characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-06-30T00:24:29Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-06-30T00:24:29Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA113577871
characteristics.characteristic: External Id
characteristics.text: CARDIFF UNIVERSITY
characteristics.characteristic: INSDC center name
characteristics.text: 2023-06-30T00:24:29Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-06-30T00:24:29Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS15572785
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-13039:KO2
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: macrophage
characteristics.characteristic: cell_type
characteristics.text: not provided
characteristics.characteristic: collection date
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: 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).
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: Gata-6 knockout
characteristics.characteristic: genotype
characteristics.text: not provided
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: peritoneal cavity
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: KO2
characteristics.characteristic: title