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Sample GSM1574307 Query DataSets for GSM1574307
Status Public on Jan 18, 2016
Title PANC1.rep1
Sample type SRA
 
Source name PANC1
Organism Homo sapiens
Characteristics cell line background: PANC1
cell type: original Pancreatic Ductal Adenocarcinoma (PDAC) cell line
Treatment protocol No treatment
Growth protocol DMEM 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
processed data file: CL-PDACs_vs_QM-PDACs.gene_exp.diff
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 Humanitas University
Lab Transcription and Chromatin Lab
Street address Via Rita Montalcini
City Pieve Emanuele (MI)
ZIP/Postal code 20090
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 SAMN03273787
SRA SRX825429

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data is available on Series record

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