|
| Status |
Public on Jun 23, 2022 |
| Title |
SUM159 SHP2 sh2 3 |
| Sample type |
RNA |
| |
|
| Source name |
SUM159 SHP2 sh2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM159
transfection: SHP2 miR2
|
| Treatment protocol |
Doxycycline, added the day after seeding the cells in cultures and refreshed every 2 days
|
| Growth protocol |
Cultures of SUM159 cells expressing inducible CTRL miR, SHP2 miR1 or SHP2 miR2 for 15 days. Cells were grown in Nutrient Mixture F-12 (Sigma #N6658-500mL), 5% FCS (Sigma #F7524), 1% Pen/Strep (Gibco #15140-122), Normocin (InvivoGen #ant-nr-1), Insulin 10µg/mL (Sigma #I5500-50mg), Hydrocortisone 500ng/mL (Sigma #H0888-1g).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After 15 days cultures, RNA was extracted with Qiagen RNeasy Kits to obtain total RNA from SUM159 cells in the presence or absence of SHP2
|
| Label |
biotin
|
| Label protocol |
100ng total RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix (GeneChip Whole Transcription Sense Target Labeling technical manual, Rev. 2).
|
| |
|
| Hybridization protocol |
Affymetrix Human Gene 1.0 st v1 GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.
|
| Scan protocol |
Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.
|
| Description |
SHP2miR2_3
|
| Data processing |
All gene arrays were processed in R (http://www.r-project.org/) using Bioconductor package oligo. Robust multi-array mean was performed using the following command: expr <- rma(read.celfiles(filenames)). Probes with the largest interquartile range were selected as representative for corresponding genes (using array annotation from Bioconductor package hugene10sttranscriptcluster.db).
|
| |
|
| Submission date |
Aug 13, 2021 |
| Last update date |
Jun 23, 2022 |
| Contact name |
Mohamed Bentires-Alj |
| E-mail(s) |
bentireslab.data@gmail.com
|
| Organization name |
University Hospital Basel
|
| Department |
DBM
|
| Lab |
THMR
|
| Street address |
Hebelstrasse 20
|
| City |
Basel |
| ZIP/Postal code |
4031 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE182033 |
SUM159 cells grown in 2D cultures in the presence or absence of SHP2 |
|
