|
| Status |
Public on Jun 15, 2013 |
| Title |
B640_K562_SCR |
| Sample type |
RNA |
| |
|
| Source name |
K562 cell lines
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
transfected with: scrambled siRNA (control)
genotype/variation: control
|
| Treatment protocol |
HepG2 and K562 cell lines were stably transfected with plasmids containing siRNA designed to specifically knock down ADAR expression (ADAR KD). Different types of siRNA were tested, and the one yielding the best ADAR reduction was chosen. The same cells transected with a plasmid containing the scrambled siRNA (SCR) were used as a control.
|
| Growth protocol |
HepG2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Beit-Haemek, Israel)). K562 cells were cultured in RPMI 1640 medium (Beit-Haemek, Israel). Both media were supplemented with 10% fetal calf serum (FCS) (Beit-Haemek, Israel), 2 mM glutamine, 100 mg/ml streptomycin and 100 units/ml penicillin (Beit-Haemek, Israel), at 370c in a humidified incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified using TRIzol.
|
| Label |
biotin
|
| Label protocol |
Affymetrix biotin labeling_ wt kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Affymetrix wt labeling protocol as described in https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf
|
| Scan protocol |
Affymetrix wt scanning protocol as described in https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf
|
| Description |
B640_K562_SCR_LIN
|
| Data processing |
RMA
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
|
| |
|
| Submission date |
Jun 14, 2013 |
| Last update date |
Oct 25, 2022 |
| Contact name |
jasmine Jacob |
| E-mail(s) |
j-jacob@sheba.health.gov.il
|
| Phone |
0523790500
|
| Organization name |
Sheba Medical Center at Tel HaShomer
|
| Street address |
haChevel 33
|
| City |
Shoham |
| State/province |
-Select- |
| ZIP/Postal code |
60850 |
| Country |
Israel |
| |
|
| Platform ID |
GPL5175 |
| Series (2) |
| GSE47945 |
Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR) [expression] |
| GSE47998 |
Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR) |
|
