was extracted from the TIFF files using Agilent Feature Extraction software and were pre-processed in R using the RINGO bioconductor package to give the raw Cy5 and Cy3 signal intensities for each spot. Individual Cy5 and Cy3 channels were normalized to each other and between arrays and then nimblegen normalised and scaled using the standard Bioconductor LIMMA package.
chromatin_normalized_matrix: Normalized Log2 (Open/Input)

source_name: DNA representative of open chromatin from HybNeo3 cells

label_protocol: For microarray hybridization,  Sample (DNA representative of open chromatin isolated from gradient fraction) and Input DNA (whole fraction DNA) were amplified using whole-genome amplification (Sigma) and 500 ng DNA was random prime labeled (ENZO) with Cy3 (Sample DNA) or Cy5 (Input DNA) and purified on a MinElute PCR purification column (Qiagen).

extract_protocol: Disrupted or ‘open’ chromatin was isolated as follows. Cell nuclei were digested with micrococcal nuclease and soluble chromatin released overnight followed by fractionation on a 6-40% isokinetic sucrose gradient in 80 mM NaCl, 0.1 mM EDTA, 0.1 mM EGTA and 250 μM PMSF. DNA purified from gradient fractions was analyzed by electrophoresis through 0.7% agarose in 1 × TPE buffer (90 mM Tris-phosphate, 2 mM EDTA) with buffer circulation. Preparative fractionation of DNA from gradient fractions was carried out by pulsed-field gel electrophoresis (PFGE) (CHEF system, Biorad) through 1% low melting point agarose in 0.5 × TBE, at 180 V, for 40 hr, with a 0.1–2 s switching time. Size markers were 1 kb (Promega) and λ-HindIII (NEB) DNA ladders. EtBr-stained gels were scanned using a 473 nm laser and a 580 nm band-pass filter on a Fuji FLA-3000. DNA of ~ 20 kb, corresponding to “open” chromatin, was isolated by β-agarase (NEB) digestion and amplified by whole genome amplification (Sigma) prior to microarray hybridization

value: alpha-amanitin (5h)

source_name: Whole fraction DNA


title: 15-4


title: HybNeo3_amanitin_open_chromatin_rep1


title: 35-5


title: HybNeo3_open_chromatin_rep3

value: Untreated


title: GM10253A_amanitin_open_chromatin_rep1

source_name: DNA representative of open chromatin from GM10253A cells

value: GM10253A cells


title: 111-2

source_name: ileum

value: ileum


title: HybNeo3_open_chromatin_rep2

value: HybNeo3 cells


title: 80-2


title: 33-3

value: UC


title: HybNeo3_CTCF_ChIP_chip_rep1

source_name: CTCF IP from HybNeo3 cells


title: 15-6

value: FALSE


title: HybNeo3_RNApolymerase_HK1_ChIP_chip_rep1

source_name: RNApolymerase_HK1 IP from HybNeo3 cells


title: GM10253A_open_chromatin_rep3


title: 42-2


title: 108-3

value: yes


title: GM10253A_open_chromatin_rep2


title: GM10253A_RNApolymerase_HK1_ChIP_chip_rep1

source_name: RNApolymerase_HK1 IP from GM10253A cells

source_name: Input from GM10253A cells


title: GM10253A_open_chromatin_rep1


title: 80-1


title: HybNeo3_RNApolymerase_D2_ChIP_chip_rep3

source_name: RNApolymerase_D2 IP from HybNeo3 cells


title: GM10253A_CTCF_ChIP_chip_rep1

source_name: CTCF IP from GM10253A cells


title: 15-7


title: GM10253A_RNApolymerase_D2_ChIP_chip_rep4

source_name: RNApolymerase_D2 IP from GM10253A cells


title: HybNeo3_RNApolymerase_D2_ChIP_chip_rep2

source_name: Input from HybNeo3 cells


title: 101-6

source_name: sigmoideum

value: sigmoideum


title: 26-1


title: HybNeo3_open_chromatin_rep1


title: 32-3

source_name: descendens


title: 76-G1

source_name: bulbus durodenum

value: TRUE

value: bulbus durodenum


title: 97-1

source_name: transversum


title: 4-5

value: non


title: 24-2


title: 79-G1

value: CD


title: 77-G1


title: GM10253A_RNApolymerase_D2_ChIP_chip_rep3


title: 4-6

source_name: rectum

value: rectum


title: 92-4

value: descendens


title: GM10253A_RNApolymerase_D2_ChIP_chip_rep2


title: HybNeo3_H3K9me3_ChIP_chip_rep1

source_name: H3K9me3 IP from HybNeo3 cells


title: GM10253A_H3K36me3_ChIP_chip_rep1

source_name: H3K36me3 IP from GM10253A cells


title: HybNeo3_RNApolymerase_D2_ChIP_chip_rep1


title: HybNeo3_H3K36me3_ChIP_chip_rep1

source_name: H3K36me3 IP from HybNeo3 cells


title: GM10253A_RNApolymerase_D2_ChIP_chip_rep1


title: GM10253A_H3K9me3_ChIP_chip_rep1

source_name: H3K9me3 IP from GM10253A cells


title: HybNeo3_H3K9me2_ChIP_chip_rep1

source_name: H3K9me2 IP from HybNeo3 cells


title: 21-2


title: 78-G1

value: Control


title: 46-3


title: GM10253A_H3K9me2_ChIP_chip_rep1

source_name: H3K9me2 IP from GM10253A cells


title: GM10253A_amanitin_open_chromatin_rep2

source_name: DNA representative of open chromatin from GM10253A cells

source_name: Whole fraction DNA


title: HybNeo3_H3K4me2_ChIP_chip_rep2

source_name: H3K4me2 IP from HybNeo3 cells


title: 127-2


title: GM10253A_H3K4me2_ChIP_chip_rep2

source_name: H3K4me2 IP from GM10253A cells

source_name: Input from GM10253A cells


title: 4-2

source_name: ascendens

value: ascendens


title: 75-2


title: 124-2


title: 4-4


title: 4-3

value: transversum


title: 123-2

source_name: coecum

value: coecum


title: hippocampus-HFD-treated 16 weeks-rep5

city: Xi'an

first: Yan

last: Niu

state: Shaanxi

address: Xi tai road #777

department: Clinical Experimental Center

institute: Xi'an International Medical Center Hospital

description: The expression of circRNAs of hippocampus after HFD -treated

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.Scanned images were imported into Agilent Feature Extraction software for raw data extraction.  Quantile normalization and subsequent data processing were performed using the R software limma package.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 1 out of 10 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

