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| Status |
Public on Jun 04, 2018 |
| Title |
TNF-α_mRNA_Seq_rep3 |
| Sample type |
SRA |
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| Source name |
TNF-α, HT-29 cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: colon
cell line: colon adenocarcinoma cell line HT29
treatment: TNF-α
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| 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.
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| 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.
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Description |
DMSO_vs_TNF-alpha_DESeq.csv
TNF-alpha_vs_TSZ_DESeq.csv
TNF-alpha_vs_TSZ_Nec-1s_DESeq.csv
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| 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
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| Submission date |
Dec 29, 2017 |
| Last update date |
Jun 04, 2018 |
| Contact name |
Zaijun Ma |
| E-mail(s) |
[email protected]
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| Organization name |
Chinese Academy Science
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| Street address |
Qiuyue Road 26
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL21697 |
| Series (1) |
| GSE108621 |
Transcriptional profiling of HT-29 cells with different treatments |
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| Relations |
| BioSample |
SAMN08275315 |
| SRA |
SRX3520889 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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