|
| Status |
Public on Oct 06, 2023 |
| Title |
M230_DMSO_expt_2 |
| Sample type |
SRA |
| |
|
| Source name |
M230
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: M230
cell type: Melanoma cell line
treatment: DMSO
|
| Treatment protocol |
Cells were plated a day ahead of treatment with DMSO (control), recombinant Human IFNg (Peprotech, 100 U/ml) and/or Ulixertinib (SelleckChem, 6 µM). Cells were harvested 24 hours later and total RNA was prepared for RNAseq.
|
| Growth protocol |
M230 and M238 cells were cultured in RPMI supplemented with 10% fetal bovine serum (FBS), 10 mM HEPES, and antibiotic and antimycotic agents. Cultured cells were grown in a 37C incubator with 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cell pellets were solubilized in TRIzol and the RNA containing aqueous phase obtained after chloroform addition was applied to RNeasy (Qiagen) columns. Total RNA was eluted in 50 µl UltraPure water (Invitrogen) after following standard RNeasy kit protocol.
Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit with RiboErase Kit following the recommended kit protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
m230_d_2
|
| Data processing |
Sequencing was performed on Illumina HiSeq 3000 for Single-End 1 x 50 bp run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.
Raw FASTQ files were aligned to the GRCh38 genome using HISAT2 version 2.1.0 using default parameters.
Gene expression was quantified by HTseq-counts version 0.6.1p1 and Stringtie version v1.3.3b, outputting counts and FPKM (Fragments Per Kilobase per Million) respectively.
Assembly: GRCh38
Supplementary files format and content: Tab delimited file containing raw counts for all samples
Supplementary files format and content: Tab delimited file containing FPKM values for all samples
|
| |
|
| Submission date |
Jun 20, 2023 |
| Last update date |
Oct 06, 2023 |
| Contact name |
Ameya Champhekar |
| E-mail(s) |
achamphekar@mednet.ucla.edu
|
| Organization name |
University of California, Los Angeles
|
| Department |
Medicine, HemOnc Division
|
| Street address |
700 Tiverton Ave, 11-272 Factor Bldg
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095-1678 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE235235 |
ERK signaling plays an essential role in the IFNg-mediated apoptosis of melanoma cells. [RNAseq] |
| GSE235238 |
ERK signaling plays an essential role in the IFNg-mediated apoptosis of melanoma cells. |
|
| Relations |
| BioSample |
SAMN35801014 |
| SRA |
SRX20726246 |
