title: 501mel_KO1.8_R2

city: New York

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

description: viral transduction

data_processing:
Single-end 75 bp reads were aligned to the human reference genome (GRCh37) with STAR v2.6.0.c using the parameters --sjdbOverhang 100 --outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated.
Rsubread featureCounts (Liao, Smyth and Shi, 2014) was used to map reads to coding genes.
Genome_build: hg19
Supplementary_files_format_and_content: two comma-delimited text matrix including raw counts values of each gene in each sample

source_name: 501mel melanoma cell lines

growth_protocol: DMEM 10% FBS 1% P/S

extract_protocol:
RNA was extracted using QIAGEN RNeasy minikit
1µg of quality-verified RNA was used for library preparation
PolyA-RNA was processed into sequencing libraries using the NETFLEX Rapid Directional RNA-seq Kit 2.0  kit following manufacturer’s protocol.

tag: melanoma molecular subtype

tag: disease state

value: metastatic melanoma

tag: construct

value: Lenti-CRISPR V2 Cas9 + sgRNA


title: 501mel_KO1.8_R1

status: Public on Apr 05 2022

type: SRA

country: USA

description: viral transduction

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens


title: CT2_1

city: Palo Alto

first: Haiyu

last: Zhang

state: CA

address: 300 Pasteur Dr.

institute: Stanford University

data_processing:
Sequence reads, after filtering for read quality, were re-filtered by fastx (fastx_artifacts_filter) (http://hannonlab.cshl.edu/fastx_toolkit/index.html).
Reads that passed the filter were mapped to the human transcriptome hg19 (refMrna, downloaded from the UCSC genome browser, http://www.genome.ucsc.edu/) by using SOAP2, allowing at most two mismatches (Guo X, 2013, PMID: 24342436).
Total numbers of sequence reads (read counts) for each gene symbol from the transcriptome mapping were determined and were used to create the gene-expression profile matrix (Guo X, 2013, PMID: 24342436).
Genome_build: Human transcriptome hg19
Supplementary_files_format_and_content: The processed data files are text files (tab delimited). It contains the gene symbols in column A and the raw read counts of each gene in column B. For CT2, Nextseq generated 4 sequence files for each sample, and each of the sequence files were processed independently and then combined into one processed data file for each sample.

source_name: Peripheral blood_CT2

extract_protocol:
Blood total RNAs were extracted using columns after red blood cell lysis. Specifically, Blood Total RNA Isolation kit (Mo Bio, Carlsbad, CA) was used for samples of CT1, and QIAamp RNA Blood Mini kit (Qiagen) was used for samples of CT2.
3SEQ (3’-end sequencing for expression quantification) analyses (Beck AH, 2010, PMID: 20098735) were performed on blood RNA samples. 3SEQ is a type of RNA-seq that focuses on quantitative analysis of transcriptome by generating a directional sequencing library targeting 3’UTRs and flanking regions upstream of poly-A tail, ensuring that one read is produced and measured per transcript. 3SEQ libraries were constructed based on the previously published method (Beck AH, 2010, PMID: 20098735) with modifications. Briefly, mRNAs were enriched by poly-A selection using Dynabeads mRNA Purification kit (Thermo Fisher Scientific, Waltham, MA) and heat-fragmented to 100-200 nucleotides. First-strand cDNAs were synthesized using Superscript III reverse transcriptase with Rd2SP-oligodT primer, followed by second-strand cDNA synthesis. Adenine was added to the 3’-end of the double-stranded cDNA and then ligated to the P5-R1SP adapter. The ligated product was amplified by PCR for 15 cycles using primers P5-Rd1SP and P7-index-Rd2SP. Six Illumina indexes, each with six bases, were introduced in the P7 primers. Qualities of the libraries were examined using Agilent DNA 1000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Libraries were quantified by Qubit 2.0 fluorometer using Qubit dsDNA BR assay kit (Thermo Fisher Scientific, Waltham, MA). Six or five samples with different indexes were pooled together for next generation sequencing on HiSeq 2000 system for CT1 and on NextSeq (Illumina Inc., San Diego, CA) for CT2. Index associated 36 bp sequences from the P5 primer end, providing the 5’-end sequences of the polyA-containing mRNA fragments, were generated.

treatment_protocol: Patients were not on treatment during sample collection period except that CT2 received a platelet transfusion on day 2.

tag: subject id

value: patient 2 (CT2)

tag: disease

value: Cyclic thrombocytopenia

tag: tissue

value: Peripheral blood


title: CTCF-ChIP-D9-shLuci_SSEA1+ [ChIP-seq]

city: Guangzhou

first: ya

middle: wei

last: song

state: Guangdong

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

country: China

institute: Guangzhou Institute of Biomedicine and Health,Chinese Academy of Sciences

library_source: genomic

data_processing:
ChIP-seq raw reads were first assessed with FastQC tool and trimmed with trim galore if they contained adaptors.
Processed reads were mapped to the mm10 assembly using Bowtie2 with parameters “—very-sensitive –end-to-end –no-unal”. Any reads overlapped with mm10 blacklist regions (from ENCODE project) were filtered with bedtools, then proper-aligned and high-quality reads (MAPQ>30) were extracted with samtools, duplicated reads were removed using picard tools. Peaks were called by MACS2. Peak annotation, motif discovery, and the gene ontology analysis were performed using HOMER annotatePeaks.pl, or findMotifsGenome.pl. Differential binding sites were identified by MACS2bdgdiff tool with default parameters, or with glbase.redefine_peaks. Heatmaps from ChIP-seq was created with glbase or deeptools.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Peak files were generated using MACS2, coupled to redefine_peaks() from glbase3. Bigwig files were generated from normalized bdg files using bedGraphToBigWig tool.

molecule: genomic DNA

organism: Mus musculus

source_name: Reprogramming cells, control shRNA, SSEA1+ subpopulations

growth_protocol: mESCs and iPSCs were cultured in DMEM/High glucose medium (Hyclone) supplemented with beta-mercaptoethanol (10 mM), sodium pyruvate (10 mM), non-essential amino acids (10 mM), GlutaMAX (10 mM), 15% fetal bovine serum (Gibco), 1000 U/ml leukemia inhibitory factor (LIF), 1 μM MEK inhibitor PD0325901 and 3 μM GSK3 inhibitor CH99021. MEF cells were cultured in 10% FBS medium supplemented with non-essential amino acids (10 mM) and GlutaMAX (10 mM).

extract_protocol:
ChIP experiments were performed as previously described. Briefly, 1×10e7 cells were crosslinked with 1% formaldehyde at room temperature for 10 min. Then the reaction was stopped by adding glycine (final concentration, 0.125 M). Crosslinked cells were lysed in ChIP SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8.0)) containing 1 X Protease Inhibitor Cocktail and PMSF, then sonicated to achieve a chromatin sized of 200-400 bp. After sonication, the supernatant was diluted with IP buffer and then co-incubated with antibodies–Dynabeads protein A/G (1:1 mixed) at 4°C overnight with rotation. Immune complexes were washed with the following buffers: low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0), 150 mM NaCl), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0), 500 mM NaCl), LiCl wash buffer (0.25 M LiCl, 1% IGEPAL-CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 10 mM Tris-HCl (pH 8.0)) and TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). Antibody-bound chromatin was reverse-crosslinked, and the ChIPed DNA samples were purified for ChIP-Seq library generation. The ChIPmentation experiments were performed as previously described. Briefly, 1×10e5 cells were crosslinked with 1% formaldehyde at room temperature for 10 min. Then the reaction was stopped by adding glycine (final concentration, 0.125 M). Crosslinked cells were lysed in lysis buffer (10 mM Tris-HCl,100 mM NaCl (pH 8.0),1 mM EDTA, 0.5 mM EGTA,0.1% NaDeoxycholate, 0.5% N-lauroylsarcosine, 1 x protease inhibitors), then sonicated to achieve a chromatin sized of 200-700 bp.Triton X-100 was added to a final concentration of 1%. After centrifuge, the supernatant was co-incubated with antibodies–Dynabeads protein A/G (1:1 mixed) at 4°C overnight with rotation. Immune complexes were washed with the following buffers: low salt wash buffer, high salt wash buffer, LiCl wash buffer, TE buffer and 10 mM Tris-HCl (pH 8.0). For tagmentation, bead bound chromatin was resuspended in 45 μl of tagmentation buffer, 5 μl of transposase (Vazyme) was added and samples were incubated at 37°C for 10 min followed by two washes with low-salt buffer. Antibody-bound chromatin was reverse-crosslinked, and the ChIPed DNA samples were purified for ChIP-seq library generation.
ChIP-seq sequencing libraries were constructed using the VAHTSTM Universal DNA Library Prep Kit for Illumina® V2.

treatment_protocol:
20,000 MEFs at passage 2 were plated in a 12-well plate and then infected twice with retroviral stocks generated with Plat-E cells. 3 volumes of the supernatants of OSKM transcription factors were mixed with 1 volume of fresh MEF medium containing polybrene at a final concentration of 8 μg/ml. The infection efficiency was tested by MEFs transduced with virus of pMXs-EGFP. pMXs-CTCF and shRNAs were also transfected into OG2-MEFs by retrovirus generated from Plat-E cells. For infecting OG2-MEFs, the medium of OG2-MEFs was replaced with 2 ml of infection mixture per well in a 12-well plate. Infected cells were cultured with mESC medium containing 50 μg/ml Vitamin C (Sigma) post infection and renewed daily. For polycistronic OSKM-mediated reprogramming experiments, MEFs were transduced with 1 volume inducible lentivirus of OSKM and 2 volume rtTA retroviruses generated from HEK293T cells. Infected cells were cultured in mESC medium containing 50 μg/ml Vitamin C and 2 μg/ml doxycycline (Sigma) for 12 days to count GFP positive colonies. To ensure proper CTCF knockdown efficiency before transfecting these virus supernatants into MEFs, we concentrated virus supernatant produced from Ctcf shRNAs.
Lentivirus of lenti-birAV5 and pSIN-FLBio-SMARCA5 were assembled with psPAX2, pMD2.G vectors. mESCs were then infected with lenti-birAV5 lentivirus and selected with 10 μg/ ml of blastcidin for 5 days. BirAV5 overexpression was detected with anti-V5 antibody by Western blot. Then BirAV5-overexpressed cells were infected with pSIN-FLBio-Smarca5 lentivirus. Thereafter, cells were selected with 2 μg /ml of puromycin for 5 days, then single clones were picked up. Finally, in vivo biotinylation of SMARCA5 was detected with Anti-BIOTIN antibody (Cell Signaling Technology, CatLog: #7075) with a dilution ratio of 1:1000.
Three sets of oligonucleotides were cloned into an U6-sgRNA vector, separately, to create paired sgRNA target sites for SpCas9-nickase in the first or second exon of Smarca5. CRISPR/Cas9 target sites in Smarca5 (NM_053124.2) were designed by http://zifit.partners.org/ZiFiT/CSquare9Nuclease.aspx. The sequences of these three oligos were listed in Key Resources Table. Then these three sets of oligonucleotides were synthesized and inserted into the Bbs I site of the U6-gRNA vector. To generate stable Smarca5-/- mESC lines, two of the three gRNAs were used together, 2×10e6 mESCs were transfected with 20 μg of U6-sgRNA vector and 50 μg of pcDNA3.3-hCas9 plasmids. Cells were selected with 500 μg/ml of G418 (Sigma) after 24 hr of infection and were maintained in selection for 72 hr. Single clones were separated and were seeded in each well of a 48-well plate. Genotype of each colony was examined through Western blot.

