title: RNA-Seq data from epiphyseal growth plates of young male rats, healthy control rats and dextran sodium sulfate (DSS) induced colitis treated rats
design: RNA-Seq data from epiphyseal growth plates of young male rats, healthy control rats and dextran sodium sulfate (DSS) induced colitis treated rats
library_construction_protocol: Epiphyseal growth plates were acquired from young male rats following a DSS induced colitis model. Rats were euthanized and then EGPs were sterility scraped from bone.  RNA was extracted using QIAGEN mirNeasy RNA extraction kit Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt [6]; resulting reads shorter than 30bp were discarded. Reads were mapped to the RatMine reference genome Rnor_6.0 using STAR [2], supplied with gene annotations downloaded from Ensembl (and with EndToEnd option and outFilterMismatchNoverLmax was set to 0.04). Reads with the same UMI were removed using the PICARD MarkDuplicate tool using the BARCODE_TAG parameter. Expression levels for each gene were quantified using htseq-count [3], using the gtf above. Differentially expressed genes were identified using DESeq2 [5] with the betaPrior, cooksCutoff and independentFiltering parameters set to False. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Pipeline was run using snakemake [4]
identifiers.namespace: European Bioinformatics Institute
identifiers.id: E-MTAB-16246:D9_p