|
| Status |
Public on Jan 18, 2016 |
| Title |
BxPc3.rep1 |
| Sample type |
SRA |
| |
|
| Source name |
BxPc3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line background: BxPc3
cell type: original Pancreatic Ductal Adenocarcinoma (PDAC) cell line
|
| Treatment protocol |
No treatment
|
| Growth protocol |
RPMI-1640 supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine and 1% Pen/Strep
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: PDACs.genes.fpkm_tracking
|
| Data processing |
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the human hg19 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches and with a mean distance between pairs (-r) of 200bp
Transcripts abundance were quantified using Cufflinks 2.1.1 (PMID: 23222703)
Differentially expressed genes were called using Cuffdiff 2.1.1 (PMID: 23222703)
Genome_build: hg19 (NCBI build GRCh37), transcripts from Illumina iGenome UCSC hg19
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression (FPKM), *.diff list the statistics for differential expression comparisons (refer to http://cole-trapnell-lab.github.io/cufflinks/manual/ for details)
|
| |
|
| Submission date |
Dec 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Chiara Balestrieri |
| E-mail(s) |
balestrieri.c@gmail.com
|
| Organization name |
IRCCS San Raffaele Scientific Institute
|
| Department |
Center for Omics Sciences
|
| Street address |
Via Olgettina 58
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE64558 |
Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer [RNA-seq] |
| GSE64560 |
Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer. |
|
| Relations |
| BioSample |
SAMN03273836 |
| SRA |
SRX825417 |