tag: cell type

value: Reprogramming cells

tag: day of reprogramming

tag: chip antibody

value: CTCF(Active motif Cat# 61311)


title: DDX3X-displaced tracer tRNA replicate 1

city: Vienna

first: Schaefer

last: Matthias

state: AT

address: Schwarzspanierstrasse 17-I

department: Cell and Developmental Biology

country: Austria

institute: Medical University Vienna, Center for Anatomy & Cell Biology

data_processing:
basecalling was performed by VBCF sequencing facility
Reads (if libraries were pair-end sequenced, only R1 mate was further processed) were trimmed for adapter sequences and low quality bases with q score less than 10 were removed from the 3' end using the cutadapt software. Command line: cutadapt -q 10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC input.fastq > output_trimmed.fastq
Reads were further mapped to the collapsed tRNA annotation originating from https://github.com/FlorianPichot/tRNA_reference_construction . Command line:  bowtie2 --no-unal --no-1mm-upfront -D 15 -R 2 -N 0  -L 10 -i S,1,1.15 -x index -U sample.fastq -S output.sam 2> sample_mapping_report.txt
Sam files were converted to bam file, sorted and indexed using samtools (samtools view -S -b; samtools sort; samtools index)
Number of reads mapping to individual tRNA cluster was extracted by samtools idxstats. Command line samtools idxstats sample_sorted.bam > sample_idxstats.txt
Genome_build: custom collapsed human tRNA space (PMID: 33435213). FASTA available on series record and at https://github.com/FlorianPichot/tRNA_reference_construction/blob/main/Available_references/Homo_sapiens/
Supplementary_files_format_and_content: tsv files containing number of reads mapping to individual tRNA clusters

molecule: total RNA

growth_protocol: HEK293 cells cultured in a humidified incubator at 37°C, 5% CO2 in standard DMEM supplemented with antibiotic/antimycotics, 2 mM L-glutamine and 10% fetal bovine serum.

extract_protocol:
Cells were collected from culture dish and solubilized in Trizol. Total RNA was extracted, and separated using UREA-PAGE. tRNAs were excised, eluted from crushed gel pieces and precipitated by isopropanol. Refolded tRNAs were further treated with recombinant angiogenin endonuclease, radiolabeled using P32-gamma-ATP and used to monitor DDX3X helicase unwinding activity
Libraries were prepared according to NEBNext small RNA cloning protocol (E7580S)

tag: enzymatic treatment

value: Cleaved with recombinant Angiogenin and subjected to DDX3X unwinding assay

tag: biochemical separation

value: Separated by native PAGE prior to library cloning

tag: cell line

tag: molecule subtype

value: tRNA


title: 501mel_NTC_R2

description: viral transduction


title: D12-CAR T rep3

city: Hangzhou

first: XIN

last: GUO

state: Zhejiang

address: yuhangtang road

institute: Zhejiang University

data_processing:
Cutadapt software (v 1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100)
Sequenced reads were aligned to the human reference genome (GRCh38) using the HISAT2  software (version 2.0.4).
The mapped reads of each sample were assembled using StringTie(v1.3.4) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(v0.9.8). StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM
Principal component analysis and differential expression analysis were performed using edgeR package  (v 3.26.8) in R (v 3.6.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix tables with raw gene counts or FPKM values for every gene and every sample

source_name: human T cells

growth_protocol: Positive transduced T cells were sorted 5 days post initial activation and expanded in culture for 6 days. Fresh IL-2-containing medium was changed every 2 days.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Peripheral blood was obtained from healthy volunteers. All blood samples were handled following the required ethical and safety procedures. Peripheral blood mononuclear cells were isolated by density gradient centrifugation. T cells were purified and stimulated with anti-CD3/CD28 beads (Life Technologies) at a 3:1 bead:cell ratio in T cell medium for 24 hours prior to lentiviral transduction. Condensed viral supernatant was used for transduction in accordance with a multiplicity of infection (MOI) of 2. Positive transduced T cells were sorted 5 days post initial activation and expanded in culture for 6 days. Day-6 T cells, Day-6 CAR-T and Day-11 CAR-T cells were used to extract RNA.

value: blood

value: T cells

tag: culture duration

value: long-term


title: 501mel_KO5.2_R1

description: viral transduction


title: D12-CAR T rep2


title: CTCF-ChIP-D9-shCTCF_SSEA1-Thy1- [ChIP-seq]

source_name: Reprogramming cells, CTCF shRNA, SSEA1-Thy1- subpopulations


title: Liver Naive ZT20 rep 3

city: Manchester

first: Polly

last: Downton

address: Oxford Road

country: United Kingdom

institute: University of Manchester

description:
PD58
liver_fc.txt

data_processing:
Sequencing library preparation and sequencing were performed by the University of Manchester Genomic Technologies Core Facility. Sample quality was determined using a 2200 TapeStation (Agilent Technologies). Libraries were generated using the TruSeq Stranded mRNA assay (Illumina, Inc.) according to the manufacturer’s protocol. The multiplexed libraries were analysed by paired-end sequencing on a HiSeq 4000 instrument (76 + 76 cycles, plus indices), then demultiplexed and converted using bcl2fastq software (v2.17.1.14, Illumina).
Joint fastqs were concatenated prior to processing.
Adaptors were removed and ends trimmed using Trimmomatic (v0.36), then reads were mapped against the mouse genome (mm10/GRCm38) using STAR (v2.5.3).
Reads were counted in R using the Rsubread (v1.28.1).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_fc.txt: Space-delimited matrix tables with raw gene counts for every gene and every sample.

source_name: Liver

extract_protocol:
Joint tissue was ground with liquid nitrogen using a pestle and mortar, then transferred to a Lysing Matrix D tube containing Trizol. Tissue was homogenised using a BeadMill homogeniser (3 x 4 m/s for 40s). RNA was extracted using chloroform then precipitated using isopropanol. After washing with 75% ethanol, the RNA pellet was resuspended in RNase-free water.
RNA was purified from liver samples using the SV Total RNA kit (Promega), according to the manufacturer’s instructions. Tissue was homogenised using Lysing Matrix D tubes loaded into a BeadMill homogeniser (4 m/s for 20s). RNA was eluted in RNase-free water.
RNA was purified from muscle samples using the ReliaPrep Tissue kit (Promega), following the manufacturer’s instructions for the purification of RNA from fibrous tissue. Muscle tissue was homogenised using the same protocol as for joint, and eluted in RNase-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Male DBA/1 mice (8-10 weeks) were administered bovine type II collagen emulsified in Complete Freund’s Adjuvant (both MD Bioscience, Zurich, Switzerland) by intradermal injection under anaesthesia (2 x 50 ml of 1 mg/ml collagen in CFA). After 21 days, mice were given an intraperitoneal booster injection of collagen (200 ml of 1 mg/ml collagen in saline). Tissue collection occurred at ZT0, 4, 8, 12, 16 or 20 on day 7 after the development of disease symptoms in CIA mice, or at matched time points in naive control mice.

tag: strain

tag: Sex

value: Male

value: Liver

tag: treatment

value: Naive

tag: time


title: 501mel_NTC_R1

description: viral transduction

tag: melanoma molecular subtype

tag: disease state


title: CTCF-ChIP-D6-shCTCF_SSEA1-Thy1- [ChIP-seq]


title: Liver Naive ZT20 rep 2

description:
PD57
liver_fc.txt


title: CTCF-ChIP-D6-shCTCF_SSEA1+ [ChIP-seq]

source_name: Reprogramming cells, CTCF shRNA, SSEA1+ subpopulations


title: CTCF-ChIP-D6-shLuci_SSEA1+ [ChIP-seq]


title: D12-CAR T rep1


title: Skmel147_KO3.20_R2

description: viral transduction

source_name: SKmel147 melanoma cell line

tag: construct

value: Lenti-Cas9 + PLKO sgRNA stable infection


title: 501mel_KO5.2_R2

description: viral transduction

value: metastatic melanoma


title: Liver Naive ZT16 rep 1

description:
PD51
liver_fc.txt


title: D6-CAR T rep2

value: short-term


title: CTCF-ChIP-D0-shCTCF_rep2 [ChIP-seq]

source_name: Reprogramming cells, CTCF shRNA


title: Liver Naive ZT16 rep 5

description:
PD55
liver_fc.txt


title: Liver Naive ZT16 rep 4

description:
PD54
liver_fc.txt


title: Skmel147_KO3.20_R1

description: viral transduction


title: CTCF-ChIP-D0-shCTCF_rep1 [ChIP-seq]


title: Skmel147_KO1.5_R2

description: viral transduction


title: Liver Naive ZT12 rep 4

description:
PD49
liver_fc.txt


title: 501mel_Par_R2


title: D6-T rep3


title: D6-T rep2


title: CTCF-ChIP-D6-shLuci_SSEA1-Thy1- [ChIP-seq]

source_name: Reprogramming cells, control shRNA, SSEA1-Thy1- subpopulations


title: Liver Naive ZT16 rep 3

description:
PD53
liver_fc.txt


title: 501mel_Par_R1


title: Liver Naive ZT20 rep 1

description:
PD56
liver_fc.txt


title: CTCF-ChIP-D3-shLuci-Thy1+ [ChIP-seq]

source_name: Reprogramming cells, control shRNA, Thy1+ subpopulations


title: Liver Naive ZT16 rep 2

description:
PD52
liver_fc.txt


title: Skmel147_KO1.4_R2

description: viral transduction


title: CTCF-ChIP-D0-shLuci_rep1 [ChIP-seq]

source_name: Reprogramming cells, control shRNA


title: Liver Naive ZT12 rep 2

description:
PD47
liver_fc.txt


title: Liver Naive ZT12 rep 5

description:
PD50
liver_fc.txt


title: Skmel147_KO1.4_R1

description: viral transduction


title: D6-CAR T rep3


title: D6-CAR T rep1


title: CTCF-ChIP_D12_shCTCF_Oct4+_rep3 [ChIP-seq]

source_name: Reprogramming cells, CTCF shRNA, GFP+ subpopulations


title: Liver Naive ZT12 rep 3

description:
PD48
liver_fc.txt


title: CTCF-ChIP-D0-shLuci_rep2 [ChIP-seq]


title: Skmel147_KO1.5_R1

description: viral transduction


title: CTCF-ChIP_D12_shCTCF_Oct4+_rep1 [ChIP-seq]


title: D6-T rep1


title: CTCF-ChIP-D3-shCTCF-Thy1+ [ChIP-seq]


title: SKmel147_Par_R2


title: Liver Naive ZT8 rep 4

description:
PD44
liver_fc.txt


title: Liver Naive ZT12 rep 1

description:
PD46
liver_fc.txt


title: MSC_19

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

description:
rRNA-depleted total RNA
rRNA-depleted stranded RNA-Seq

data_processing:
The high quality of sequence reads was confirmed using FastQC tool.
The pooled libraries were sequenced on two lanes, hence 2 sets of paired-end sequence files were generated. The R1 and R2 files for each samples were concatenated prior to analysis.
Reads were then mapped to the human UCSC hg38 reference assembly using HISAT2 v2.1.0 with options "-k 1 -5 10 --rna-strandness RF".
Gene expression was quantified by counting the number of uniquely mapped reads with featureCounts with option "-s 1".
For differential gene expression analysis, we masked sex-linked genes and retained genes that had an expression level of minimum 5 counts per million reads (CPM) in at least 5 of the samples. We performed normalization using glmQLFit model. Differential gene expression analyses were conducted using the edgeR Bioconductor package (R version 3.6.0).
For data visualization in IGV genome browser, bigwig scaled per million reads mapping onto gene exons were generated using a succession of genomeCoverageBed and wigToBigWig tools.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: MSC_RNASeq_QLFit_cpm_counts.txt: Matrix table with CPM values after quantile normalization.
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with raw gene counts for every gene in each sample as generated by featureCounts (gene annotation: UCSC hg38).
Supplementary_files_format_and_content: *.bw: Bigwig files scaled per million reads mapping onto gene exons.

source_name: mesenchymal stromal cells derived from bone marrow

growth_protocol: Clinical grade allogeneic BM-MSC were generated using good manufacturing practices (GMP) following the European Medical Agency guideline on Human Cell Based Medicinal Product (EMA/CHMP/410860/2006) and “Établissement Français du Sang” standard operating procedures. In brief, BM aspirate, harvested from the donor iliac crest, was directly seeded at 50,000 nucleated cells/cm2 in culture chambers with Minimal Essential Medium Alpha (MEM-alpha) (Macopharma, France), 5% human platelet lysate (HPL) (Centre de Transfusions des Armées (CTSA), France) and 2 IU/mL heparin (Medium 1) until reaching >50% confluence (passage 0, P0). BM-MSC were further expanded in new culture chambers seeded at 4,000 cells/cm2 in MEM-alpha medium, 8% HPL and 2 IU/mL heparin (Medium 2). When reaching confluence, final product BM-MSC (passage 1, P1) were harvested and re-suspended at a maximal concentration of 2x106 BM-MSC/mL in NaCl 0.9% containing 0.5% of human albumin.

