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| Status |
Public on May 24, 2023 |
| Title |
PUB23 |
| Sample type |
SRA |
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| Source name |
Pancreas
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Nfic_KO -/- (KO)
age: 8-10 week-old mice
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total pancreatic RNA was isolated using guanidine thiocyanate, followed by acid phenol-chloroform extraction. 1µg of total RNA samples, each containing an equal amount of ERCC ExFold RNA Spike-In Mix 1 (Ambion 4456739), was used as provided by the user. Average sample RNA Integrity Number was 8.4 (range 7.8 - 9.2) when assayed on an Agilent 2100 Bioanalyzer. 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 Sample Preparation Part # 15031047 Rev. D" 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 on an Illumina instrument (see below) by following manufacturer's protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of Illumina BCL files to bam format was performed with the Illumina2bam tool (Wellcome Trust Sanger Institute - NPG).
RNA seq analysis was performed using Nextpresso analysis pipeline. Graña, Osvaldo & Rubio-Camarillo, M & Fdez-Riverola, F & Pisano, David & Glez-Peña, Daniel. (2018). Nextpresso: Next Generation Sequencing Expression Analysis Pipeline. Current Bioinformatics. 13. 583-591. 10.2174/1574893612666170810153850.
Genome_build: mm10
Supplementary_files_format_and_content: HOMER.rawCount.txt : raw count matrix text file.
Supplementary_files_format_and_content: HOMER.rawTPM.txt : annotated normalized counts text file.
Supplementary_files_format_and_content: NFICwt.vs.NFICko.scatter.txt : differential expression analysis DESeq2 text file.
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| Submission date |
Feb 21, 2019 |
| Last update date |
May 24, 2023 |
| Contact name |
Jaime Martinez de Villarreal |
| E-mail(s) |
jmartinezv@cnio.es
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| Phone |
+34 917328000
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| Organization name |
CNIO
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| Department |
Molecular Oncology Programme
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| Lab |
Epithelial Carcinogenesis Group
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| Street address |
Melchor Fernández Almagro, 3
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| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE126907 |
RNA-Seq of wild type and Nfic-/- mice pancreata |
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| Relations |
| BioSample |
SAMN10985127 |
| SRA |
SRX5405872 |
| 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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