title: WTCHG_380869_205249: M38+ Gut single cell


title: 031U_MSCB-076

status: Public on Mar 12 2019

type: SRA

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

library_source: transcriptomic

data_processing:
Primary data analysis was carried out with the standard Illumina pipeline following the manufacturer's protocol. Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Sequenced reads were filtered for low-complexity or low-quality sequence.
MARS-Seq libraries were mapped as single-end reads with the GEMTools 1.7.0 RNA pipeline on the mouse  genome reference.
For MARS-seq samples, gene quantification was performed using UMI corrected transcript information to correct for amplification biases.
Genome_build: Assembly GRCm38. Gencode release M8.
Supplementary_files_format_and_content: Tab-separated values (.tsv) files containing gene expression values (rows) as UMI counts for each cell (columns).

molecule: polyA RNA

organism: Mus musculus

source_name: bone marrow

growth_protocol: We used 'reprogrammable mice' containing a doxycycline-inducible OSKM cassette and thetetracycline transactivator. pre-B cells were isolated from 8- to 16-week-old female mice. Mice were housed in standard cages under 12-h light–dark cycles and fed ad libitum with a standard chow diet.    After isolation, pre-B cells were grown in RPMI medium supplemented with 10% FBS and 10ng/ml IL-7 (Peprotech), L-glutamine, nonessential amino acids, β-mercaptoethanol (Life Technologies) as well as penicillin/streptomycin. All cell lines were routinely tested for mycoplasma contamination.

extract_protocol:
CD19+ pre-B cells were isolated from the bone marrow of these mice using monoclonal antibody to CD19 (clone 1D3, BD Pharmingen #553784) and MACS sorting (Miltenyi Biotech). Cell purity was confirmed to be >98% CD19+ by FACS using an LSRII machine (BD).
To construct single cell libraries from polyA-tailed RNA, we applied massively parallel single-cell RNA sequencing (MARS-Seq; Jaitin et al., Science 2014).  This methodology generates paired-end reads where read 1 contains the transcript sequence and read 2 the cell and UMI barcodes. Briefly, single cells were FACS-sorted into 384-well plates, containing lysis buffer and reverse-transcription (RT) primers. The RT primers contained the single cell barcodes and unique molecular identifiers (UMIs) for subsequent de-multiplexing and correction for amplification biases, respectively.

treatment_protocol: For transdifferentiation pre-B cells were infected with C/EBPα-ER-hCD4 retrovirus produced by the PlatE retroviral packaging cell line (Cell Biolabs, # RV-101). The cells were expanded for 48hrs on Mitomycin C-inactivated S17 feeders grown in RPMI medium supplemented with 10 ng/mL each of IL-7 (Peprotech) and hCD4+ were sorted (FACSaria, BD). For transdifferentiation C/EBPα was induced by treating the cells with 100 nM β-Estradiol (E2) in medium supplemented with 10 ng/mL each of IL-7 (Peprotech), IL-3 (Peprotech) and human colony-stimulating factor 1 (hCSF-1). For reprogramming hCD4+ cells were plated at 500 cells/cm2 in gelatinized plates (12 wells) on irradiated MEF feeders in RPMI medium and pre-treated for 18h with E2 to induce C/EBPα. After E2 washout the cultures were switched to serum-free N2B27 medium supplemented with 10 ng/ml IL-4, IL-7 and IL-15 at 2 ng/ml and treated with 2 μg/ml of doxycycline to activate OSKM. From day 2 onwards the N2B27 medium was supplemented with 20% KSR (Life Technologies), 3 μM CHIR99021 and 1uM PD0325901(2i medium).

tag: cell type

value: pre-B cell

tag: treatment

value: reprogramming

tag: induction

value: OSKM

tag: fate

value: iPSCs

tag: time point

value: day 6


title: WTCHG_380869_204249: M38+ Gut single cell

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

country: United Kingdom

institute: University of  Oxford

data_processing:
RNA-seq reads were aligned to reference genome sequences using STAR(Dobin et al., 2013) aligner software. Mapped reads were assigned to genomic features using Rsubread(Liao et al., 2013)  R package(Team, 2014).
Pre-processing, gene and sample filtering, data visualization and analysis were performed using Scater (McCarthy et al, 2017),scran (Lun  et al, 2016), EdgeR (Robinson et al, 2010), WGCNA (Langefekder et al,2008) R packages. Data sets results comparisons were performed using GSEA ( Subramanian, Tamayo et al, 2005).TCR repertoire was inferred using TraCeR software (Stubbington et al,2016)
Hierarchical clustering analysis of cell transcription profiles was conducted in R employing highly variable genes (IQR >0.75(Gentleman et al., 2004)) and Euclidian distance.
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts_w_ercc.txt: Raw mapped genes read counts
Supplementary_files_format_and_content: sce_k_G1_tmm_voom_quant_norm_entrezIDs.txt: Normalized, voom transformed (log cpm) gene expression values. Filtered genes and samples.

source_name: Gut IEL

extract_protocol:
Extraction and reverse transcription was as described by Picelli et al. (Nature Protocols, 2014). Briefly, single cells were lysed with 2ul buffer containing 0.2% (vol/vol) Triton X-100 and 2Uµ-1 Rnase inhibitorand mixed 1µl oligo-dT primer and 1µl of dNTP mix. Samples were incubated at 72°C for 3 mins.  Reverse transcription mix containing SuperScript II (Invitrogen) reverse transcriptase 100 U, RNAase inhibitor 10 U, SuperScript II first-strand buffer, DTT 5mM, betaine 1 M, MgCl2 6mM, TSO 1 µM and nuclease free water, was added to the samples. Samples where incubated at 45°C for 90mins followed by 10 cycles of 50°C for 2mins and 42°C for 2 min.
Library preparation of purified amplified cDNA was performed using Nextera XT library preparation (Illumina, AUS). Following QC, 150 pg of cDNA was tagmented (simultaneously fragmented with adaptors inserted) using Nextera transposons. Molecular barcodes were incorporated during 12 cycles of amplification followed by purification using AMPure XP. The libraries passed a quality checkpoint (Qubit and Bioanalyser HS DNA) prior to normalization and pooling before loading onto the HiSeq 2500 (Illumina, AUS) for paired end sequencing.

treatment_protocol: MCMV (Strain Smith, ATCC: VR194) was  injected i.v. at a dose of 1 x 106 pfus. Spleen and gut was obtained day 28 post infection. Spleen was minced, passed through a 40µm filter and red blood cells lysed. To obtain IELs, Peyer’s patches and fecal content were first removed from intestines. The intestines were then flushed with PBS and cut open longitudinally. To separate IELs from intestinal tissue, intestinal tissue was incubated in HBSS supplemented with 5mM EDTA, 10% FCS, 25 mM HEPES for 20 min at 200 rpm at 37°C, passed through a 40 µm nylon filter and purified by Percoll (GE healthcare, Little Chalfont, UK) gradient centrifugation. CD8+ T-cells were enriched by negative selection using the Miltenyi Biotec GmbH CD8a+ T-cell isolation kit (Bergisch Gladbach, Germany) as per manufacturer’s instructions. After M38-tetramer and surface staining, tetramer+ CD3+ CD8+ single-cells were sorted in two 96-well plates using a SH800S cell sorter (Sony, Tokyo, Japan).

tag: tissue

value: Gut intraepithelium (IEL)

tag: cell population

value: Live CD3+CD8+M38tetramer+

tag: genotype/variation

value: MCMV infected

tag: sample number

tag: sample id


title: 031U_MSCB-074


title: 031U_MSCB-084


title: WTCHG_380869_203249: M38+ Gut single cell


title: WTCHG_380869_202249: M38+ Gut single cell


title: WTCHG_380869_201249: M38+ Gut single cell


title: 031U_MSCB-072


title: 031U_MSCB-071


title: LD

city: Durham

first: Daniel

last: Saban

state: NC

address: 2351 Erwin Rd, Duke Eye Center

country: USA

institute: Duke University

description: with light damage

data_processing:
The raw FASTQ files were processed using 10x Genomics Cell Ranger software (v2.0.0)
Data were demultiplexed, alignmented with the reference transcriptome (mm10), and aggregated
Gene expression matrices were created.

molecule: total RNA

source_name: retinal Cx3cr1+ cells

extract_protocol:
Isoalted retinas from 5 to 8 mice per group were pooled and digested in 1.5 mg/ml collagenase A and 0.4 mg/ml DNase I (Roche) for 30 min at 37 °C  to generate single cell suspensions. Cells were stained with PE before FACS sorting. Live Cx3cr1YFP+ cells were sorted by FACS
Single Cell RNA libraries were prepared using standard 10x Genomics 3' end library protocols

treatment_protocol: Animals were dark-adapted over night. Eyes were dilated with with 1% atropine sulfate and 10% phenylephrine hydrochloride, light damaged with 10k lux LED light for 4h and then returned to normal lighting for 5 days.

tag: strain

value: CB6F1. Cx3cr1-YFP

value: retina

tag: cell

value: Cx3cr1+ cells

tag: sex and age

value: male, 8 months of age


title: 031U_MSCB-073


title: WTCHG_380869_201250: M38+ Gut single cell


title: ctrl

description: no light damage


title: 031U_MSCB-068


title: 031U_MSCB-077


title: WT1

city: Chicago

first: Issam

last: Awad

state: IL

address: 5841 S. Maryland Avenue

department: Department of Neurology

institute: The University of Chicago

data_processing:
Illumina CASAVA was applied to perform base calling
R & Bioconductor were used to normalize and analyze the data
Hierarchical clustering and Principal Component Analysis were performed on the normalized data to assess the sample relationship and variability.
Differential expression between different experiments were assessed by DESeq2, with negative binomial linear models and Wald test for significance testing.
False discovery rate was estimated by Benjamini-Hochberg procedure.
Genome_build: mm9
Supplementary_files_format_and_content: Raw reads were then processed by trimming adaptors. Fastq and count files were generated.

source_name: Lung epithelial cells

growth_protocol: Tomato+ lineage labeled type II cells from WT or Dlk1ΔAT2 mice were isolated by flow cytometry sorting. Total RNA was isolated using Qiagen RNeasy mini kit (Qiagen).

extract_protocol:
Tomato+ type II cells were isolated from WT (H) and Dlk1ΔAT2 (I) lungs and cultured for 8 days.
TruSeq mRNA-Seq libraries were the prepared for each sample, followed by sequencing using the Illumina NextSeq500 platform at the Genomics Core of Northwestern University. All samples were sequenced together on a flow cell to avoid batch effect.

treatment_protocol: 10 day after PA injection

value: Lung epithelial cells

tag: genotype

value: SpC-CreER/ROSA-Tomato

tag: condition

value: Pseudomonas aeruginosa (PA) induced acute lung injury

tag: time

value: 10 days after injury


title: 031U_MSCB-066


title: WT3


title: Mutant1


title: WT2


title: Mutant3


title: Mutant2


title: 031U_MSCB-069


title: 031U_MSCB-075


title: 031U_MSCB-063


title: 031U_MSCB-067


title: 031U_MSCB-064


title: 031U_MSCB-065


title: 031U_MSCB-061


title: 031U_MSCB-062


title: OHC_374

city: Philadelphia

first: Paul

middle: T

last: Ranum

state: PA

address: 3501 Civic Center Blvd.

department: Center for Cellular and Molecular Therapy

institute: The Children's Hospital of Philadelphia

description: Single-Cell SmartSeq2 Illumina

data_processing:
For Illumina data processing begin with R1.gz and R2.gz paired end read files for each sample.  Process each sample individually.
Perform Kallisto pseudoalignment to the mm10 transcriptome to generate gene expression .tsv file for each sample.
Perform Star alignment to the mm10 genome to generate .sam output for each cell.
Use samtools view to convert the .sam file to .bam format
Use samtools sort tool to sort the .bam file
Corresponding publication includes extensive discussion of mRNA transcript structure and splicing.   Transcript structure features are visualized using .bam files.  The .bam files can be regenerated using the provided raw data files (fastq).
Genome_build: mm10
Supplementary_files_format_and_content: Output files are in .tsv format.