extract_protocol:
The cryopreserved P1 BM-MSC from 17 donors were stabilized in RNAStill (Real Biotech Corporation) prior to thawing. Cells were thawed on ice and recovered by centrifugation. Total RNA was extracted with the Aurum total RNA mini kit (Biorad) including an on-column DNase I digestion step. RNA was quantified using a BioDrop (Montreal Biotech) and the integrity evaluated on an Agilent TapeStation; the RNA integrity numbers were in average 9.7 [±0.2].
Ribosomal RNAs were depleted and libraries were prepared with the TruSeq stranded total RNA kit (Illumina), then multiplexed and sequenced on an Illumina NovaSeq 6000 Sprime flow cell in a paired-end 50bp configuration.

value: female

value: healthy

value: BM-MSC


title: MSC_20


title: SKmel147_NT_R2

description: viral transduction


title: CTCF-ChIP_D12_shLuci_Oct4+_rep3 [ChIP-seq]

source_name: Reprogramming cells, control shRNA, GFP+ subpopulations

value: Reprogramming cells


title: MSC_18


title: Liver Naive ZT8 rep 5

description:
PD45
liver_fc.txt


title: SKmel147_NT_R1

description: viral transduction


title: CTCF-ChIP_D12_shCTCF_Oct4+_rep2 [ChIP-seq]

value: CTCF(Active motif Cat# 61311)


title: Liver Naive ZT8 rep 2

description:
PD42
liver_fc.txt


title: MSC_21


title: MSC_17


title: Liver Naive ZT8 rep 1

description:
PD41
liver_fc.txt


title: 501mel_ATAC_KO5.2_R2

description: paired end

data_processing:
XL ChIP-seq: Reads were aligned using Bowtie (version 0.12.7) with parameters -k 1 -m 1 --best -S -n 2 -l 65 -q. BAM files were generated using SAMtools. duplicated reads were removed using SAMtools. bigwig files were generated from BAM files using deepTools bamCoverage (version 2.4.1) with parameters –normalizeUsingRPKM –binsize 10. Significant peaks were called using MACS2 callpeak (version 2.1.1.2) with parameters -f BAM -g 2.7e9 -s 100 --bw 200 —slocal 1000 -q 0.01.
ATAC-seq: Reads (40bp Paired-end) were aligned using Bowtie2 (version  2.1.0) with parameters -q -X 2000. BAM files were generated using SAMtools. Reads that align to mtDNA, with quality value Q<30, as well as duplicated reads, were discarded using in-house scripts and Samtools.. bigwig files were generated from BAM files using deepTools bamCoverage (version 2.4.1) with parameters –normalizeUsingRPKM –binsize 10. Significant peaks were called using MACS2 callpeak (version 2.1.1.2) with parameters –nomodel –nolambada –keepdup all –slocal 10000
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: fastq - raw illumina reads. bigwig - aligned reads pileup with deeptools

source_name: 501mel ARID2 KO

extract_protocol:
XL ChIP-seq: For ARID2, SS18, BRG1, TEAD4, FOSL2, CTCF, and MITF cells were cross-linked with 2 mM disuccinimidyl glutarate (DSG, Pierce 20593) in PBS for 45 min  followed by 1% FA for 10 min at RT. For H3K27ac and H3K27me3 cells were cross-linked with  1% FA for 10 min at RT. ChIP was performed  as previously described (Fontanals-Cirera B, Hasson D, Vardabasso C, Di Micco R et al. Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene. Mol Cell 2017 Nov 16;68(4):731-744.e9)
ChIP-seq: Libraries for ChIP-seq were done as previously described  (Fontanals-Cirera B, Hasson D, Vardabasso C, Di Micco R et al. Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene. Mol Cell 2017 Nov 16;68(4):731-744.e9)
ATAC-seq: For all ATAC-seq libraries,  50k cells were harvested, tagmented with 2.5-5uL Nextera Tn5 Transposes from nextera for 30 min, amplified up to 10 cycles and purified essentially as previously described in ATAC protocols. Purified libraries were then size selected on 2% agarose gel (150-700bp).

value: Lenti-CRISPR V2 Cas9 + sgRNA

tag: antibody


title: MSC_14

value: male


title: Liver Naive ZT4 rep 5

description:
PD40
liver_fc.txt

tag: tissue


title: Liver Naive ZT8 rep 3

description:
PD43
liver_fc.txt


title: MSC_15

tag: cell type


title: 501mel_ATAC_KO5.2_R1

description: paired end


title: Liver Naive ZT4 rep 4

description:
PD39
liver_fc.txt


title: MSC_13


title: E14_oeSmarca5_input [ChIP-seq]

source_name: E14Tg2a, overexpression of Flag-biotin-Smarca5

value: Embryonic stem (ES) cell line,E14Tg2a

tag: passages


title: 501mel_ATAC_KO1.8_R2

description: paired end


title: CTCF-ChIP_D12_shLuci_Oct4+_rep1 [ChIP-seq]

tag: day of reprogramming

tag: chip antibody


title: E14_oeSmarca5_SMARCA5_rep2 [ChIP-seq]

value: Dynabeads M-280 Streptavidin(Thermo Fisher Scientific Cat# 11205D)


title: MSC_16


title: SKmel147_Par_R1


title: 501mel_ATAC_KO1.8_R1

description: paired end


title: E14_oeSmarca5_SMARCA5_rep1 [ChIP-seq]


title: 501mel_ATAC_NT

description: paired end

source_name: 501mel ARID2 WT


title: MSC_12


title: CTCF-ChIP_D12_shLuci_Oct4+_rep2 [ChIP-seq]


title: D12_shCTCF_GFP+_rep2 [RNA-seq]

data_processing:
RNA-seq raw datasets were qualified with FastQC tool and trimmed with trim galore if containing adaptors.
Reads were aligned to mm10 genome using rsem with options "--star". Counts were extracted from sample.genes.results file and merged together. RNA-seq raw counts were normalized with EDAseq.
Genome_build: mm10 (GRCm38), Ensembl v95
Supplementary_files_format_and_content: tsv files were generated from normalized RNAseq data.

extract_protocol:
Total RNAs were extracted with TRIzol.
RNA sequencing libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit from Illumina (NEB).

treatment_protocol: 20,000 MEFs at passage 2 were plated in a 12-well plate and then infected twice with retroviral stocks generated with Plat-E cells. 3 volumes of the supernatants of OSKM transcription factors were mixed with 1 volume of fresh MEF medium containing polybrene at a final concentration of 8 μg/ml. The infection efficiency was tested by MEFs transduced with virus of pMXs-EGFP. pMXs-CTCF and shRNAs were also transfected into OG2-MEFs by retrovirus generated from Plat-E cells. For infecting OG2-MEFs, the medium of OG2-MEFs was replaced with 2 ml of infection mixture per well in a 12-well plate. Infected cells were cultured with mESC medium containing 50 μg/ml Vitamin C (Sigma) post infection and renewed daily. For polycistronic OSKM-mediated reprogramming experiments, MEFs were transduced with 1 volume inducible lentivirus of OSKM and 2 volume rtTA retroviruses generated from HEK293T cells. Infected cells were cultured in mESC medium containing 50 μg/ml Vitamin C and 2 μg/ml doxycycline (Sigma) for 12 days to count GFP positive colonies. To ensure proper CTCF knockdown efficiency before transfecting these virus supernatants into MEFs, we concentrated virus supernatant produced from Ctcf shRNAs.


title: MSC_11


title: MSC_08


title: 501mel_ATAC_Par

description: paired end


title: Liver Naive ZT4 rep 2

description:
PD37
liver_fc.txt


title: Liver Naive ZT4 rep 1

description:
PD36
liver_fc.txt


title: SKmel147_ATAC_KO3.20_R2

description: paired end

source_name: SKmel147 ARID2 KO


title: MSC_07


title: D12_shCTCF_GFP+_rep1 [RNA-seq]


title: MSC_06


title: SKmel147_ATAC_KO3.20_R1

description: paired end


title: D12_shLuci_GFP+_rep1 [RNA-seq]


title: Liver Naive ZT4 rep 3

description:
PD38
liver_fc.txt


title: Liver Naive ZT0 rep 4

description:
PD34
liver_fc.txt


title: SKmel147_ATAC_KO1.4_R2

description: paired end


title: Liver Naive ZT0 rep 3

description:
PD33
liver_fc.txt


title: MSC_04


title: Liver Naive ZT0 rep 2

description:
PD32
liver_fc.txt


title: MSC_05


title: MSC_02


title: SKmel147_ATAC_KO1.4_R1

description: paired end


title: D9_shCTCF_SSEA1-Thy1-_rep2 [RNA-seq]


title: D12_shLuci_GFP+_rep2 [RNA-seq]


title: Liver Naive ZT0 rep 5

description:
PD35
liver_fc.txt


title: D9_shCTCF_SSEA1-Thy1-_rep1 [RNA-seq]


title: SKmel147_ATAC_NT

description: paired end

source_name: SKmel147 ARID2 WT


title: SKmel147_ATAC_Par

description: paired end


title: 501-KO1-8-H3K27ac

description: single end

value: H3K27ac - Abcam #ab4729


title: D9_shLuci_SSEA1-Thy1-_rep1 [RNA-seq]


title: D9_shLuci_SSEA1-Thy1-_rep2 [RNA-seq]


title: 501-KO5-2-H3K27ac

description: single end


title: Liver CIA ZT20 rep 5

description:
PD30
liver_fc.txt

value: CIA


title: D9_shCTCF_SSEA1+_rep1 [RNA-seq]


title: Liver CIA ZT20 rep 4

description:
PD29
liver_fc.txt

value: Male


title: 501-Par-H3K27ac

description: single end


title: D9_shLuci_SSEA1+_rep1 [RNA-seq]

source_name: Reprogramming cells, control shRNA, SSEA1+ subpopulations


title: 501-NT-H3K27ac

description: single end


title: D9_shLuci_SSEA1+_rep2 [RNA-seq]


title: 501-KO5-2-MITF

description: single end

value: MITF - Sigma A. #HPA003259


title: Liver CIA ZT20 rep 1

description:
PD26
liver_fc.txt

value: Liver


title: 501-KO1-8-MITF

description: single end


title: D9_shCTCF_SSEA1+_rep2 [RNA-seq]


title: Liver Naive ZT0 rep 1

description:
PD31
liver_fc.txt

value: Naive


title: Liver CIA ZT20 rep 2

description:
PD27
liver_fc.txt


title: D9_shCTCF_Thy1+_rep2 [RNA-seq]

source_name: Reprogramming cells, CTCF shRNA, Thy1+ subpopulations


title: Liver CIA ZT16 rep 5

description:
PD25
liver_fc.txt

source_name: Liver


title: Liver CIA ZT16 rep 3

description:
PD23
liver_fc.txt


title: 501-NT-MITF

description: single end

value: metastatic melanoma


title: D9_shCTCF_Thy1+_rep1 [RNA-seq]


title: Liver CIA ZT20 rep 3

description:
PD28
liver_fc.txt


title: Liver CIA ZT16 rep 2

description:
PD22
liver_fc.txt


title: D9_shLuci_Thy1+_rep1 [RNA-seq]


title: 501-ARID2KO-5-2

description: paired end

value: SS18 - Cell Signaling #21792 D6I4Z


title: D6_shCTCF_SSEA1-Thy1-_rep2 [RNA-seq]

source_name: Reprogramming cells, CTCF shRNA, SSEA1-Thy1- subpopulations


title: 501-Par-MITF

description: single end


title: D6_shCTCF_SSEA1-Thy1-_rep1 [RNA-seq]


