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Sample GSM5384476 Query DataSets for GSM5384476
Status Public on Apr 29, 2024
Title SK-HEP1 Non-Target Expressing cells (Replicate_2)
Sample type SRA
 
Source name SK-HEP1 cell lines
Organism Homo sapiens
Characteristics genotype/variation: Non-Target ALK Expressing control cells
cell line: SK-HEP1
Treatment protocol HepG2, SK-HEP1 and SNU449 cells stably expressing either Non-Targeting or ALK targeted inhibition were used for preparing the total RNA and to perfrom gene expression array.
Growth protocol HepG2 and SK-HEP1 cells stably expressing either Non-Targeting or ALK Targeted inhibition were grown in DMEM medium with 10% Fetal bovine serum and Penicilline and Streptomycin at 37 C under 5% CO2 condition. SNU449 cells were growth in RPMI-1640 with 10% FBS plus Penicilline and Streptomycin at the same condition as the other two cell lines.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description C8
Data processing The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample
 
Submission date Jun 15, 2021
Last update date Apr 29, 2024
Contact name Narendra Wajapeyee
E-mail(s) nwajapey@uab.edu
Phone 205-934-5331
Organization name University of Alabama at Birmingham
Department Department of Biochemistry and Molecular Genetics
Street address 720 20th Street South, Kaul 540A
City Birmingham
State/province AL
ZIP/Postal code 35233
Country USA
 
Platform ID GPL21290
Series (1)
GSE178211 ALK inhibitors suppress HCC and synergize with anti-PD-1 therapy and ABT-263 in preclinical models
Relations
BioSample SAMN19708246
SRA SRX11146093

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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