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Sample GSM2858946 Query DataSets for GSM2858946
Status Public on Jan 09, 2018
Title MS42_0ng
Sample type SRA
 
Source name expandable arterial endothelial precursors (eAEPs)
Organism Homo sapiens
Characteristics cell type: mature endothelial progeny of eAEP line MS42, obtained by the downregulation of MYCN and SOX17 for four days
culture medium: EGM2 (Lonza) supplemented with 10 mM HEPES
tissue of origin: cord blood
Extracted molecule total RNA
Extraction protocol from RLT+ cell lysates using the RNeasy Plus Micro Kit (Qiagen) with genomic DNA elimination (gDNA Eliminator Spin Columns)
The following is an excerpt from Hou et al, Sci Rep. 2015; 5:9570, the manuscript that details the protocol employed. Poly-A-tailed mRNA is isolated from total RNA using oligo-dT beads. Purified mRNA is then fragmented with heat in fragmentation buffer. First strand cDNA is then synthesized using random hexamer oligos containing partial Illumina 3′ adaptor sequence. After RNA removal, a modified oligo containing partial Illumina's 5′ adaptor is then ligated to the 5′ of the single stranded cDNA. The library is then amplified by PCR using oligos that contain full Illumina adaptor sequences and our in-house index sequences.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description s049129_0049988
Data processing Basecalls/demuxxing performed using Illumina bcl2fastq v1.8.4.
Reads were filtered and trimmed for adapters and quality. Expression estimates were calculated using RSEM v1.2.3 with alignments by bowtie v0.12.9
Genome_build: hg19
Supplementary_files_format_and_content: gzipped tab-delimited file containing RSEM's calculated Expected Counts gene expression estimates.
 
Submission date Nov 16, 2017
Last update date May 15, 2019
Contact name David Vereide
E-mail(s) dvereide@morgridge.org
Organization name Morgridge Institute for Research
Department Regenerative Biology
Street address 330 North Orchard Street
City Madison
State/province WI
ZIP/Postal code 53715
Country USA
 
Platform ID GPL16791
Series (1)
GSE106991 RNA-seq analysis of human expandable arterial endothelial precursors (eAEPs), expandable mesenchymal precursors (eMPs), and controls
Relations
BioSample SAMN08032614
SRA SRX3398860

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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