|
Status |
Public on Apr 27, 2024 |
Title |
SW48_D2 |
Sample type |
SRA |
|
|
Source name |
Colon
|
Organism |
Homo sapiens |
Characteristics |
cell line: SW48 cell type: colorectal cancer cell line drug treatment: trametinib
|
Treatment protocol |
Colorectal cancer cell lines in condition with trametinib
|
Growth protocol |
SW48, SW620 human colorectal cancer cells were cultured in DMEM supplemented with 10% FBS and antibiotics (100 units/mL of penicillin, 100 μg/ml of streptomycin, and 0.25 μg/ml of Fungizone; Life Technologies Corp.) at 37°C in 5% CO2.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols. RNA libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Illumina Casava1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using trimmomatic), then mapped to hg38 whole genome using STAR Read count extraction were performed using featureCounts Genome_build: hg38 Supplementary_files_format_and_content: tsv
|
|
|
Submission date |
Sep 24, 2021 |
Last update date |
Apr 27, 2024 |
Contact name |
Jeong-Ryeol Gong |
E-mail(s) |
jrgong@kaist.ac.kr
|
Organization name |
KAIST
|
Lab |
SBIE
|
Street address |
291, Daehak-ro
|
City |
Yuseong-gu |
State/province |
Daejeon |
ZIP/Postal code |
34141 |
Country |
South Korea |
|
|
Platform ID |
GPL18573 |
Series (1) |
GSE184731 |
A scalable derivative-free optimizer trained through learning to optimize approach to interpret drug response mechanism network |
|
Relations |
SRA |
SRX12326632 |
BioSample |
SAMN21593940 |