title: 501-ARID2KO-1-8

description: paired end


title: Liver CIA ZT16 rep 1

description:
PD21
liver_fc.txt


title: Liver CIA ZT12 rep 4

description:
PD19
liver_fc.txt


title: Liver CIA ZT12 rep 5

description:
PD20
liver_fc.txt


title: 501-NT-SS18

description: paired end


title: D6_shLuci_SSEA1-Thy1-_rep1 [RNA-seq]


title: 501-Parental

description: paired end


title: Liver CIA ZT16 rep 4

description:
PD24
liver_fc.txt


title: Liver CIA ZT12 rep 3

description:
PD18
liver_fc.txt


title: D6_shLuci_SSEA1+_rep2 [RNA-seq]


title: D6_shCTCF_SSEA1+_rep2 [RNA-seq]

source_name: Reprogramming cells, CTCF shRNA, SSEA1+ subpopulations


title: Liver CIA ZT8 rep 5

description:
PD15
liver_fc.txt


title: Liver CIA ZT12 rep 1

description:
PD16
liver_fc.txt


title: D6_shCTCF_SSEA1+_rep1 [RNA-seq]


title: 147-KO3-20-Fosl2

description: single end

value: Lenti-Cas9 + PLKO sgRNA stable infection

value: FOSL2 - Santa Cruz #sc-604


title: D6_shLuci_SSEA1+_rep1 [RNA-seq]


title: 147-KO1-4-Fosl2

description: single end


title: Liver CIA ZT8 rep 4

description:
PD14
liver_fc.txt


title: 147-KO3-20-Tead4

description: single end

value: TEAD4 - Santa Cruz #sc-101184


title: D9_shLuci_Thy1+_rep2 [RNA-seq]

value: Reprogramming cells


title: Liver CIA ZT12 rep 2

description:
PD17
liver_fc.txt


title: 147-NT-Tead4

description: single end


title: D6_shCTCF_Thy1+_rep2 [RNA-seq]


title: Liver CIA ZT8 rep 2

description:
PD12
liver_fc.txt


title: D6_shLuci_Thy1+_rep2 [RNA-seq]


title: D6_shCTCF_Thy1+_rep1 [RNA-seq]


title: D6_shLuci_SSEA1-Thy1-_rep2 [RNA-seq]


title: Liver CIA ZT8 rep 1

description:
PD11
liver_fc.txt


title: 147-Par-Tead4

description: single end


title: 147-KO1-4-Tead4

description: single end


title: Liver CIA ZT8 rep 3

description:
PD13
liver_fc.txt


title: 147_KO3_20_ARID2

description: single end

value: ARID2 - Cell signaling #82342 D8D8U


title: D3_shCTCF_SSEA1-Thy1-_rep2 [RNA-seq]


title: Liver CIA ZT4 rep 4

description:
PD9
liver_fc.txt


title: D6_shLuci_Thy1+_rep1 [RNA-seq]


title: 147-NT-Fosl2

description: single end


title: 147-Par-Fosl2

description: single end


title: Liver CIA ZT4 rep 2

description:
PD7
liver_fc.txt


title: 147_KO1_4_ARID2

description: single end


title: D3_shCTCF_SSEA1-Thy1-_rep1 [RNA-seq]


title: Liver CIA ZT0 rep 5

description:
PD5
liver_fc.txt


title: 147_KO3_20_H3K27me3

description: single end

value: H3K27me3 - Epicypher #13-0030


title: Liver CIA ZT4 rep 3

description:
PD8
liver_fc.txt


title: Liver CIA ZT0 rep 4

description:
PD4
liver_fc.txt


title: 147_KO1_4_H3K27me3

description: single end


title: 147_NT_ARID2

description: single end


title: D3_shLuci_SSEA1-Thy1-_rep1 [RNA-seq]


title: D3_shCTCF_SSEA1+_rep2 [RNA-seq]


title: 147_Par_H3K27me3

description: single end


title: D3_shLuci_SSEA1-Thy1-_rep2 [RNA-seq]


title: D3_shLuci_SSEA1+_rep2 [RNA-seq]


title: 147_NT_H3K27me3

description: single end


title: D3_shLuci_SSEA1+_rep1 [RNA-seq]


title: Liver CIA ZT4 rep 5

description:
PD10
liver_fc.txt


title: Liver CIA ZT0 rep 1

description:
PD1
liver_fc.txt


title: 147_NT_CTCF

description: single end

value: CTCF - Millipore #07-729


title: D3_shCTCF_SSEA1+_rep1 [RNA-seq]


title: 147_KO3_20_CTCF

description: single end


title: D3_shCTCF_Thy1+_rep2 [RNA-seq]


title: Liver CIA ZT0 rep 3

description:
PD3
liver_fc.txt


title: D3_shCTCF_Thy1+_rep1 [RNA-seq]


title: Plasma exosome 6 of  Legg-Cavé-Perthes patient

city: Nanning

first: Qian

last: Huang

state: Guangxi

address: Shuangyong road 22

institute: Guangxi Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts.
The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures.
Known miRNA used miFam.dat (http://www.mirbase.org/ftp.shtml) to look for families; novel miRNA precursor was submitted to Rfam (http://rfam.sanger.ac.uk/search/) to look for Rfam families.
Predicting the target gene of miRNA was performed by psRobot_tar in psRobot for plants or miRanda for animals.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Plasma exosome

extract_protocol:
In brief, all patients and volunteers fasted for 8 hours and abandoned the first tube after early morning blood draw. Then, 10 mL of whole blood was collected using an EDTA anticoagulant tube and centrifuged at 3000× g speed for 15 min to remove blood cells and fragments. Plasma exosomes were extracted with exoEasy Maxi Kit (QIAGEN, Germany) in accordance with the manufacturer’s instructions. Finally, 200 μl of exosomes were obtained and stored separately at −80 °C.Small RNA libraries were prepared from the exosomal RNA isolated from each sample in the Perthes group and the control group by using the exoRNeasy Maxi Kit (QIAGEN, Germany) in accordance with 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.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500 platform and 50bp single-end reads were generated.

value: Legg-Cavé-Perthes


title: 147_Par_CTCF

description: single end


title: D3_shLuci_Thy1+_rep2 [RNA-seq]


title: Plasma exosome 1 of  Legg-Cavé-Perthes patient


title: D3_shLuci_Thy1+_rep1 [RNA-seq]


title: Liver CIA ZT0 rep 2

description:
PD2
liver_fc.txt


title: Plasma exosome 0 of  Legg-Cavé-Perthes patient


title: D0_shCTCF_rep1 [RNA-seq]

source_name: Reprogramming cells, CTCF shRNA


title: Liver CIA ZT4 rep 1

description:
PD6
liver_fc.txt


title: Plasma exosome 8 of  healthy volunteer

value: healthy


title: D0_shLuci_rep2 [RNA-seq]


title: D0_shCTCF_rep2 [RNA-seq]


title: D0_shLuci_rep1 [RNA-seq]


title: 147_Par_H3K27ac

description: single end

value: H3K27ac - Abcam #ab4729


title: 147_KO3_20_H3K27ac

description: single end


title: 147_NT_H3K27ac

description: single end


title: Plasma exosome 9 of  healthy volunteer


title: 147_Par_BRG1

description: single end

value: BRG1 - Abcam #ab110641


title: 147_KO3_20_SS18

description: single end


title: SNU-JAX-G187 (patient)

city: Seoul

first: Jong-Il

last: Kim

address: 101 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

description:
Sample name in figure:
R08
patient; SUVmax=3.91

data_processing:
Transcriptome sequencing data were mapped to the reference using STAR 2.5.3a
Sorting and marking duplicate reads were performed using Picard 2.9 MarkDuplicates.
Quality control for RNA-seq data using RNA-SeQC 1.1.9
Genome_build: GTEX_Homo_sapiens_assembly19.fa
Supplementary_files_format_and_content: raw counts

source_name: Tumor

extract_protocol:
Tumor tissues were homogenized and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols(TruSeq RNA Library Prep Kit v1).

tag: host strain

value: gastric cancer tumor

tag: suvmax


title: SNU-JAX-G139 (patient)

description:
Sample name in figure:
R07
patient; SUVmax=5.9


title: Plasma exosome 7 of  healthy volunteer


title: SNU-JAX-G420 (patient)

description:
Sample name in figure:
R06
patient; SUVmax=8.8


title: 147_KO1_4_SS18

description: single end


title: 147_KO1_4_CTCF

description: single end


title: tumor-case-50

type: genomic

city: Lübeck

first: Axel

last: Künstner

address: Ratzeburger Allee 160

department: LIED

country: Germany

institute: University of Lübeck

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Arrays were hybridized, washed, and stained in Affymetrix fluidics station according to manufacturer's protocols.

data_processing: Raw data (CEL files) were processed using the R package EaCoN (v0.3.6-2) with SEQUENZA as segmentation algorithm. L2R files in CBS format were used as input for GISTIC (v2.0.22) to identify regions that are significantly amplified or deleted across all samples (confidence level 0.95, focal length cutoff 0.5, q-value threshold 0.1).

label: Biotin

source_name: tumor

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: As per manufacturer (Affymetrix)

value: Blastic plasmacytoid dendritic cell neoplasm (BPDCN)

value: tumor

tag: age

tag: gender

value: female

tag: primary location

value: Skin


title: tumor-case-49

value: male

value: Skin thorax


title: 147_KO1_4_H3K27ac

description: single end

value: Lenti-Cas9 + PLKO sgRNA stable infection

value: metastatic melanoma


title: SNU-JAX-G415 (patient)

description:
Sample name in figure:
R05
patient; SUVmax=12


title: tumor-case-51


title: SNU-JAX-G141 (patient)

description:
Sample name in figure:
R04
patient; SUVmax=13


title: tumor-case-48

value: LN cervical


title: 147_Par_SS18

description: single end

value: SS18 - Cell Signaling #21792 D6I4Z


title: tumor-case-47


title: tumor-case-45

value: BM, LN


title: UMUC3Drg3

city: Utrecht

first: Frank

last: Riemers

address: Uppsalalaan 8

country: Netherlands

institute: Utrecht University

data_processing:
quality control on FastQ files using FastQC-0.11.4
align reads of each sample in a run against reference genome using STAR-2.4.2a
add read groups using picard-tools-1.141 and Index BAM Sambamba v0.5.4
perform quality control on generated BAM files picard-tools-1.141
count reads in features using HTSeq-count
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: UM-UC-3 cell line

growth_protocol: RPE1-hTERT cells were cultured in DMEM, UM-UC-3 cells were cultured in EMEM. Both were supplemented with 10% FBS and 1% pen/strep.

