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| Status |
Public on Nov 02, 2020 |
| Title |
MKN1_4h_unb_3 |
| Sample type |
SRA |
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| Source name |
MKN1_untreated_4h
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MKN1
cell type: Gastric cancer cell line
time: 4h
treat: untreated
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| 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
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| 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)
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
ID105_S24
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| 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
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| Submission date |
Dec 03, 2019 |
| Last update date |
Nov 02, 2020 |
| Contact name |
Robert Geffers |
| E-mail(s) |
[email protected]
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| Phone |
+49 531-6181-3058
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| Organization name |
HCI - Helmholtz Centre for Infection Research
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| Department |
Dep. Molecular Bacteriology
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| Lab |
Genome Analytics
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| Street address |
Inhoffenstr. 7
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| City |
Braunschweig |
| ZIP/Postal code |
38124 |
| Country |
Germany |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE141352 |
Effects of EGF, cetuximab, trastuzumab and afatinib on gene expression in gastric cancer cell lines |
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| Relations |
| BioSample |
SAMN13471306 |
| SRA |
SRX7262272 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4201765_MKN1_4h_unb_3.txt.gz |
268.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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