2025-11-30
ENA first public
ERC000011
ENA-CHECKLIST
Tel Aviv University
INSDC center name
public
INSDC status
ERS27405547
SRA accession
E-MTAB-16246:C1
Submitter Id
48
day
age
ArrayExpress
broker name
not collected
collection date
Norway rat
common name
Protocols: 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]
description
postnatal day 48
developmental stage
disease
not collected
geographic location (country and/or sea)
not applicable
isolate
Rattus norvegicus
organism
Rattus norvegicus
organism
cartilage
organism part
Rattus norvegicus
scientific_name
male
sex
Sprague Dawley
strain
C1
title