source_name: Cochlea

extract_protocol:
Individual cells were dissociated from mouse cochlear tissue using a collagenase digestion and gentle tituration.  Cells were then isolated using pulled glass micropipettes, washed to remove extracellular contaminants and re-isolated.
Single cell reverse transciption and PCR amplification was performed using Smartseq2

tag: age

tag: background

value: OHC


title: OHC_376

description: Single-Cell SmartSeq2 Illumina

tag: cell type


title: OHC_375

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-060

value: pre-B cell

tag: treatment

tag: induction


title: IHC_373

description: Single-Cell SmartSeq2 Illumina

value: IHC


title: 031U_MSCB-059

value: reprogramming

value: OSKM

tag: fate

tag: time point


title: 031U_MSCB-070

value: iPSCs

value: day 6


title: 031U_MSCB-058


title: Deiter_341

description: Single-Cell SmartSeq2 Illumina

value: Deiter


title: 031U_MSCB-057


title: 031U_MSCB-056


title: Deiter_340

description: Single-Cell SmartSeq2 Illumina


title: Deiter_339

description: Single-Cell SmartSeq2 Illumina


title: Deiter_338

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-055


title: Deiter_337

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-053


title: Deiter_336

description: Single-Cell SmartSeq2 Illumina


title: Deiter_335

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-052


title: 031U_MSCB-051


title: Deiter_333

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-054


title: 031U_MSCB-049


title: 031U_MSCB-050


title: 031U_MSCB-048


title: Deiter_328

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-047


title: Deiter_332

description: Single-Cell SmartSeq2 Illumina


title: Deiter_330

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-044


title: Deiter_327

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-045


title: Deiter_329

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-043


title: 031U_MSCB-046


title: 031U_MSCB-042


title: OHC_287

description: Single-Cell SmartSeq2 Illumina


title: OHC_288

description: Single-Cell SmartSeq2 Illumina


title: OHC_286

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-041


title: IHC_334

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-039


title: 031U_MSCB-038


title: OHC_284

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-037


title: Deiter_331

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-036


title: OHC_285

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-040


title: Deiter_282

description: Single-Cell SmartSeq2 Illumina


title: OHC_269

description: Single-Cell SmartSeq2 Illumina


title: OHC_270

description: Single-Cell SmartSeq2 Illumina


title: OHC_268

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-033


title: Deiter_326

description: Single-Cell SmartSeq2 Illumina


title: OHC_267

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-035


title: Deiter_265

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-032


title: 031U_MSCB-034


title: OHC_266

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-030


title: IHC_264

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-031


title: 031U_MSCB-027


title: 031U_MSCB-026


title: OHC_259

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-028


title: 031U_MSCB-023


title: 031U_MSCB-024


title: OHC_251

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-025


title: OHC_253

description: Single-Cell SmartSeq2 Illumina


title: OHC_258

description: Single-Cell SmartSeq2 Illumina


title: Deiter_250

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-021


title: 031U_MSCB-020


title: OHC_252

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-018


title: 031U_MSCB-019


title: 031U_MSCB-017


title: 031U_MSCB-022


title: IHC_248

description: Single-Cell SmartSeq2 Illumina


title: IHC_245

description: Single-Cell SmartSeq2 Illumina


title: OHC_249

description: Single-Cell SmartSeq2 Illumina


title: IHC_246

description: Single-Cell SmartSeq2 Illumina


title: OHC_247

description: Single-Cell SmartSeq2 Illumina


title: Deiter_263

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-016


title: OHC_262

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-015


title: 031U_MSCB-029


title: OHC_260

description: Single-Cell SmartSeq2 Illumina


title: IHC_243

description: Single-Cell SmartSeq2 Illumina


title: IHC_242

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-012


title: IHC_241

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-014


title: 031U_MSCB-013


title: 031U_MSCB-011


title: IHC_239

description: Single-Cell SmartSeq2 Illumina


title: IHC_240

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-009


title: IHC_244

description: Single-Cell SmartSeq2 Illumina


title: IHC_232

description: Single-Cell SmartSeq2 Illumina


title: IHC_237

description: Single-Cell SmartSeq2 Illumina


title: IHC_231

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-004


title: IHC_238

description: Single-Cell SmartSeq2 Illumina


title: Deiter_233

description: Single-Cell SmartSeq2 Illumina


title: IHC_230

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-005


title: IHC_234

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-002


title: 031U_MSCB-007


title: IHC_235

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-003


title: 031U_MSCB-006


title: IHC_229

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-001


title: Deiter_228

description: Single-Cell SmartSeq2 Illumina


title: 030U_MSCB-192


title: 030U_MSCB-191


title: IHC_227

description: Single-Cell SmartSeq2 Illumina


title: 031U_MSCB-010


title: IHC_226

description: Single-Cell SmartSeq2 Illumina


title: 030U_MSCB-190


title: 031U_MSCB-008


title: 030U_MSCB-188


title: Deiter_223

description: Single-Cell SmartSeq2 Illumina


title: Deiter_225

description: Single-Cell SmartSeq2 Illumina


title: 030U_MSCB-185


title: 030U_MSCB-186


title: 030U_MSCB-184


title: 030U_MSCB-183


title: Deiter_217

description: Single-Cell SmartSeq2 Illumina


title: Deiter_222

description: Single-Cell SmartSeq2 Illumina


title: IHC_218

description: Single-Cell SmartSeq2 Illumina


title: 030U_MSCB-187


title: Deiter_224

description: Single-Cell SmartSeq2 Illumina


title: 030U_MSCB-182


title: IHC_216

description: Single-Cell SmartSeq2 Illumina


title: Deiter_215

description: Single-Cell SmartSeq2 Illumina


title: 030U_MSCB-189


title: Deiter_212

description: Single-Cell SmartSeq2 Illumina


title: 030U_MSCB-178


title: 030U_MSCB-179


title: 030U_MSCB-180


title: IHC_211

description: Single-Cell SmartSeq2 Illumina


title: Deiter_213

description: Single-Cell SmartSeq2 Illumina


title: 030U_MSCB-176


title: 030U_MSCB-177


title: Deiter_209

description: Single-Cell SmartSeq2 Illumina


title: Deiter_221

description: Single-Cell SmartSeq2 Illumina


title: 030U_MSCB-175


title: 030U_MSCB-174


title: Deiter_208

description: Single-Cell SmartSeq2 Illumina


title: IHC_219

description: Single-Cell SmartSeq2 Illumina


title: Deiter_207

description: Single-Cell SmartSeq2 Illumina


title: 030U_MSCB-181


title: Deiter_206

description: Single-Cell SmartSeq2 Illumina


title: Deiter_214

description: Single-Cell SmartSeq2 Illumina


title: 030U_MSCB-173


title: OHC_204

description: Single-Cell SmartSeq2 Illumina


title: OHC_203

description: Single-Cell SmartSeq2 Illumina


title: 030U_MSCB-172


title: 030U_MSCB-168


title: 030U_MSCB-169


title: Deiter_210

description: Single-Cell SmartSeq2 Illumina


title: OHC_201

description: Single-Cell SmartSeq2 Illumina


title: OHC_199

description: Single-Cell SmartSeq2 Illumina


title: OHC_200

description: Single-Cell SmartSeq2 Illumina


title: 030U_MSCB-167


title: WTCHG_380869_256275: 10pg human brain RNA

organism: Homo sapiens

source_name: 10pg human brain RNA

tag: tissue

value: 10pg human brain RNA

tag: cell population

value: 10pg human brain RNA_132


title: WTCHG_380869_205253: 10pg human brain RNA

tag: genotype/variation

tag: sample number

value: 10pg human brain RNA_53


title: 030U_MSCB-165


title: 030U_MSCB-166


title: 030U_MSCB-164


title: 030U_MSCB-162


title: 030U_MSCB-163


title: DCM5

city: Houston

first: AJ

last: Marian

state: Texas

address: 3742 Arnold St

department: Institute of Molecular Medicine

institute: The University of Texas Health Science Center Houston

data_processing:
Data was mapped to the mouse geneome using TopHat2 and the UCSC mm10 mouse genome as reference.
Gene expression was quantified using Cufflinks 2 and the Genecode reference.
Differential gene expression was determined using EdgeR.
Supplementary_files_format_and_content: xlsx file contains the cpm for the Samples and the calculated log2ratio for the KO samples compared to the NTG samples along with the FDR and pvalue for the comparison.

source_name: Heart

growth_protocol: not applicable

extract_protocol:
A miRNeasy Mini Kit  (Qiagen, Cat:217004) was used to isolate the RNA following the manufacturer's guidelines
A Illumina TruSeq kit was used in library preparation following the manufacturer's guidelines.

treatment_protocol: not applicable

tag: Sex

value: Male

tag: group

value: DCM


title: DCM3


title: 030U_MSCB-160


title: 030U_MSCB-161


title: DCM2

value: Female


title: DCM4


title: 030U_MSCB-159


title: DCM1


title: 030U_MSCB-158


title: 030U_MSCB-171


title: Deiter_205

description: Single-Cell SmartSeq2 Illumina


title: 030U_MSCB-157


title: 030U_MSCB-170


title: Control4

value: Control


title: Control5


title: Control3


title: 030U_MSCB-156


title: Control1


title: 030U_MSCB-155


title: 030U_MSCB-154


title: 030U_MSCB-153


title: 030U_MSCB-152


title: Control2


title: hTransMSC_FOXO32SA/2SA_1 Bisulfite-Seq

city: Beijing

first: Ping

last: Lu

address: 5 Yiheyuan Road

country: China

institute: Peking University

description: Bisulfite treated  genomic DNA

library_source: genomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
RNA: Raw reads with low-quality bases (N > 10%) and adaptor contaminants were removed, and the clean reads were mapped to hg19 human reference (UCSC) using TopHat (version 2.0.12). The transcripts were assembled and quantified using Cufflinks (version 2.2.1) with default parameters.
DNA: Raw reads with low-quality bases (N > 10%) and adaptor contaminants were removed. The clean reads were aligned to hg19 human reference genome by bowtie2 (version 2.2.3). The wild type samples without CNVs were selected as standard controls. The CNVs were calculated with HMMcopy (version 1.21.0) (Ha et al., 2012) by estimating the copy number in each 1Mb window.
PBAT: Trim Galore (v0.3.3) was used to remove the first 9 bases of random primer, adaptor sequences and low quality bases were also trimmed with the command ‘trim_galor’ --quality 20 --stringency 3 --length 36 --clip_R1 9 --clip_R2 9 --paired --trim1 --phred33’.   In order to recover more sequencing reads, we used Bismark (v0.7.6) to map the clean reads to human reference genome hg19 with paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module (paired-end parameters: bismark --fastq --non_directional –unmapped --phred33-quals -1 $trim_fq1 -2 $trim_fq2; unmapped read1 single-end parameters: bismark –fastq --non_directional --phred33-quals $unmap_fq1; unmapped read2 single-end parameters: bismark –fastq --non_directional --phred33-quals $unmap_fq2). After alignment, PCR duplificates were removed using SAMtools(v0.1.18). Single cytosine site methylation level was estimated using comstomized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: RNA: Txt files which include the FPKM of RefSeq genes. DNA: Wig files which include the depth of 1Mb window in order to estimate the copy number. PBAT: Txt files which include the methylation level of cytosines.

