|
| Status |
Public on Jan 09, 2018 |
| Title |
MS51_100ng |
| Sample type |
SRA |
| |
|
| Source name |
expandable mesenchymal precursors (eMPs)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: eMP line MS51, maintained in culture with the ectopic expression of MYCN and SOX17
culture medium: EGM2 (Lonza) supplemented with 10 mM HEPES and 100 ng/mL doxycycline
tissue of origin: adult bone marrow
|
| 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 |
s053107_0062801
|
| 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 |
SAMN08032653 |
| SRA |
SRX3398879 |
