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Sample GSM2907098 Query DataSets for GSM2907098
Status Public on Jun 04, 2018
Title TSZ,Nec-1s_mRNA_Seq_rep2
Sample type SRA
 
Source name TSZ,Nec-1s, HT-29 cells
Organism Homo sapiens
Characteristics tissue: colon
cell line: colon adenocarcinoma cell line HT29
treatment: TNF-α, SM-164, zVAD,Nec-1s
Treatment protocol HT-29 were treated with DMSO, 10 ng/ml TNF-α (T), or the combination of 10 ng/ml TNF-α (T), 50 nM SM-164 (S) and 20 μM zVAD (Z) in the presence or absence of 10 μM Nec-1s for 8 h.
Growth protocol HT-29 cells were cultured in McCoy's 5A medium (GIBCO, Grand Island, NY, USA), supplemented with 10% FBS (Gibco), penicillin and streptomycin.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted and purified using RNAiso Plus (TaKaRa)
RNA libraries were prepared according to instructions of NEB Ultra RNA library prep kit (NEB, E7530L).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 550
 
Description DMSO_vs_TSZ_Nec-1s_DESeq.csv
TSZ_vs_TSZ_Nec-1s_DESeq.csv
Data processing For RNA-Seq comparison, Sequencing reads were mapped to hg38 with STAR by default parameter. The read counts for each genes were calculated by HTSeq-count. The count files were used as input to DESeq for differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: DESeq was used for calling differential expression.tab-delimited text files include normalized read counts,foldChange,pvalue
 
Submission date Dec 29, 2017
Last update date Jun 04, 2018
Contact name Zaijun Ma
E-mail(s) mazj@sioc.ac.cn
Organization name Chinese Academy Science
Street address Qiuyue Road 26
City Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL21697
Series (1)
GSE108621 Transcriptional profiling of HT-29 cells with different treatments
Relations
BioSample SAMN08275310
SRA SRX3520894

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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