{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":[null],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15029"],"description":["Pancreatic RalGAPβ deficiency induces inflammation and neoplasia. RNA sequencing of isolated acinar cells was performed to identify underlying processes."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - For RNA library preparation, 0.5-1 x 10^6 MPx1-positive FACS sorted cells were used for RNA isolation using the Quick-RNA Microprep Kit (Zymo Research, R1051) according to manufacturer’s instructions.","Sequencing - Single-end read sequencing was performed using a NextSeq ® 2000 System with a read length of 72 bp. The samples were demultiplexed with the Illumina® DRAGEN™ Bio-IT Platform. Quality control was done using FastQC version 0.11.9. Trimmomatic version 0.39 was used for adapter and low quality end trimming as well as for general quality trimming utilizing a sliding window of 4 bp with a minimal average base quality of 15. Reads below a minimum read length of 15 bp were discarded.","Sample Collection - Pancreata were resected, washed in PBS and minced into small pieces (1-2 mm) in 2 ml RPMI-1640 without phenol red (Sigma-Aldrich, R7509) supplemented with 2 % FBS (Biowest, S1810), 10 mM L-glutamine (Sigma-Aldrich, G7513) and 50 U Penicillin-Streptomycin (Thermo Fisher Scientific, 15070063). After two washing steps with 5 ml RPMI/2% FBS, each minced pancreas was digested in 2 mg/ml Collagenase, Type 4 (Worthington-Biochemical, LS004188), 2 mg/ml Dispase II (Sigma-Aldrich, D4693) and 20 µg/ml DNase I (AppliChem, A3778) dissolved in 15 ml HBSS (Sigma-Aldrich, H6648) at 37 °C with 5 % CO2 for 1 h, including thorough pipetting every 15 min to enhance dissociation. The isolated cells were then washed two times with 35 ml. PBS (400xg, 5 min, 4 °C). The cells were resuspended in 0.5 ml RPMI/2 % FBS, filtered through a 35 µm cell strainer, the filter washed with 0.5 ml RPMI/2 % FBS and 0.1 mg/ml Soybean Trypsin Inhibitor (Thermo Fisher Scientific, 17075029) was added. For acinar cell sorting, the cells were stained 1:25 with rat MPx1 MICO-2A6 (gift from C. Dorrell; Dorrell, C. et al. Isolation of mouse pancreatic alpha, beta, duct and acinar populations with cell surface markers. Mol. Cell. Endocrinol. 339, 144–150 (2011)) for 20 min on ice, then washed three times with 3 ml RPMI/2 % FBS (400xg, 5 min, 4 °C) and stained 1:200 with FITC goat anti-rat (BioLegend, 554016) for 10 min on ice. After a washing step with 3 ml RPMI/2 % FBS (400xg, 5 min, 4 °C), the cells were counterstained with APC rat anti-CD45 (BioLegend, 103112) and PE-Cy7 rat anti-CD19 (BD Biosciences, 55284, clone 1D3) for 20 min. After a final washing step, the cells were stained 1:100 with 7-AAD Viability Staining Solution (BioLegend, 420404). Cell sorting was performed on a FACSAria II using the FACSDiva version 9.0.1 and FACSuite version 1.0.6 software (BD Biosciences). Flow cytometry data were analysed using FlowJo software version 10.5.3 (BD Life Sciences).","Library Construction - Library preparation of the total RNA was performed with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, E7760) and NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490)."],"figure_sub":["MINSEQE Score","Assays and Data","Processed Data","organisation","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - The resulting reads were aligned to the Ensembl GRCm39 reference genome, using HISAT2 version 2.2.1  and sorted using SAMtools version 1.16.1.","Data Transformation - Gene based read counting was done using HTSeq version 2.0.3 with the Ensembl annotation version 107. Differential expression analysis was performed using the R package DESeq2 version 1.38.3. The R package biomaRt version 2.54.0 was used to convert Ensembl IDs to mgi symbols."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"additional_accession":["E-MTAB-15030"],"pubmed_authors":["Andrea Oeckinghaus","Lisa Apken"]},"is_claimable":false,"name":"RNA-sequencing of isolated pancreatic acinar cells from RalGAPβ knockout mice against control mice","description":"Pancreatic RalGAPβ deficiency induces inflammation and neoplasia. RNA sequencing of isolated acinar cells was performed to identify underlying processes.","dates":{"release":"2025-06-03T00:00:00Z","modification":"2025-06-04T09:40:44.322Z","creation":"2025-04-15T12:06:55.716Z"},"accession":"E-MTAB-15029","cross_references":{"ENA":["ERP171647"],"Biostudies":["E-MTAB-15030"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}