molecule: genomic DNA

source_name: Human TransMSCs

growth_protocol: Wild type hESCs (Line H9, WiCell Research) and derived FOXO32SA/2SA hESCs were cultured on Mitomycin C-inactivated mouse embryonic fibroblasts (MEF) with cDF12 medium or Matrigel-coated plates with mTeSR1 medium, as previously described (Duan et al., 2015; Liu et al., 2014a; Pan et al., 2016; Zhang et al., 2015b). hVECs were maintained on collagen-coated plates in EGM2 medium (Lonza) supplemented with 10 nM SB431542, 50 ng/mL VEGF and 20 ng/mL bFGF (Pan et al., 2016). hVSMCs were cultured in VSMC medium with PDGF-AB (Pepro Tech, 10 ng/ml). hMSCs were cultured in a-MEM (Invitrogen) medium supplemented with 10% fetal bovine serum (Gibco), 0.1 mM non-essential amino acids (Gibco), 1% penicillin/streptomycin (Gibco), and 1 ng/ml bFGF (Joint Protein Central). hTMSCs were maintained in hMSC medium without bFGF (Joint Protein Central). No mycoplasma contamination was observed during cell culture (Yang et al., 2017).

extract_protocol:
Total RNA was extracted from one million cells using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Genomic DNA extraction from cell pellets was performed according to the DNeasy Blood & Tissue Kit (Qiagen) protocol.
RNA library construction protocol: The mRNA was isolated from 2 ug of total RNA using the NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB). Subsequently, the isolated mRNA was sheared, and the synthesized cDNA was used for RNA library construction using NEBNext ultra RNA library prep kit for Illumina (NEB). DNA library construction protocol: 500 ng of genomic DNA was sheared into approximately 300-bp fragments by Covaris S2. Then the DNA library was constructed using a NEBNext ultra DNA library prep kit for illumina (NEB). PBAT library construction protocol: Samples of 50 ng of genomic DNA were used to construct the PBAT library as previously described with several modifications. Briefly, together with 1% unmethylated lambda DNA (Thermo Scientific), genomic DNA was bisulfite converted and purified with EZ-96 DNA Methylation-Direct™MagPrep (Zymo) according to the manufacturer’s instructions. The bisulfite-converted DNA was subjected to four rounds of random priming and extension with biotinylated random primers containing a truncated Illumina P5 adaptor and supplemented with klenow exo– polymerase (Enzymatic). The excess primers were digested by exonuclease I (NEB). After purification of DNA with 0.8× Ampure XP beads (Beckman), the newly synthesized DNA strands were bound to the Dynabeads M280 Streptavidin (Invitrogen), and the bisulfite-converted DNA templates were removed with two rounds of 0.1 N NaOH washes. Next, the second strands were synthesized with random primers containing a truncated P7 Illumina adaptor. The M280 beads were washed again and the library was amplified with KAPA HiFi ReadyMix (Kapa biosysems) for 6-8 cycles. The generated libraries were purified twice with 0.8× Ampure XP beads. All the generated libraries were pooled and sequenced on Illumina HiSeq 4000 platforms with paired-end 150-bp sequencing.
RNA-Seq; whole-genome sequencing; Bisulfite-Seq

treatment_protocol: Generation of FOXO3 enhanced hESCs  Helper-dependent adenoviral vector (HDAdV) for FOXO32SA/2SA (Ser253Ala and Ser315Ala) knock-in was generated as previously described, with some modifications (Li et al., 2011; Liu et al., 2012; Liu et al., 2014a; Yang et al., 2017). In brief, part of intron 2 and exon 3 of the FOXO3 gene was PCR-amplified from RP11-653O20 BAC DNA (BACPAC Resources) and subcloned into the pCR2.1-TOPO vector (Invitrogen). The Ser253Ala and Ser315Ala mutations at exon 3 were introduced using the GeneTailor Site-Directed Mutagenesis System (Invitrogen). An FRT-PGK-EM7-neo-bpA-FRT marker fragment was subcloned into intron 2 in the 2SA mutated plasmid, and the generated DNA fragment was recombined into RP11-653O20 BAC DNA using BAC recombineering (Datsenko and Wanner, 2000). A total of 20.9 kb of homology arms for FOXO3 gene, including the Ser253Ala and Ser315Ala mutations and marker cassette, was subcloned into the HDAdV backbone plasmid pCIHDAdGT8-4 (Addgene #26421). The generated plasmids were packaged into HDAdVs following a previous report (Yang et al., 2017). To generate heterozygous FOXO32SA/2SA mutation knock-in hESCs, hESCs were infected with FOXO32SA/2SA HDAdV at MOI of 0.6-6 btu/cell, as described previously (Yang et al., 2017). To generate homozygous FOXO32SA/2SA hESCs, we repeated a 2nd round of mutation knock-in using the generated heterozygous FOXO32SA/2SA clones.  Directed differentiation of hESCs into hVECs  Differentiation of hESCs into hVECs was performed as previously described with minor modifications (Patsch et al., 2015). Briefly, after 1 day in culture in mTeSR1-media, the medium was changed to M1 medium, containing IWP2 (3 mM), BMP4 (25 ng/ml), CHIR99021 (3 mM) and bFGF (4 ng/ml) for 3 days. The following day, M1 medium was removed and replaced with M2 medium with addition of VEGF (50 ng/ml), bFGF (20 ng/ml) and IL6 (10 ng/ml) to promote endothelial cell emergence for another 3 days. At day 6 after differentiation, adherent cells were harvested by TryPLE (Gibco), and then counted after anti-human CD201 and human CD34 staining. Flow cytometry detection of the cell surface antigens and cells sorting were performed on BD FACS Aria II.     Directed differentiation of hESCs into hVSMCs  Differentiation of hESCs into hVSMCs was performed as previously described with minor modifications (Patsch et al., 2015). Firstly, after 4-5 days in culture in mTeSR1 medium on matrigel coated plates, the hESCs were dissociated into single cells using TrypLE and seeded onto matrigel coated plates with a concentration of 3×104 cells / cm2. The following day, mTeSR1 medium was replaced with M1 medium and maintained for 3 days. Then, the M1 medium was removed and replaced with M2 medium for 2 days. At day 5, cells were harvested with TrypLE, purified with CD140b and cultured on collagen (Biocoat) coated plates with VSMC culture medium.     Directed differentiation of hESCs into hMSCs   Differentiation of hESCs into hMSCs was performed as previously described (Yang et al., 2017; Zhang et al., 2015a). In brief, embryoid bodies were cultured in hMSC differentiation medium (αMEM (Invitrogen) supplemented with 10% FBS (Gibco), 10 ng/ml bFGF, 5 ng/ml TGFβ (HumanZyme) and 1% penicillin/streptomycin (Gibco)) for 10 days, while fibroblast-like cells appeared. The hMSCs were purified with hMSC-specific markers CD73, CD90, and CD105 by FACS Aria II. Negative hMSC markers CD34, CD43 and CD45 were also analyzed by FACS. Anti-IgG-FITC, anti-IgG-PE, and anti-IgG-APC antibodies were used as isotype controls. To identify function of hMSCs, they were further differentiated towards bone, cartilage and adipocytes. Histochemical staining with von Kossa (osteogenesis), Toluidine blue O (chondrogenesis), and Oil red O (adiopogenesis) was then performed to evaluate the tri-lineage differentiation potential, respectively.     Generation of CSRP1 overexpressed hMSCs  WT hMSCs were transfect with lentivirus encoding full length CSRP1 and Luc (control), respectively.     Generation of transformed hMSCs  The in vitro oncogenic transformation was conducted based on previous reports (Scaffidi and Misteli, 2012; Yang et al., 2017). hMSCs were transduced sequentially with pBABE-neo-hTERT, pBABE-zeo-largeTgenomic and pBABE-puro-RasV12 retroviruses. At the same time, cells were selected using G418 (100 μg/mL, 7 days, Invitrogen), zeocin (100 μg/mL, 7 days, Invitrogen) and puromycin (1 μg/mL, 3 days, Invitrogen), respectively. The selected cells were transfected with the pLVTHM-shRNA-P53 vector for reducing P53 expression. The generated hTMSCs were regarded as passage 1 (P1), and cultured in hTMSC medium.

