|
| Status |
Public on Sep 09, 2020 |
| Title |
CF-U-2 |
| Sample type |
SRA |
| |
|
| Source name |
CFPAC-1-siUBE2C
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Pancreatic cancer cell line
cell line: CFPAC-1
genotype/variation: UBE2C knock-down
|
| Treatment protocol |
After transfecting CFPAC-1 cells with siUBE2C for 36 hours, three matched control samples
|
| Growth protocol |
Pancreatic cancer cell line were used for our research.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the samples using the TRIzol method. The total RNA extracted from the samples was tested by a NanoDrop 2000 and denaturing gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Sequenced raw reads were preprocessed by removing rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads with Seqtk (https:// github.com/lh3/seqtk).
Obtained clean reads were mapped to the hg38 reference genome with two mismatches by Hisat2 (version 2.0.4). After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM (fragments per kilobase of exon model per million mapped reads)values for known gene models.
The p-value significance threshold was set by the false discovery rate (FDR) strictly controlled using the Benjamini and Hochberg algorithm. The fold-changes were estimated according to the FPKM in each sample. Differentially expressed genes were identified using Cuffdiff with the following filter criteria: FDR≤0.05 and fold-change≥2.
Genome_build: GRCh38 (hg38)
|
| |
|
| Submission date |
Sep 10, 2019 |
| Last update date |
Sep 09, 2020 |
| Contact name |
wang xianxing |
| E-mail(s) |
wxx0819@outlook.com
|
| Organization name |
State Key Laboratory of Silkworm Genome Biology, the Institute of Sericulture and Systems Biology, Southwest University
|
| Street address |
No. 2 Tiansheng Rd., Beibei District
|
| City |
Chongqing |
| ZIP/Postal code |
400716 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE137172 |
RNA-seq analysis CFPAC-1-siNC and CFPAC-1-siUBE2C |
|
| Relations |
| BioSample |
SAMN12721637 |
| SRA |
SRX6824777 |
