|
| Status |
Public on Aug 03, 2019 |
| Title |
ZH487_shSOX10_3_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
gliomasphere patient-derived cell line
|
| Organism |
Homo sapiens |
| Characteristics |
subtype: RTK_I-like glioblastoma cell line
gender: male
treatment: shSOX10
|
| Treatment protocol |
Inducible SOX10 knockdown cells were established by infecting cells with pLKO-Tet-On non-targeting (nt) shRNA and pLKO-Tet-On SOX10 shRNA (TRCN0000018988) lentiviral particles and puromycin selection (1 µg/ml) for 7 days. shRNA expression was induced by adding 0.1 µg/ml doxycycline to the medium for at least 7 days.
|
| Growth protocol |
The human glioblastoma cell line LN229 was obtained from ATCC (cat. CRL-2611). Cells were cultured in DMEM containing 1 g/L glucose (D5921, Sigma) supplemented with 10% tetracycline-free fetal bovine serum (Clontech), 1% penicillin and streptomycin (P/S) mix, and glutamine (0.5 mM). The ZH487 glioblastoma spheroid primary cells were originally established at the University of Zurich Hospital. ZH487 cells were cultured in Neurobasal medium (Cat. 12348017, NBM) supplemented with 2% B27 (cat. 12587010, retinoic acid-free, Invitrogen), EGF (20 ng/ml, AF-100-15, Peprotech), FGF (20 ng/ml, cat. 100-18B, Peprotech) and glutamine (0.5 mM). DNA methylation array (Illumina EPIC) analysis classified the ZH487 primary tumour and derived cell line as part of the RTK I subtype. All cell lines were cultured under 10% CO2 at 37℃ with humidity. Cell identities were verified by the Multiplex human Cell line Authentication Test (MCA). Cells were also tested for mycoplasma contamination with the Multiplex cell test (Multiplexion GmbH, Friedrichshafen, Germany).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Microkit (Qiagen) according to the manufacturer's standard protocol.
|
| Label |
biotin
|
| Label protocol |
Affymetrix standard protocol
|
| |
|
| Hybridization protocol |
Affymetrix standard protocol
|
| Scan protocol |
Affymetrix standard protocol
|
| Data processing |
Raw microarray .CEL files were read into R (3.4.3) and normalized using the ‘gcrma’ R package (2.50.0). Probes without an annotated gene were removed from the analysis, leaving 41941 annotated probes. R annotation package versions: hgu133plus2probe_2.18.0, hgu133plus2cdf_2.18.0, hgu133plus2.db_3.2.3
|
| |
|
| Submission date |
Jul 31, 2019 |
| Last update date |
Aug 04, 2019 |
| Contact name |
Bernhard Radlwimmer |
| E-mail(s) |
b.radlwimmer@dkfz-heidelberg.de
|
| Organization name |
Deutsches Krebsforschungszentrum / German National Cancer Research Centre
|
| Department |
Department of Molecular Genetics
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE121718 |
Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype - cell line gene expression microarray data |
| GSE121723 |
Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype |
|