tag: gender

value: female


title: hTransMSC_FOXO3+/+_2 Bisulfite-Seq

description: Bisulfite treated  genomic DNA


title: hTransMSC_FOXO32SA/2SA_2 Bisulfite-Seq

description: Bisulfite treated  genomic DNA


title: 030U_MSCB-151


title: hMSC_FOXO32SA/2SA_1 Bisulfite-Seq

description: Bisulfite treated  genomic DNA

source_name: Human MSCs

tag: passages


title: 030U_MSCB-146


title: hMSC_FOXO3+/+_2 Bisulfite-Seq

description: Bisulfite treated  genomic DNA


title: 030U_MSCB-144


title: hTransMSC_FOXO3+/+_1 Bisulfite-Seq

description: Bisulfite treated  genomic DNA


title: 030U_MSCB-150


title: 030U_MSCB-149


title: 030U_MSCB-143


title: 030U_MSCB-148


title: hMSC_FOXO32SA/2SA_2 Bisulfite-Seq

description: Bisulfite treated  genomic DNA


title: 030U_MSCB-147


title: hMSC_FOXO3+/+_1 Bisulfite-Seq

description: Bisulfite treated  genomic DNA


title: 030U_MSCB-145


title: hVSMC_FOXO3+/+_1 Bisulfite-Seq

description: Bisulfite treated  genomic DNA

source_name: Human VSMCs


title: hEC_FOXO32SA/2SA_2 Bisulfite-Seq

description: Bisulfite treated  genomic DNA

source_name: Human ECs


title: hVSMC_FOXO32SA/2SA_2 Bisulfite-Seq

description: Bisulfite treated  genomic DNA


title: hVSMC_FOXO32SA/2SA_1 Bisulfite-Seq

description: Bisulfite treated  genomic DNA


title: 030U_MSCB-140


title: 030U_MSCB-142


title: 030U_MSCB-141


title: hEC_FOXO32SA/2SA_1 Bisulfite-Seq

description: Bisulfite treated  genomic DNA


title: hVSMC_FOXO3+/+_2 Bisulfite-Seq

description: Bisulfite treated  genomic DNA


title: 030U_MSCB-139


title: hEC_FOXO3+/+_1 Bisulfite-Seq

description: Bisulfite treated  genomic DNA


title: 030U_MSCB-138


title: hEC_FOXO3+/+_2 Bisulfite-Seq

description: Bisulfite treated  genomic DNA


title: 030U_MSCB-136


title: hESCs_FOXO32SA/2SA_1

description: Genomic DNA

source_name: Human ESCs


title: 030U_MSCB-135


title: 030U_MSCB-133


title: hESCs_FOXO3+/+_2

description: Genomic DNA


title: 030U_MSCB-132


title: hTransMSC_FOXO32SA/2SA_1

description: Genomic DNA


title: hTransMSC_FOXO32SA/2SA_2

description: Genomic DNA


title: hTransMSC_FOXO32SA/2SA_3

description: Genomic DNA


title: hESCs_FOXO3+/+_1

description: Genomic DNA


title: 030U_MSCB-130


title: hTransMSC_FOXO3+/+_2

description: Genomic DNA


title: hTransMSC_FOXO3+/+_3

description: Genomic DNA


title: hTransMSC_FOXO3+/+_1

description: Genomic DNA


title: 030U_MSCB-128


title: 030U_MSCB-127


title: hMSC_FOXO32SA/2SA_2

description: Genomic DNA


title: hMSC_FOXO32SA/2SA_3

description: Genomic DNA


title: 030U_MSCB-125


title: 030U_MSCB-137


title: 030U_MSCB-126


title: 030U_MSCB-124


title: hMSC_FOXO32SA/2SA_1

description: Genomic DNA


title: 030U_MSCB-123


title: 030U_MSCB-122


title: hMSC_FOXO3+/+_2

description: Genomic DNA


title: 030U_MSCB-121


title: 030U_MSCB-131


title: hMSC_FOXO3+/+_3

description: Genomic DNA


title: hVSMC_FOXO32SA/2SA_3

description: Genomic DNA


title: 030U_MSCB-120


title: 030U_MSCB-118


title: hVSMC_FOXO32SA/2SA_1

description: Genomic DNA


title: 030U_MSCB-134


title: hMSC_FOXO3+/+_1

description: Genomic DNA


title: 030U_MSCB-117


title: hVSMC_FOXO3+/+_3

description: Genomic DNA


title: hVSMC_FOXO3+/+_1

description: Genomic DNA


title: hVSMC_FOXO32SA/2SA_2

description: Genomic DNA


title: hVSMC_FOXO3+/+_2

description: Genomic DNA


title: 030U_MSCB-129


title: 030U_MSCB-114


title: 030U_MSCB-116


title: hEC_FOXO32SA/2SA_2

description: Genomic DNA


title: hEC_FOXO3+/+_2

description: Genomic DNA


title: hEC_FOXO32SA/2SA_1

description: Genomic DNA


title: 030U_MSCB-115


title: 030U_MSCB-112


title: hEC_FOXO3+/+_1

description: Genomic DNA


title: hTransMSC_FOXO32SA/2SA_3 RNA-Seq

description: polyA RNA


title: 030U_MSCB-110


title: hTransMSC_FOXO32SA/2SA_2 RNA-Seq

description: polyA RNA


title: 030U_MSCB-119


title: hTransMSC_FOXO32SA/2SA_1 RNA-Seq

description: polyA RNA


title: 030U_MSCB-108


title: 030U_MSCB-109


title: hTransMSC_FOXO3+/+_3 RNA-Seq

description: polyA RNA


title: hTransMSC_FOXO3+/+_1 RNA-Seq

description: polyA RNA


title: hMSC_CSRP1_3 RNA-Seq

description: polyA RNA


title: 030U_MSCB-105


title: hMSC_CSRP1_1 RNA-Seq

description: polyA RNA


title: hMSC_Luc_3 RNA-Seq

description: polyA RNA


title: 030U_MSCB-102


title: 030U_MSCB-103


title: 030U_MSCB-106


title: 030U_MSCB-104


title: 030U_MSCB-113


title: hMSC_Luc_2 RNA-Seq

description: polyA RNA


title: hMSC_FOXO32SA/2SA_4 RNA-Seq P7

description: polyA RNA


title: 030U_MSCB-111


title: 030U_MSCB-098


title: 030U_MSCB-099


title: 030U_MSCB-100


title: hMSC_FOXO32SA/2SA_3 RNA-Seq P7

description: polyA RNA


title: 030U_MSCB-097


title: hMSC_FOXO32SA/2SA_2 RNA-Seq P7

description: polyA RNA


title: hMSC_FOXO32SA/2SA_1 RNA-Seq P7

description: polyA RNA


title: 030U_MSCB-107


title: 030U_MSCB-096


title: 030U_MSCB-095


title: hTransMSC_FOXO3+/+_2 RNA-Seq

description: polyA RNA


title: hMSC_FOXO3+/+_4 RNA-Seq P7

description: polyA RNA


title: hMSC_CSRP1_2 RNA-Seq

description: polyA RNA


title: hMSC_FOXO3+/+_3 RNA-Seq P7

description: polyA RNA


title: hMSC_FOXO3+/+_2 RNA-Seq P7

description: polyA RNA


title: 030U_MSCB-093


title: 030U_MSCB-101


title: hMSC_FOXO3+/+_1 RNA-Seq P7

description: polyA RNA


title: 030U_MSCB-092


title: 030U_MSCB-091


title: 030U_MSCB-090


title: hMSC_FOXO32SA/2SA_3 RNA-Seq P3

description: polyA RNA


title: hMSC_FOXO32SA/2SA_2 RNA-Seq P3

description: polyA RNA


title: hMSC_FOXO32SA/2SA_4 RNA-Seq P3

description: polyA RNA


title: 030U_MSCB-088


title: 030U_MSCB-089


title: 030U_MSCB-087


title: hMSC_Luc_1 RNA-Seq

description: polyA RNA


title: 030U_MSCB-094


title: 030U_MSCB-086


title: 030U_MSCB-085


title: hMSC_FOXO3+/+_2 RNA-Seq P3

description: polyA RNA


title: hMSC_FOXO3+/+_1 RNA-Seq P3

description: polyA RNA


title: hMSC_FOXO3+/+_4 RNA-Seq P3

description: polyA RNA


title: 030U_MSCB-084


title: hVSMC_FOXO32SA/2SA_2 RNA-Seq

description: polyA RNA


title: hMSC_FOXO32SA/2SA_1 RNA-Seq P3

description: polyA RNA


title: 030U_MSCB-083


title: 030U_MSCB-082


title: 030U_MSCB-081


title: hVSMC_FOXO32SA/2SA_1 RNA-Seq

description: polyA RNA


title: hVSMC_FOXO3+/+_3 RNA-Seq

description: polyA RNA


title: hVSMC_FOXO32SA/2SA_3 RNA-Seq

description: polyA RNA


title: hMSC_FOXO3+/+_3 RNA-Seq P3

description: polyA RNA


title: 030U_MSCB-080


title: 030U_MSCB-079


title: hEC_FOXO32SA/2SA_3 RNA-Seq

description: polyA RNA


title: hVSMC_FOXO3+/+_2 RNA-Seq

description: polyA RNA


title: 030U_MSCB-078


title: 030U_MSCB-076


title: 030U_MSCB-074


title: 030U_MSCB-075


title: hEC_FOXO32SA/2SA_2 RNA-Seq

description: polyA RNA


title: hEC_FOXO3+/+_3 RNA-Seq

description: polyA RNA


title: hEC_FOXO32SA/2SA_1 RNA-Seq

description: polyA RNA


title: hEC_FOXO3+/+_2 RNA-Seq

description: polyA RNA


title: 030U_MSCB-073


title: hEC_FOXO3+/+_1 RNA-Seq

description: polyA RNA


title: 030U_MSCB-072


title: 030U_MSCB-069


title: 030U_MSCB-071


title: 030U_MSCB-068


title: 030U_MSCB-070


title: 030U_MSCB-066


title: 030U_MSCB-065


title: hVSMC_FOXO3+/+_1 RNA-Seq

description: polyA RNA


title: 030U_MSCB-077


title: 030U_MSCB-064


title: 030U_MSCB-067


title: 030U_MSCB-062


title: 030U_MSCB-061


title: 030U_MSCB-063


title: 030U_MSCB-059


title: 030U_MSCB-060


title: 030U_MSCB-055


title: 030U_MSCB-058


title: 253G1_SALL3 shRNA, biological rep3

type: RNA

city: Setagaya

first: Takuya

last: Kuroda

state: Tokyo

address: 1-18-1 Kamiyoga

department: Division of cell-based therapeutic products

country: Japan

institute: National Institute of Health and Sciences

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The TGT value is 500.

label: biotin

source_name: 253G1 infected shRNA to SALL3

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy  Mini Kit, Qiagen)

tag: shRNA

value: shRNA to SALL3


title: 253G1_control shRNA, biological rep.1

source_name: 253G1 infected control shRNA

value: control shRNA


title: ATCC-DYR0103hiPSc, biological rep5

tag: cell line


title: 253G1_SALL3 shRNA, biological rep2


title: 253G1_control shRNA, biological rep.3


title: ATCC-DYR0103hiPSc, biological rep3


title: 253G1_SALL3 shRNA, biological rep1


title: 030U_MSCB-056

value: pre-B cell


title: 253G1_control shRNA, biological rep.2


title: ATCC-DYR0103hiPSc, biological rep2


title: ATCC-DYR0103hiPSc, biological rep6


title: ATCC-DYR0100hiPSc, biological rep6


title: ATCC-DYR0100hiPSc, biological rep3


title: ATCC-DYR0103hiPSc, biological rep4


title: 030U_MSCB-054


title: 030U_MSCB-050


title: 030U_MSCB-057


title: 030U_MSCB-053


title: 030U_MSCB-052


title: ATCC-DYR0100hiPSc, biological rep5


title: 030U_MSCB-051


title: ATCC-DYR0100hiPSc, biological rep1


title: ATCC-DYR0103hiPSc, biological rep1


title: 030U_MSCB-043


title: mc-iPS, biological rep3

source_name: mc-iPS

value: mc-iPS


title: ATCC-DYR0100hiPSc, biological rep2


title: mc-iPS, biological rep4


title: mc-iPS, biological rep5


title: 030U_MSCB-048

value: reprogramming


title: ATCC-DYR0100hiPSc, biological rep4


title: mc-iPS, biological rep6


title: Tic, biological rep6

source_name: Tic

value: Tic


title: mc-iPS, biological rep2


title: 030U_MSCB-040

value: OSKM

value: iPSCs


title: 030U_MSCB-047

value: day 6


title: 030U_MSCB-046


title: 030U_MSCB-045


title: UV-RIP-seq 0h

city: hangzhou

first: Hongyu

last: Lin

address: Zijingang Campus of Zhejiang University, 866 Yuhangtang Road, Xihu District

institute: Zhejiang University School of Medicine

data_processing:
Primary sequencing data that produced by Illumina Xten, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
Raw data quality control was performed by FastQC, and raw data filter was performed by scripts.
Trimmomatic and Fastx-toolkit were used to trim adaptor contamination and low quality bases.
Clean data mapped to mm10 reference genome by HISAT2.
Assemble of RNA-Seq alignments into mm10 transcripts was processed by Stringtie.
Differential expression analysis between sample 1 and 2 was performed using the Cuffmerge and Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: isoforms.fpkm_tracking

source_name: RAW264.7 cells

growth_protocol: RAW264.7 cells stably expressing Flag-tagged TRIM25 were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
RIP experiment was performed according to the manufacturer’s instructions. The isolated RNA was further assessed by RNA-seq analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RAW264.7 cells stably expressing Flag-tagged TRIM25 were mock treated with PBS or VSV infection for 8 hr and  were subjected to crosslinking with 0.3 J/cm2 of 254 nm UV light in a crosslinker HL-2000 (UVP). RIP experiment was performed using anti-Flag antibody, and then co-purified RNAs were analyzed using Illumina HiSeq4000 sequencing.

value: RAW264.7 cells

value: murine macrophage cell line

tag: strain

tag: rip antibody

value: flag-tag (Millipore, MAB3118,clone 2EL-1B11 )

tag: infection

value: without VSV infection


title: mc-iPS, biological rep1


title: 030U_MSCB-044

source_name: bone marrow

tag: cell type

tag: treatment


title: 030U_MSCB-049

tag: induction

tag: fate


title: 030U_MSCB-042

tag: time point


title: 030U_MSCB-041


title: Tic, biological rep3


title: HiPS-RIKEN-12A, biological rep5


title: 030U_MSCB-037


title: HiPS-RIKEN-12A, biological rep6


title: 030U_MSCB-039


title: UV-RIP-seq 8h

value: VSV infection for 8 hr


title: Tic, biological rep1


title: Tic, biological rep2


title: Tic, biological rep5


title: 030U_MSCB-038


title: P8a cerebellum

city: Shanghai

first: Peng

last: Jian

address: 320 Yue Yang Road

department: Institute of Neuroscience

institute: University of Chinese Academy of Sciences

data_processing:
Basecalls performed using CellRanger 2.1
reads were aligned to the mm10 genome assembly using cellranger 2.1 with the following configurations…
cellranger count --id=result --transcriptome=/ion/luozg_group/pengjian/2_refdata/1_mm/refdata-cellranger-mm10-1.2.0 --fastqs=/ion/luozg_group/pengjian/1_rawdata --sample=P0 \ ##P8a or P8b
--expect-cells=5000
Data were filtered using the following specifications…filtering out outliers with extremely low (less than 1000) and high (more than 6500) gene numbers
Cluster were perform using Seurat in R
26 bp Read1 (10× cell barcode and UMI), 8 bp i7 Index (sample index), and 98 bp Read2 (insert)is biological,otherwise is technical
Genome_build: mm10
Supplementary_files_format_and_content: [.csv]  raw counts

source_name: Total cerebellum cell

extract_protocol:
Samples were sheared in 1×Hank’s balanced salt solution (HBSS) and digested for 15-20 min in 0.25% trypsin solution
All procedures followed the guidelines provided by 10x Genomics, Inc Dissociated cells in each sample were partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs) in a limiting dilution to lower multiplet rate. Then, single-cell GEMs were incubated with reverse-transcription reagents, including several primers for cell and transcript barcoding in cDNA synthesis, followed by cDNA amplification and library construction

tag: developmental stage

value: postnatal day 8

tag: tissue

value: cerebellum


title: P0 cerebellum

value: postnatal day 0


title: Tic, biological rep4


title: HiPS-RIKEN-12A, biological rep3


title: HiPS-RIKEN-12A, biological rep4


title: P8b cerebellum


title: 030U_MSCB-033


title: MK801_6

first: Jialu

last: Zhao

address: You an men wai Xi tou tiao Road 10

institute: Capital Medical University

data_processing:
Illumina CASAVA(v1.8.2) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to MusGRC38.71 using Tophat (version tophat-2.1.1.Linux_x64)
After adding up the read counts use HTSeq(version 0.9.1), the differential expression analysis was performed using DEseq2(version 1.16.1)
Genome_build: MusGRC38.71
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample.

