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Sample GSM3070090 Query DataSets for GSM3070090
Status Public on Jun 25, 2019
Title ADGFP2365
Sample type SRA
Source name PDAC cell lines
Organism Mus musculus
Characteristics cell line: PDAC
genotype/variation: K-Ras+/FSFG12V;Tp53frt/frt;Elas-tTA/tetO-Flp(o);Tg.hUBC-CreERT2;c-Raflox/lox;Egfrlox/lox
infected with: 25 MOI of AdGFP
Treatment protocol 25 MOI of AdGFP
Extracted molecule polyA RNA
Extraction protocol RNA extraction protocol from Quiagen
1ug of total RNA from the samples was used. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA LT Sample Prep Kit" (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced in paired-end format (Illumina NovaSeq 6000), leading to 101bp paired-end reads.
Strand-specific RNA-Seq (dUTP)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing RNA-seq analysis:
RNA-seq data were analysed with the nextpresso pipeline (, as follows: RNA-seq reads were aligned to the mouse genome (NCBI37/mm9) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing two mismatches and twenty multihits. Differential expression tests were done with DESeq2, using the mouse NCBI37/mm9 genome annotations from
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Normalized counts calculated with DESeq2
Submission date Mar 28, 2018
Last update date Jun 25, 2019
Contact name Osvaldo Graña
Organization name CNIO
Department Structural Biology
Lab Bioinformatics Unit
Street address C/ Melchor Fernández Almagro, 3
City Madrid
State/province Comunidad de Madrid
ZIP/Postal code 28029
Country Spain
Platform ID GPL24247
Series (1)
GSE112434 RNA sequencing data
BioSample SAMN08804858
SRA SRX3856554

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

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