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Sample GSM8294307 Query DataSets for GSM8294307
Status Public on Jun 01, 2024
Title GBM15_GSK_DF3
Sample type RNA
 
Source name primary cell culture
Organism Homo sapiens
Characteristics cell type: patient derived glioblastoma cells (GBM15)
treatment: GSK126
Treatment protocol Tumor cell cultures were treated witht the substances (GSK126, Abemaciclib, combination or DMSO as control) for 2 x 72 hours, with a complete medium change after 72 hours.
Growth protocol Tumor pieces were homogenized using a cell strainer (100 μm) and seeded in 6-well plates containing DMEM/Hams F12 130 medium, supplemented with 20% FCS, 6 mM L-glutamine, and 1% penicillin/streptomycin and incubated at 37°C in a humidified atmosphere of 5% CO2. Continually growing cell cultures were serially passaged and regularly stored at low passages.
Extracted molecule total RNA
Extraction protocol Spheroids were grown in AggreWell™400 plates, treated as described, harvested and pelleted by centrifugation. The total RNA was isolated using Rneasy Kit (Qiagen), including column-based DNase I digestion
Label biotin
Label protocol 100 ng total RNA was labeled using WT-labeling protocol (Affymetrix/Thermofisher).
 
Hybridization protocol Hybridization was performed for 16 hours at 45 degrees celsius using the GeneChip Hybridization Oven 645 (Affymetrix, St. Clara, USA).
Scan protocol Scanning was done using the GeneChip Scanner 3000/7G (Affymetrix, St. Clara, USA) with 0.7 micron resolution.
Description Gene expression data of glioblastoma cells treated with GSK126
M_GBM15_GSK_DF3
Data processing The gene expression datasets were filtered with an adjusted p-value < 0.01 and a FC ± > 2 to identify differentially expressed genes (DEGs)
probe group file: Clariom_S_Human.r1.pgf and meta-probeset file: Clariom_S_Human.r1.na36.hg38.a1.transcript.csv were used.
Transcriptome Analysis Console 4.0.3.14.
 
Submission date May 29, 2024
Last update date Jun 01, 2024
Contact name Dirk Koczan
E-mail(s) dirk.koczan@med.uni-rostock.de
Phone +493814945885
Organization name University of Rostock
Department Institute for Immunology
Street address Schillingallee 70
City Rostock
ZIP/Postal code 18057
Country Germany
 
Platform ID GPL23159
Series (1)
GSE268563 Combined inhibition of EZH2 and CDK4/6 perturbs endoplasmic reticulum-mitochondrial 1 homeostasis and increases antitumor activity against glioblastoma

Data table header descriptions
ID_REF
VALUE log2 values generated by SST-RMA normalization

Data table
ID_REF VALUE
TC0100006437.hg.1 3.51
TC0100006476.hg.1 3.84
TC0100006479.hg.1 5.03
TC0100006480.hg.1 5.3
TC0100006483.hg.1 4.46
TC0100006486.hg.1 6.65
TC0100006490.hg.1 3.77
TC0100006492.hg.1 3.8
TC0100006494.hg.1 6.71
TC0100006497.hg.1 3.54
TC0100006499.hg.1 5.31
TC0100006501.hg.1 5.73
TC0100006502.hg.1 4.35
TC0100006514.hg.1 3.38
TC0100006516.hg.1 4.14
TC0100006517.hg.1 3.66
TC0100006524.hg.1 5.92
TC0100006540.hg.1 4.38
TC0100006548.hg.1 3.62
TC0100006550.hg.1 3.77

Total number of rows: 21448

Table truncated, full table size 485 Kbytes.




Supplementary file Size Download File type/resource
GSM8294307_M_GBM15_GSK_DF3_Clariom_S_Human_.CEL.gz 967.9 Kb (ftp)(http) CEL
GSM8294307_M_GBM15_GSK_DF3_Clariom_S_Human_.sst-rma-gene-full.chp.gz 270.7 Kb (ftp)(http) CHP

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