source_name: Prefrontal cortex

extract_protocol:
After behavioral evaluations, mice were killed by decapitation. The brains were rapidly removed from the skull and were flash frozen in liquid nitrogen, stored at –80 ℃.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prefrontal cortex

tag: classfication

value: male

tag: age

value: post natal day 56-63


title: 030U_MSCB-034

value: pre-B cell


title: MK801_5


title: 030U_MSCB-035

value: reprogramming


title: 030U_MSCB-036


title: 030U_MSCB-032


title: MK801_4


title: MK801_3


title: MK801_2


title: HiPS-RIKEN-12A, biological rep2


title: HiPS-RIKEN-12A, biological rep1


title: HiPS-RIKEN-2A, biological rep5


title: 030U_MSCB-030


title: 030U_MSCB-028


title: HiPS-RIKEN-2A, biological rep4


title: HiPS-RIKEN-2A, biological rep1


title: Control_3

value: Control


title: HiPS-RIKEN-1A, biological rep6


title: HiPS-RIKEN-2A, biological rep2


title: 030U_MSCB-025

value: OSKM


title: HiPS-RIKEN-2A, biological rep3


title: 030U_MSCB-031

value: iPSCs


title: Control_1


title: HiPS-RIKEN-2A, biological rep6


title: 030U_MSCB-027

value: day 6


title: 030U_MSCB-026


title: Control_2


title: HiPS-RIKEN-1A, biological rep5


title: DCM5 Input

data_processing:
Data alignement  Bowtie v2.1
Downsizing using Downsampke SAM feature of picard
peak calling using EDD (Enriched domain detector)
Reads were aligned to the hg19 release of the human genome by Bowtie v2.1 and each pair of input and anti-LMNA samples was adjusted so that the same read depth was achieved, using the DownsampleSam feature of Picard software on the larger of the two files. Peaks (lamin-associated domains, LADs) were calculated using EDD (Enriched domain detector) with bin size = 11 kb, gap penalty = 9, FDR = 0.05
Genome_build: HG19
Supplementary_files_format_and_content: Chromosome coordinates of the peaks present in atleast 3 samples
Supplementary_files_format_and_content: Bed coordinates for peaks for all the samples

source_name: PCM1 positive cardiac myocyte nuclei

growth_protocol: Not applicable

extract_protocol:
Cardiomyocyte nuclei were isolated by FACS using anti PCM1 antibody. The nuclei were crosslinked using 1% formaldehyde for 2 min at room temperature. Crosslinked nuclei were fragmented using Bioruptor Pico (Diagenode) to achieve frgament size of 200-500bp. A portion of nuclear extract was kept aside to serve as input. Immunoprecipitation was carried out using  anti LMNA A/C antibody. Immunecomplexes were washed, eluted the DNA and reverse crosslinked at 65 O/N. the DNA was precipitated after phenol chloroform extraction by glycogen.
ChIP libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, Inc.) following the manufacturer’s protocol. Sequencing was done  on an Illumina HiSeq3000 for sequencing using a Single Read 50 bp run.

treatment_protocol: Not applicable

tag: Sex

value: Male

tag: group

value: DCM


title: HiPS-RIKEN-1A, biological rep4


title: MK801_1

tag: gender


title: HiPS-RIKEN-1A, biological rep3


title: HiPS-RIKEN-1A, biological rep1


title: DCM4  α-LMNA ChIP

tag: antibody

value: anti LMNA A/C


title: 409B2, biological rep6

tag: cell line


title: 030U_MSCB-023


title: 030U_MSCB-020


title: DCM2 Input


title: DCM5  α-LMNA ChIP


title: HiPS-RIKEN-1A, biological rep2


title: DCM3 Input

value: Female


title: 030U_MSCB-022


title: 030U_MSCB-019


title: DCM3  α-LMNA ChIP


title: 030U_MSCB-021


title: 409B2, biological rep5


title: DCM1  α-LMNA ChIP


title: 409B2, biological rep2


title: DCM4 Input


title: 409B2, biological rep3


title: 409B2, biological rep4


title: DCM1 Input


title: 030U_MSCB-017


title: 030U_MSCB-018


title: Control 5 α-LMNA ChIP


title: 030U_MSCB-013


title: 030U_MSCB-014


title: DCM2  α-LMNA ChIP


title: Control 5 Input


title: 030U_MSCB-015


title: Control 4 Input


title: Control 4 α-LMNA ChIP


title: Control 3 α-LMNA ChIP


title: 030U_MSCB-016


title: 030U_MSCB-012


title: Control 3 Input


title: 253G1, biological rep5


title: 253G1, biological rep6


title: 253G1, biological rep2


title: 409B2, biological rep1


title: 030U_MSCB-009


title: 030U_MSCB-010


title: 030U_MSCB-011


title: 253G1, biological rep4


title: Control 1 α-LMNA ChIP


title: 253G1, biological rep1


title: Control 2 α-LMNA ChIP


title: 030U_MSCB-007


title: 030U_MSCB-008


title: Control 1 Input


title: Control 2 Input


title: 201B7, biological rep6


title: 253G1, biological rep3


title: 201B7, biological rep5


title: Activated myeloid cells at day 1 pi

city: Oakland

first: Laura

last: Hertel

state: CA

address: 5700 Martin Luther King Jr Way

institute: Children's Hospital Oakland Research Institute

data_processing:
CellRanger v1.2 software pipeline
Genome_build: hg19 + TB40/E (NCBI accession EF999921.1)
Supplementary_files_format_and_content: Genes.tsv - Tab-delimited text file includes Ensembl gene ID (first column) and HGNC gene Symbol (second column)
Supplementary_files_format_and_content: Barcodes.tsv - Tab-delimited text file includes illumina barcodes in the first column
Supplementary_files_format_and_content: Matrix.mtx - The .mtx file contains the filtered  gene-barcode matrix. Each element of the matrix is the number of UMIs associated with a gene and barcode (i.e. indvidual cell) as output from the cellranger pipeline. Genes correspond to row indices and cells to column indices.

source_name: Activated myeloid cells infected with TB40/E at 1 dpi

growth_protocol: Umbilical cord blood CD34+ HSC purchased from StemCell Technologies were pre-amplified in alpha-Minimum Essential Medium supplemented with 20% heat-inactivated fetal bovine serum, 375 ng/ml of Flt3 ligand, 50 ng/ml of stem cell factor and 50 ng/ml of thrombopoietin for 8-10 days at a density of 1 x 104 cells/well in 48-well tissue culture plates. Cells were then differentiated in serum-free X-VIVO 15 medium supplemented with 1,500 IU/ml of granulocyte-macrophage colony-stimulating factor, 150 ng/ml of Flt3 ligand, 10 ng/ml of stem cell factor, 2.5 ng/ml of tumor necrosis factor- and 0.5 ng/ml of transforming growth factor 1 for 8 days at a density of 1 x 105 cells/well in 48-well plates. Differentiated cells were then activated by exposure to X-VIVO 15 medium containing 10% standard fetal bovine serum, 1,500 IU/ml of granulocyte-macrophage colony-stimulating factor, 200 ng/ml of CD40 ligand and 500 ng/ml of lipopolysaccharide for 2 days at a density of 1 x 105 cells/well in 48-well plates.

extract_protocol:
10,000 cells were loaded onto a single channel of the 10X Chromium Controller. Messenger RNA from approximately ~ 7,000 cells, captured and lysed within nanoliter-sized gel beads in emulsion, was reverse transcribed and barcoded using polyA primers with unique molecular identifier sequences before being pooled, amplified, and used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were  infected with CMV strain TB40/E at an MOI of 10, washed five times, and further incubated in activation medium for 24 hours.

value: Activated myeloid cells

tag: virus

value: Day 1 post-infection


title: 030U_MSCB-004


title: 030U_MSCB-005


title: D18 SIX2CRE lineage tracing organoid

city: Parkville

first: Andrew

last: Lonsdale

state: VIC

address: 50 Flemington Rd

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
Transcripts for reporters mTagBFP, mCherry and eGFP were added to the hg38 genome.
The 10x Genomics Cell Ranger pipeline (v1.3.1) was used to align, filter and de-duplicate reads before counting those overlapping genes to produce count matrices.
Celllranger datasets consist of (for each sample) matrix files (matrix.mtx) containing the UMI count values, barcode files (barcodes.tsv) containing the detected cell barcodes and genes files (genes.tsv)  containing the ENSEMBL ids of the detected genes.  The first 26 bp of R1 reads contain the barcode (16bp) and UMI (10bp) respectively.
Genome_build: hg38
Supplementary_files_format_and_content: Cell Ranger output files, compressed.

source_name: SIX2:cre/GAPDH:dual lineage tracing reporter

growth_protocol: Kidney organoids were made according to a published protocol (Takasato et al., Generation of kidney organoids from human pluripotent stem cells, Nature protocols 2016, PMID:27560173.) with the following adjustments: E6 was used in place of APEL and the organoids were produced by bioprinting from a cell paste instead of pelleting in a centrifuge.

extract_protocol:
Organoids were harvested by pooling 3 organoids, cutting into small pieces with a scalpel blade and dissociating in 1mL Accutase at 37 degrees Celcius, pipetting every 3 minutes. The incubation was stopped after 15 minutes by placing on ice. The cell solution was passed through a 40um cell strainer into a FACS tube and then washed with 2mL E6 (room temperature). FACS tubes were spun (1500 rpm, 3 minutes) and resuspended in 500uL of E6 media. Samples were cell counted and tested for viability and diluted to the required density for the sequencing protocol (300-1000 cells per uL) in E6 media. The cells were then transported to the sequencing facility on ice (30 minutes total).
Chromium Single Cell Library kit V2
Illumina HiSeq HT chemistry- 100bp paired end sequencing

value: iPSC-derived kidney organoid

tag: day of differentiation


title: 030U_MSCB-006


title: 030U_MSCB-003


title: 030U_MSCB-001


title: 030U_MSCB-002


title: 1254800_30hpi

city: Singapore

first: Radoslaw

middle: Igor

last: Omelianczyk

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Hybridization of labeled cDNA was performed as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

scan_protocol: Scanning and image acquisition of the hybridized microarray chips was performed using the PowerScannerTM (Tecan) at 10µM resolution under automated photomultiplier (PMT) balancing. Hybridized spots were analysed and preprocessed using GenePix® ProMicroarray Image Analysis Software v6.0 (Axon Instruments).

