|
| Status |
Public on Mar 01, 2022 |
| Title |
KRIB-WB |
| Sample type |
RNA |
| |
|
| Source name |
KRIB cells, control
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KRIB
|
| Treatment protocol |
KRIB cells were transduced with GIPZ lentivirus for shRNA expression and isolated by sorting for GFP expression, as previously described (PMID: 28698375).
|
| Growth protocol |
KRIB cells were maintained at 37 °C in 5% CO2 in DMEM with 10% FBS and 10 mg/mL penicillin-streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of harvested cells was extracted using a mirVana miRNA Isolation Kit (Invitrogen). RNA integrity was determined using the 2100 Bioanalyzer and RNA 6000 Nano Kit (Agilent Technologies).
|
| Label |
biotin
|
| Label protocol |
100 nanograms of total RNA was amplified and biotin-labeled through a two-round Eberwine procedure using MessageAmp II and Illumina TotalPrep RNA amplification kits (Ambion).
|
| |
|
| Hybridization protocol |
Amplified cRNA was hybridized to Illumina human HT12v4.0 whole-transcriptome arrays.
|
| Scan protocol |
As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.
|
| Description |
replicate 2
|
| Data processing |
The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated by starting from the non-normalized data, then modified by methods previously described (PMID: 20805315). In brief, probe-level values were quantile-normalized and adjusted by a model-based background correction method (PMID: 18450815). After this, the only probe results that are kept for the normalized matrix are those for reliable probes (PMID: 19923232) in which the detection p value is <0.05, in at least 25% of the samples.
|
| |
|
| Submission date |
Dec 19, 2021 |
| Last update date |
Mar 02, 2022 |
| Contact name |
Richard Eric Davis |
| E-mail(s) |
redavis1@mdanderson.org
|
| Phone |
4437456831
|
| Organization name |
MD Anderson Cancer Center
|
| Street address |
7455 Fannin Street
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE191215 |
IL11RA signaling and EZH2 activity in osteosarcoma |
|
