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Sample GSM2858987 Query DataSets for GSM2858987
Status Public on Jan 09, 2018
Title MS58_Control_Day4
Sample type SRA
Source name expandable arterial endothelial precursors (eAEPs)
Organism Homo sapiens
Characteristics cell type: eAEP line MS58 cultured without exposure to PD173074, as a negative control for sample MS58_PD17_Day4
culture medium: EGM2 (Lonza) supplemented with 10 mM HEPES and 100 ng/mL doxycycline
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 3000
Description s060552_0088857
Data processing Basecalls/demuxxing performed using Illumina bcl2fastq2, v2.17.1.14
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
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 GPL21290
Series (1)
GSE106991 RNA-seq analysis of human expandable arterial endothelial precursors (eAEPs), expandable mesenchymal precursors (eMPs), and controls
BioSample SAMN08032631
SRA SRX3398901

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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