source_name: hippocampus tissue,replicate 1

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Array v2 (8x15K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

treatment_protocol: 6-week-old mice were randomly divided into two groups, fed with standard diet (HFD) and high-fat diet(HFD), respectively. Hippocampal tissue was isolated for circRNA detection after 16 weeks of high-fat feeding

value: hippocampus

tag: Sex

value: male

tag: diet

value: HFD

tag: std/hfd-treated time

value: 16 weeks


title: hippocampus-STD-treated 16 weeks-rep3

description: The expression of circRNAs of hippocampus after STD -treated

value: STD


title: 121-4

value: FALSE


title: 74-5

source_name: sigmoideum

value: yes

value: sigmoideum


title: 45-4

source_name: descendens

value: UC


title: hippocampus-HFD-treated 16 weeks-rep4


title: 33-4


title: hippocampus-STD-treated 16 weeks-rep1


title: hippocampus-STD-treated 16 weeks-rep5


title: 74-6

source_name: rectum


title: hippocampus-STD-treated 16 weeks-rep2

source_name: hippocampus tissue,replicate1


title: 120-1

value: non


title: hippocampus-HFD-treated 16 weeks-rep2


title: hippocampus-STD-treated 16 weeks-rep4


title: 4-1B


title: 3-6


title: 40-6

value: CD


title: 74-4


title: hippocampus-HFD-treated 16 weeks-rep3


title: 4-1A

source_name: ileum

value: ileum


title: 73-1

value: TRUE


title: 74-3

source_name: transversum


title: 115-1


title: 1-5

value: Control


title: 30-1

value: descendens


title: hippocampus-HFD-treated 16 weeks-rep1


title: Sham1 [miRNA_expression_tissue]

city: Shenzhen

first: Xinjin

last: Chi

state: Guagndong

address: No. 628, Zhenyuan Road, Guangming New District

institute: he Seventh Affiliated Hospital of Sun Yat-Sen University

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp(version 0.20.0) softeware with default parameters in pair end mode.
The clean data were obtained for downstream analyses by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
The clean reads were mapped to reference of mouse mRNAs and lncRNAs using bowtie2(version 2.3.1) with parameters -q -L 16 --phred64 -p 6
TPM value and read counts of each transcript were obtained by eXpress(version 1.5.1) with parameters --no-update-check --rf-stranded.
Assembly: mm10
Supplementary files format and content: abundance measurements

source_name: Intestine

extract_protocol:
Total RNA of intestine samples was extracted respectively using the TRIzol (Thermo Scientific, USA) reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). A total amount of 1 µg RNA per sample was used as initial material for the RNA sample preparations. Ribosomal RNA was removed using Ribo-off™ rRNA Depletion Kit (Human/Mouse/Rat) (Vazyme, China).
The sequencing libraries were generated following manufacturer recommendations with varied index label by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, USA). The libraries were sequenced on an BGISEQ-500 platform.

value: C57BL/KsJ db/db

value: Intestine

value: 10～12 weeks old

tag: treatment

value: Sham Operation


title: CLP2 [miRNA_expression_tissue]

value: CLP


title: Sham2 [miRNA_expression_tissue]


title: 1-4


title: CLP1 [miRNA_expression_tissue]


title: 40-4


title: high IL-2, bio rep 1

city: Chongqing

first: Haiyang

last: He

address: Gaotanyan street

institute: Arm medical university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perlscripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Reference genome GrCM38/mm10 and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.16.1), Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed
Assembly: mm10
Supplementary files format and content: xlsx file includes RPKM values
Supplementary files format and content: xlsx file includes diffgenes

source_name: spleen

growth_protocol: Cells were maintained in RPMI1640 complete medium supplemented with 10% fetal bovine serum (FBS) and antibiotics at 37 °C in 5% CO2

extract_protocol:
Total RNA were extracted using RNeasy Plus Micro or Mini Kit (Qiagen). A total amount of 3 µg RNA per sample was used as input material for the RNA libraries preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol:
Naïve CD8+ T cells from  spleen of wild type C57BL/6 recipient mice were negatively sorted and activated with Dynabeads® Mouse T-Activator CD3/CD28 (Life Technologies) for 48 h.
Then, cells were cultured in flanks at a density of 100000/mlwith low IL-2/7 (4 ng/ml IL-2 and 10 ng/ml IL-7) or high IL-2 (100 ng/ml IL-2) for 8 days

value: spleen

value: CD8+ T

tag: genotype

value: WT

value: cultivation with 100 ng/ml IL-2


title: low IL2/7, bio rep 3

tag: tissue

value: cultivation with 4 ng/ml IL-2 and 10 ng/ml IL-7


title: high IL-2, bio rep 3

tag: strain


title: 74-1

value: FALSE


title: low IL2/7, bio rep 1


title: low IL2/7, bio rep 2


title: 111-1

value: yes


title: 35-7

value: UC

value: rectum


title: 108-2

value: sigmoideum


title: 32-1

value: Control

value: non

value: ileum


title: high IL-2, bio rep 2


title: 73-G1

source_name: bulbus durodenum

value: TRUE

value: bulbus durodenum


title: 3-2

value: coecum


title: 101-5

value: descendens


title: 3-1


title: 73-2

value: transversum


title: 100-3

value: CD

value: ascendens


title: 6-6


title: 26-2


title: 72-G1


title: 62898-cpd-30mpk-8weeks

city: Croissy-sur-Seine

first: Fabien

last: MELCHIORE

address: 125 chemin de Ronde

country: France

institute: Servier IdRS

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated and normalized by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes TPM values for all Samples (mutiple-Samples file)

source_name: liver

extract_protocol:
Total RNA was extracted using Qiagen RNA extraction kits following manufacturer’s instructions (RNeasy lipid mini kit).
Librairies for RNAseq were prepared using Illumina Stranded mRNA Prep (polyA capture) following manufacturer's protocol instructions

treatment_protocol: DIO NASH mice were kept on AMLN diet (Gubra NAsH mouse model) and received either S217879 (30mg/kg, PO, QD) or vehicle (HEC 1%) for 8 weeks

