title: KO2
organism: Mus musculus
description: 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).
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2023-06-30T00:24:29Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2023-06-30T00:24:29Z
attributes.tag: External Id
attributes.value: SAMEA113577871
attributes.tag: INSDC center alias
attributes.value: CARDIFF UNIVERSITY
attributes.tag: INSDC center name
attributes.value: CARDIFF UNIVERSITY
attributes.tag: INSDC first public
attributes.value: 2023-06-30T00:24:29Z
attributes.tag: INSDC last update
attributes.value: 2023-06-30T00:24:29Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-13039:KO2
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell_type
attributes.value: macrophage
attributes.tag: collection date
attributes.value: not provided
attributes.tag: common name
attributes.value: house mouse
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: genotype
attributes.value: Gata-6 knockout
attributes.tag: geographic location (country and/or sea)
attributes.value: not provided
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism part
attributes.value: peritoneal cavity
attributes.tag: sample name
attributes.value: E-MTAB-13039:KO2
attributes.tag: scientific_name
attributes.value: Mus musculus