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| Status |
Public on Jan 18, 2023 |
| Title |
RNA-seq on RUES2 - 4DNEX2Y8O58V |
| Sample type |
SRA |
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| Source name |
biosource_summary: RUES2
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| Organism |
Homo sapiens |
| Characteristics |
cell_line: RUES2
tissue: stem cell
modifications_summary: None
Sex: female
treatments_summary: None
biosample_type: stem cells
biosource_vendor: WiCell.org
url: https://data.4dnucleome.org/biosamples/4DNBSV76CF3L/
life_stage: embryonic
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| Treatment protocol |
description: Protocol for passaging hPSCs and differentiating them to endothelial cells
download: https://data.4dnucleome.org/protocols/5390905f-7a27-4c82-816f-5a848c1ae21d/@@download/attachment/Alavattam-Mitzelfelt_endothelial-cells_protocol_passaging-differentiation.pdf
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| Extracted molecule |
total RNA |
| Extraction protocol |
description: Protocol for Illumina TruSeq Stranded Total RNA Human/Mouse/Rat
download: https://data.4dnucleome.org/protocols/bd3a9473-196d-4191-8e89-c49e05618907/@@download/attachment/truseq-stranded-total-rna-sample-prep-guide-15031048-e.pdf
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEX2Y8O58V
strandedness: reverse
submitted_by: Kris Alavattam
experiment_type: RNA-seq
contributing_labs: William Noble, UW
biosample_quantity: 1.0 ug
url: https://data.4dnucleome.org/experiments-seq/4DNEX2Y8O58V/
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| Data processing |
https://data.4dnucleome.org/resources/data-analysis/rnaseq-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/888eb1d5-7c87-4264-9bfa-625bff89c014/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIBI4ZOH4.fastq.gz, 4DNFIJT1NWFG.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (plus)
file_format: bw
file name: 4DNFI2WUB1RH.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/888eb1d5-7c87-4264-9bfa-625bff89c014/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIBI4ZOH4.fastq.gz, 4DNFIJT1NWFG.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (minus)
file_format: bw
file name: 4DNFISSA8YO4.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/888eb1d5-7c87-4264-9bfa-625bff89c014/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIBI4ZOH4.fastq.gz, 4DNFIJT1NWFG.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: gene expression
file_format: tsv
file name: 4DNFI2M1FK6T.tsv
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/888eb1d5-7c87-4264-9bfa-625bff89c014/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFIBI4ZOH4.fastq.gz, 4DNFIJT1NWFG.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: isoform expression
file_format: tsv
file name: 4DNFIAMNA6YD.tsv
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| Submission date |
Jan 06, 2023 |
| Last update date |
Jan 18, 2023 |
| Contact name |
4DN DCIC |
| E-mail(s) |
support@4dnucleome.org
|
| Organization name |
4D Nucleome - Data Coordination and Integration Center
|
| Street address |
10 Shattuck St
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE222305 |
4DNESNTQV8XL - Replicate experiments of RNA-seq on RUES2 |
| GSE222551 |
Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation |
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| Relations |
| BioSample |
SAMN32545280 |
| SRA |
SRX18991169 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6919592_4DNFI2M1FK6T.tsv.gz |
3.2 Mb |
(ftp)(http) |
TSV |
| GSM6919592_4DNFI2WUB1RH.bw |
107.0 Mb |
(ftp)(http) |
BW |
| GSM6919592_4DNFIAMNA6YD.tsv.gz |
9.9 Mb |
(ftp)(http) |
TSV |
| GSM6919592_4DNFISSA8YO4.bw |
103.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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