value: liver


title: 62848-cpd-30mpk-8weeks


title: 62776-cpd-30mpk-8weeks


title: 62745-cpd-30mpk-8weeks


title: 62801-cpd-30mpk-8weeks


title: 62802-cpd-30mpk-8weeks


title: 62734-cpd-30mpk-8weeks


title: 73-3


title: 3-3


title: 62719-cpd-30mpk-8weeks


title: 62707-cpd-30mpk-8weeks


title: 1-2


title: 24-1


title: 62887-mouse-HEC1%-8weeks

value: vehicle


title: 62713-cpd-30mpk-8weeks


title: 21-3

value: FALSE


title: 73-4


title: 62822-mouse-HEC1%-8weeks


title: 62861-mouse-HEC1%-8weeks


title: 92-3


title: 62817-mouse-HEC1%-8weeks


title: 49-1


title: 126-3

value: yes


title: 3-4


title: 71-G1


title: 3-7


title: 96-5


title: 62795-mouse-HEC1%-8weeks


title: 47-3

value: UC


title: 62728-mouse-HEC1%-8weeks


title: 62726-mouse-HEC1%-8weeks


title: 62840-mouse-HEC1%-8weeks


title: 124-1


title: 3-5


title: 62800-mouse-HEC1%-8weeks


title: 45-3


title: WT1 and STAP-1 KO1 Tag

city: Sapporo

first: Junichi

last: Kashiwakura

state: Hokkaido

address: 15-4-1, Maeda 7-jo, Teine-ku

institute: Hokkaido University of Science

description:
S4 flowcell
A0301 = WT replicate 1
A0302 = WT replicate 2
A0303 = KO replicate 1
A0304 = KO replicate 2

library_source: transcriptomic single cell

data_processing:
Demultiplexing of each cell by hashtag read count was performed according to the previous report.
Assembly: GRCm38 release-101
Supplementary files format and content: barcode sequence-separated values files and matrix files

source_name: spinal cords

extract_protocol:
hashtag-stained single cell suspension was pooled and approximately 32607 cells were loaded onto the BD Rhapsody system (BD Biosciences). After loading unique cell barcode-immobilized magnetic beads, cells were lysed, and reverse transcription of polyA RNA and hashtag oligos derived from each single cell were performed according to the manufacture’s instructions. Exonuclease I treatment and cDNA/hashtag amplification were performed by using TAS-Seq protocol.
Sequencing libraries were prepared by using NEBNext Ultra II FS library prep kit for Illumina (New England Biolabs) and quantified by KAPA library quantification kit (KAPA Biosystems) and a MultiNA system (Shimazu).

value: spinal cords

value: CD45+ cells

value: WT1 and STAP-1 KO1

value: EAE induction


title: 62733-mouse-HEC1%-8weeks


title: 1-6

value: Control

value: non

value: rectum


title: 123-1

source_name: valvula

value: valvula


title: 1-3


title: 40-3


title: day28mouse3_visium

city: Birmingham

first: Matthew

middle: David

last: Cheung

state: AL

address: 1825 University Blvd

institute: University of Alabama at Birmingham School of Medicine

description: Visium spatial transcriptomics

data_processing:
10x Genomics Cell Ranger version 6.0
10x Genomics Space Ranger version 1.2.2
Assembly: mm10

source_name: kidney

extract_protocol: RNA was isolated according to manufacturer's instructions for 3' Chromium gene expression and Visium spatial transcriptomics kits

tag: disease state

value: BIRI

value: kidney


title: day6mouse1_visium

description: Visium spatial transcriptomics


title: day28mouse2_visium

description: Visium spatial transcriptomics


title: day28mouse1_visium

description: Visium spatial transcriptomics


title: day6mouse3_visium

description: Visium spatial transcriptomics


title: 121-3


title: day6mouse2_visium

description: Visium spatial transcriptomics


title: 75-1


title: day1mouse3_visium

description: Visium spatial transcriptomics


title: 32-2


title: day1mouse2_visium

description: Visium spatial transcriptomics


title: 117-2


title: 64-G1

value: TRUE

value: bulbus durodenum


title: 54-2

value: sigmoideum


title: 1-1

value: coecum


title: day1mouse1_visium

description: Visium spatial transcriptomics


title: 39-2

value: FALSE


title: WT1 and STAP-1 KO1 cDNA


title: day0p5mouse3_visium

description: Visium spatial transcriptomics


title: 44-1


title: day0p5mouse2_visium

description: Visium spatial transcriptomics


title: 113-4

value: CD


title: 5-8

value: yes


title: 63-G1


title: quiescentmouse1_visium

description: Visium spatial transcriptomics

value: quiescent/uninjured


title: quiescentmouse2_visium

description: Visium spatial transcriptomics


title: day0p5mouse1_visium

description: Visium spatial transcriptomics


title: day28mouse3_GEX

description: 3' gene expression of CD11b+ cells, KRMs are isolated using C1q > 4


title: quiscentmouse3_visium

description: Visium spatial transcriptomics


title: day28mouse2_GEX


title: 110-2

value: UC


title: day28mouse1_GEX


title: day6mouse3_GEX

description: 3' gene expression of F4/80hi,CD11bint cells


title: day6mouse2_GEX


title: 60-G1


title: day1mouse3_GEX


title: day6mouse1_GEX


title: PK-15 cells, NC, Day10 [PK15_NC_3]

city: Zhengzhou

first: Wang

last: Dong

address: No. 6 Longzi Hubei Road

institute: Henan University of Animal Husbandry and Economy

data_processing:
Trimmomatic
The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated and raw reads for each sample were generated.
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.  containing ploy-N and the low quality reads were removed to obtain the clean reads
The clean reads were mapped to reference genome using hisat2Then, the clean reads were mapped to the Sus scrofa genome (GCF_000003025.6_Sscrofa11.1) using HISAT2
Supplementary files format and content: Sus scrofa genome (GCF_000003025.6_Sscrofa11.1)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Sus scrofa

growth_protocol: PK-15 cells  were cultured in high-glucose DMEM (GIBCO, UK) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (HyClone, USA) at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: PK-15 cells were infected with lentivirus products expressing NS4A, then were selected with 6 μg/mL of puromycin (Thermo, USA) for 10 days.

