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Sample GSM2247286

Query DataSets for GSM2247286

Status

Public on Jan 29, 2018

Title

Big278

Sample type

SRA

Source name

pancreas

Organism

Mus musculus

Characteristics

tissue: pancreas
nr5a2 genotype: +/+
treatment: Caerulin 24h
mouse background: C57BL

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.

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

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."

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina Genome Analyzer IIx

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

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

Organization name

Spanish National Cancer Research Centre (CNIO)

Department

Cancer Cell Biology Programme