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Status |
Public on Jan 29, 2018 |
Title |
Big278 |
Sample type |
SRA |
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Source name |
pancreas
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Organism |
Mus musculus |
Characteristics |
tissue: pancreas nr5a2 genotype: +/+ treatment: Caerulin 24h mouse background: C57BL
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Treatment protocol |
A mild acute pancreatitis was induced by seven hourly injections of the CCK analog caerulein (Bachem) at 50 ug/kg. Briefly, animals were weighted before the beginning of the procedure and caerulein was administered i.p. Mice were sacrificed by cervical dislocation 8h, 24h,and 48h after the first injection.
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Growth protocol |
All animal procedures were approved by local and regional ethics committees (Institutional Animal Care and Use Committee and Ethics Committee for Research and Animal Welfare, Instituto de Salud Carlos III, Madrid, Spain) and performed according to the European Union guidelines
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Extracted molecule |
polyA RNA |
Extraction protocol |
Total pancreatic RNA was isolated using guanidine thiocyanate, followed by acid phenol chloroform extraction. RNA quality was assessed on an Agilent 2100 Bioanalyzer. 1 µg of total RNA samples was used as provided by the user. RNA Integrity Numbers were in the range 6.6 to 9.2 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer. PolyA+ RNA fraction was extracted 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 RNA Sample Preparation Guide" (Part # 15008136 Rev. A; for samples Big104, Big90, Big92, Big18, Big277, Big 278, Big33, Big87, Big94, Big113, Big17, Big86) or in Illumina's "TruSeq RNA Sample Preparation v2 Protocol" (Part # 15026494 Rev. C; for samples Big408, Big409, Big410, Big416, Big417, Big423, Big454, Big459, Big461, Big465, Big467 and Big470). Adapter-ligated library was completed by limited-cycle PCR with Illumina PE primers (10 cycles or 8 for samples v2 protocol). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols."
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer IIx |
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Data processing |
Image analysis and per-cycle basecalling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format and sequence alignment with the ELAND algorithm (v2e) was performed with CASAVA-1.8 (Illumina).
Tophat5 (version 2.0.4) was used for alignment with the following parameters: --bowtie1, --max-multihits 5, --genome-read-mismatches 1 --segment-mismatches 1 --segment-length 20 --splice-mismatches 0.
Gene expression levels were quantified with cufflinks (version 2.0.2) with the following parameters: -N, -u
Further, gene expression values were normalized for library size with cuffnorm following parameters: -o -L --library-norm-method classic-fpkm
The result was a matrix of normalized FPKM values
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: A tabular file with the normalized FPKM values for each sample
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Submission date |
Jul 21, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Enrique Carrillo de Santa Pau |
E-mail(s) |
enrique.carrillo@imdea.org
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Organization name |
Spanish National Cancer Research Centre (CNIO)
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Department |
Cancer Cell Biology Programme
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Lab |
Epithelial Carcinogenesis group
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Street address |
C/ Melchor Fernández Almagro, 3
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City |
Madrid |
ZIP/Postal code |
28029 |
Country |
Spain |
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Platform ID |
GPL11002 |
Series (1) |
GSE84659 |
Transcriptional regulation by NR5A2 couples cell differentiation |
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Relations |
BioSample |
SAMN05425745 |
SRA |
SRX1967751 |
Supplementary data files not provided |
SRA Run Selector |
Processed data are available on Series record |
Raw data are available in SRA |
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