tag: cell line

value: epithelial cell

value: WT

value: lentivirus products expressing empty vector infection


title: PK-15 cells, NC, Day10 [PK15_NC_1]


title: 33-2

value: non

value: ascendens


title: 5-9

value: rectum


title: 5-4


title: 61-G1

value: Control


title: 101-4

value: transversum


title: day1mouse2_GEX

value: BIRI

value: kidney


title: 54-3


title: PK-15 cells, NS4A, Day10 [PK15_4A_3]

value: lentivirus products expressing NS4A infection


title: day1mouse1_GEX


title: 29-2

value: descendens


title: PK-15 cells, NS4A, Day10 [PK15_4A_2]


title: day0p5mouse3_GEX

description: 3' gene expression of CD45+ cells


title: PK-15 cells, NC, Day10 [PK15_NC_2]


title: day0p5mouse2_GEX

description: 3' gene expression of CD45+ cells


title: day0p5mouse1_GEX

description: 3' gene expression of CD45+ cells


title: quiscentmouse3_GEX


title: quiescentmouse1_GEX


title: quiescentmouse2_GEX


title: A20 with non-targeting control sgRNA replicate 1

city: Parkville

first: Yunshun

last: Chen

state: VIC

address: 1G Royal Parade

department: ACRF Cancer Biology and Stem Cells

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Adapters and reads of poor quality scores were trimmed using TrimGalore v0.6.7
Reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using bismark v0.20.0
Duplicated reads were removed using bismark's deduplicate_bismark function.
Methylation calls were made using bismark's bismark_methylation_extractor function
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text giving chromosome number, start and end position of the CpG site, methylation proportion, the number of methylated Cs, and the number of unmethylated Cs

source_name: A20 B cell lymphoma cell line

growth_protocol: RPMI 1640 with 2 mM GlutaMAX, 50 μM β-mercaptoethanol and 10% heat-inactivated foetal calf serum (FCS).

extract_protocol:
DNeasy Blood & Tissue kit (Qiagen)
NEBNext Enzymatic Methyl-seq kit (NEB)

treatment_protocol: Cells transduced with lentiviral vector overexpressing the TETact system together with either the non-targeting control sgRNA or CD4-promoter targeting sgRNA.

value: A20 B cell lymphoma cell line

value: BALB/C

tag: activation


title: PK-15 cells, NS4A, Day10 [PK15_4A_1]


title: A20 with non-targeting control sgRNA replicate 2


title: A20 with sgRNA activating CD4 gene replicate 2


title: bulk_mESC_rep1

city: Beijing

first: Fuchou

last: Tang

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Biomedical Pioneering Innovation Center, Peking University

description: Bulk short-read ATAC-seq of mouse embryonic stem cell

data_processing:
Raw Illumina paired-end reads were trimmed by cutadapt (v3.2) to remove adaptors, including 'AGATGTGTATAAGAGACAG' at 5' ends and 'CTGTCTCTTATACACATCT' at 3' ends. It also filtered reads with quality < 20 or length < 30bp at either end.
Trimmed paired-end reads were aligned to reference genome by Bowtie2 (v2.4.2) with `--no-unal` parameter to suppress reads failed to align recorded into bam. Reads with mapping quality less than 30 were filtered. Then duplicates in aligned reads were removed by `picard MarkDuplicates`, including both PCR duplicates and Illumina sequencing optical duplicates.
ATAC-seq peaks were called from bam files by `callpeak` function of MACS2 (v2.2.7.1). We set other macs2 parameters as `--nomodel --shift -75 --extsize 150` to adapt to ATAC-seq data. The false discovery rate of peak calling was controlled by setting `-q` parameter to 0.01.
Genome_build: hg38 for human; mm10 for mouse
Supplementary_files_format_and_content: Bigwig files recorded ATAC-seq signal strength tracks. Bed files recorded coordinates of ATAC-seq peaks.

source_name: Mouse embryonic stem cell

growth_protocol: K526 cells were cultured in RPMI-1640 (Gibco; 11875093) supplemented with 10% fetal bovine serum (Gibco; 26140079). HEK293T and HFF1 cells were cultured in DMEM (Gibco; 11995040) supplemented with 10% fetal bovine serum.  GM12878 cells were cultured in RPMI-1640 supplemented with 15% fetal bovine serum. eHAP1 cells were cultured in IMDM (Gibco; 12440053) supplemented with 10% fetal bovine serum. Mouse embryonic stem cells (mESCs) were cultured without feeders in equal volume of Dulbecco’s modified eagle’s medium (DMEM/F-12, Gibco; 11320033) and Neurobasal Medium (Gibco; 21103049) supplemented with 1,000 U/ml leukemia inhibitory factor (LIF, Millipore, ESG1107), 0.5× N-2 (Gibco, 17502048), 0.5× B-27 (Gibco, 10889038), 50 μg/ml Bovine Serum Albumin (BSA, Sigma-Aldrich, A3311), 2 mM L-Glutamine (Gibco, 2503081), 0.1 mM β-Mercaptoethanol (Sigma-Aldrich, M7522), 1× MEM Non-Essential Amino Acids Solution (NEAA, Gibco, 11140050), 100 U/ml Penicillin and 0.1mg/ml Streptomycin (Gibco, 15140122).

extract_protocol:
Cells (100,000-200,000 cells before freezing) were quickly thawed at 37℃ and centrifuged at 500 g for 5 min at 4℃. Then nuclei were isolated with Omni-ATAC lysis buffer (10 mM Tris-HCl (pH 7. 4), 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA630, 0.1% Tween-20, 0.01% digitonin) and incubated on ice for 3-5 min.
Nuclei were isolated with Omni-ATAC protocol lysis buffer. Then nuclei were resuspended in 50 μl tagmentation mix with Tn5 from the NovoNGS DNA Library FlashPrep Kit for Illumina, Cat. No. N233. The tagmentation reaction was performed on a thermomixer at 800 rpm, 37 °C, 30 min. To stop the tagmentation reaction, 50 μl of tagmentation stop buffer (10 mM Tris-HCl, pH 8.0, 20 mM EDTA, pH 8.0) was added to tagged nuclei. Around 20,000 nuclei stained with DAPI was sorted into 200μl tubes by FACS. The nuclei were resuspended in lysis buffer and incubated at 65℃ for 30 minutes to release Tn5. Equal volume of 10% TWEEN-20 was added to ~30ng lysed product. 2X KAPA PCR Mix was added to perform library amplification PCR: 72℃ 10 minutes; 98℃ 5 minutes; [98℃ 10 seconds, 63℃ 30 seconds, 72℃ 20 seconds] x 15 cycle; 4℃ hold. Libraries were size selected(200bp-700bp) with 2% agarose gel and sequenced on Illumina NovaSeq 6000.

