Hiseq 4000 pe100 sequencing system

Total RNAs from wild-type, Hdac1- or Hdac2-deleted enteroids were purified with the RNeasy mini kit (Qiagen) (n = 4), and quantified. RNA integrity was evaluated with a 2100 Bioanalyzer (Agilent Technologies). Only samples with RNA Integrity Number (RIN) > 6.5 were selected. cDNA library preparation and transcriptome analysis with the Illumina HiSeq. 4000 PE100 sequencing system (Illumina) were performed at the McGill University and Génome Québec Innovation Center. Sequence alignment was performed with the Star 2.4.0.1 software package based on genome reference Mus_musculus:GRCm38. Differentially expressed genes were identified with DESeq adjusted p-value ≤ 0.05^{88 (link)}. Only transcripts increased or decreased more than 2-fold between wild-type, Hdac1- or Hdac2-deleted enteroids were selected for further bioinformatics analysis. RNA-Seq data have been deposited in the Gene Expression Omnibus database (GSE124146).

Jejunal IEC from three-month-old wild-type and villin-Cre Hdac1^−/−; Hdac2^−/− mice were enriched by EDTA treatment. Jejunal IEC RNAs were isolated with the ToTALLY RNA™ (Thermo Fisher Scientific) and Rneasy kits (Qiagen) (n = 3). Samples with RNA integrity number over 6.5 were selected with a 2100 Bioanalyser (Agilent Technologies). cDNA libraries were prepared and the transcriptome was determined with the Illumina HiSeq4000 PE100 sequencing system (Illumina, San Diego, CA, USA) at the McGill University and Génome Québec Innovation Center. Sequences were aligned with the Star 2.4.0.1 software package based on the genome reference Mus_musculus:GRCm38. Differentially expressed genes were identified with DESeq adjusted p-value ≤ 0.05 [31 (link)]. Two-fold increased or decreased transcripts between control and Hdac1^−/−; Hdac2^−/− IEC were selected for additional bioinformatics analysis. RNA-Seq data have been deposited in the Gene Expression Omnibus database (GSE158522).