extract_protocol:
RNA was isolated using the QIAGEN RNAeasy kit according to manufacturers’ recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells where treated with the combination of CHK1 inhibitor Prexasertib (CHK1i) (10nM) and Gemcitabine (4uM) or vehicle, and harvested after 16 hours

tag: doxycycline

value: Drg


title: tumor-case-43

value: BM, Skin


title: SNU-JAX-G284 (patient)

description:
Sample name in figure:
R02
patient; SUVmax=16.6


title: UMUC3Ctr3

tag: treatment

value: Ctr


title: SNU-JAX-G364 (patient)

description: patient; SUVmax=15.7


title: SNU-JAX-G218 (patient)

description:
Sample name in figure:
R03
patient; SUVmax=14.3


title: 147_NT_SS18

description: single end


title: UMUC3Drg1


title: UMUC3Ctr2


title: tumor-case-42

value: LN hilar, Gall bladder, Spleen, BM


title: SNU-JAX-G220 (patient)

description:
Sample name in figure:
R01
patient; SUVmax=19.2


title: tumor-case-44

value: BM


title: UMUC3Drg2


title: SNU-JAX-G304 (patient)

description: patient; SUVmax=8.44

value: gastric cancer tumor


title: F432HrasVehCtr1

source_name: RPE1-hTERT cell line

value: Veh


title: SNU-JAX-G417 (patient)

description: patient; SUVmax=4.4


title: SNU-JAX-G263 (patient)

description: patient; SUVmax=3.9


title: SNU-JAX-G251 (patient)

description: patient; SUVmax=7.8


title: tumor-case-40

value: Blastic plasmacytoid dendritic cell neoplasm (BPDCN)

value: tumor

value: BM, LN mesenterial, retroperitoneal, mediastinal, Osseous tissue, pleura


title: F432HrasVehDrg1


title: UMUC3Ctr1


title: tumor-case-38

value: female


title: F432HrasDoxDrg1

value: Dox


title: SNU-JAX-G250 (patient)

description: patient; SUVmax=12.8


title: tumor-case-37

value: male


title: F432HrasDoxCtr1


title: tumor-case-46

value: Skin thorax


title: SNU-JAX-G213 (patient)

description: patient; SUVmax=9.4


title: tumor-case-34


title: F411HrasVehDrg1


title: SNU-JAX-G130 (patient)

description: patient; SUVmax=28


title: SNU-JAX-G208 (patient)

description: patient; SUVmax=4.3


title: F411HrasVehDrg2


title: SNU-JAX-G088 (patient)

description: patient; SUVmax=9.49


title: F411HrasVehCtr1


title: tumor-case-41

value: Skin occipital


title: tumor-case-30

value: LN, Skin


title: SNU-JAX-G080 (patient)

description: patient; SUVmax=5.91


title: F411HrasVehCtr2


title: SNU-JAX-G114 (patient)

description: patient; SUVmax=8.8


title: tumor-case-32

value: LN cervical, BM


title: F411HrasDoxCtr2


title: tumor-case-33


title: SNU-JAX-G042 (patient)

description: patient; SUVmax=6.06


title: tumor-case-29

value: LN cervical


title: SNU-JAX-G015 (patient)

description: patient; SUVmax=4.12


title: F411HrasDoxDrg1

value: Drg


title: tumor-case-28

value: Mucous membrane paranasal sinus


title: tumor-case-27

value: Skin forearm


title: SNU-JAX-G001 (patient)

description: patient; SUVmax=8.82


title: F411HrasDoxDrg2


title: 12_PF382_IACS_CB839_2

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

data_processing:
Raw sequencing reads were pseudoaligned using Kallisto v0.44.059 with 30 bootstrap samples to a transcriptome index based on the human GRCh38.92 release (Ensembl)
Genome_build: GRCh38.92 release (Ensembl)
Supplementary_files_format_and_content: mRNA quantification of all samples

extract_protocol:
Total RNA was extracted from 4 ×106 cells using the RNeasy Mini Kit (Qiagen; cat. 74104). RNA concentration was determined by a NanoDrop 2000 spectrophotometer (ThermoFisher Scientific), and RNA quality was assessed with an Agilent Bioanalyzer. Approximately 100 million reads per sample were run on an Illumina Nextseq 500 system using 75 × 75 paired end (PE) reads for stranded whole-transcriptome sequencing
The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer’s instructions and amplified for five cycles

tag: cell line

value: leukemia cell line

tag: genotype/variation


title: tumor-case-26

tag: disease state

value: Skin


title: SNU-JAX-G417 (PDX)

description: xenograft; SUVmax=0.453

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ

value: gastric cancer tumor


title: tumor-case-25

value: Blastic plasmacytoid dendritic cell neoplasm (BPDCN)

value: tumor

value: LN


title: 11_PF382_IACS_CB839_1


title: tumor-case-31

value: female

value: Skin, Mucous membrane, LN cervical, axillary, left nuchal, right hilar, skin right chest, eye suspected


title: tumor-case-24

value: Skin, LN inguinal


title: 6_PF382_CB839_2


title: SNU-JAX-G364 (PDX)

description: xenograft; SUVmax=1.15


title: SNU-JAX-G354 (PDX)

description: xenograft; SUVmax=0.713


title: SNU-JAX-G367 (PDX)

description: xenograft; SUVmax=0.827


title: tumor-case-23

value: male

value: Skin, BM


title: 5_PF382_CB839_1


title: 4_PF382_IACS_2

value: IACS


title: tumor-case-21


title: SNU-JAX-G344 (PDX)

description: xenograft; SUVmax=1.433


title: 3_PF382_IACS_1


title: F411HrasDoxCtr1

value: Dox

value: Ctr


title: SNU-JAX-G311 (PDX)

description: xenograft; SUVmax=0.643


title: 2_PF382_control2

value: control


title: tumor-case-19

value: Adipose tissue peritoneal


title: tumor-case-18


title: SNU-JAX-G263 (PDX)

description: xenograft; SUVmax=0.687


title: tumor-case-20

value: Skin upper arm


title: SNU-JAX-G255 (PDX)

description: xenograft; SUVmax=0.64


title: tumor-case-16

value: Skin


title: SNU-JAX-G251 (PDX)

description: xenograft; SUVmax=0.517

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ


title: 1_PF382_control_1

value: leukemia cell line


title: SNU-JAX-G250 (PDX)

description: xenograft; SUVmax=0.585

value: gastric cancer tumor


title: i3_Lin_3

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

description: DESeq2_i3_MS_vs_i3_Lin, DESeq2_i3_MS_vs_Col_MS

data_processing:
Galaxy platform
adaptors were removed with Trimmomatic (Bolger et al., 2014)
sequencing quality was accessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were mapped to the Arabidopsis genome (TAIR10) with the gapped-read mapper TopHat 2.1.1 (Kim et al., 2013) set for Forward Read (FR) unstranded libraries and adjusting the maximum intron length to 5000 bp.
Reads were counted with featureCounts (Liao et al., 2014) with the help of the gene annotation in Araport11 (www.araport.org/data/araport11).
Genome_build: TAIR10
Supplementary_files_format_and_content: DESeq2 output

organism: Arabidopsis thaliana

source_name: 5-d-old seedlings

growth_protocol: Surface-sterilized seeds were sown on Murashige and Skoog plates containing 0.8% (w/v) agar (pH 5.8), and stratified for at least 2 days at 4°C. The growth medium contained 1% (w/v) sucrose. Seedlings were grown at 22°C under continuous illumination (100 µmol photons m-2 sec-1) provided by white fluorescent lamps. For inhibitor experiments, MS medium was supplemented with 50 µg/ml lincomycin (Sigma-Aldrich, Darmstadt, Germany)

extract_protocol:
Total RNA from plants was isolated using Trizol (Invitrogen, Carlsbad, USA) and purified using Direct-zol™ RNA MiniPrep Plus columns (Zymo Research, Irvine, USA) according to the manufacturer’s instructions. RNA integrity and quality was assessed by an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).
Illumina Tru-Seq

treatment_protocol: continuous light

tag: genotype

value: irx3-2 mutant

tag: growth medium

value: LIN

value: seedlings

value: 5 days old


title: i3_Lin_2

tag: tissue


title: tumor-case-15

value: Blastic plasmacytoid dendritic cell neoplasm (BPDCN)

value: tumor

value: LN Jaw angle


title: tumor-case-22

value: male

value: LN inguinal


title: SNU-JAX-G247 (PDX)

description: xenograft; SUVmax=0.723


title: tumor-case-14


title: i3_MS_2

value: MS


title: SNU-JAX-G222 (PDX)

description: xenograft; SUVmax=0.665


title: tumor-case-12

value: BM


title: SNU-JAX-G213 (PDX)

description: xenograft; SUVmax=0.767


title: tumor-case-13


title: Col_Lin_1

description: DESeq2_Col_Lin_vs_Col_MS, DESeq2_Col_Lin_vs_i3_Lin


title: tumor-case-10

value: female

value: LN, Liver


title: SNU-JAX-G238 (PDX)

description: xenograft; SUVmax=0.697


title: tumor-case-11

value: Skin, BM


title: tumor-case-17

value: Skin


title: i3_MS_1


title: SNU-JAX-G304 (PDX)

description: xenograft; SUVmax=0.797

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ


title: SNU-JAX-G210 (PDX)

description: xenograft; SUVmax=0.513

value: gastric cancer tumor


title: SNU-JAX-G208 (PDX)

description: xenograft; SUVmax=0.647


title: tumor-case-09

value: Skin frontal


title: SNU-JAX-G182 (PDX)

description: xenograft; SUVmax=0.63


title: Col_MS_3


title: tumor-case-07


title: tumor-case-08


title: Col_MS_2


title: SNU-JAX-G130 (PDX)

description: xenograft; SUVmax=0.727


title: SNU-JAX-G150 (PDX)

description: xenograft; SUVmax=0.867


title: tumor-case-06

value: LN, BM


title: tumor-case-05


title: SNU-JAX-G114 (PDX)

description: xenograft; SUVmax=0.955


title: 5KO,DS,Inp,rep1

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

country: Japan

institute: RIKEN

data_processing:
Adaptor sequences and low quality bases in reads were trimmed using Trim Galore version 0.3.7
Then trimmed reads were aligned to the mouse GRCm38 genome assembly using bowtie version 0.12.7
Duplicated reads were removed using samtools version 0.1.18
BigWig files were produced by bamCoverage 2.5.4-1-eca29f6
RPKM value in each 10kb bin was calculated by featureCounts and house perl script, then Log2(FC) against input was calculated and quantile normalization was performed by house perl script
Assembly: mm10
Supplementary files format and content: wig or bigWIg

extract_protocol: The ChIP DNA was fragmented by Picoruptor (Diagenode) for 10 cycles of 30 seconds on, 30 seconds off. Then, ChIP library was constructed by KAPA Hyper Prep Kit (KAPA BIOSYSTEMS) and SeqCap Adapter Kit A (Roche) according to manufacturer instructions. The concentration of the ChIP-seq library was quantified by KAPA Library quantification kit (KAPA BIOSYSTEMS). ChIP sequencing was performed on a HiSeq X platform (Illumina).

tag: cell type

value: iMEFs


title: 5KO,DMSO,Inp,rep2

value: DMSO


title: Col_Lin_3

value: LIN

value: seedlings

value: 5 days old


title: SNU-JAX-G088 (PDX)

description: xenograft; SUVmax=0.81


title: tumor-case-01

value: Blastic plasmacytoid dendritic cell neoplasm (BPDCN)

value: tumor

value: male

value: LN


title: SNU-JAX-G042 (PDX)

description: xenograft; SUVmax=0.477


title: SNU-JAX-G080 (PDX)

description: xenograft; SUVmax=0.703


title: 5KO,DS,LaminAC,rep2


title: 5KO,DMSO,Inp,rep1


title: 5KO,DMSO,LaminAC,rep2


title: 5KO,DS,Inp,rep2


title: 5KO,DS,BS,rep2

data_processing:
Adaptor sequences and low quality bases in reads were trimmed using Trim Galore version 0.3.7
The trimmed reads were mapped to the mouse GRCm38 genome assembly using Bismark v0.14.1 with single-end and non-directional mapping parameters
The methylation level of each CpG site was calculated as follows: number of methylated reads/number of total reads.
Assembly: mm10
Supplementary files format and content: txt

extract_protocol: 500 ng of genomic DNA was sheared by sonication to 100-500 bp using a Covaris S220 and purified by AMPure XP beads (Agencourt Bioscience Corp.). Genomic DNA libraries were constructed as ChIP-seq library. After adapter ligation, the DNA was treated with sodium bisulfite using EZ DNA Methylation GOLD kit (ZYMO RESEARCH) following the manufacturer’s instructions. Enrichment for adapter-ligated DNA was carried out through 10 PCR cycles using Pfu Turbo Cx Hotstart DNA polymerase (Agilent).