value: Mouse embryonic stem cell


title: A20 with sgRNA activating CD4 gene replicate 1


title: 26-3

tag: biopsy

value: FALSE

value: sigmoideum


title: 56-2

tag: age

value: UC


title: Wild-type A20 replicate 2


title: Wild-type A20 replicate 1


title: 5-1

value: CD

tag: gastroscopy

value: yes

value: ileum


title: Gallus gallus utricle, cell-300

city: South San Francisco

first: Daniel

middle: C

last: Ellwanger

state: CA

address: 1120 Veterans Blvd

department: Genome Analysis Unit

institute: Amgen Inc

data_processing:
Reads were aligned to the NCBI Gallus gallus v6.0 (GCF_000002315.6) reference genome and gene expression values were quantified with a customized STAR-RSEM pipeline for single-cell data.
FastQC and Scater were used for quality control.
Low-quality cells, ERCC spike-in transcripts, and low-level expressed genes were removed.
Assembly: NCBI Gallus gallus v6.0 (GCF_000002315.6) reference genome
Supplementary files format and content: Tab-separated values file reporting counts

organism: Gallus gallus

source_name: Utricle sensory epithelia

extract_protocol:
Utricles were dissected in ice-cold Medium 199, otolithic membranes were mechanically removed, and tissue was incubated in thermolysin (0.5 mg/mL M199 medium) for 20 minutes at 37°C. Thermolysin activity was attenuated with 10% FBS in M199. The sensory epithelia were carefully peeled off from the underlying stromal cells using a 30- gauge 1⁄2-inch hypodermic needle attached to a 1 mL syringe. For each experiment, we pooled 4-8 sensory epithelia. The epithelia were dissociated using 1X Accutase for 20 minutes at 37°C, followed by mild mechanical trituration, and washed twice with PBS using a centrifugation step (300 x g, 5 min, room temperature (RT)). Viable single cells were isolated with a Becton Dickinson FACSAria Fusion flow cytometer (Ellwanger et al., 2018). Two independent batches of 270 cells were deposited into individual wells of 96-well plates, prefilled with 4 μl of a premade lysis solution with 1 U/μl of recombinant RNase inhibitor, 0.1% Triton X-100, 2.5 mM dNTP mix, 2.5 μM oligo d(T)30 VN (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, IDT). Plates containing sorted cells were immediately sealed, frozen on dry ice, and stored at −80°C.
Single-cell RNA-seq was performed via Picelli and colleagues’ method (Picelli et al., 2014) using SMARTscribe for reverse transcription followed by 22 amplification cycles. Amplified cDNAs were purified by AMPure Beads cleanup using a Biomek FX automated platform and assessed with a fragment analyzer (Agilent) for quantitation and quality assurance. Barcoded libraries were synthesized using a scaled-down Nextera XT protocol (Mora-Castilla et al., 2016) in a total volume of 4 μl. A total of 384 libraries were pooled, and paired-end sequenced (2 x 150 bp) on a NextSeq 500/550 High Output flow cell.

value: Utricle sensory epithelia

value: Wildtype

value: Posthatch day 7 (P7)

tag: well plate

tag: plate position


title: bulk_mESC_rep2


title: Gallus gallus utricle, cell-299


title: Gallus gallus utricle, cell-298


title: 100-2

tag: patient

tag: diagnosis

tag: inflammation


title: 96-4


first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

data_processing:
Reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using Rsubread::align.
Genewise counts were obtained using featureCounts with Rsubread's inbuilt mm10 annotation.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text giving Entrez Gene IDs, gene length (number of bases in union of all exons) and the number of read-pairs assigned to that read.

extract_protocol:
NucleoSpin RNA Plus (Macherey-Nagel) with gDNA removal column
Illumina TruSeq RNA (100ng plus) v1.0 protocol

value: Control


title: Gallus gallus utricle, cell-297


title: Gallus gallus utricle, cell-295


title: Gallus gallus utricle, cell-296


title: 5-3


title: 23-1

value: non


title: 5-7


title: 92-2


title: EtOH fed 8 weeks plus 3 binges 3

city: Rockville

first: Bryan

last: Mackowiak

state: MD

address: 5625 Fishers Lane, 2S12

institute: NIH

hyb_protocol: Blocking buffer and Hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software. Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: Mouse liver with EtOH diet for 8 weeks plus 3 EtOH binges (5 g/kg)

label_protocol: cDNA was generated with SuperScript® Indirect cDNA Labeling Core kit (Invitrogen) and labeled with Cy3/Cy5-mono reactive dye pack (GE healthcare), and the labeled cDNA was purified with Qiagen kit (#28004)

extract_protocol: Total RNA extracted using Trizol from liver and purified with QIAGEN kit (#74104) following manufacturer's instructions.

treatment_protocol: Collected tissues from fresh liver

tag: gender

value: Male

value: Liver

source_name: Ambion Mouse Assorted Total RNA

value: liver


title: 22-5

source_name: descendens

value: descendens


title: EtOH fed 8 weeks plus 3 binges 4


title: EtOH fed 8 weeks plus 3 binges 1


title: EtOH fed 8 weeks plus 3 binges 2


title: EtOH fed 8 weeks plus 3 binges 5


title: Gallus gallus utricle, cell-294


value: BALB/C


title: Gallus gallus utricle, cell-292


title: Gallus gallus utricle, cell-291


title: Gallus gallus utricle, cell-290


title: 69-2


title: Wild-type A20 replicate 2


title: Gallus gallus utricle, cell-286


title: Gallus gallus utricle, cell-287


title: Gallus gallus utricle, cell-285


title: 2-2

source_name: ascendens

value: ascendens


title: Gallus gallus utricle, cell-288


title: Gallus gallus utricle, cell-289


title: Gallus gallus utricle, cell-293


title: Wild-type A20 replicate 1


title: Gallus gallus utricle, cell-283


title: 126-2

source_name: rectum

value: FALSE

value: rectum


title: CUT&RUN Exp122 JUN MG132

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

data_processing:
Sequencing libraries were subjected to Illumina NextSeq 500 and NextSeq 2000 sequencing according to the manufacturer’s instructions. After base calling with Illumina’s FASTQ Generation software v1.0.0 (NextSeq 500 sequencing), high quality PF-clusters were selected for further analyses and sequencing quality was ascertained using FastQC. ChIP samples were mapped to human hg19 and ChIP-Rx samples were mapped separately to the human hg19 and to the murine mm10 genome using Bowtie1 79 or Bowtie 2 80 with -N 1 parameters. For ChIP-Rx spike-in normalized reads were calculated by dividing the number of mapped reads mapped to hg19 by the number of reads mapped to mm10 for each sample and multiplying this ratio with the smallest number of reads mapped to mm10 for any sample.
CUT&RUN samples were mapped separately to the human hg19 and either to the murine mm10 genome using Bowtie 2 with -N 1 option. For CUT&RUN spike-in normalized reads were calculated by dividing the number of mapped reads mapped to hg19 by the number of reads mapped to mm10 for each sample and multiplying this ratio with the smallest number of reads mapped to mm10 for any sample.
Assembly: hg19
Supplementary files format and content: bw

