|
| Status |
Public on Jul 01, 2024 |
| Title |
HAP1, wild-type |
| Sample type |
RNA |
| |
|
| Source name |
HAP1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HAP1
cell line source: Near-haploid cell line derived from the KBM-7 cell line
tumor stage: Chronic myelogenous leukemia
genotype: Wild-type
treatment: untreated
trpm7 status: control
gender: Male
|
| Treatment protocol |
Samples 1-3: Wild-type, TRPM7 KO-01 and TRPM7 KO-04 HAP1 cells were cultured in IMDM medium supplemented with 10 mM MgCl2 (IMDM-Mg medium). At 50% confluence, the IMDM-Mg was exchanged to the regular IMDM medium and the cells were cultured for additional 24h. Sample 4: At 50% confluence, wild-type HAP1 cells were exposed to the fresh medium containing 30 µM NS8593 and cultured for an additional 24 h.
|
| Growth protocol |
HAP1 cells were maintained in 25 cm flasks with IMDM containing 10% fetal bovine serum, 100 U/ml penicillin and 100 µg/ml streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the GenElute mammalian total RNA purification kit (Sigma-Aldrich).
|
| Label |
Biotin
|
| Label protocol |
Biotinylated single-stranded DNA were prepared according to the standard Affymetrix protocol (Whole Transcript Expression arrays) from 100 ng total RNA using the WT terminal labeling kit
|
| |
|
| Hybridization protocol |
2.5 µg of fragmented and labeled ssDNA were hybridized for 16-18h hr at 45°C on GeneChip Human Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Description |
SAMPLE 1
Derived from a 39-year-old man with chronic myeloid leukemia in blast crisis
|
| Data processing |
The data were analyzed with Affymetrix Expression Console (version 1.4.0) using Affymetrix default analysis settings and RMA as processing algorithm.
|
| |
|
| Submission date |
May 13, 2022 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Vladimir Chubanov |
| E-mail(s) |
vladimir.chubanov@lrz.uni-muenchen.de
|
| Phone |
+4989218075740
|
| Organization name |
Ludwig-Maximilians-Universität München
|
| Department |
Walther-Straub-Institut
|
| Lab |
AG Chubanov
|
| Street address |
Goethestraße 33
|
| City |
Munich |
| State/province |
Non-US/Canada |
| ZIP/Postal code |
80336 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE203013 |
Whole-genome profiling of human HAP1 cells after the genetic and pharmacological inactivation of TRPM7 |
|
