|
| Status |
Public on Oct 23, 2018 |
| Title |
U6_1 |
| Sample type |
SRA |
| |
|
| Source name |
CRC cell line SW480
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: colorectal cancer cell
cell line: SW480
shRNA: control vehicle cells
|
| Treatment protocol |
SW480 cells were infected with the recombinant lenti-viruses from control shRNA and CABLES2 shRNA vevtors respectivly
|
| Growth protocol |
SW480 CRC cell line (from the American Type Culture Collection, ATCC) was cultured in RPMI-1640 medium which was supplemented with 10% fetal bovine serum (GIBCO, Cat No. 10099), and 1% penicillin/streptomycin (GIBCO, Cat No. 15140). Cells were maintained in a 37 °C incubator with 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The cells were extracted with Trizol reageant (Invitrogen)
RNA libraries were prepared according the standard BGISEQ-500 library construction protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Basecalls performed by BGISEQ-500 basecalling Software
Raw reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence to generate clean data using SOAPnuke V1.5.2 with parameters -l 15 -q 0.5 -n 0.1.
Clean data were mapped to the human genome (hg38) using the Bowtie2 tool
Expression levels of genes were measured by Fragments Per Kilobase of transcripts per Million mapped reads (FPKM) using RSEM V1.2.12
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Oct 22, 2018 |
| Last update date |
Oct 23, 2018 |
| Contact name |
Weiqiang Lin |
| E-mail(s) |
wlin@zju.edu.cn
|
| Phone |
+86-86971990
|
| Organization name |
Zhejiang University
|
| Street address |
866 Yuhangtang Rd
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE121553 |
Integrative genomic analyses revealed colorectal cancer susceptibility genes in risk loci identified in genome-wide association studies |
|
| Relations |
| BioSample |
SAMN10266217 |
| SRA |
SRX4910552 |
