biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsChew Weng ChengIllumina HiSeq 4000IlluminaRNA-seq of coding RNAMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13110Non-alcoholic fatty liver disease (NAFLD), a chronic liver condition characterised by excessive fat in the liver, is associated with insulin resistance (as in type II diabetes), obesity and lipidaemia. The progression of NAFLD to NASH is multifactorial, however, the underlying mechanisms are not well understood and whilst a population of patients develop NASH some, with the same co-morbidities and risk factors, just have a fatty liver. Recently a pilot GWAS in patients with NAFLD looked at genetic variants significantly associated with hepatic histology. They identified rs887304 on chromosome 12 in EFCAB4B to be associated with lobular inflammation. It is important therefore to understand the contribution of CRACR2A and Rab46 to liver function. Here we utilized an Efcab4b global knockout mouse to explore the gene expression in liver.biostudies-arrayexpressSample Collection - Homozygous (Efcab4b-/-) and wild-type (Efcab4b+/+) WT mice were weighed at 8 weeks and 12 weeks where they were sacrificed.Library Construction - The library preparation was constructed using the TruSeq Stranded mRNA kit (Illumina), following the manufacturer’s recommended protocol.Nucleic Acid Extraction - Liver tissue was placed in a tube with a metal lysis bead with 1 ml Trizol Reagent. Tubes were then placed in a tissue lyser and agitated at 26 Hz for 3 x 1 min sessions. The resultant liquid was transferred to 1.5 ml centrifuge tubes, 200 μl of phenol-chloroform were added and left to settle for 3 mins at room temperature, then spun at 12000g (4°C) for 15 mins. The supernatant (top aqueous phase) was transferred to new tubes and 500 μl of isopropanol were added to each tube and gently mixed before being left to stand for 10 mins. The samples were then spun for 15 mins at 12000g (4°C), and the supernatant discarded. The pellets were re-suspended in 1 ml of 75% ethanol (in dH2O) before a further spin at 8000g (4°C) for 5min. The supernatant was removed carefully, the pellet dried and then 20-50 μl of RNA-free dH2O was added to each sample which were then stored at -80°C. RNA was quantified using a NanoDrop®.Sequencing - The libraries were sequenced on the HiSeq 4000 platform with 150 bp paired-end strategy.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesLynn McKeownChew Weng ChengfalseRab46 and the liverNon-alcoholic fatty liver disease (NAFLD), a chronic liver condition characterised by excessive fat in the liver, is associated with insulin resistance (as in type II diabetes), obesity and lipidaemia. The progression of NAFLD to NASH is multifactorial, however, the underlying mechanisms are not well understood and whilst a population of patients develop NASH some, with the same co-morbidities and risk factors, just have a fatty liver. Recently a pilot GWAS in patients with NAFLD looked at genetic variants significantly associated with hepatic histology. They identified rs887304 on chromosome 12 in EFCAB4B to be associated with lobular inflammation. It is important therefore to understand the contribution of CRACR2A and Rab46 to liver function. Here we utilized an Efcab4b global knockout mouse to explore the gene expression in liver.2025-06-23T00:00:00Z2023-06-23T10:30:39.334Z2023-06-23T10:30:39.334ZE-MTAB-13110ERP148613EFO_0002944EFO_0004170EFO_0005518EFO_0003738EFO_0004184