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Sample GSM3310590 Query DataSets for GSM3310590
Status Public on Jul 01, 2021
Title Gefitinib 2
Sample type SRA
 
Source name NSCLC cell line
Organism Homo sapiens
Characteristics cell type: PC9ER cells (PMID: 29212784)
treatment: Gefitinib 1microM
cell line: NSCLC
Treatment protocol Cells were treated for 72 h with DBZ (250 nM) (or DMSO as vehicle), then serum-starved overnight and treated with 1µM gefitinib for the final 6h of incubation.
Growth protocol Cells were cultured in RPMI1640 containing 10 % FCS in an atmosphere of humidified 5% CO2 at 37°C and passed twice a week.
Extracted molecule total RNA
Extraction protocol total RNA were extracted using the Rneasy kit from qiagen. RNA integrity was checked with the Agilent RNA 6000 nano kit
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description gefi.2
Data processing Trimming of first 15bp of each read to eliminate compositional bias
STAR alignment in 2 passes with default parameters against Ensembl human genome GRCh38
Read count extraction with HTSeq-count
Only "protein coding" genome features were kept for subsequent processing
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: notch-counts-all.txt
Supplementary_files_format_and_content: normalized-counts-coding.txt
 
Submission date Jul 30, 2018
Last update date Jul 01, 2021
Contact name Jacques Colinge
E-mail(s) jacques.colinge@inserm.fr
Organization name Inserm
Lab IRCM
Street address 208, avenue des Apothicaires
City Montpellier
ZIP/Postal code 34000
Country France
 
Platform ID GPL21290
Series (1)
GSE117846 Gefitinib treatment in human EGFR-driven-Gefitinib resistant tumoral cell line
Relations
BioSample SAMN09738025
SRA SRX4483273

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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