data_processing:
Features with flag>0 and with median foreground intensity greater than 1.5 fold median background intensity for either channel passed quality control and were accepted. Local background correction using normexp, followed by lowess normalization across all features were carried out to generate the normalized Log2 gene expression ratios.
Processed matrix contains lowess normalized log2-transformed expression ratio of the RNA sample/3D7 reference pool

organism: Plasmodium falciparum

source_name: Plasmodium falciparum

label_protocol: Labeling of cDNA was performed as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

growth_protocol: All P. falciparum strains were cultivated at 3.5% haematocrit of O+ erythrocytes. RPMI 1640 medium was completed with 10% Albumax, 25mM Hepes Buffer and 0.05mg/ml gentamicin (all Gibco). Parasites were incubated at 37°C in 90% nitrogen, 5% oxygen and 5% carbon dioxide.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions and as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

tag: genotype/variation

value: transfectant

tag: multigene family

value: rifin

value: In vitro, blood stage

tag: hours post invasion

source_name: mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle

tag: sample type

value: reference


title: 0421300_30hpi

value: var


title: 1149900_18hpi

value: stevor


title: 1254800_18hpi


title: 1254800_24hpi


title: 1149900_30hpi


title: 0421300_24hpi


title: 0421300_18hpi


title: 211_NMuMg_BC0STOP

city: Milano

first: gabriele

last: bucci

state: MI

address: via olgettina 58

department: CTGB

country: Italy

institute: IRCCS Ospedale San Raffaele

data_processing:
base calls RTA 2.4.11
demultiplexing bcl2fastq v2.0
pseudocounts were computed from fastq with kallisto v0.43.1 on gencode M15 (GRCm38.p5) transcriptome reference
Genome_build: HG38
Supplementary_files_format_and_content: tab separated kallisto pseudocounts transcripts abundances

source_name: NMuMg

growth_protocol: NMuMG cultured in DMEM 10% FCS, 0.01 mg/ml

extract_protocol:
Total RNA was extracted using miRNeasy (Qiagen)
Libraries were prepared according to TruSeq Stranded Total RNA illumina protocol , generating paired-end 75 base-pair reads on NextSeq_1_1_4

treatment_protocol: Cells have been stably transfected with pBICEP-based recombinant expression vector and selected with G418 to obtain transfectant pools

value: NMuMg

tag: genotype

value: overexpressed point-mutant transcript


title: 210_NMuMg_BC0STOP


title: 3D7_30hpi

value: parental


title: 201B7, biological rep2


title: 3D7_24hpi


title: 208_NMuMg_BC030870

value: overexpressed full transcript


title: 201B7, biological rep4


title: 201B7, biological rep3


title: 209_NMuMg_BC0STOP


title: 201B7, biological rep1


title: 205_NMuMg_mock

value: mock


title: 207_NMuMg_BC030870


title: D25 MAFB:GATA3 reporter organoid

source_name: MAFB:mTagBFP2/GATA3:mCherry reporter

tag: cell type


title: 204_NMuMg_mock


title: 1149900_24hpi


title: 203_NMuMg_mock


title: GBM-17 with TTF treatment for 10 days

city: New York

first: Longfei

last: Gao

state: NY

address: 650 West 168th Street

institute: Columbia University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: human primary glioblastoma tissues

growth_protocol: GBM-387 and GBM-17 cells were cultured in serum-free medium, which was consisted of Neurobasal medium (Gibco), 1X N2 (Gibco), 1X B27 (Gibco), 1X non-essential amino acid (Millipore), 1X sodium pyruvate (Sigma), 1X glutamax (Gibco), 10 ng/ml bFGF (Invitrogen), and 10 ng/ml EGF (Invitrogen)

extract_protocol:
Cells were harvested with Trizol reagent after the medium was aspirated. RNA was isolated following manufacturer’s instructions.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were  generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: G387-d0 or G17-d0 were GBM-387 or GBM-17 cells without drug treatment. G387-d2 or G17-d2 were GBM-387 or GBM-17 cells treated with TTF cocktail (50 µM TMZ, 100 µM Tranilast, and 50 µM Fasudil) for 2 days in neuron induction medium (BrainPhys medium (Stemcell Technologies) supplemented with 1X B27, 1X N2, 10 ng/ml brain-derived neurotrophic factor (Peprotech), 10 ng/ml glial cell-derived neurotrophic factor (Peprotech), 10 ng/ml insulin-like growth factor (Peprotech), 0.2 μM ascorbic acid (Sigma), and 100 μM N6, 2’-O-Dibutyryladenosine 3’, 5’-cyclic monophosphate sodium salt (Sigma)). G387-d10 or G17-d10 were GBM-387 or GBM-17 cells treated with TTF cocktail (50 µM TMZ, 100 µM Tranilast, and 50 µM Fasudil) for 10 days in neuron induction medium

value: glioblastoma cells

tag: passages

tag: treatment

value: with TTF treatment for 10 days


title: Biological replicate 3. Cells transduced with an empty vector

city: Stockholm

first: Nik

middle: V

last: Kuznetsov

address: Nobels vag 16

country: Sweden

institute: Karolinska Institute

description:
Anderson RNAseq Analysis.xlsx
1701_20151124_GFP.fastq

data_processing:
cDNA libraries for each sample was loaded onto an Ion P1 chip and run on the Ion Proton.
Raw sequence data was aligned to the hg 19 human reference genome using Ion torrent alignment plug-in.
Subsequent aligned bam files were loaded into StrandNGS bioinformatic software.
After determining post-alignment QC, the total reads were filtered based on read metrics (Alignment score>90, Match count, venders QC).
The filtered reads for each sample was quantified and then normalized and baseline transformed by the DE-seq algorithm.
Genome_build: hg19
Supplementary_files_format_and_content: Fastq

source_name: T cells

growth_protocol: Human PBMCs were separated after Ficoll (GE Healthcare) gradient centrifugation. Highly purified cell populations (>95%) of CD4+ naïve T cells (CD4+ CD25- CD45RA+) were obtained using fluorescence activated cell sorting (FACS)

extract_protocol:
RNA was extracted using Qiagen's RNeasy Mini Kit (Cat#74104) and mRNA enrichment was done by Dynabeads® mRNA DIRECT™ Micro Kit (Catolog # 61021)
The library was prepared using Total RNA-Seq Kit v2 from Life Technologies (Cat# 4479789)

treatment_protocol: Sequences coding for FOXP3 isoforms were cloned into second generation lentivral pHAGE-IRES-ZsGreen plasmid. Lentiviruses encoding for FOXP3 isoform were produced by Turku Centre for Biotechnology lentivirus core facility. Sorted CD4+ naïve T cells were activated with anti-CD3/anti-CD28 beads (Miltenyi) in XVIVO-15 medium supplemented with 1% Penicillin-Streptomycin (both from Lonza) and 300 U/ml IL-2 (Preprotech). Lentiviral particules were added to the culture 12h after activation. Cells were then cultured for 3 days before being moved to IL-2 only conditions. On day 7 post-activation, CD4+ 7AAD- ZsGreen+ cells were sorted using FACSJazz (BD Biosciences).

tag: transducer

value: empty vector


title: Biological replicate 3. Cells transduced with FOXP3[delta]2

description:
Anderson RNAseq Analysis.xlsx
1703_20121124d2.fastq


title: human neuron

description:
human neuron total RNA purchased from ScienCell (Cat. #1525 )
hN

value: human neuron cells

value: human neuron


title: Biological replicate 2. Cells transduced with FOXP3fl

description:
Anderson RNAseq Analysis.xlsx
1699_20151110_FL.fastq


title: GBM-17 without TTF treatment

value: without TTF treatment


title: Biological replicate 2. Cells transduced with FOXP3[delta]2

description:
Anderson RNAseq Analysis.xlsx
1700_20151110_d2.fastq


title: Biological replicate 2. Cells transduced with an empty vector

description:
Anderson RNAseq Analysis.xlsx
1698_20151110_GFP.fastq

value: empty vector.


title: GBM-17 with TTF treatment for 2 days

value: with TTF treatment for 2 days


title: 206_NMuMg_BC030870


title: Biological replicate 1. Cells transduced with FOXP3fl

description:
Anderson RNAseq Analysis.xlsx
1696_201550807a_FL.fastq


title: Biological replicate 1. Cells transduced with FOXP3[delta]2

description:
Anderson RNAseq Analysis.xlsx
1697_20150807a_d2.fastq


title: Biological replicate 1. Cells transduced with an empty vector

description:
Anderson RNAseq Analysis.xlsx
1695_20150807a_GFP.fastq


title: IonXpress_022

city: Pisa

first: Gabriella

last: Fontanini

state: Italy

address: Via Roma 57

department: Department of Surgical, Medical, Molecular Pathology and Critical Area

institute: University of Pisa

data_processing:
Raw sequencing reads were evaluated on the Torrent Server using the ampliSeqRNA plug-in
Raw counts for each gene in the UCSC coding gene annotation (hg19) were measured with HTSeq (http://www-huber.embl.de/users/anders/HTSeq/) version 0.5.3p3. Genes with at least a count of 10 in all samples were retained.
Raw read count data was first scaled to library size followed by normalizing with weighted trimmed mean of M values (TMM) to consider the compositional bias in sequenced libraries, using edgeR version 2.6.8.
Genome_build: hg19
Supplementary_files_format_and_content: normalized data.rpm.bcmatrix.xls: normalized reads per million counts

source_name: Lung

extract_protocol:
Four 5µm unstained sections underwent standard deparaffinization. All samples were enriched by manual microdissection. Total RNA was isolated using Qiagen RNeasy FFPE kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions
Ten ng of total RNA  was reverse transcribed to cDNA using the Invitrogen SuperScript VILO cDNA Synthesis kit (Applied Biosystem - ThermoFisher Scientific, San Francisco, CA, USA).   Transcriptome libraries were generated according to the manufacturer’s instructions. Briefly, after primers digestion, adapters and molecular barcodes were ligated to the amplicons followed by magnetic bead purification; then libraries were amplified and purified. Amplicon size and DNA concentration were measured using an Agilent high sensitivity DNA kit (Agilent Technologies, Waldbronn, Germany).

tag: tissue

value: Lung

tag: histology

value: carcinosarcoma

tag: specimen

value: surgical formalin-fixed paraffin-embedded tissue

value: Male

tag: age

tag: t stage

tag: n stage


title: IonXpress_020

value: pleomorphic carcinoma

tag: gender

value: KRAS p.G12V


title: IonXpress_021

value: spindle cell carcinoma


title: IonXpress_025

value: normal lung parenchyma


title: IonXpress_024


title: IonXpress_023


title: 3D7_18hpi

value: parental

value: In vitro, blood stage

value: reference


title: WT_A

city: Ithaca

first: Jeffrey

last: Pleiss

address: 453 Biotech

institute: Cornell University

data_processing:
Library strategy: MPE-seq
Reads were trimmed using Trimmomatic v0.35
Trimmed reads were aligned with hisat2 v.2.1.0
Counts per feature were completed with custom scripts based off of HTSeq-count
Genome_build: Pombase v2.30
Supplementary_files_format_and_content: text file with 4 columns: 1) Gene ID 2) Exonic: Number of reads that mapped completely within an exon. 3) Mature: Number of reads that mapped across a splice junction. 4) Premature: Number of reads that mapped across an exon-intron border, completely within an intron, or across an intron-exon border.

organism: Schizosaccharomyces pombe

source_name: Culture

growth_protocol: Single colony innoculated into YES. Grown at 30˚C until OD600 = .8

extract_protocol:
Phenol-chloroform extraction
Libraries were prepared according to Xu et al, Nature Methods 2018

tag: strain

value: Bioneer WT

tag: growth phase

value: Log

tag: media

value: YES


title: IonXpress_018

value: giant cell carcinoma


title: IonXpress_017


title: IonXpress_014

value: Female

value: ALK rearrangement


title: WT6_HiC_2 reanalysis

first: Ryan

middle: D

last: Fine

address: 435 E 30th Street

department: Center for Human Genetics and Genomics

institute: NYU Langone

data_processing:
Heatplots appearing in the publication were produced entirely by python scripts from the Mirny Lab hiclib library publicly available at (http://mirnylab.bitbucket.org/hiclib/index.html).
Briefly, reads were mapped using the iterative mapping program, which uses Bowtie2 to map reads and iteratively trims unmapped reads to increase the total number of mapped reads.
Reads were then parsed into an hdf5 python data dictionary for storage and further analysis.  Mapped reads of the same strains were concatenated using the hiclib library's "Merge" function.
Mapped reads were then run through the fragment filtering program using the default parameters as follows: filterRsiteStart(offset=5), filterDuplicates, filterLarge, filterExtreme (cutH=0.005, cutL=0).
Finally, raw heat maps were futher filtered to remove diagonal reads and iteratively corrected using the heat map processing program.
Genome_build: sacCer3
Supplementary_files_format_and_content: All processed data files are mapped reads stored in .hdf5 format.  This is a highly compressed python data dictionary format that can be analyzed with the Mirnylab hiclib library available at (http://mirnylab.bitbucket.org/hiclib/index.html).