title: 5KO,DS,BS,rep1


title: SNU-JAX-G039 (PDX)

description: xenograft; SUVmax=0.78


title: 5KO,DMSO,BS,rep2


title: WT,DS,Inp,rep2

value: WT


title: SNU-JAX-G037 (PDX)

description: xenograft; SUVmax=0.937


title: 5KO,DMSO,BS,rep1


title: WT,DMSO,Inp,rep2


title: SNU-JAX-G015 (PDX)

description: xenograft; SUVmax=0.577


title: SNU-JAX-G017 (PDX)

description: xenograft; SUVmax=1.01


title: TKO,DMSO,BS,rep2

source_name: TKO

value: TKO


title: SNU-JAX-G019 (PDX)

description: xenograft; SUVmax=1.157


title: WT,DS,Inp,rep1


title: SNU-JAX-G001 (PDX)

description: xenograft; SUVmax=0.663


title: TKO,DMSO,BS,rep1


title: Fibrolamellar carcinoma #8

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
FLC34_YROP
Sample from fibrolamellar carcinoma patient #8

data_processing:
Alignment using STAR
Quantification using Salmon
Differential expression analysis using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: DESeq2 normalized counts and differential expression in csv format

extract_protocol:
Resection of normal or cancerous liver from human patients
TruSeq Stranded mRNA Library Prep Kit

value: Liver

value: fibrolamellar carcinoma


title: 5KO,DS,LaminAC,rep1


title: WT,DMSO,Inp,rep1


title: WT,DMSO,BS,rep1


title: 5KO,DMSO,LaminAC,rep1


title: WT,DS,LaminAC,rep1


title: WT,DMSO,LaminAC,rep2


title: WT,DS,LaminAC,rep2


title: Fibrolamellar carcinoma #7

description:
FLC33_NYTS
Sample from fibrolamellar carcinoma patient #7


title: Fibrolamellar carcinoma #6

description:
FLC32_UOTX
Sample from fibrolamellar carcinoma patient #6


title: Fibrolamellar carcinoma #5

description:
FLC31_OTOK
Sample from fibrolamellar carcinoma patient #5


title: shcontrol_D10_rep2 [BL-Hi-C]

data_processing:
Raw sequence data of BL-Hi-C were subjected to trimLinker tool from ChIA-PET2 to remove linker sequences with parameters "-m 1 -k 2 -e 1 -l 15 -A ACGCGATATCTTATC -B AGTCAGATAAGATAT". The trimmed reads were processed using HiC-Pro.
The resulting valid pairs were balanced and transformed into hic format using juicer tools.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: NOT PROVIDED

source_name: Reprogramming cells, OSKM knock down control

extract_protocol:
The BL-Hi-C libraries were performed as previous described. Briefly, the cells were treated with 1% formaldehyde for 10 min at RT and the crosslink was quenched by adding 2.5 M glycine. Then, the cells were treated with 0.1% SDS FA lysis buffer and 1% SDS FA lysis buffer. After that, the genome was digested with enzyme HaeIII into fragments with blunt-ends, which were treated with adenine and ligated with bridge linker containing biotin for 4 hr at 16°C. The unligated DNA fragments were digested with DNA exonuclease. Next, the cells were treated with SDS and proteinase K to digest proteins, and the DNA was purified using phenol-chloroform extraction with ethanol precipitation. Then, the DNA was fragmented into 300 bp on average by sonication and the biotin-labeled DNA fragments were pulled down with streptavidin coated M280 beads.
The BL-Hi-C libraries were constructed into standard Illumina libraries.

value: Reprogramming cells


title: shCTCF_D10_rep2 [BL-Hi-C]

source_name: Reprogramming cells, OSKM knock down CTCF


title: 5KO, input, rep2

data_processing:
Adaptor sequences and low quality bases in reads were trimmed using Trim Galore version 0.3.7
Then trimmed reads were aligned to the mouse GRCm38 genome assembly using bowtie version 0.12.7
Duplicated reads were removed using samtools version 0.1.18
BigWig files were produced by bamCoverage 2.5.4-1-eca29f6 or bamCompare 2.5.4-1-eca29f6
Assembly: mm10
Supplementary files format and content: bigWIg


title: shCTCF_D10_rep1 [BL-Hi-C]


title: shcontrol_D10_rep1 [BL-Hi-C]


title: 4F-144h-3

city: Houston

first: Tamer

last: Mohamed

state: TX

address: 6770 Bertner Avenue

institute: Baylor College of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM counts

source_name: 60-day-old mature hiPS-CMs_4F-144h

growth_protocol: hiPS-CMs cultured for 60 days post differentiation

extract_protocol:
RNA from hiPS-CMs were isolated using the Qiagen, miRNeasy Micro Kit, #210874, following homogenization of the tissue in QIAzol (Qiagen).
Using the Ovation RNA-seq System v2 Kit (NuGEN),

treatment_protocol: Adenovirus were added for 24, 48, or 72 hours

value: hiPS-CMs

tag: time point

value: 60 days post differentiation

tag: medium

value: Cellular dymnamics medium


title: oeCTCF_shSmarca5_D10_rep2 [BL-Hi-C]

source_name: Reprogramming cells, OSKM plus CTCF, in addition to Smarca5 knockdown

tag: day of reprogramming


title: Fibrolamellar carcinoma #4

description:
FLC30_KPKS
Sample from fibrolamellar carcinoma patient #4


title: 5KO, input, rep1

value: iMEFs


title: WT,DMSO,BS,rep2

value: DMSO


title: WT, input, rep2


title: Fibrolamellar carcinoma #3

description:
FLC29_QLXW
Sample from fibrolamellar carcinoma patient #3


title: oeCTCF_shSmarca5_D10_rep1 [BL-Hi-C]


title: 4F-144h-1


title: Fibrolamellar carcinoma #2

description:
FLC06_SLVP
Sample from fibrolamellar carcinoma patient #2


title: WT, input, rep1


title: 4F-72h-3

source_name: 60-day-old mature hiPS-CMs_4F-72h


title: Non-malignant liver #1

description:
FLC34_PMVV
Sample from non-malignant patient #1

value: normal


title: 5KO, H3K27me3, rep2


title: oeCTCF_D10_rep2 [BL-Hi-C]

source_name: Reprogramming cells, OSKM plus CTCF


title: oeCTCF_D10_rep1 [BL-Hi-C]


title: 4F-72h-2


title: WT,DMSO,LaminAC,rep1


title: Fibrolamellar carcinoma #1

description:
FLC06_DZIS
Sample from fibrolamellar carcinoma patient #1

source_name: Liver


title: 4F-72h-1


title: D10 rep2

city: Madrid

first: Ignacio

last: Palmero

state: Madrid

address: Arturo Duperier, 4.

country: Spain

institute: CSIC

description:
IMR90 fibroblasts treated with conditioned medium from IMR90-ER:RAS fibroblasts at day 10 of senescence induction with 4-OHT.
processed data file: Processed_data_Paracrine_Senescence.txt

data_processing:
Image analysis, per-cycle basecalling and quality score assignment were performed with Illumina Real Time Analysis software.
Illumina BCL files were converted to bam format with Illumina2bam.
Sequencing reads were aligned to the transcriptome and quantitated with STAR (v 2.5), a spliced read mapper for RNA-seq.
Differential gene expression analysis was performed with DESeq2.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Processed_data_Paracrine_Senescence.txt: Tab-delimited text file includes non-normalised counts, as calculated with STAR, and RPM (reads per million) for each sample. Genes with 0 raw counts in all samples have been removed.

source_name: fibroblast

extract_protocol:
Total RNA from two independent experiments was prepared using Trizol reagent. 1 ug of total RNA was used for construction of sequencing libraries.
PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments using Illumina's TruSeq Stranded Library Prep Kit. Adapter-ligated library was completed by PCR with Illumina PE.

treatment_protocol: IMR90 primary human fibroblasts were incubated for 3 days with conditioned medium obtained from IMR90-ER:RAS fibroblasts at day 0, 4, 7 and 10 of senescence induction with 4-OHT.

value: Fibroblasts

value: Conditioned medium from IMR90-ER:RAS fibroblasts at day 10 of senescence induction


title: 4F48h-3

source_name: 60-day-old mature hiPS-CMs_4F48h


title: WT, H3K27me3, rep2


title: oecontrol_D10_rep1 [BL-Hi-C]

source_name: Reprogramming cells, OSKM overexpress  control


title: D10 rep1


title: D7 rep2

description:
IMR90 fibroblasts treated with conditioned medium from IMR90-ER:RAS fibroblasts at day 7 of senescence induction with 4-OHT.
processed data file: Processed_data_Paracrine_Senescence.txt

value: Conditioned medium from IMR90-ER:RAS fibroblasts at day 7 of senescence induction


title: OSKM_D10_rep2 [BL-Hi-C]

source_name: Reprogramming cells, OSKM


title: 4F-144h-2


title: OSKM_D10_rep1 [BL-Hi-C]


title: WT, H3K9me2, 6D11, rep2


title: D7 rep1


title: 4F48h-1


title: WT, H3K9me2, 6D11, rep1


title: OG2MEF_rep2 [BL-Hi-C]

source_name: Mouse embryonic fibroblasts

value: MEF cells

tag: passages


title: 5KO, H3K27me3, rep1


title: oecontrol_D10_rep2 [BL-Hi-C]


title: WT, H3K9me3, 2F3, rep1


title: 4F-24h-3

source_name: 60-day-old mature hiPS-CMs_4F-24h


title: OG2MEF_rep1 [BL-Hi-C]


title: D4 rep1

description:
IMR90 fibroblasts treated with conditioned medium from IMR90-ER:RAS fibroblasts at day 4 of senescence induction with 4-OHT.
processed data file: Processed_data_Paracrine_Senescence.txt

value: Conditioned medium from IMR90-ER:RAS fibroblasts at day 4 of senescence induction


title: D0 rep2

description:
IMR90 fibroblasts treated with conditioned medium from IMR90-ER:RAS fibroblasts at day 0 of senescence induction with 4-OHT.
processed data file: Processed_data_Paracrine_Senescence.txt

value: Conditioned medium from IMR90-ER:RAS fibroblasts at day 0 of senescence induction


title: 4F-24h-2


title: 4F-24h-1


title: D4 rep2


title: Fenofibrate-Ppara-/-2 (3 mouse liver mix)

city: Bethesda

middle: J.

last: Gonzalez

state: MD

address: 37 Convent Drive. Bldg37/Rm3106

department: National Cancer Institute

institute: National Institutes of Health

description: Fenofibrate-Ppara-:-2_3 mouse liver mix_KO_FEN_2_S33

data_processing:
Basecalling was performed by Illumina RTA 1.18.61. Demultiplexing was performed by Bcl2fastq v2.17.
Filtering (Adaptor and quality) was performed by Trimmomatic 0.30
Alignment was performed by TopHat v2.0.8
RNA Statistics and Duplication Statistics were performed by Picard 1.84
Insert Size Statistics was performed by RseQC 2.3.5
raw counts, RPKM values, and the associated statistical analyses by Qiagen CLC Genomics Workbench software
Genome_build: mm10

source_name: Fenofibrate-Ppara-/-

extract_protocol:
Total RNA was extrated from euthanized mouse livers. RNeasy plus mini kit (Qiagen) was used for preparing high purity RNA.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library Prep.

treatment_protocol: Mice were fed with either a normal diet, a 0.1% Wy14,643-chow diet or a 0.5% Fenofibrate-chow diet for 48 houre.

tag: strain background

value: C57BL/6 and SV129 mixed

value: 8 weeks old

value: Ppara-null (Ppara-/-)

value: PPARA agonist (Fenofibrte)

value: liver


title: 4F48h-2

value: hiPS-CMs


title: WT, H3K27me3, rep1

value: WT


title: LacZ-144h-3

source_name: 60-day-old mature hiPS-CMs_LacZ-144h

value: 60 days post differentiation

value: Cellular dymnamics medium


title: D0 rep1


title: E14_Smarca5-KO_input [ChIP-seq]

data_processing:
ChIP-seq raw reads were first assessed with FastQC tool and trimmed with trim galore if they contained adaptors.
Processed reads were mapped to the mm10 assembly using Bowtie2 with parameters “—very-sensitive –end-to-end –no-unal”. Any reads overlapped with mm10 blacklist regions (from ENCODE project) were filtered with bedtools, then proper-aligned and high-quality reads (MAPQ>30) were extracted with samtools, duplicated reads were removed using picard tools. Peaks were called by MACS2. Peak annotation, motif discovery, and the gene ontology analysis were performed using HOMER annotatePeaks.pl, or findMotifsGenome.pl. Differential binding sites were identified by MACS2bdgdiff tool with default parameters, or with glbase.redefine_peaks. Heatmaps from ChIP-seq was created with glbase or deeptools.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Peak files were generated using MACS2, coupled to redefine_peaks() from glbase3. Bigwig files were generated from normalized bdg files using bedGraphToBigWig tool.

