 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 17, 2024 |
| Title |
A498 parental replicate 3 [4_veh3] |
| Sample type |
SRA |
| |
|
| Source name |
786-O
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 786-O
cell type: advanced clear cell renal cell carcinoma (ccRCC)
drug resistance: none
treatment: none
batch: N122415
|
| Growth protocol |
Two human advanced renal cell carcinoma cell lines A498 and 786-O were purchased from ATCC. They were cultured in DMEM growth media containing 25mM glucose and glutamine supplemented with 10% heat-inactivated foetal bovine serum and 1% penicillin-streptomycin at 37⁰C in a humidified atmosphere of 5% CO2. Sunitinib (SU11248) malate was purchased from Selleckchem. For the development of sunitinib-resistant cells, parental cells were exposed to increasing concentrations of sunitinib. In brief, the RCC cell lines were treated with varying concentrations of sunitinib (0, 1, 2, 3, 4, 5, 7, 10, 20, and 50μM). With the passage of time of every four days, it has been observed that A498 cells showed stable growth and eventually became confluent at a concentration of 2µM, while 798-O cells showed stable growth to confluence at a concentration of 4µM. It can be assumed that cells that grew to confluence had developed stable sunitinib-resistance after a period of four months or >20 passages. The cells were constantly in sunitinib containing medium throughout the selection process.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from cultured cells according to the QIAGEN RNeasy mini kit protocol.
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Sample prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base calling with bcl2fastq2 version 2.19.0
Sequencing reads were trimmed using trimmomatic (version 0.36.6; parameters: SLIDINGWINDOW:4:20 MINLEN:50)
Trimmed reads were aligned to GRCh38/hg38 using HISAT2 (version 2.1.0; parameters: --n-ceil L,0.0,0.15 --mp 6,2 --no-softclip --np 1 --rdg 5,3 --rfg 5,3 --sp 2,1 --score-min L,0.0,-0.2 --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --min-intronlen 20 --max-intronlen 500000).
Gene counts were estimated using featureCounts (version 1.6.3; parameters: -s 1 -t 'exon' -g 'gene_id' -J -Q 12 --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0) with GENCODE gene annotation (GENCODE version 33; Ensembl version 99).
Assembly: hg38
Supplementary files format and content: tab-delimited text file include gene counts for each Sample
|
| |
|
| Submission date |
Oct 25, 2022 |
| Last update date |
Apr 17, 2024 |
| Contact name |
Alexis L Norris |
| E-mail(s) |
alexis.norris@fda.hhs.gov
|
| Organization name |
US FDA
|
| Street address |
7500 Standish Place
|
| City |
Rockville |
| State/province |
MD |
| ZIP/Postal code |
20855 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE216494 |
Impact of sunitinib resistance on clear cell renal cell carcinoma therapeutic sensitivity in vitro |
|
| Relations |
| BioSample |
SAMN31437012 |
| SRA |
SRX18013997 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