source_name: Bone Marrow

growth_protocol: Cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin

extract_protocol:
ChIP-seqCells were treated with 1% formaldehyde for 5 min at 37°C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <300 bp using Covaris. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used. CUT&RUN: cells were harvested using Accutase (Sigma) for cell detachement. Cells were counted and washed in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine). After washing, cells were coupled to ConA-coated magnetic beads (Polysciences Europe) and subsequently permeabilized and followed by addition of primary antibody in antibody binding buffer (wash buffer, 0.05% digitonin, 2 mM EDTA) over night at 4 °C. Cells were wased in Dig-Wash buffer (Wash buffer, 0.05% digitonin) and MNase (700ng/ml) was added to each sample for 1 hr at 4 °C. After washing with Dig-wash buffer and Low-salt Rinse buffer (20 mM HEPES pH 7.5, 0.5 mM Spermidinge, 0.05% digitonin) incubation buffer (3.5 mM HEPES pH 7.5, 10 mM CaCl2, 0.05% digitoin) was added for 30 min at 4°C. STOP buffer (170 mM NaCL, 20 mM EGTA, 0.05% digitonin, 20 ug/ml RMAse A, 25 ug/ml Glycogen was added to stop the MNase digestion. DNA fragments were released at 37 °C for 30 min and proteins digested for 1 h at 50 °C after adding 0.01 % SDS and 10 mg/ml Proteinase K followed by Phenol Chloroform extraction. Precipitated DNA was resuspended in 30 ul 0.1x TE buffer
ChIP-seq Libraries were prepared according to instructions accompanying the NEBNext Ultra™ II DNA Library Prep Kit for Illumina. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and eluted. DNA fragments were amplified by 12 to 17 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using a picogreen assay. CUT&RUN: NEBnext Ultra II DNA Library Prep Kit (New England Biolabs) was used. Pre-PCR samples were purified using AmpureXP beads with a ratio of 1.75x. Then half of the eluted material was used with 12-17 PCR cycles. The libraries were cleaned using Agentcourt AMPure XP Beads (ratio 1.1x, Beckman Coulter), quality, quantity and fragment size assessed on the Fragment Analyzer (Agilent) using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent)

treatment_protocol: Treatment as indicated

value: Bone Marrow

value: U-2 OS MYC-tet-on

tag: cell type

value: osteosarcoma cell line

value: Dox inducible MYC overexpression

value: DOX, 1µg/ml, 8 hrs


title: CUT&RUN Exp122 MAX MG132

tag: treatment


title: CUT&RUN Exp122 MAX CTL

tag: genotype


title: Gallus gallus utricle, cell-282

tag: tissue

value: Utricle sensory epithelia

value: Wildtype


title: 54-1

source_name: transversum

value: UC

value: transversum


title: 5-6

value: CD

value: yes


title: 49-G1

value: non

value: bulbus durodenum


title: 47-2

source_name: sigmoideum

value: sigmoideum


title: CUT&RUN Exp122 JUN CTL


title: 123-8


title: CUT&RUN Exp122 IgG merged

value: merged


title: Gallus gallus utricle, cell-279

value: Posthatch day 7 (P7)


title: Gallus gallus utricle, cell-277


title: Gallus gallus utricle, cell-278


title: Gallus gallus utricle, cell-276


title: Gallus gallus utricle, cell-274


title: 58-1

value: FALSE


title: Gallus gallus utricle, cell-275


title: Gallus gallus utricle, cell-281


title: 5-5

value: ascendens


title: Gallus gallus utricle, cell-273


title: Gallus gallus utricle, cell-280


title: Gallus gallus utricle, cell-270


title: 45-6

value: rectum


title: Gallus gallus utricle, cell-271


title: Gallus gallus utricle, cell-269


title: CUT&RUN Exp122 EXOSC10 CTL

value: Bone Marrow

value: U-2 OS MYC-tet-on

value: osteosarcoma cell line


title: Gallus gallus utricle, cell-268

value: Utricle sensory epithelia


title: Gallus gallus utricle, cell-272

value: Wildtype


title: CUT&RUN Exp122 EXOSC10 BI8626

value: Dox inducible MYC overexpression

value: DOX, 1µg/ml, 8 hrs


title: CUT&RUN Exp97 IgG H2O HU merged


title: CUT&RUN Exp122 EXOSC10 MG132 + BI8626


title: CUT&RUN Exp122 EXOSC10 MG132


title: Gallus gallus utricle, cell-266


title: 57-1

source_name: ileum

value: UC

value: ileum


title: CUT&RUN Exp97 FANCD2 HU rep2

value: HU, 5mM, 2 hrs


title: Gallus gallus utricle, cell-264


title: CUT&RUN Exp97 FANCD2 HU rep1


title: Gallus gallus utricle, cell-263


title: 122-3

value: non


title: Gallus gallus utricle, cell-265


title: 36-2

value: yes


title: Gallus gallus utricle, cell-262


title: 121-2

source_name: coecum

value: Control

value: coecum


title: 66-G1

source_name: bulbus durodenum

value: TRUE

value: bulbus durodenum


title: Gallus gallus utricle, cell-258

value: Posthatch day 7 (P7)


title: Gallus gallus utricle, cell-259


title: Gallus gallus utricle, cell-267


title: CUT&RUN Exp97 FANCD2 H2O rep1

value: Bone Marrow

value: CTL


title: Gallus gallus utricle, cell-261


title: 5-2

value: CD

value: FALSE


title: CUT&RUN Exp97 FANCD2 H2O rep2

value: U-2 OS MYC-tet-on

value: osteosarcoma cell line


title: CUT&RUN Exp95 U-2 OS MYC-tet-on pS4S8RPA HU BI8626

value: Dox inducible MYC overexpression


title: Gallus gallus utricle, cell-256

value: Utricle sensory epithelia

value: Wildtype


title: Gallus gallus utricle, cell-255


title: Gallus gallus utricle, cell-257


title: Gallus gallus utricle, cell-254


title: Gallus gallus utricle, cell-253


title: Gallus gallus utricle, cell-251


title: Gallus gallus utricle, cell-252


title: 108-1

value: UC

value: transversum


title: CUT&RUN Exp95 U-2 OS MYC-tet-on pS4S8RPA Control

value: Dox, 1ug/ml, 24h


title: Gallus gallus utricle, cell-250


title: CUT&RUN Exp80 IgG merged rep2

value: merged


title: 68-G1

value: Control

value: non


title: Gallus gallus utricle, cell-284


title: 30-3

value: yes

value: rectum


title: CUT&RUN Exp95 U-2 OS MYC-tet-on pS4S8RPA HU

value: Bone Marrow

value: Dox, 1ug/ml, 24h + HU, 2.5mM, 4h


title: Gallus gallus utricle, cell-246

value: Posthatch day 7 (P7)