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown at 30C in YEP medium with 2% Glucose as the Carbon source.

extract_protocol:
DNA was extracted by pestle and mortar liquid Nitrogen grinding and SDS solubilization.  Triton X-100 was used to quench the SDS before O/N digestion with HindIII.  Digested DNA ends were then biotinylated and blunt-end ligated under dilute conditions.  Unligated biotinylated ends were removed with T4 DNA Polymerase and crosslinks were reversed.  The DNA was concentrated using a Zymogen Clean and Concentrate Kit-5 and sonicated in a Diagenode Bioruptor.
Biotinylated ligation junctions were capture by Streptavidin coupled Dynabeads and libraries were constructed on the beads using Nextera Mate Pair Reagents (Illumina).

treatment_protocol: Log-Phase cultures were cross-linked with 3% formaldehyde for 20 mins.  Cross-linking was quenched with a 2X formaldehyde volume of 2.5M Glycine.

tag: re

value: HindIII


title: IonXpress_012

value: Lung

value: BRAF p.D594V


title: IonXpress_010

value: surgical formalin-fixed paraffin-embedded tissue

value: Male

value: MET p.H997Y


title: WT_B


title: IonXpress_008

value: pulmonary blastoma


title: IonXpress_006

value: carcinosarcoma


title: IonXpress_004

value: PIK3CA p.H1047R


title: Biological replicate 3. Cells transduced with FOXP3fl

description:
Anderson RNAseq Analysis.xlsx
1702_20151124_FL.fastq


title: S8

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Count on FAST DB gene annotations (GenoSplice) and normalization using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes deseq normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2013_2 were also provide

source_name: Sam68 -/- spermatids

growth_protocol: C57BL/6 mice were maintained on a normal 12 hr light/dark cycle.

extract_protocol:
RNA was extracted and DNAse treated using the miRNeasy Mini Kit (Qiagen).
Library was prepared using the TruSeq Stranded mRNA kit protocol (Illumina technology) with an input total RNA of 1µg

treatment_protocol: Spermatocytes and spermatids were collected from 12-week-old male mice by gravimetric decantation (Sta-put).

value: spermatids


title: S7


title: IonXpress_002

value: pleomorphic carcinoma

value: EGFR Exon 19 deletion


title: 030U_MSCB-029

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

address: C. Baldiri Reixac, 4; Barcelona Science Park

institute: Centro Nacional de Análisis Genómico

data_processing:
Primary data analysis was carried out with the standard Illumina pipeline following the manufacturer's protocol. Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Sequenced reads were filtered for low-complexity or low-quality sequence.
MARS-Seq libraries were mapped as single-end reads with the GEMTools 1.7.0 RNA pipeline on the mouse  genome reference.
For MARS-seq samples, gene quantification was performed using UMI corrected transcript information to correct for amplification biases.
Genome_build: Assembly GRCm38. Gencode release M8.
Supplementary_files_format_and_content: Tab-separated values (.tsv) files containing gene expression values (rows) as UMI counts for each cell (columns).

extract_protocol:
CD19+ pre-B cells were isolated from the bone marrow of these mice using monoclonal antibody to CD19 (clone 1D3, BD Pharmingen #553784) and MACS sorting (Miltenyi Biotech). Cell purity was confirmed to be >98% CD19+ by FACS using an LSRII machine (BD).
To construct single cell libraries from polyA-tailed RNA, we applied massively parallel single-cell RNA sequencing (MARS-Seq; Jaitin et al., Science 2014).  This methodology generates paired-end reads where read 1 contains the transcript sequence and read 2 the cell and UMI barcodes. Briefly, single cells were FACS-sorted into 384-well plates, containing lysis buffer and reverse-transcription (RT) primers. The RT primers contained the single cell barcodes and unique molecular identifiers (UMIs) for subsequent de-multiplexing and correction for amplification biases, respectively.

value: pre-B cell

value: reprogramming

tag: induction

value: OSKM

tag: fate

value: iPSCs

tag: time point

value: day 6


title: S6

tag: cell type

tag: genotype


title: WT12_HiC_2 reanalysis

value: HindIII


title: S5


title: SH

source_name: Sam68 -/- spermatocytes

value: spermatocytes


title: WT6_HiC_1 reanalysis


title: SG


title: SF


title: IonXpress_003

value: Lung

value: spindle cell carcinoma

value: KRAS p.G13C


title: SE


title: IonXpress_005

value: surgical formalin-fixed paraffin-embedded tissue

value: Female


title: 030U_MSCB-024

tag: treatment


title: RNAseq_GPS2_LKO4

city: Huddinge

first: Rongrong

last: Fan

address: Hälsovägen 7c

institute: Karolinska Institutet

data_processing:
ChIP-seq raw files (fastq files) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Raw tag counts files are in txt format and contain the merged peaks, annotation and raw tag counts of the respective peaks in the indicated samples.  Bed files contain the genomic coordinates, tag counts, fold changes and p value of each peak.
RNA-seq raw files (fastq files) were aligned to GRCm38/mm10 version of the mouse reference genome, using HISAT2 with defalt settings. SAM files were converted to BAM files and then sorted using SAMtools. featureCounts were then used to count tag in all exons.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq subreads counts files are in txt format and contain gene id and tag counts  in the indicated samples.

source_name: Liver

extract_protocol:
Total RNA was extracted from snap-frozen liver tissues using Trizol Reagent and RNeasy RNA Mini Kit. RNA quality was assessed by Agilent TapeStation 2200.
PolyA RNA selection was performed using the Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer's protocol. RNA-seq libraries were prepared and sequenced on the Illumina HiSeq 2000.

treatment_protocol: GPS2 WT and LKO mice under normal chow diet

value: 8-12 week

tag: genotype/variation

tag: tissue

value: liver


title: WT12_HiC_1 reanalysis


title: scRNA data of peripheral blood mononuclear cells from healthy donor_sample 2_KC

city: Pittsburgh

first: Zhe

last: Sun

address: 130 DeSoto Street

institute: University of Pittsburgh

description: scRNA data from peripheral blood mononuclear cells

data_processing:
Standard 10X Genomics CellRanger pipeline;  R1 read is technical (16bp Chromium barcode and 10bp UMI), R2 is biological and I1 is 8bp sample index.
Genome_build: hg19
Supplementary_files_format_and_content: For each sample, there are one mtx file with filtered gene expressing UMI counts for each sample; a tsv file containing gene names; a tsv file with cell barcodes.

source_name: peripheral blood

extract_protocol:
Sorted cells were loaded into the Single Cell Chip and processed through the 10X controller for droplet generation, resulting in droplets containing a single cell and bead per droplet
Chromium Single Cell 3' RNA-seq libraries were prepared for sequencing using standard 10X Genomics protocols

tag: subject status

value: healthy donor

value: whole blood

value: peripheral blood mononuclear cells (PBMCs)


title: MM7866

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

data_processing:
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to mm10 whole genome using Tophat (Galaxy tool version 0.9).
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.0).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include transcript id and their FPKM values along with confidence intervals for each sample.

source_name: Smad2/3 cKO_uterus cells

growth_protocol: All mouse lines used in this study were maintained on a mixed C57BL/6/129S6/SvEv genetic background and handled under protocols approved by the Institutional Animal Care and Use Committee at Baylor College of Medicine. Smad2 and Smad3 double cKO mice were previously generated using the Cre-LoxP system, where loxP sites were introduced to flank exons 9 and 10 for Smad2 (Smad2flox/flox ) and exons 2 and 3 for Smad3 (Smad3flox/flox). To obtain tissue-specific deletion in this study, Smad2flox/flox and Smad3flox/flox females were mated to males expressing the progesterone receptor-cre (Pgr-cre) knock-in allele. Previous studies indicated that Pgr-cre is expressed postnatally in the ovary, uterus, oviduct, mammary gland and pituitary gland. Using this mating strategy Smad2flox/flox;Smad3flox/flox;Pgr-cre (herein called Smad2/3 cKO) mice were produced.

extract_protocol:
These libraries were prepared using Illumina mRNA Kit.
Total RNA samples were made into cDNA using the NuGEN Ovation® RNA‑Seq System V2 kit (using both random priming and poly d(T) priming). cDNA from the NuGEN kit were taken into the Illumina TruSeq DNA Sample Prep Kit for library construction. Completed libraries were sequenced on the Illumina HiSeq 2500.

tag: strain background

value: mixed C57BL/6/129S6/SvEv

value: Smad2/3 cKO

value: uterine epithelium

value: uterus cells


title: scRNA data of peripheral blood mononuclear cells from healthy donor_sample 4_TC


title: MM7863


title: Veh-4

city: San Diego

first: Tomohiro

last: Terasaka

address: 9500 Gilman DR LBR 332AA/BB

institute: UCSD

description:
SAMPLE 8
Replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label_protocol: Standard Illumina label protocol

extract_protocol: Cells were lysed with  lysis buffer (PEB buffer with 1% TritonX-100, 10µM NaF, 1mM Na3VO4, 10µM β-glycerophosphate, 1mM PMSF and 160IU/ml RNase OUT: Invitrogen™) and incubated for 30 minutes on ice with pipetting gently for lysis.  The cleared samples with Protein G Dynabeads and IgG were incubated with Protein G Dynabeads™ precoated with 5µg of ELAVL1 antibody (Santa Cruz, sc-5261).  Beads were collected on a magnetic stand and washed with NT-2 buffer 6 times and RNA extracted with TRIzol (Thermo-Fisher).

treatment_protocol: 30min Vehicle or GnRH treatment after serum starved for 16 hours.

tag: cell line

value: 30min Vehicle after serum starved for 16 hours

tag: molecule subtype

value: ELAVL1-RIP RNA


title: scRNA data of peripheral blood mononuclear cells from healthy donor_sample 1_CS


title: Veh-3

description:
SAMPLE 5
Replicate 3


title: Gn-3

description:
SAMPLE 6
Replicate 3

value: 30min GnRH treatment after serum starved for 16 hours


title: RNAseq_GPS2_LKO1

tag: age


title: Veh-2

description:
SAMPLE 4
Replicate 2


title: 1 CG, biological rep1

city: Naples

first: Annamaria

last: mancini

address: Via Medina, 40

department: DISMEB

institute: Università Parthenope

description: Gene expression data from  muscle biopsies derived from veteran football players (VPG) and of healthy age-matched untrained controls (CG)

hyb_protocol: The biotinylated DNA was hybridized to the Human Genechip HTA 2.0 Arrays (Affymetrix), containing more than 285.000 full length transcripts covering 44.700 coding genes and 22.800 non-coding genes selected from H. sapiens genome databases RefSeq, ENSEMBL and GenBank.

