|
| Status |
Public on Oct 28, 2023 |
| Title |
U87-MG cells, Normoxia 24h, replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
U87-MG GBM cells conditioned at 21% of O2 for 24h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U87-MG
tissue: Brain
tumor: Glioblastoma (GBM)
|
| Treatment protocol |
For experiments requiring hypoxia, cells were incubated in a humidified SCI-TIVE N-N Hypoxia workstation (Baker Ruskinn Technology) set at 5% CO2, 1% O2, and 37 °C for 24 h. For normoxic controls, cells were kept in a humidified 21% O2 and 5% CO2 incubator at 37 °C for the 24h period.
|
| Growth protocol |
U87-MG (ATCC, RRID: CVCL_0022) human high-grade glioma cells, authenticated by ATCC via STR, karyotyping, morphology, and cytochrome C oxidase I (COI) analysis, were routinely cultured in high-glucose DMEM (HyClone, GE) medium supplemented with 2 mmol/L L-glutamine (Sigma Aldrich, G7513), 100 U/ml Penicillin, 100 µg/ml Streptomycin (PEST; Sigma Aldrich, P0781), and with 10% (v/v) FBS (Sigma Aldrich, F7524) (full medium)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For profiling of U87-MG mRNA, cells were grown in serum-free DMEM and pre-conditioned to 24 h normoxia or hypoxia in triplicates. Total RNA was extracted with RNeasy mini kit (Qiagen).
|
| Label |
not provided
|
| Label protocol |
RNA was labelled with Modified Illumina TotalPrep-96 RNA Amplification Kit (Cat #4393543)
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization with Illumina Whole-Genome Gene Expression with IntelliHyb Seal 11226030 Rev C protocol
|
| Scan protocol |
Standard Illumina scanning protocol with Illumina iScan
|
| Description |
Sample_Probe_Summary.txt
Control_Probe_Summary.txt
200118400033_G
|
| Data processing |
Downstream background correction, normalization, and differential expression analysis were performed with limma r package followed by gene annotation with illuminaHumanv4.db r package. Detection pvalues were obtained with lumi r package (v2.52.0)
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| |
|
| Submission date |
Oct 19, 2023 |
| Last update date |
Oct 28, 2023 |
| Contact name |
Mattias Belting |
| E-mail(s) |
mattias.belting@med.lu.se
|
| Organization name |
Lund University
|
| Department |
Clinical Sciences Lund
|
| Lab |
Tumor Microenvironment
|
| Street address |
Barngatan
|
| City |
Lund |
| State/province |
Skåne |
| ZIP/Postal code |
SE-221 85 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE245800 |
Proteotranscriptomic decoding of the surface-endocytome in primary glioblastoma cells identifies potential target antigens in the hypoxic tumor niche [U87_mRNA_Norm_Hyp] |
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