source_name: E14Tg2a_Smarca5 knock out

extract_protocol:
ChIP experiments were performed as previously described. Briefly, 1×10e7 cells were crosslinked with 1% formaldehyde at room temperature for 10 min. Then the reaction was stopped by adding glycine (final concentration, 0.125 M). Crosslinked cells were lysed in ChIP SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8.0)) containing 1 X Protease Inhibitor Cocktail and PMSF, then sonicated to achieve a chromatin sized of 200-400 bp. After sonication, the supernatant was diluted with IP buffer and then co-incubated with antibodies–Dynabeads protein A/G (1:1 mixed) at 4°C overnight with rotation. Immune complexes were washed with the following buffers: low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0), 150 mM NaCl), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0), 500 mM NaCl), LiCl wash buffer (0.25 M LiCl, 1% IGEPAL-CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 10 mM Tris-HCl (pH 8.0)) and TE buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). Antibody-bound chromatin was reverse-crosslinked, and the ChIPed DNA samples were purified for ChIP-Seq library generation. The ChIPmentation experiments were performed as previously described. Briefly, 1×10e5 cells were crosslinked with 1% formaldehyde at room temperature for 10 min. Then the reaction was stopped by adding glycine (final concentration, 0.125 M). Crosslinked cells were lysed in lysis buffer (10 mM Tris-HCl,100 mM NaCl (pH 8.0),1 mM EDTA, 0.5 mM EGTA,0.1% NaDeoxycholate, 0.5% N-lauroylsarcosine, 1 x protease inhibitors), then sonicated to achieve a chromatin sized of 200-700 bp.Triton X-100 was added to a final concentration of 1%. After centrifuge, the supernatant was co-incubated with antibodies–Dynabeads protein A/G (1:1 mixed) at 4°C overnight with rotation. Immune complexes were washed with the following buffers: low salt wash buffer, high salt wash buffer, LiCl wash buffer, TE buffer and 10 mM Tris-HCl (pH 8.0). For tagmentation, bead bound chromatin was resuspended in 45 μl of tagmentation buffer, 5 μl of transposase (Vazyme) was added and samples were incubated at 37°C for 10 min followed by two washes with low-salt buffer. Antibody-bound chromatin was reverse-crosslinked, and the ChIPed DNA samples were purified for ChIP-seq library generation.
ChIP-seq sequencing libraries were constructed using the VAHTSTM Universal DNA Library Prep Kit for Illumina® V2.

value: Embryonic stem (ES) cell line,E14Tg2a

tag: chip antibody

value: Smarca5 knock out


title: LacZ-144h-2


title: 36-sham

city: Changsha

first: Changsheng

state: Hunan

address: 87 Xiangya Road

department: Department of Anesthesiology

institute: Xiangya Hospital, Central South University

data_processing:
Solexa pipeline version 1.8 (off line base caller software, version 1.8) software was used for image processing and base recognition.
Fastqc software was used to evaluate the quality of sequencing, and then the reads of splices were removed with cutadapt after quality filtering by Solexa CHASTITY.
The rat reference genome (UCSC rn6) was compared by Hisat2 software (v2.0.4).
The transcription abundance was estimated by using StringTie software (v1.2.3) referring to the annotation information of official database, and then the Fragments Per Kilobase of exon model per Million mapped reads (FPKM) calculation of gene level was carried out by Balldown software.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: spinal cord

extract_protocol:
Total RNA was extracted and then quality controled by agarose gel electrophoresis. After detecting the concentratin, qualified total RNA was enriched with oligo (DT) magnetic beads .If the RNA was degraded or prokaryotic, it was directly treated with rRNA Removal Kit.
RNA libraries were prepared for sequencing using KAPA Stranded RNA-Seq Library Prep Kit（Illumina）

tag: strain

value: Sprague Dawley

value: spinal cord

tag: age

value: 8 weeks

value: sham

tag: timepoint


title: Wy14,643-Ppara-/-3 (4 mouse liver mix)

description: Wy14,643-Ppara-:-3_4 mouse liver mix_KO_WY_3_S27

tag: treatment

value: PPARA agonist (Wy14,643)


title: Fenofibrate-Ppara-/-1 (3 mouse liver mix)

description: Fenofibrate-Ppara-:-1_3 mouse liver mix_KO_FEN_1_S26


title: E14_Smarca5-KO_CTCF [ChIP-seq]

city: Guangzhou

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institute of Biomedicine and Health,Chinese Academy of Sciences

value: CTCF(Active motif Cat# 61311)


title: E14_WT_CTCF [ChIP-seq]

source_name: E14Tg2a_Wild type

value: Wild type


title: Wy14,643-Ppara-/-2 (3 mouse liver mix)

description: Wy14,643-Ppara-:-2_3 mouse liver mix_KO_WY_2_S20

value: C57BL/6 and SV129 mixed

value: 8 weeks old


title: Fenofibrate-Ppara-/-3 (4 mouse liver mix)

description: Fenofibrate-Ppara-:-3_4 mouse liver mix_KO_FEN_3_S19

value: Ppara-null (Ppara-/-)

value: PPARA agonist (Fenofibrte)


title: 34-sham


title: D10_oeCTCF_shSmarca5_input [ChIP-seq]

value: Reprogramming cells


title: LacZ-72h-3

source_name: 60-day-old mature hiPS-CMs_LacZ-72h

value: hiPS-CMs


title: Wy14,643-Ppara-/-1 (3 mouse liver mix)

description: Wy14,643-Ppara-:-1_3 mouse liver mix_KO_WY_1_S34

value: liver


title: D10_oeCTCF_input [ChIP-seq]


title: LacZ-72h-2

value: 60 days post differentiation

value: Cellular dymnamics medium


title: 29-CCI14d

value: chronic constriction injury (CCI)


title: LacZ-72h-1


title: D10_control_input [ChIP-seq]

source_name: Reprogramming cells, OSKM control


title: E14_WT_input [ChIP-seq]

value: Embryonic stem (ES) cell line,E14Tg2a


title: Control-Ppara-/-2 (4 mouse liver mix)

description: Control-Ppara-:-2_4 mouse liver mix_KO_CON_2_S35

source_name: Control-Ppara-/-

value: control


title: Control-Ppara-/-3 (5 mouse liver mix)

description: Control-Ppara-:-3_5 mouse liver mix_KO_CON_3_S28


title: D10_oeCTCF_shSmarca5_CTCF [ChIP-seq]

source_name: Reprogramming cells, OSKM plus CTCF, in addition to Smarca5 knockdown


title: 28-CCI14d

value: Sprague Dawley

value: spinal cord

value: 8 weeks


title: LacZ-48h-3

source_name: 60-day-old mature hiPS-CMs_LacZ-48h


title: Control-Ppara-/-1 (4 mouse liver mix)

description: Control-Ppara-:-1_4 mouse liver mix_KO_CON_1_S13


title: 27-CCI14d


title: LacZ-48h-2


title: 22-CCI7d


title: LacZ-144h-1


title: 19-CCI7d


title: LacZ-48h-1


title: D10_control_CTCF [ChIP-seq]

value: CTCF(Active motif Cat# 61311)


title: LacZ-24h-3

source_name: 60-day-old mature hiPS-CMs_LacZ-24h


title: 33-sham

value: sham


title: 18-CCI7d


title: D10_shCTCF_rep2 [RNA-seq]

data_processing:
RNA-seq raw datasets were qualified with FastQC tool and trimmed with trim galore if containing adaptors.
Reads were aligned to mm10 genome using rsem with options "--star". Counts were extracted from sample.genes.results file and merged together. RNA-seq raw counts were normalized with EDAseq.
Genome_build: mm10 (GRCm38), Ensembl v95
Supplementary_files_format_and_content: tsv files were generated from normalized RNAseq data.

source_name: Reprogramming cells, CTCF shRNA


title: Fenofibrate-Ppara+/+1 (3 mouse liver mix)

description: Fenofibrate-Ppara+:+1_3 mouse liver mix_WT_FEN_1_S16

source_name: Fenofibrate-Ppara+/+

value: C57BL/6 and SV129 mixed

value: Wild type (Ppara+/+)


title: Wy14,643-Ppara+/+2 (4 mouse liver mix)

description: Wy14,643-Ppara+:+2_4 mouse liver mix_WT_WY_2_S24

value: 8 weeks old

value: PPARA agonist (Wy14,643)


title: LacZ-24h-1


title: LacZ-24h-2


title: Wy14,643-Ppara+/+3 (5 mouse liver mix)

description: Wy14,643-Ppara+:+3_5 mouse liver mix_WT_WY_3_S39


title: 14-CCI3d


title: D10_shcontrol_rep2 [RNA-seq]

source_name: Reprogramming cells, control shRNA

value: Reprogramming cells


title: 13-CCI3d


title: D10_shcontrol_rep1 [RNA-seq]


title: Wy14,643-Ppara+/+1 (4 mouse liver mix)

description: Wy14,643-Ppara+:+1_4 mouse liver mix_WT_WY_1_S17


title: Fenofibrate-Ppara+/+3 (3 mouse liver mix)

description: Fenofibrate-Ppara+:+3_3 mouse liver mix_WT_FEN_3_S38

value: PPARA agonist (Fenofibrte)


title: D10_oeCTCF_CTCF [ChIP-seq]

source_name: Reprogramming cells, OSKM plus CTCF


title: Control-Ppara+/+3 (5 mouse liver mix)

description: Control-Ppara+:+3_5 mouse liver mix_WT_CON_3_S32

source_name: Control-Ppara+/+

value: liver


title: Control-Ppara+/+2 (5 mouse liver mix)

description: Control-Ppara+:+2_5 mouse liver mix_WT_CON_2_S25


title: 9-CCI1d


title: 10-CCI1d


title: D10_shCTCF_rep1 [RNA-seq]


title: D10_oeCTCF_rep2 [RNA-seq]


title: 15-CCI3d


title: 7-CCI1d


title: D10_oeCTCF&shSmarca5_rep1 [RNA-seq]


title: Control-Ppara+/+1 (5 mouse liver mix)

description: Control-Ppara+:+1_5 mouse liver mix_WT_CON_1_S18


title: D10_oeCTCF_rep1 [RNA-seq]


title: 4-CCI12h


title: D10_oeCTCF&shSmarca5_rep2 [RNA-seq]


title: D10_oecontrol_rep2 [RNA-seq]


title: iPSCs [RNA-seq]

data_processing:
RNA-seq raw datasets were qualified with FastQC tool and trimmed with trim galore if containing adaptors.
Reads were aligned to mm9 genome using rsem with options "--star". Counts were extracted from sample.genes.results file and merged together. RNA-seq raw counts were normalized with EDAseq.
Genome_build: mm9
Supplementary_files_format_and_content: tsv files were generated from normalized RNAseq data.

source_name: induced pluripotent stem cells

value: iPSCs


title: MEFs [RNA-seq]

source_name: Mouse embryonic fibroblast

value: MEF cells


title: 2-CCI12h

value: chronic constriction injury (CCI)


title: D10_oecontrol_rep1 [RNA-seq]


title: 1-CCI12h


title: Fenofibrate-Ppara+/+2 (3 mouse liver mix)

description: Fenofibrate-Ppara+:+2_3 mouse liver mix_WT_FEN_2_S31


title: o9R pmel + MSA-oIL2 (2)

status: Public on Apr 04 2022

city: Stanford

first: Anusha

last: Kalbasi

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford

description: single-end RNAseq

data_processing:
Reads were aligned to the mouse reference genome (mm9/GRCm38) using HISAT2 (v2.0.4)(44).
Gene expression was quantified using HTSeq-counts(v0.6.1)(45).
Assembly: GRCm38 - mm10
Supplementary files format and content: raw count data frame

source_name: in vitro T cell culture

extract_protocol:
Total RNA was extracted from T cells using the AllPrep DNA/RNA Micro Kit (Qiagen).
RNA sequencing (RNAseq) libraries were prepared using the KAPA mRNA stranded library preparation kit, according to the manufacturer’s recommendations.
Libraries were pooled and sequenced on the Illumina HiSeq3000 platform (50bp reads).

