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Sample GSM2400238 Query DataSets for GSM2400238
Status Public on Dec 07, 2016
Title total RNA-seq from mesenchymal stem cell of adipose (ENCLB555ATX)
Sample type SRA
 
Source name Homo sapiens mesenchymal of adipose stem cell female adult (37 years)
Organism Homo sapiens
Characteristics cell_type: mesenchymal stem cell of adipose
biomaterial_type: stem cell
description: Mesenchymal Stem Cells from subcutaneous adipose tissue (hMSC-AT) that were surgically ressected from the abdomen of a 37 year old caucasian female
biosample encode accession: ENCBS458ENC (SAMN06044611)
dev stage: adult
Sex: female
donor_id: ENCDO133AAA
age: 37 year
health state: negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV
passage number: 2
lab: Thomas Gingeras, CSHL
link: ENCBS458ENC at ENCODE; https://www.encodeproject.org/ENCBS458ENC/
link: Derived from ENCODE donor ENCDO133AAA; https://www.encodeproject.org/ENCDO133AAA/
link: certificate of analysis; https://www.encodeproject.org/documents/f33e88f2-0d8a-4cba-92d4-3cc529adc475/@@download/attachment/hMSCAT9061601.12_Gingeras_protocol.pdf
link: ENCODE dbxrefs Cellosaurus CVCL_Y509; http://web.expasy.org/cellosaurus/CVCL_Y509
link: ENCODE dbxrefs hMSC-AT; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=hMSC-AT
link: ENCODE dbxrefs hMSC-AT_9061601.12; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=hMSC-AT_9061601.12
link: PromoCell sample source; http://www.promocell.com/nc/products/human-stem-and-blood-cells/mesenchymal-stem-cells/human-mesenchymal-stem-cells-from-adipose-tissue-hmsc-at/?sword_list%5B%5D=hMSC-AT
Extracted molecule total RNA
Extraction protocol extraction method: see document
general protocol: https://www.encodeproject.org/documents/2eb5d790-fede-48ee-9a4c-22d93f349ed1/@@download/attachment/LID47098.pdf
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description https://www.encodeproject.org/experiments/ENCSR000CTZ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from mesenchymal adipose derived stem cells, hMSC-AT isolated from independent donors. They are stranded PE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CTZ
assay title: total RNA-seq
assembly: GRCh38, hg19
encode release date: 2012-06-21
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ATX
size range: >200
spikeins used: /references/ENCSR470JZL/
Data processing See GSM*_README.txt supplementary file linked below
 
Submission date Nov 22, 2016
Last update date May 15, 2019
Contact name ENCODE DCC
E-mail(s) encode-help@lists.stanford.edu
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
 
Platform ID GPL11154
Series (1)
GSE90271 total RNA-seq from mesenchymal stem cell of adipose (ENCSR000CTZ)
Relations
BioSample SAMN06044611
SRA SRX2370554
Named Annotation GSM2400238_ENCFF782EZH_plus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM2400238_ENCFF858FGO_plus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation GSM2400238_ENCFF074QEQ_minus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM2400238_ENCFF655ICD_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Supplementary file Size Download File type/resource
GSM2400238_ENCFF074QEQ_minus_strand_signal_of_all_reads_GRCh38.bigWig 372.9 Mb (ftp)(http) BIGWIG
GSM2400238_ENCFF123BAB_minus_strand_signal_of_all_reads_hg19.bigWig 368.4 Mb (ftp)(http) BIGWIG
GSM2400238_ENCFF196QCY_minus_strand_signal_of_unique_reads_hg19.bigWig 348.3 Mb (ftp)(http) BIGWIG
GSM2400238_ENCFF434KKM_transcript_quantifications_GRCh38.tsv.gz 7.9 Mb (ftp)(http) TSV
GSM2400238_ENCFF486SGY_gene_quantifications_GRCh38.tsv.gz 2.7 Mb (ftp)(http) TSV
GSM2400238_ENCFF567ZGA_transcript_quantifications_hg19.tsv.gz 7.8 Mb (ftp)(http) TSV
GSM2400238_ENCFF655ICD_minus_strand_signal_of_unique_reads_GRCh38.bigWig 346.9 Mb (ftp)(http) BIGWIG
GSM2400238_ENCFF675WXT_plus_strand_signal_of_all_reads_hg19.bigWig 388.0 Mb (ftp)(http) BIGWIG
GSM2400238_ENCFF782EZH_plus_strand_signal_of_all_reads_GRCh38.bigWig 392.3 Mb (ftp)(http) BIGWIG
GSM2400238_ENCFF858FGO_plus_strand_signal_of_unique_reads_GRCh38.bigWig 368.1 Mb (ftp)(http) BIGWIG
GSM2400238_ENCFF879TUK_gene_quantifications_hg19.tsv.gz 2.5 Mb (ftp)(http) TSV
GSM2400238_ENCFF951KZB_plus_strand_signal_of_unique_reads_hg19.bigWig 369.7 Mb (ftp)(http) BIGWIG
GSM2400238_ENCLB555ATX_README.txt.gz 1.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file
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