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| Status |
Public on Oct 31, 2022 |
| Title |
TRP_1 |
| Sample type |
SRA |
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| Source name |
colorectum
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| Organism |
Homo sapiens |
| Characteristics |
tissue: colorectum
cell line: Pericyte
cell type: Tumor pericyte
treatment: overexpression of TRPM8
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol Reagent (Servicebio, Wuhan, China) at a ratio of 106 cells per mL of reagent according to the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
The index of the reference genome was built using Hisat2 (v2.0.5), and the paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
For the quantification of gene expression level, FeatureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Analysis of differential expression was performed using the DESeq2 R package (1.16.1)
The differentially expressed mRNAs and genes were selected with statistical significance (P < 0.05) by R package-edgeR.
Assembly: hg18
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Oct 28, 2022 |
| Last update date |
Oct 31, 2022 |
| Contact name |
Qun Miao |
| E-mail(s) |
[email protected]
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| Organization name |
Jinan University
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| Street address |
Huangpu avenue
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| City |
Guang Zhou |
| ZIP/Postal code |
510000 |
| Country |
China |
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| Platform ID |
GPL10999 |
| Series (1) |
| GSE216780 |
Effect of overexpression of TRPM8 on gene expression of tumor pericytes |
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| Relations |
| BioSample |
SAMN31505786 |
| SRA |
SRX18059601 |
| 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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