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Sample GSM2400239 Query DataSets for GSM2400239
Status Public on Dec 07, 2016
Title total RNA-seq from mesenchymal stem cell of adipose (ENCLB555ALU)
Sample type SRA
 
Source name Homo sapiens mesenchymal of adipose stem cell female adult (42 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 42 year old caucasian female
biosample encode accession: ENCBS457ENC (SAMN06044610)
dev stage: adult
Sex: female
donor_id: ENCDO132AAA
age: 42 year
health state: negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV
passage number: 2
lab: Thomas Gingeras, CSHL
link: ENCBS457ENC at ENCODE; https://www.encodeproject.org/ENCBS457ENC/
link: Derived from ENCODE donor ENCDO132AAA; https://www.encodeproject.org/ENCDO132AAA/
link: certificate of analysis; https://www.encodeproject.org/documents/8e366b42-130b-4428-ab2a-ae15d0941031/@@download/attachment/hMSCAT0102604.12_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_0102604.12; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=hMSC-AT_0102604.12
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/51c8db2e-abda-4fb8-a489-190293cb85fa/@@download/attachment/LID47097.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: 1
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: ENCLB555ALU
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 SAMN06044610
SRA SRX2370555
Named Annotation GSM2400239_ENCFF871OMV_plus_strand_signal_of_unique_reads_GRCh38.bigWig
Named Annotation GSM2400239_ENCFF469NJZ_minus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM2400239_ENCFF297PYD_plus_strand_signal_of_all_reads_GRCh38.bigWig
Named Annotation GSM2400239_ENCFF449AFY_minus_strand_signal_of_unique_reads_GRCh38.bigWig

Supplementary file Size Download File type/resource
GSM2400239_ENCFF297PYD_plus_strand_signal_of_all_reads_GRCh38.bigWig 215.1 Mb (ftp)(http) BIGWIG
GSM2400239_ENCFF303ORC_transcript_quantifications_GRCh38.tsv.gz 7.8 Mb (ftp)(http) TSV
GSM2400239_ENCFF326SJI_plus_strand_signal_of_unique_reads_hg19.bigWig 201.8 Mb (ftp)(http) BIGWIG
GSM2400239_ENCFF449AFY_minus_strand_signal_of_unique_reads_GRCh38.bigWig 196.6 Mb (ftp)(http) BIGWIG
GSM2400239_ENCFF469NJZ_minus_strand_signal_of_all_reads_GRCh38.bigWig 210.0 Mb (ftp)(http) BIGWIG
GSM2400239_ENCFF517JRG_gene_quantifications_hg19.tsv.gz 2.5 Mb (ftp)(http) TSV
GSM2400239_ENCFF682MOO_minus_strand_signal_of_all_reads_hg19.bigWig 206.7 Mb (ftp)(http) BIGWIG
GSM2400239_ENCFF782AIE_plus_strand_signal_of_all_reads_hg19.bigWig 211.9 Mb (ftp)(http) BIGWIG
GSM2400239_ENCFF785NCI_minus_strand_signal_of_unique_reads_hg19.bigWig 195.5 Mb (ftp)(http) BIGWIG
GSM2400239_ENCFF834XIQ_transcript_quantifications_hg19.tsv.gz 7.7 Mb (ftp)(http) TSV
GSM2400239_ENCFF871OMV_plus_strand_signal_of_unique_reads_GRCh38.bigWig 199.2 Mb (ftp)(http) BIGWIG
GSM2400239_ENCFF964RZR_gene_quantifications_GRCh38.tsv.gz 2.6 Mb (ftp)(http) TSV
GSM2400239_ENCLB555ALU_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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