{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Sandhya Visweswariah"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15690"],"description":["The experiment was designed to detemine changes in gene expression between wild type mice and mice with a mutation in receptor guanylyl cyclase C at the Serine 839 position converted to an Isoleucine. This mutation mimics the mutation seen in human patients with familial GUCY2C diarrhoea  syndrome."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - The sequence data was generated using Illumina HiSeq","Library Construction - RNA was quantified by QUBIT 3 Fluorometer using Ribogreen Dye. 1 microgram of total RNA was used to enrich the mRNA Oligo dT magnetic beads, and the mRNA was chemically fragmented in a magnesium-based buffer at 94°C for 15 minutes. The fragmented mRNAs were primed with random hexamers, and reverse transcribed to form cDNA. The cDNA fragments obtained were cleaned up by using AM pure beads. The DNA underwent end repair wherein the mix converts the overhangs resulting from fragmentation into blunt ends. The 3’ to 5’ exonuclease activity of end repair mix removes the 3’ overhangs and polymerase activity fills in the 5’ overhangs. To the blunt ended fragments adenylation was performed by adding single ‘A’ nucleotide to the 3’ ends. To the adenylated fragments loop adapters were ligated and cleaved with uracil-specific excision reagent (USER) enzyme. The samples were further purified using AMPure beads and The DNA was then enriched by PCR with 12 cycles using NEBNext Ultra II Q5 master mix, illumina universal primer and sample-specific octamer primers. The amplified products were cleaned up by using AM pure beads and the final mRNA library was eluted in 15 microlitres  of 0.1X TE buffer.","Nucleic Acid Extraction - Samples were then processed using the Qiagen RNeasy mini kit as per manufacturer's instructions. Total RNA was isolated and sent for RNAseq analysis","Sample Collection - A 1cm piece from the ileum, close to the ilea-ceaecal junction was harvested and placed in 1 ml of Trizol and snap frozen."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The data was anslysed using the Ingenuity Pathway RNAseq Analysis Portal","Sequence Alignment - Data was analysed using the Ingenuity Pathway RNAseq Analysis Portal (workflow version 1.1) after uploading the raw fastq files. Reads were aligned to  Mus musculus (GRCm38.101)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Sandhya Visweswariah"],"additional_accession":[]},"is_claimable":false,"name":"Bulk RNAseq analysis of the terminal ileum from C57BL6N mice, either wild type of mice harbouring a mutation in the Gucy2c gene","description":"The experiment was designed to detemine changes in gene expression between wild type mice and mice with a mutation in receptor guanylyl cyclase C at the Serine 839 position converted to an Isoleucine. This mutation mimics the mutation seen in human patients with familial GUCY2C diarrhoea  syndrome.","dates":{"release":"2025-10-31T00:00:00Z","modification":"2026-05-27T16:12:18.21Z","creation":"2025-10-10T12:27:14.399Z"},"accession":"E-MTAB-15690","cross_references":{"ENA":["ERP181349"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}