scan_protocol: Chips scanned on the Affymetrix Complete GeneChip® Instrument System, generating digitized image data (DAT) files.

data_processing: The data were analyzed with RMA from expression console software version 1.1.

source_name: Vastus lateralis muscle, untrained controls

label_protocol: Single strand cDNA is then purified and fragmented with a mixture of uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 (Affymetrix) in conjunction with incorporated dUTPs. DNA fragments are then terminally labeled by terminal deoxynucleotidyl transferase (Affymetrix) with biotin.

extract_protocol: Total RNA was extracted from the muscle biopsies using an miRNeasy ® kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Muscle biopsies were obtained under standardized conditions after an overnight fast between 7 and 10 a.m. from the vastus lateralis under local anaesthesia (1% Lidocaine, Amgros 742122, Copenhagen, Denmark) using the Bergstrom technique. The muscle sample (40 mg wet weight) was immediately frozen in liquid N2 and stored at -80°C until further analysis.

value: Vastus lateralis muscle


title: MM7860


title: 1 VPG, biological rep1

source_name: Vastus lateralis muscle, football players


title: 3 CG, biological rep1


title: 2 VPG, biological rep1


title: 3 VPG, biological rep1


title: Gn-2

description:
SAMPLE 3
Replicate 2


title: Gn-4

description:
SAMPLE 7
Replicate 4


title: RNAseq_GPS2_WT4

tag: strain


title: RNAseq_GPS2_LKO3


title: Control_SALL3_hs_i90

city: Setagaya

first: Takuya

last: Kuroda

address: 1-18-1 Kamiyoga

institute: National Institute of Health and Sciences

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings
Alignment information for each read is stored in the BAM format.
Since the 5 ́-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3 ́- ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp).
Since the 5 ́-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3 ́- ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp).
To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files also provide the peak metrics in the Active Motif analysis program. The generic term “Interval” is used to describe genomic regions with local enrichments in tag numbers. Intervals are defined by the chromosome number and a start and end coordinate. The two main peak callers used at Active Motif are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009). MACS is suitable to identify the binding sites of transcription factors that bind to discrete sites (often containing a consensus DNA sequence) as well as many active histone marks and methyl-C enriched regions, while SICER is used to study proteins that bind to extended regions in the genome (such as repressive histone marks or RNA polymerase II). Both methods look for significant enrichments in the ChIP/IP data file when compared to the Input data file (~ random background).

source_name: undifferentiated hiPSC (253G1)

growth_protocol: hiPSCs were maintained on Matrigel (Corning)-coated dishes in mTeSR1 medium (StemCell Technologies)

extract_protocol:
Active Motif Epigenetic Services performed ChIP assays. Cells fixed with 1% formaldehyde for 15 min were quenched with 0.125 M lysine, and then swollen in lysis buffer for 30 min on ice. Chromatin was isolated after sonication to shear the DNA to an average length of 300-500 bp.
ChIP and input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3' ends. Illumina adaptors were added and the library was size-selected (175-225 bp) on an agarose gel. The adaptor- ligated libraries were amplified for 18 cycles. The resulting DNA libraries were purified, quantified, and tested by qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions. DNA libraries then were sequenced on the Illumina Genome Analyzer II.

value: Human induced pluripotent stem cell (iPSC)

tag: chip antibody


title: RNAseq_GPS2_LKO2


title: RNAseq_GPS2_WT3


title: MM7042


title: 2 CG, biological rep1


title: RNAseq_GPS2_WT2


title: Gn-1

description:
SAMPLE 2
Replicate 1


title: Veh-1

description:
SAMPLE 1
Replicate 1


title: MM7857

source_name: control_uterus cells

value: control


title: scRNA data of peripheral blood mononuclear cells from healthy donor_sample 3_TB


title: MM7854


title: H3K27ac_ChIPseq_GPS2_LKO_1

extract_protocol:
Fresh mouse livers were crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 30 min, followed by 1% formaldehyde for 10 min at room temperature. Nuclei were isolated, sonicated and incubated with magnetic bead-antibody complexes.
ChIPed DNA was processed using Rubicon ThruPLEX DNA-seq kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.

treatment_protocol: All mice under normal chow diet

value: H3K27ac (Abcam, ab4729)


title: H3K27ac_ChIPseq_GPS2_LKO_2


title: MM7851


title: H3K27ac_ChIPseq_GPS2_WT_2


title: MM7048


title: H3K27ac_ChIPseq_GPS2_WT_1


title: WT_KK_rep1

city: State College

first: Santhosh

last: Girirajan

address: 205A Life Sciences Building

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

data_processing:
Trimmomatic (Bolger et al., 2014) v.0.36 was first used to trim reads as necessary, based on FastQC (bioinformatics.babraham.ac.uk/projects/fastqc) output.
TopHat2 v.2.1.1 (Kim et al., 2013) was used to align the raw sequencing data to the reference fly genome and transcriptome.
HTSeq-Count v.0.6.1 (Anders et al., 2015) was used to calculate raw read counts for each gene.
Genome_build: Dmel 6.08
Supplementary_files_format_and_content: Tab-delimited text files of raw read counts for all transcripts (two-three technical replicates per biological sample in each file).

organism: Drosophila melanogaster

source_name: Drosophila whole head

growth_protocol: Flies were reared with Elav-Gal4 driver at 25°C on conventional cornmeal-sucrose-dextrose-yeast medium.

extract_protocol:
F1 female progeny were collected in groups of 40-50, quickly frozen in liquid nitrogen, and stored at −80°C. For RNA extraction, heads were separated from the bodies by repetitive cycles of freezing in liquid nitrogen and vortexing. Total RNA was isolated using TRIZOL (Invitrogen, Carlsbad, CA, USA).
We prepared cDNA libraries using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA).

value: Drosophila whole head

tag: tissue-specific knockdown

value: neuronal

tag: RNAi driver

tag: human genotype

value: wild-type

tag: fly genotype

value: wild-type (VDRC KK)

tag: fly rnai line (vdrc)

tag: vdrc genetic background

value: KK


title: WT_KK_rep3


title: WT_GD_rep3

value: wild-type (VDRC GD)

value: wVDRC

value: GD


title: WT_KK_rep2


title: H3K4me3_ChIPseq_GPS2_LKO_2

value: 8-12 week

value: liver

value: H3K4me3 (Abcam, ab8580)


title: WT_GD_rep2


title: RNAseq_GPS2_WT1


title: H3K4me3_ChIPseq_GPS2_LKO_1


title: WT_GD_rep1


title: H3K4me3_ChIPseq_GPS2_WT_1


title: GPS2_ChIPseq_GPS2_LKO


title: PAK2_rep2

value: Pak


title: PAK2_rep3


title: PAK2_rep1


title: H3K4me3_ChIPseq_GPS2_WT_2


title: NCBP2_FBXO45_rep3


title: Control_Input_hs_i93

tag: cell type

value: none (input)


title: NCBP2_FBXO45_rep2


title: NCBP2_FBXO45_rep1


title: NCBP2_DLG1_rep2


title: NCBP2_DLG1_rep3


title: shPML.IFN-Pos.Input

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

institute: University of Glasgow

data_processing:
Analysis of the ChIP-seq data was performed by assessing read quality using FASTQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) and trimming reads using Trim-Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Single-end ChIP-seq reads were aligned to the human genome (hg19) using Bowtie2.
Additional quality and filtering steps were undertaken; demarking duplicate reads with Picard Tools (http://picard.sourceforge.net) as well as by retaining reads that map uniquely to single loci.
Peak calling was performed using USeq (v8.6.0) [124], with window and extension sizes of 200 bp and 150 bp, respectively, utilizing non-specific input DNA as a control.
Genome_build: hg19
Supplementary_files_format_and_content: bed files – peaks

growth_protocol: Native ChIP was performed for HIRA as described [69] using an equimolar mixture of mouse mAbs to HIRA (WC15, WC19, WC117, WC 119, a gift from Professor Peter Adams (Beatson Institute for Cancer Research, University of Glasgow) or mouse mAb to HA tag (Covance, MMS-101R) as a species and class-matched negative control.

extract_protocol:
Fragmented chromatin was incubated with antibodies to HIRA and preimmobilized on Dynabeads.
Libraries were prepared from 10–20 ng of ChIP or input DNA using New England Biolabs ChIP-seq kit according to the manufacturer’s instructions
Resulting libraries were sequenced on an Illumina GAIIx to yield ∼30 million to 40 million raw reads.

treatment_protocol: For HIRA ChIP, native ChIP was performed using benzonase endonuclease for chromatin solubilization and fragmentation. After quenching with glycine, the cells were harvested and sonicated to produce soluble chromatin with DNA fragments in the range of 300–500 base pairs.

value: Short-hairpin targeting PML

tag: treatment

value: Interferon Stimuated


title: shPML.IFN-Pos.ChIP

tag: genotype/variation

value: mouse mAbs to HIRA


title: Input_hs_i96

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings
Alignment information for each read is stored in the BAM format.
Since the 5 ́-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3 ́- ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp).
To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.
bigWig files also provide the peak metrics in the Active Motif analysis program. The generic term “Interval” is used to describe genomic regions with local enrichments in tag numbers. Intervals are defined by the chromosome number and a start and end coordinate. The two main peak callers used at Active Motif are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009). MACS is suitable to identify the binding sites of transcription factors that bind to discrete sites (often containing a consensus DNA sequence) as well as many active histone marks and methyl-C enriched regions, while SICER is used to study proteins that bind to extended regions in the genome (such as repressive histone marks or RNA polymerase II). Both methods look for significant enrichments in the ChIP/IP data file when compared to the Input data file (~ random background).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: Input DNA

extract_protocol:
Active Motif Epigenetic Services performed ChIP assays. Cells fixed with 1% formaldehyde for 15 min were quenched with 0.125 M lysine, and then swollen in lysis buffer for 30 min on ice. Chromatin was isolated after sonication to shear the DNA to an average length of 300-500 bp.
ChIP and input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3' ends. Illumina adaptors were added and the library was size-selected (175-225 bp) on an agarose gel. The adaptor- ligated libraries were amplified for 18 cycles. The resulting DNA libraries were purified, quantified, and tested by qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions.

value: Human induced pluripotent stem cell (iPSC)


title: NCBP2_DLG1_rep1

tag: tissue

value: Drosophila whole head


title: NCBP2_rep2

value: neuronal


title: NCBP2_rep3


title: NCBP2_rep1


title: shCntrl.IFN-Pos.Input

value: Short-hairpin control


title: benign T cell [3_CD4]

type: genomic

city: Hannover

first: Anke

middle: Katharina

last: Bergmann

address: OE 6300, Carl-Neuberg-Str. 1

department: human genetics

country: Germany

institute: Medical School Hannover

description:
benign T cell
3_CD4

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were scanned using the Illumina iScan using standard recommended Illumina scanner settings

data_processing: GenomeStudio software (version2011.1; Methylation Analysis Module version 1.9.0, Illumina)

label: cy3, cy5

source_name: benign

label_protocol: Standard Illumina Protocol

extract_protocol: Whole genomic DNA was extracted from frozen tumor cells containing samples and the benign controls using the Gentra purification kit (Qiagen, Hilden, Germany).

tag: disease state

value: benign


title: SALL3_KD_DNMT3B_hs_i85

source_name: 253G1_SALL3 shRNA_DNMT3B_ChIPSeq

tag: genotype

value: SALL3 KD


title: shCntrl.IFN-Pos.ChIP


title: shCntrl.IFN-Neg.Input

value: Control


title: Control_DNMT3B_hs_i70

source_name: 253G1_Control shRNA_DNMT3B_ChIPSeq


title: FBXO45_rep2

value: Fsn


title: benign T cell [2_CD4]

description:
benign T cell
2_CD4