2024-07-24
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA115029658
External Id
UH
INSDC center name
2023-12-14T10:49:06Z
INSDC last update
public
INSDC status
ERS17476495
SRA accession
E-MTAB-13631:Sample 8
Submitter Id
9 to 10
week
age
ArrayExpress
broker name
not collected
collection date
house mouse
common name
Protocols: Distal colon 5-10mm tissue pieces were dissected from each mouse and placed in RNA later. Mice were treated with 3% DSS in the drinking water for 7 days followed by 3 days recovery. RNA was extracted using the commercial kit for DNA, RNA and protein purification from Macherey-Nagel. 3′ RNA sequencing was performed by the Biomedicum Functional Genomics Unit at the Helsinki Institute of Life Science and Biocenter, Finland, at the University of Helsinki. 3′ UTR RNAseq ‘Bulkseq’ is based upon the Dropseq method for single-cell sequencing (Macosko et al., 2015). The method involves priming mRNA with an oligo-dT primer that also contains a 12 bp barcode and an 8 bp unique molecular identifier (UMI) sequence, which can be used to remove PCR duplicates during data analysis. Single-stranded cDNA is then converted to double-stranded cDNA using the template-switch effect, and double-stranded cDNA product is then amplified with PCR and another set of primers (SMART PCR primer). Samples were pooled and PCR sequencing pools were made with Nextera i7 primers and the Dropseq P5 primers.
description
adult
developmental stage
Lkb1fl/+
genotype
not collected
geographic location (country and/or sea)
24
individual
not applicable
isolate
Mus musculus
organism
Mus musculus
organism
colon
organism part
Mus musculus
scientific_name
male
sex
3% DSS
stimulus
ICR mixed background
strain
Sample 8
title