|
| Status |
Public on Nov 01, 2016 |
| Title |
A13-Pr2_rep2 [RNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
Patient A13
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary tumor
protocol: 10% FBS
|
| Growth protocol |
Unless otherwise stated, cells were grown to 70% (A38-Lg) or 100% (A38-Per) confluence in DMEM with 10% Fetal Bovine Serum (FBS)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, RNA was extracted with Trizol reagent.
RNA-Seq libraries were generated using TruSeq Stranded mRNA protacol (Illumina). 2ug of total RNA was used for library generation and 6 minutes of fragmentation. For enrichment of cDNA fragments 11 PCR cycles were used.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
primary tumor
all_gene_raw_readcounts2.txt
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Paired-end HiSeq2000 sequencing reads were aligned against human genome (hg19) by OSA (version 2.0.1) with default parameters. After alignment, only uniquely aligned reads were kept for further analysis.
Reads count for each gene of all samples were estimated using HTSeq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) and then were used to identify differentially expressed (DE) genes using DESeq package. Genes with adjusted p-value < 0.01 and fold-change > 2 between A38-41 and A38-5 were considered as DE genes.
Genome_build: hg19
Supplementary_files_format_and_content: text file, raw read counts of each gene for all samples
|
| |
|
| Submission date |
Apr 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xin Li |
| E-mail(s) |
lixin4306ren@gmail.com
|
| Organization name |
Sun Yat-sen University
|
| Department |
School of Medicine
|
| Street address |
132 Daxuecheng Outer Ring E Rd
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510006 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE63124 |
Large-scale epigenetic reprogramming is punctuated late during the evolution of pancreatic cancer progression [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN04889736 |
| SRA |
SRX1722803 |
