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Status |
Public on Feb 23, 2022 |
Title |
GSK126-treated cells rep2 |
Sample type |
SRA |
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|
Source name |
mouse B16F10 melanoma cells
|
Organism |
Mus musculus |
Characteristics |
treatment: GSK126 cell line: mouse B16F10 melanoma cells
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Treatment protocol |
B16F10 melanoma cells were treated with GSK126 at 10 μM
|
Growth protocol |
B16F10 melanoma cells were grown in Dulbecco's modified Eagle's medium (DMEM) or RPMI-1640 supplemented with 10% fetal bovine serum (FBS, GIBCO, CA, USA), 50 IU/mL penicillin, and 50 mg/mL streptomycin (Invitrogen, CA, USA). All cells were cultured at 37 ℃ in a humidified incubator in the presence of 5% CO2.
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Extracted molecule |
total RNA |
Extraction protocol |
RNA was isolated using RNeasy Mini Kit (Qiagen) RNA libraries were prepared for sequencing using standard Illumina protocols
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
Basecalls performed using CASAVA version 1.8 aligned to the GRCm38.p4 (mm10) genome assembly using Hisat2(version:2.0.4) Uniquely mapped reads with mapping quality >=20 were retrieved for downstream analysis. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: GRCm38.p4 (mm10) Supplementary_files_format_and_content: files include counts and RPKM values for each Sample
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|
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Submission date |
Dec 11, 2020 |
Last update date |
Feb 23, 2022 |
Contact name |
Qianqian Yin |
Organization name |
Peking University Third Hospital
|
Department |
Center of Basic Medical Research
|
Street address |
49 North Garden Road, Haidian District
|
City |
BEIJING |
ZIP/Postal code |
100191 |
Country |
China |
|
|
Platform ID |
GPL24247 |
Series (1) |
GSE163078 |
Dysregulated lipid metabolism blunts the sensitivity of B16F10 melanoma cells to EZH2 inhibitor |
|
Relations |
BioSample |
SAMN17062964 |
SRA |
SRX9675386 |