|
| Status |
Public on Jul 13, 2018 |
| Title |
PANC-1 NC3 |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PANC-1
tissue: pancreatic cancer cell line
treatment: negative control
|
| Treatment protocol |
cells were seeded onto 6-well culture plates. PANC-1 cell lines were transfected with CD73 siRNA or negative control in serum-free medium, transfection was performed using Lipofectamine 3000 following the manufacturer’s protocol.
|
| Growth protocol |
PANC-1 was cultured in DMEM medium with 10% fetal bovine serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of cells was isolated and purified by miRNeasy Mini Kit (Qiagen, Maryland, USA), following the manufacturer’s instructions.
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 |
bcl2fastq software were used for basecalling.
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).The steps are: 1) trim Smart-seq2 public primer sequence from the Reads; 2) remove the contaminated reads for adapters; 3) remove the low quality reads; and 4) remove the reads whose N base more than 5% for total bases.
Sequenced reads were mapped to hg38 using Bowtie2 v2.2.3 software.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0. and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Trapnell, C. et al., Nat. Biotechnol, 2010.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
Jul 12, 2018 |
| Last update date |
Jul 13, 2018 |
| Contact name |
Liangjing Zhou |
| E-mail(s) |
124929619@qq.com
|
| Organization name |
Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
|
| Department |
Department of General Surgery
|
| Street address |
no. 3,QingChun east road,Jianggan District, Hangzhou City, Zhejiang Province
|
| City |
Hangzhou City, Zhejiang Province |
| ZIP/Postal code |
310000 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE117012 |
CD73 knockdown effect in pancreatic cancer cell lines |
|
| Relations |
| BioSample |
SAMN09651011 |
| SRA |
SRX4385575 |
