|
| Status |
Public on Mar 10, 2017 |
| Title |
TS616_sparse_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
TS616 glioma cells sparse
|
| Organism |
Homo sapiens |
| Characteristics |
group: cancer
cell line: TS616
density: sparse
|
| Treatment protocol |
none
|
| Growth protocol |
Primary glioma cells were splated at either sparse plating density (5x104 cells/mL) or dense (3x105 cell/mL). NHAs were plated at either sparse plating density (3.5x105 cells/55cm2 dish) or dense (5.2x106/55cm2 dish) at a final conc of 5x104 cells/mL and 3x105 cell/mL. Cells were incubated for 5 days prior to RNA harvest.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Rneasy Mini
|
| Label |
biotin
|
| Label protocol |
Affymetrix GeneChip 3'IVT Express Kit, as in manufacturer's instructions.
|
| |
|
| Hybridization protocol |
10 ug of fragmented, labeled, antisense RNA, hyb'ed overnight at 45 degrees on PrimeView Affymetrix Human Gene Expression Array
|
| Scan protocol |
Scanned on Affymetrix GeneChip Scanner
|
| Description |
TS616 glioma cells sparse
|
| Data processing |
In Partek Genomics Suite, normalization was performed using RMA background correction with the following settings: adjust for GC content, quantile normalization, probeset summarization = mean. Batch removal was performed across experimental replicates.
|
| |
|
| Submission date |
Mar 11, 2016 |
| Last update date |
Mar 10, 2017 |
| Contact name |
Jayne M Stommel |
| E-mail(s) |
jayne.stommel@nih.gov
|
| Organization name |
National Cancer Institute
|
| Street address |
10 Center Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL15207 |
| Series (1) |
| GSE79097 |
Cell density effects on normal astrocytes and glioma cells |
|