value: pmel T cells

tag: transduced with


title: o9R pmel + MSA-oIL2 (3)

description: single-end RNAseq


title: o9R pmel + MSA-IL2 (1)

description: single-end RNAseq


title: o9R pmel + MSA-IL2 (2)

description: single-end RNAseq


title: o9R pmel + MSA-oIL2 (1)

description: single-end RNAseq


title: o2R pmel + MSA-oIL2 (3)

description: single-end RNAseq


title: HK-2cell_72h_high glucose 3

type: RNA

city: Zhengzhou

first: Yi

last: Song

address: 1 Jianshe East Road

institute: The First Affiliated Hospital of Zhengzhou University

hyb_protocol: 1. Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing.  2. Equilibrate water bath to 60°C.  3. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube:  4. Mix well but gently on a vortex mixer.  5. Incubate at 60°C for exactly 30 minutes to fragment RNA.   6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction.  7. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles.  8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction.  9. Place sample on ice and load onto the array as soon as possible.   10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar.  11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner.  12. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.   13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.  14. Hand-tighten the clamp onto the chamber.  15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles.  16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm.  17. Hybridize at 65°C for 17 hours.

scan_protocol: 1. Assemble the slides into an slide holder.   2. Place assembled slide holders into scanner carousel.  3. Verify scan settings for one-color scans.  4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: 1. Open the Agilent Feature Extraction (FE) software.  2. Add the images (.tif) to be extracted to the FE Project.  3. Set FE Project Properties.  4. Check the Extraction Set Configuration.  5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location.  6. Select Project > Start Extracting and export data to txt.

source_name: HK-2 cell,72h, high glucose

label_protocol: 1. Add 1ug of total RNA to a 1.5-mL microcentrifuge tube.   2. Add 1.2 μL of T7 Promoter Primer.   3. Use nuclease-free water to bring the total reaction volume to 11.5 μL.  4. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes.  5. Place the reactions on ice and incubate for 5 minutes.  6. Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice  7. Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice.  8. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down.  9. Incubate samples at 40°C in a circulating water bath for 2 hours.  10. Move samples to a 65°C circulating water bath and incubate for 15 minutes.  11. Move samples to ice. Incubate for 5 minutes.  12. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid.  13. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature.  14. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting.  15. Incubate samples in a circulating water bath at 40°C for 2 hours.

growth_protocol: HK-2 cell were cultured with normal glucose and high glucose for 72h

extract_protocol: Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The amount of TRIzol Reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present.2. Phase Separation  Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization.  RNA Precipitation  Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C.   RNA Wash  Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C.  Redissolving the RNA  At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C.

treatment_protocol: normal and high glucose

value: HK-2 cell

tag: glucose level

value: high


title: o9R pmel + MSA-IL2 (3)

description: single-end RNAseq


title: o2R pmel + MSA-oIL2 (2)

description: single-end RNAseq


title: o2R pmel + MSA-oIL2 (1)

description: single-end RNAseq


title: o2R pmel + MSA-IL2 (3)

description: single-end RNAseq


title: o2R pmel + MSA-IL2 (1)

description: single-end RNAseq


title: HK-2cell_72h_high glucose 2


title: HK-2cell_72h_high glucose 1


title: Morphine injection  [T2]

city: shijiazhuang

first: xiaojie

last: li

address: 361 Zhongshan East Road, Chang'an District, Shijiazhuang, Hebei Province

institute: Hebei Medical University

data_processing:
Illumina Casava1.7 software used for basecalling
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.

source_name: test

extract_protocol:
nucleus accumbens were removed, flash frozen on dry ice, and RNA was harvest using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: nucleus accumben

value: Morphine injection


title: Saline injection  [NS3]

source_name: saline

value: Saline injection


title: Morphine injection   [T1]


title: HK-2cell_72h_normal glucose 3

source_name: HK-2 cell,72h, normal glucose

value: normal


title: HK-2cell_72h_normal glucose 1


title: HK-2cell_72h_normal glucose 2


title: Morphine injection  [T3]


title: Genomic DNA from whole blood 71

city: Santiago de Compostela

first: Sara

last: Pischedda

state: A Coruña

address: Avenida da Choupana s/n

department: Instituto de Investigación Sanitaria de Santiago de Compostela

institute: Hospital Clinico Universitario de Santiago de Compostela

description: Sample 71

hyb_protocol: Whole blood DNA was bisulfite converted using the EZ-96 DNA Bisulfite Zymo Research conversion protocol according to the manufacturer’s instructions.

scan_protocol: The array was imaged using the Illumina iScan system.

data_processing:
R software (minfi package).
MatrixSignal.txt: Unmethylated and methylated signal intensities.
MatrixProcessed.txt: Average Beta (quantile normalization).

label: not provided

source_name: blood

label_protocol: Standard Illumina Protocol.

extract_protocol: DNA was extracted from whole blood collected from the 77 patients.

value: Blood

tag: disease state

value: Asthma

tag: group

tag: gender

value: Male


title: Genomic DNA from whole blood 75

description: Sample 75

tag: tissue


title: Saline injection  [NS2]


title: Saline injection  [NS1]


title: Genomic DNA from whole blood 72

description: Sample 72


title: Genomic DNA from whole blood 74

description: Sample 74


title: Genomic DNA from whole blood 77

description: Sample 77

value: Complete recovery

value: Female


title: Genomic DNA from whole blood 73

description: Sample 73


title: Genomic DNA from whole blood 76

description: Sample 76


title: Genomic DNA from whole blood 70

description: Sample 70


title: Genomic DNA from whole blood 67

description: Sample 67


title: o2R pmel + MSA-IL2 (2)

description: single-end RNAseq

tag: cell type


title: Genomic DNA from whole blood 66

description: Sample 66

value: Recurrent wheezing


title: Genomic DNA from whole blood 64

description: Sample 64


title: Genomic DNA from whole blood 69

description: Sample 69


title: Genomic DNA from whole blood 63

description: Sample 63


title: Genomic DNA from whole blood 68

description: Sample 68


title: Genomic DNA from whole blood 65

description: Sample 65


title: Genomic DNA from whole blood 62

description: Sample 62


title: Genomic DNA from whole blood 60

description: Sample 60


title: Genomic DNA from whole blood 59

description: Sample 59


title: Genomic DNA from whole blood 61

description: Sample 61


title: Genomic DNA from whole blood 55

description: Sample 55


title: Genomic DNA from whole blood 56

description: Sample 56


title: Genomic DNA from whole blood 58

description: Sample 58


title: Genomic DNA from whole blood 57

description: Sample 57


title: Genomic DNA from whole blood 54

description: Sample 54


title: Genomic DNA from whole blood 53

description: Sample 53


title: Genomic DNA from whole blood 52

description: Sample 52


title: Genomic DNA from whole blood 42

description: Sample 42


title: Genomic DNA from whole blood 48

description: Sample 48


title: Genomic DNA from whole blood 44

description: Sample 44


title: Genomic DNA from whole blood 45

description: Sample 45


title: Genomic DNA from whole blood 46

description: Sample 46


title: Genomic DNA from whole blood 41

description: Sample 41


title: Genomic DNA from whole blood 49

description: Sample 49


title: Genomic DNA from whole blood 39

description: Sample 39


title: Genomic DNA from whole blood 37

description: Sample 37


title: Genomic DNA from whole blood 43

description: Sample 43


title: Genomic DNA from whole blood 35

description: Sample 35


title: Genomic DNA from whole blood 38

description: Sample 38


title: Genomic DNA from whole blood 36

description: Sample 36


title: Genomic DNA from whole blood 33

description: Sample 33


title: Genomic DNA from whole blood 28

description: Sample 28


title: Genomic DNA from whole blood 29

description: Sample 29


title: Genomic DNA from whole blood 32

description: Sample 32


title: Genomic DNA from whole blood 40

description: Sample 40


title: Genomic DNA from whole blood 30

description: Sample 30


title: Genomic DNA from whole blood 26

description: Sample 26


title: Genomic DNA from whole blood 27

description: Sample 27


title: Genomic DNA from whole blood 34

description: Sample 34


title: Genomic DNA from whole blood 24

description: Sample 24


title: Genomic DNA from whole blood 25

description: Sample 25


title: Genomic DNA from whole blood 50

description: Sample 50


title: Genomic DNA from whole blood 47

description: Sample 47


title: Genomic DNA from whole blood 21

description: Sample 21


title: Genomic DNA from whole blood 19

description: Sample 19


title: Genomic DNA from whole blood 23

description: Sample 23


title: Genomic DNA from whole blood 14

description: Sample 14


title: Genomic DNA from whole blood 11

description: Sample 11


title: Genomic DNA from whole blood 22

description: Sample 22


title: Genomic DNA from whole blood 12

description: Sample 12


title: Genomic DNA from whole blood 16

description: Sample 16


title: Genomic DNA from whole blood 20

description: Sample 20


title: Genomic DNA from whole blood 18

description: Sample 18


title: Genomic DNA from whole blood 17

description: Sample 17


title: Genomic DNA from whole blood 13

description: Sample 13


title: Genomic DNA from whole blood 6

description: Sample 6


title: Genomic DNA from whole blood 31

description: Sample 31


title: Genomic DNA from whole blood 15

description: Sample 15


title: Genomic DNA from whole blood 9

description: Sample 9


title: Total RNA from cells expressing CrtSPARTA

city: Wageningen

first: Daan

middle: C.

last: Swarts

address: Stippeneng 4

department: Laboratory of Biochemistry

institute: Wageningen University

description: RNA purified from E. coli cells in which CrtSPARTA was expressed

data_processing:
For small RNA and DNA reads, adapter sequences and were trimmed and paired-end read files (fastq) were combined using BBMerge (BBtools version 38.90). Parameters: in1=R1.fast.gz in2=R2.fast.gz R2input.fast.gz out=merged.fastq.gz mininsert=10 minlength=10 minoverlap=10 entropy=f
For total RNA, adapter were trimmed using trimgalore (Cutadapt version 0.6.6). Parameters: --paired --length 10 R1.fastq.gz R2.fastq.gz
For small RNAs, read length was trimmed to 60 nt using BBbreformat (Bbtools version 38.90). Parameters: in=merged.fastq.gz out=output.fastq.gz maxlength=60
Reads were aligned against a .gff file in which the genome of E. coli BL21 DE3 and the expression plasmid pBK092 (CrtSPARTA) or pBK082 (MapSPARTA) were combined using HISAT2 (Version 2.1.0). Parameters for small RNAs and DNA: index --no-spliced-alignment -x index -U output.fastq.gz -S output.sam. Parameters for long RNAs and DNA: index --no-spliced-alignment -1 R1_trimmed_1.fq.gz R2_trimmed_2.fq.gz mapped.sam
Read summarization was performed using featureCounts (version 2.0.1). Parameters: -O -M --fraction -p -a genome.gff3 -t gene -g Name -o output.txt input.sam
Genome_build: Custom build comprised of CP053602.1 (Escherichia coli BL21(DE3) chromosome, complete genome) and expression plasmid (pBK086 or pBK092).
Supplementary_files_format_and_content: An Excel file with featureCounts results is provided

organism: Escherichia coli BL21(DE3)

source_name: Crenatolea thermophila SPARTA complex, heterologously expressed in E. coli

growth_protocol: 37C in LB, expression from pColADuet-1 vector

extract_protocol:
Small RNAs  were extracted from SPARTA complexes after a proteinase K treatment using PCI extraction and subsequent ethanol precipitation
Small RNA-Seq libraries were prepared by GenomeScan (Leiden, The Netherlands)

treatment_protocol: SPARTA complexes where purified using his-MBP tag by niNTA and amylose affinity chromatography

value: BL21 DE3

tag: expressing

value: Crenatolea thermophila SPARTA complex

tag: molecule subtype

value: Total RNA


title: Genomic DNA from whole blood 7

description: Sample 7


title: Genomic DNA from whole blood 5

description: Sample 5


title: Genomic DNA from whole blood 8

description: Sample 8


title: Genomic DNA from whole blood 1

description: Sample 1