title: Gallus gallus utricle, cell-248


title: Gallus gallus utricle, cell-249


title: 117-1

value: FALSE

value: sigmoideum


title: CUT&RUN Exp80 FANCD2 EtOH rep2

value: U-2 OS MYC-tet-on

value: osteosarcoma cell line

value: CTL


title: CUT&RUN Exp80 IgG merged rep1

value: Dox inducible MYC overexpression


title: Gallus gallus utricle, cell-245

value: Utricle sensory epithelia

value: Wildtype


title: Gallus gallus utricle, cell-244


title: 6-2

value: transversum


title: CUT&RUN Exp80 FANCD2 EtOH rep1


title: 35-2

value: UC

value: ascendens


title: Gallus gallus utricle, cell-243


title: 2-5

value: Control

value: non


title: 113-3

value: CD


title: Gallus gallus utricle, cell-241


title: Gallus gallus utricle, cell-240


title: CUT&RUN Exp80 FANCD2 DOX rep1

value: Bone Marrow

value: Dox (1 µg/ml, 9 hrs)


title: 42-1

value: ileum


title: 58-2

value: FALSE

value: yes

value: rectum


title: 2-3


title: Gallus gallus utricle, cell-247

value: Posthatch day 7 (P7)


title: Gallus gallus utricle, cell-239


title: CUT&RUN Exp80 ATR DOX rep2

value: U-2 OS MYC-tet-on

value: osteosarcoma cell line


title: Gallus gallus utricle, cell-237

value: Utricle sensory epithelia


title: Gallus gallus utricle, cell-235

value: Wildtype


title: 110-1

value: sigmoideum


title: CUT&RUN Exp80 ATR CTL rep2

value: Dox inducible MYC overexpression

value: CTL


title: Gallus gallus utricle, cell-242


title: Gallus gallus utricle, cell-236


title: Gallus gallus utricle, cell-233


title: CUT&RUN Exp80 ATR DOX rep1


title: Gallus gallus utricle, cell-238


title: CUT&RUN Exp80 ATR CTL rep1


title: Gallus gallus utricle, cell-232


title: 67-G1

value: Control

value: TRUE

value: bulbus durodenum


title: CUT&RUN Exp80 FANCD2 DOX rep2

value: Bone Marrow


title: Gallus gallus utricle, cell-230


title: Gallus gallus utricle, cell-231


title: ChIP-seq Exp126 RNAPII MG132 Rep2


title: Gallus gallus utricle, cell-229


title: Gallus gallus utricle, cell-260


title: 2-1

value: non

value: coecum


title: Gallus gallus utricle, cell-227


title: 42-3

value: FALSE

value: transversum


title: ChIP-seq Exp126 RNAPII Dox

value: Dox, 1ug/ml, 10h


title: 6-3

value: descendens


title: Gallus gallus utricle, cell-228

value: Posthatch day 7 (P7)


title: ChIP-seq Exp126 RNAPII Dox MG132

value: U-2 OS MYC-tet-on

value: osteosarcoma cell line


title: Gallus gallus utricle, cell-234

value: Utricle sensory epithelia

value: Wildtype


title: 107-3

value: UC

value: yes

value: rectum


title: Gallus gallus utricle, cell-226


title: 56-1


title: Gallus gallus utricle, cell-225


title: ChIP-seq Exp126 RNAPII CTL Rep2

value: Dox inducible MYC overexpression

value: CTL


title: Gallus gallus utricle, cell-224


title: Gallus gallus utricle, cell-220


title: Gallus gallus utricle, cell-221


title: Gallus gallus utricle, cell-223


title: Gallus gallus utricle, cell-222


title: ChIP-seq Exp123 MYC Dox w/o HS rep1

value: Bone Marrow


title: ChIP-seq Exp123 MYC Dox HS rep1

value: 42°C for 30 min


title: 57-4

value: non


title: 29-3

value: CD

value: FALSE

value: sigmoideum


title: ChIP-seq Exp126 Input merge

value: merged


title: ChIP-seq Exp123 MYC Dox HS 5h Recovery rep1

value: 42°C for 30 min, 37°C for 5 h


title: Gallus gallus utricle, cell-217

value: Posthatch day 7 (P7)


title: 2-4

value: Control

value: descendens


title: 101-3

value: transversum


title: 28-1

value: UC

value: ileum


title: ChIP-seq Exp123 MYC Dox HS 0.5h Recovery rep1

value: U-2 OS MYC-tet-on

value: osteosarcoma cell line

value: 42°C for 30 min, 37°C for 30 min


title: Gallus gallus utricle, cell-216

value: Utricle sensory epithelia

value: Wildtype


title: Gallus gallus utricle, cell-212


title: Gallus gallus utricle, cell-215


title: Gallus gallus utricle, cell-214


title: Gallus gallus utricle, cell-213


title: ChIP-seq Exp123 Input merge

value: Bone Marrow

value: Dox inducible MYC overexpression


title: 100-1

value: CD

value: FALSE

value: non


title: Gallus gallus utricle, cell-218


title: Gallus gallus utricle, cell-219


title: ChIP-seq Exp112 MYC Dox w/o HS rep2

value: CTL


title: Gallus gallus utricle, cell-210

value: Posthatch day 7 (P7)


