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| Status |
Public on Jun 25, 2019 |
| Title |
ADGFP1439 |
| Sample type |
SRA |
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| Source name |
PDAC cell lines
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| 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
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| Treatment protocol |
25 MOI of AdGFP
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| 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
RNA-seq analysis:
RNA-seq data were analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/), 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 https://0-ccb-jhu-edu.brum.beds.ac.uk/software/tophat/igenomes.shtml.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Normalized counts calculated with DESeq2
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| Submission date |
Mar 28, 2018 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Osvaldo Graña |
| Organization name |
CNIO
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| Department |
Structural Biology
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| Lab |
Bioinformatics Unit
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| Street address |
C/ Melchor Fernández Almagro, 3
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| City |
Madrid |
| State/province |
Comunidad de Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
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| Platform ID |
GPL24247 |
| Series (1) |
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| Relations |
| BioSample |
SAMN08804862 |
| SRA |
SRX3856551 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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