|
| Status |
Public on Nov 29, 2018 |
| Title |
MHCC-97H-SH-UCK2-B-1 |
| Sample type |
SRA |
| |
|
| Source name |
MHCC-97H liver cancer cells, SH-UCK2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MHCC-97H liver cancer cells
genotype: UCK2 knockdown
|
| Treatment protocol |
knocking down UCK2 in MHCC-97H cell
|
| Growth protocol |
knocking down UCK2 in MHCC-97H cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
U1
MHCC-97H-SH-UCK2-B-1
|
| Data processing |
Sequenced reads were aligned to hg38-ref-mRNA using tophat/2.0.14-gcc-4.8.5
Transcripts Per Kilobase of exon model per Million mapped reads (TPM) were calculated using Htseq
Different expression genes were calculated by DESeq (Anders et al,2010) edgeR package, |log2(FoldChange)| > 1 ,Pvalue < 0.05,"https://bioconductor.org/biocLite.R"
Genome_build: hg38
Supplementary_files_format_and_content: TPMs
|
| |
|
| Submission date |
Nov 28, 2018 |
| Last update date |
Nov 29, 2018 |
| Contact name |
Shanzhou Huang |
| E-mail(s) |
575932993@qq.com
|
| Organization name |
First Affiliated Hospital of Sun Yat-sen University
|
| Street address |
No. 58 Zhongshan Second Road
|
| City |
Guangzhou |
| ZIP/Postal code |
510080 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE123039 |
mRNA expression profile in MHCC-97H-SH-NC And MHCC-97H-SH-UCK2 liver cancer cells |
|
| Relations |
| BioSample |
SAMN10492298 |
| SRA |
SRX5073862 |