title: Gallus gallus utricle, cell-211


title: Gallus gallus utricle, cell-207


title: Gallus gallus utricle, cell-209


title: Gallus gallus utricle, cell-208


title: Gallus gallus utricle, cell-205


title: ChIP-seq Exp112 MYC Dox HS 5h Recovery rep2

value: 42°C for 30 min, 37°C for 5 h


title: Gallus gallus utricle, cell-204


title: Gallus gallus utricle, cell-203


title: ChIP-seq Exp112 MYC Dox HS 0.5h Recovery rep2


title: Gallus gallus utricle, cell-206


title: Gallus gallus utricle, cell-202


title: 59-4

value: yes


title: Gallus gallus utricle, cell-201


title: ChIP-seq Exp103 RNAPII MG132 Rep1


title: 2-6

value: Control

value: rectum


title: ChIP-seq Exp103 SPT5 CTL rep2


title: Gallus gallus utricle, cell-200


title: ChIP-seq Exp112 MYC Dox HS rep2

value: 42°C for 30 min


title: Gallus gallus utricle, cell-198


title: 96-3

value: descendens


title: ChIP-seq Exp103 RNAPII CTL Rep1

value: U-2 OS MYC-tet-on

value: osteosarcoma cell line


title: Gallus gallus utricle, cell-199

value: Utricle sensory epithelia


title: 92-1

value: UC

value: coecum


title: 23-2

value: sigmoideum


title: Gallus gallus utricle, cell-196

value: Wildtype


title: 22-4

value: CD

value: FALSE

value: transversum


title: Gallus gallus utricle, cell-195

value: Posthatch day 7 (P7)


title: 7-3


title: ChIP-seq Exp103 MYC HU rep3

value: Bone Marrow

value: Dox inducible MYC overexpression

value: HU, 5mM, 2h


title: Gallus gallus utricle, cell-194


title: 55-1

value: non

value: ileum


title: Gallus gallus utricle, cell-193


title: 53-2

value: Control

value: ascendens


title: ChIP-seq Exp103 MYC CTL rep3

value: U-2 OS MYC-tet-on

value: osteosarcoma cell line

value: CTL


title: Gallus gallus utricle, cell-192

value: Utricle sensory epithelia


title: 7-2

value: coecum


title: ChIP-seq Exp103 SPT5 MG132 rep2


title: Gallus gallus utricle, cell-197

value: Wildtype


title: Gallus gallus utricle, cell-191


title: ChIP-seq Exp103 Input merge 1,2,3

value: merged


title: Gallus gallus utricle, cell-190


title: ChIP-seq Exp100 SPT5 MG132 rep1


title: ChIP-seq Exp100 SPT5 Dox rep1

value: Dox, 1ug/ml, 10h


title: Gallus gallus utricle, cell-188


title: Gallus gallus utricle, cell-186


title: ChIP-seq Exp100 SPT5 Dox MG132 rep1


title: Gallus gallus utricle, cell-187


title: Gallus gallus utricle, cell-184


title: Gallus gallus utricle, cell-189


title: ChIP-seq Exp100 SPT5 CTL rep1


title: Gallus gallus utricle, cell-183


title: Gallus gallus utricle, cell-182


title: Gallus gallus utricle, cell-180


title: Gallus gallus utricle, cell-181


title: Gallus gallus utricle, cell-179


title: 47-1

value: UC

value: FALSE

value: descendens


title: ChIP-seq Exp99 MYC HU rep2

value: Bone Marrow

value: Dox inducible MYC overexpression

value: Dox 1ug/ml 8h, HU, 5mM 2h


title: Gallus gallus utricle, cell-178

value: Posthatch day 7 (P7)


title: Gallus gallus utricle, cell-185


title: Gallus gallus utricle, cell-177


title: 7-1

value: CD

value: non

value: ileum


title: 7-5

value: sigmoideum


title: 123-7

value: yes

value: rectum


title: 55-2

value: transversum


title: ChIP-seq Exp99 MYC CTL rep2

value: U-2 OS MYC-tet-on

value: osteosarcoma cell line

value: Dox 1ug/ml 8h


title: Gallus gallus utricle, cell-175

value: Utricle sensory epithelia

value: Wildtype


title: Gallus gallus utricle, cell-176


title: 55-3

value: UC

value: FALSE

value: descendens


title: 122-2


title: 45-5


title: 7-4


title: ChIP-seq Exp99 Input merge

value: Bone Marrow

value: Dox inducible MYC overexpression

value: merged


title: Gallus gallus utricle, cell-174

value: Posthatch day 7 (P7)


title: Gallus gallus utricle, cell-173


title: 55-4


title: ChIP-seq Exp100 Input merge


title: 38-1

value: CD

value: ileum


title: Gallus gallus utricle, cell-172


title: Gallus gallus utricle, cell-171


title: 4sU-seq U-2 OS MYC-AID rep3

data_processing:
library strategy: 4sU-seq
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For 4sU-seq, reads were mapped to hg19 with  Bowtie2, reads mapping to rRNA,exons and blacklist regions were removed, and then normalized based on read depth.
Assembly: hg19
Supplementary files format and content: bw

extract_protocol:
total RNA
4sU-RNA was used for library preparation with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Ultra II Directional RNA Library Prep kit. The libraries were amplified with 10-14 PCR cycles depending on the input RNA. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq500 Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform

value: U-2 OS MYC-AID

value: Dox inducible overexpression of WT-MYC

value: Auxin, 6H

tag: molecule subtype

value: nascent RNA


title: Gallus gallus utricle, cell-170


title: Gallus gallus utricle, cell-169


title: Gallus gallus utricle, cell-168


title: 121-1

value: Control

value: non


title: 6-5

value: rectum


title: Gallus gallus utricle, cell-167

value: Utricle sensory epithelia

value: Wildtype


title: 4sU-seq U-2 OS MYC-AID WT rep3

value: osteosarcoma cell line

value: Auxin, 6H + Dox, 1µg/ml, 24 h


title: Gallus gallus utricle, cell-166


title: 4sU-seq U-2 OS MYC-AID rep1

value: Bone Marrow


title: 4sU-seq U-2 OS MYC-AID WT rep2


title: Gallus gallus utricle, cell-164


title: 57-3

value: UC

value: FALSE

value: sigmoideum


title: Gallus gallus utricle, cell-162

value: Posthatch day 7 (P7)


title: Gallus gallus utricle, cell-163


title: Gallus gallus utricle, cell-158


title: 4sU-seq U-2 OS MYC-AID Kless rep2

value: Dox inducible overexpression of Kless-MYC


title: 4sU-seq U-2 OS MYC-AID WT rep1

value: U-2 OS MYC-AID


title: Gallus gallus utricle, cell-160


title: 4sU-seq U-2 OS MYC-AID rep2

value: Dox inducible overexpression of WT-MYC


title: Gallus gallus utricle, cell-159


title: 37-1


title: Gallus gallus utricle, cell-157


title: Gallus gallus utricle, cell-156