2024-10-10
ENA first public
ERC000011
ENA-CHECKLIST
CARDIFF
INSDC center name
public
INSDC status
ERS18285485
SRA accession
E-MTAB-13782:NS1.2.3
Submitter Id
9 to 12
week
age
ArrayExpress
broker name
not collected
collection date
house mouse
common name
Protocols: Resident peritoneal macrophages (pMΦs) were obtained via peritoneal lavage with 5 ml lavage solution (PBS (Invitrogen) supplemented with 5 mM EDTA and 4% foetal calf serum (FCS)). Lavages of the same genotype were pooled together for flow cytometric cell sorting prior to nucleic acid extraction.  Total RNA extraction was performed using miRNeasy Micro Kit (Qiagen) accordingly to manufacturer’s instructions. Paired-end reads from Illumina sequencing were trimmed with Trim Galore and assessed for quality using FastQC using default parameters. Reads were mapped to the mouse GRCm38 reference genome using STAR and counts were assigned to transcripts using featureCounts with the GRCm38.84 Ensembl gene build GTF. Both the reference genome and GTF were downloaded from the Ensembl FTP site. Differential gene expression analyses used the DESeq2 packageGenes were discarded from the analysis differential expression failed to be significant (significance: adj.pval < 0.05, Benjamini-Hochberg correction for multiple testing).
description
adult
developmental stage
wild type genotype
genotype
not collected
geographic location (country and/or sea)
not applicable
isolate
control
microrna overexpression
Mus musculus
organism
Mus musculus
organism
peritoneal cavity
organism part
Mus musculus
scientific_name
female
sex
C57BL/6
strain
NS1.2.3
title