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| Status |
Public on May 01, 2020 |
| Title |
DMSO-rep2 |
| Sample type |
SRA |
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| Source name |
Colorectal cancer cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: HCT116
treatment: DMSO
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by using EASYspin RNA Mini Kit (Aidlab RN07).
RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat v2.1.1 with default parameters.
The gene expression level was calculated by Cufflinks (v 2.2.1).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.
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| Submission date |
Jan 30, 2019 |
| Last update date |
May 02, 2020 |
| Contact name |
Qinglan Li |
| E-mail(s) |
[email protected]
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| Organization name |
Wuhan University
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| Street address |
Room 5005, Life Science College, Wuhan University
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| City |
Wuhan City |
| State/province |
Hubei Province |
| ZIP/Postal code |
430062 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (2) |
| GSE125920 |
Genome-wide screen of transcription co-regulators identifies GLIS2 as a repressor for p53 target genes [RNA-seq] |
| GSE125928 |
Genome-wide screen of transcription co-regulators identifies GLIS2 as a repressor for p53 target genes |
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| Relations |
| BioSample |
SAMN10848601 |
| SRA |
SRX5312745 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3584971_DMSO-rep2-RNA.txt.gz |
183.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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