2025-10-31
ENA first public
ERC000011
ENA-CHECKLIST
Indian Institute of Science, Bangalore, India
INSDC center name
public
INSDC status
ERS26983924
SRA accession
E-MTAB-15690:WT4-Ile
Submitter Id
8
week
age
ArrayExpress
broker name
not applicable
cell line
not collected
collection date
house mouse
common name
Protocols: A 1cm piece from the ileum, close to the ilea-ceaecal junction was harvested and placed in 1 ml of Trizol and snap frozen.  Samples were then processed using the Qiagen RNeasy mini kit as per manufacturer's instructions. Total RNA was isolated and sent for RNAseq analysis RNA was quantified by QUBIT 3 Fluorometer using Ribogreen Dye. 1 microgram of total RNA was used to enrich the mRNA Oligo dT magnetic beads, and the mRNA was chemically fragmented in a magnesium-based buffer at 94°C for 15 minutes. The fragmented mRNAs were primed with random hexamers, and reverse transcribed to form cDNA. The cDNA fragments obtained were cleaned up by using AM pure beads. The DNA underwent end repair wherein the mix converts the overhangs resulting from fragmentation into blunt ends. The 3’ to 5’ exonuclease activity of end repair mix removes the 3’ overhangs and polymerase activity fills in the 5’ overhangs. To the blunt ended fragments adenylation was performed by adding single ‘A’ nucleotide to the 3’ ends. To the adenylated fragments loop adapters were ligated and cleaved with uracil-specific excision reagent (USER) enzyme. The samples were further purified using AMPure beads and The DNA was then enriched by PCR with 12 cycles using NEBNext Ultra II Q5 master mix, illumina universal primer and sample-specific octamer primers. The amplified products were cleaned up by using AM pure beads and the final mRNA library was eluted in 15 microlitres  of 0.1X TE buffer.
description
adult
developmental stage
FGDS
disease
wild type genotype
genotype
not collected
geographic location (country and/or sea)
not applicable
isolate
Mus musculus
organism
Mus musculus
organism
terminal ileum
organism part
Mus musculus
scientific_name
female
sex
C57BL/6NJ
strain
WT4-Ile
title