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| Status |
Public on Apr 27, 2024 |
| Title |
620p2_S14 |
| Sample type |
SRA |
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| Source name |
Colon
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| Organism |
Homo sapiens |
| Characteristics |
cell line: SW620
cell type: colorectal cancer cell line
drug treatment: palbociclib
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| Treatment protocol |
Colorectal cancer, breast cancer, stomach cell lines in condition with trametinib, afatinib, and palbocilib
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| Growth protocol |
SW48, SW620 human colorectal cancer cells, MKN45, NCI-N87 human stomach cells, BT-20, BT-474 human breast 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.
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
620p2_S14
GSE184731_samsung_exp_batch.tsv
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| 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
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| Submission date |
Mar 04, 2022 |
| Last update date |
Apr 27, 2024 |
| Contact name |
Jeong-Ryeol Gong |
| E-mail(s) |
jrgong@kaist.ac.kr
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| Organization name |
KAIST
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| Lab |
SBIE
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| Street address |
291, Daehak-ro
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| City |
Yuseong-gu |
| State/province |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE184731 |
A scalable derivative-free optimizer trained through learning to optimize approach to interpret drug response mechanism network |
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| Relations |
| BioSample |
SAMN26437467 |
| SRA |
SRX14371443 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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