|
| Status |
Public on Nov 07, 2007 |
| Title |
hMSC_Donor5064L_Passage2_Day7 |
| Sample type |
RNA |
| |
|
| Source name |
Passage 2 human MSC grown for 7 days
|
| Organism |
Homo sapiens |
| Characteristics |
Recovered passage 1 human Multipotent Stromal Cells (MSCs) donor 220R plated at 50 cells/cm2 in complete culture medium (CCM: alpha-MEM, 17% FBS, pen-strep, 2 mM L-glutamine) and grown for 7 days.
|
| Biomaterial provider |
Tulane University Center for Gene Therapy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAqueous Kit (Ambion)
|
| Label |
Biotin
|
| Label protocol |
5 μg of total RNA was used to synthesize double-stranded cDNA (Superscript Choice System/GIBCO BRL Life Technologies). After synthesis, the double-stranded cDNA was purified by phenol/chloroform extraction (Phase Lock Gel, Eppendorf Scientific) and concentrated by ethanol precipitation. In vitro transcription was used to produce biotin-labeled cRNA (BioArray HighYield RNA Transcription Labeling Kit, Enzo Diagnostics). The biotinylated cRNA was then cleaned (RNAeasy Mini Kit Qiagen) and fragmented with metal induced hydrolysis.
|
| |
|
| Hybridization protocol |
The biotinylated and fragmented cRNA was hybridized on the HG-U133 Plus 2.0 microarray chips (Affymetrix). After washing, microarray chip was stained with streptavidin-phycoerythrin (Molecular Probes), amplified with biotinylated anti-streptavidin (Vector Laboratories) and stained with streptavidin-phycoerythrin.
|
| Scan protocol |
The microarray was scanned for fluorescence (GeneChip Scanner 3000, Affymetrix) using the GeneChip Operating software 1.0 (GCOS, Affymetrix).
|
| Description |
Scale factor: 24.8
Background: 92.1
Noise (RawQ): 2.90
%Present: 40.8
|
| Data processing |
Data was scaled to the target value of 2500 with GCOS that also recorded intensities for perfect match (PM) and mismatch (MM) oligonucleotides, and determined whether genes were present (P), marginal (M) or absent (A).
|
| |
|
| Submission date |
Nov 05, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Joni Ylostalo |
| E-mail(s) |
[email protected]
|
| Organization name |
Texas A&M
|
| Department |
Institute for Regenerative Medicine
|
| Street address |
5701 Airport Rd., Module C
|
| City |
Temple |
| State/province |
TX |
| ZIP/Postal code |
76502 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE9520 |
Transcriptome changes in hMSCs during expansion |
|
| Relations |
| Reanalyzed by |
GSE20125 |
| Reanalyzed by |
GSE64985 |
| Reanalyzed by |
GSE119087 |
