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Sample GSM4201679 Query DataSets for GSM4201679
Status Public on Nov 02, 2020
Title MKN1_4h_EGF+Cet_1
Sample type SRA
 
Source name MKN1_EGF+Cet_4h
Organism Homo sapiens
Characteristics cell line: MKN1
cell type: Gastric cancer cell line
time: 4h
treat: EGF+Cet
Treatment protocol Cells were treated with EGF (5 ng/ml, Sigma Aldrich), cetuximab (Cet, 1 µg/ml, Merck), trastuzumab (Tra, 5 µg/ml, Roche) or afatinib (Afa, 0.5 µM, Biozol) for 4 h or 24 h
Growth protocol MKN1, MKN7 and NCI-N87 cells were grown in RPMI medium (10 % FCS, 0.5 % penicillin/streptomycin). Hs746T cells were grown in DMEM medium (10 % FCS, 0.5 % penicillin/streptomycin)
Extracted molecule polyA RNA
Extraction protocol Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). The RNA sequencing library was generated from 500ng total RNA using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Thermo Fisher)
NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs) according to manufacture´s protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description ID3_S3
Data processing fastq file generation by bcl2fastq2ConversionSoftwarev2.20 (Illumina)
raw FASTQ files were trimmed on base call quality and sequencing adapter contamination using Trim Galore! wrapper tool. Reads shorter than 20 bp were removed from FASTQ file.
Trimmed reads were aligned to the reference genome using open source short read aligner STAR (https://code.google.com/p/rna-star/) with default settings
Feature counts were determined using R package “Rsubread”.
Genome_build: hg38
Supplementary_files_format_and_content: Text file with raw counts
 
Submission date Dec 03, 2019
Last update date Nov 02, 2020
Contact name Robert Geffers
E-mail(s) robert.geffers@helmholtz-hzi.de
Phone +49 531-6181-3058
Organization name HCI - Helmholtz Centre for Infection Research
Department Dep. Molecular Bacteriology
Lab Genome Analytics
Street address Inhoffenstr. 7
City Braunschweig
ZIP/Postal code 38124
Country Germany
 
Platform ID GPL24676
Series (1)
GSE141352 Effects of EGF, cetuximab, trastuzumab and afatinib on gene expression in gastric cancer cell lines
Relations
BioSample SAMN13471344
SRA SRX7262258

Supplementary file Size Download File type/resource
GSM4201679_MKN1_4h_EGF+Cet_1.txt.gz 272.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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