|
| Status |
Public on Jan 15, 2022 |
| Title |
24h_5mgYFSJ_75uMgefitinib [Y5_G75_1] |
| Sample type |
SRA |
| |
|
| Source name |
H1975_24h_5mgYFSJ_75uMgefitinib
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1975
tumor type: non-small cell lung cancer
treatment: 24h_5mgYFSJ_75uMgefitinib
|
| Treatment protocol |
Drug treatments were designed as follows: CKI in 2 doses (1.0 mg/mL and 2.0 mg/mL), YFSJ in 2 doses (2.5 mg/ml and 5 mg/ml) and gefitinib in two doses (50 uM and 75 uM); Two doses of CKI combined with two doses of gefitinib; Two doses of YFSJ combined with two doses of gefitinib.
|
| Growth protocol |
Human EGFR mutated NSCLC cell line H1975 was purchased from ATCC (HTB-22™, VA, USA) and were cultured in RPMI-1640 medium (Thermo Fisher Scientifc, MA, USA) supplemented with 10% fetal bovine serum (Thermo Fisher Scientifc, MA, USA) at 37°C with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using PureLink™ RNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
RNA libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, Massachusetts, USA) according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
unstranded paired-end RNA-seq
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Low quality and adaptor sequences in raw reads were trimmed using Trim_galore (v0.4.2, Babraham Bioinformatics) with the following parameters: --stringency 6 --paired. Then cleaned reads were aligned to the reference genome (hg19, UCSC) using STAR_2.5.3a with the following parameters: --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --seedSearchStartLmax 30 –quantMode GeneCounts
Differential expression analysis was performed with edgeR and DE genes were selected with a False Discovery Rate (FDR) < 0.05.
Genome_build: hg19, UCSC
Supplementary_files_format_and_content: Tab delimited matrix showing raw counts of refGenes
|
| |
|
| Submission date |
Jan 31, 2019 |
| Last update date |
Jan 15, 2022 |
| Contact name |
Lizhu Lin |
| E-mail(s) |
lizhulin05@gmail.com
|
| Organization name |
Guangzhou University of Chinese Medicine
|
| Street address |
12 Jichang Street, Baiyun District
|
| City |
Guangzhou |
| ZIP/Postal code |
510000 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE125933 |
Compound kushen injection and YFSJ reduce gefitinib resistance in gefitinib resistant lung cancer cell lines |
|
| Relations |
| BioSample |
SAMN10850800 |
| SRA |
SRX5314333 |
