|
| Status |
Public on Apr 30, 2024 |
| Title |
H69M cells, cytoplasmic RNA, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
H69M
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H69M
cell type: SCLC cells
genotype: WT
treatment: normal
fraction: cytoplasmic RNA
|
| Growth protocol |
H69, H196 and H69M cells were maintained in RPMI 1640 supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37°C
|
| Extracted molecule |
cytoplasmic RNA |
| Extraction protocol |
Polysome-bound RNA were extracted from sucrose based fraction after polysome profiling using TRIzol LS (ThermoFisher) according to manufacturer’s protocol and were quantified by Nanodrop microvolume spectrophotometers (Thermo Fisher Scientific). Cytoplasmic RNA were extracted from cell lysate in hypotonic buffer (5 mM Tris-HCl pH 7.5, 2.5 mM MgCl2, 1.5 mM KCl, 100 μg.ml-1 cycloheximide, 2 mM DTT, 100 U/ml RNase inhibitor (Promega), 0.5% sodium deoxycholate, 0.5% Triton X-100) using TRIzol LS and were quantified by Nanodrop as well.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
H69M_input_3
H69_H69M_cyto_count.txt
|
| Data processing |
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR
Count data were generated using HTSeq
Assembly: hg38
Supplementary files format and content: tab delimited text file includes read counts for each sample
|
| |
|
| Submission date |
Mar 27, 2024 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Haoning Peng |
| Organization name |
West China Hospital, Sichuan University
|
| Department |
Department of Thoracic Surgery
|
| Lab |
Institute of Thoracic Oncology
|
| Street address |
No.37 Guoxue Alley, Wuhou District
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE262593 |
EIF6 conditions drug-tolerant persister-like transdifferentiation in small cell lung carcinoma (SCLC cell lines) |
| GSE262597 |
EIF6 conditions drug-tolerant persister-like transdifferentiation in small cell lung carcinoma |
|
| Relations |
| BioSample |
SAMN40629299 |
| SRA |
SRX24106088 |
