{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Abhinav Soni"],"organism":["Mus musculus"],"software":["R software"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17032"],"description":["Tumor-associated macrophages (TAMs) play important roles in cancer progression and resistance to therapy. Recent studies have shown that TAMs include both long-lived resident tissue macrophages (RTMs) and short-lived monocyte-derived macrophages (MDMs) with limited proliferative potential. RTMs and MDMs have been suggested to play divergent roles in tumorigenesis; RTMs are aligned with trophic functions, whereas MDMs are enriched for immune-regulatory pathways. Here we established a specific role for the AP-1 factor JUN in the differentiation and maintenance of MDMs and the specification of pro-tumoral trophic functions during tumor development. Alternatively, the immune-regulatory functions of TAMs remained JUN-independent. JUN was required for the specification and maintenance of pro-tumoral TAMs that support blood vessel maturation and tumor growth. Single-cell transcriptomics analysis uncovered the alternative fates for tumor-infiltrating monocytes and the development of distinct TAM states associated with trophic functions and immune-regulation. These studies demonstrate an important role for JUN in the specification of pro-tumoral monocyte-derived TAMs that could offer opportunities for selective TAM-targeted therapies for cancer."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - The libraries for RNA-seq were prepared using ILL DNA Library Prep Tagmentation LV (Pur,FA) and quality of the RNA libraries was confirmed using fragment analyser","Sample Collection - 300mg tumour fragments digested with tumour dissociation kit (Miltenyi BioTec) were stained with CD45.2-PE and CD45+ cell isolated with anti-PE beads (StemCell) after enrichment iTAM and mTAM populations were sorted by flow cytometry (10000 cells). Nucleic acid extraction protocol: Arcturus PicoPure.","Sequencing - After purification, libraries were quantified on a Fragment Analyzer (Agilent). Libraries were sequenced on an Illumina NovaSeq 6000 in 100 bp paired-end mode to a depth of 50-60 million fragments per library.   NovaSeq S4 v1.5 4XP (200cyc)  Illumina NovaSeq 6000 (sequencer)","Nucleic Acid Extraction - Sample prep (RNA-cDNA) \\\"Smart-Seq2\\\" - adapted from Picelli et al 2013 https://www.nature.com/articles/nmeth.2639, in-house method on robotics."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Post-alignment several RNA-seq QC metrics were calculated. FeatureCounts (RRID:SCR_012919) was used to read count relative to gene biotype. The code used to run the nf-core pipeline for RNA-seq analysis is the following: nextflow run nf-core/rnaseq --input Samplesheet_RNA.csv --genome mm10 --outdir results_mm10 -c config.txt -profile singularity -r 3.14.0  The count matrix generated using nf-core pipeline was extracted and further processed for differential analysis using DEseq2(v1.44.0) (RRID:SCR_015687) in R programming environment (v4.4.1).","Sequence Alignment - To process RNA-seq reads, the nf-core/rnaseq pipeline written in the Nextflow domain-specific language was used. Briefly, the nf-core pipeline for RNA-seq (v3.14.0) was used to perform a quality check on fasta files generated after sequencing, adapter and quality trimming, removal of genomic contaminants and STAR (RRID:SCR_004463) and Salmon based genome alignment and transcript quantification."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Miltenyi Biotec (cat no. 130-096-730) ,Fortessa X-20 flow cytometer (BD Biosciences)","R software","nf-core pipeline","Illumina NovaSeq 6000","Illumina DNA Tagmentation","Arcturus PicoPure"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Abhinav Soni","Toby Lawrence"],"additional_accession":[]},"is_claimable":false,"name":"RNAseq of iTAM and mTAMs isolated from tumors in Junf/f and Jun Csf1r KO mice","description":"Tumor-associated macrophages (TAMs) play important roles in cancer progression and resistance to therapy. Recent studies have shown that TAMs include both long-lived resident tissue macrophages (RTMs) and short-lived monocyte-derived macrophages (MDMs) with limited proliferative potential. RTMs and MDMs have been suggested to play divergent roles in tumorigenesis; RTMs are aligned with trophic functions, whereas MDMs are enriched for immune-regulatory pathways. Here we established a specific role for the AP-1 factor JUN in the differentiation and maintenance of MDMs and the specification of pro-tumoral trophic functions during tumor development. Alternatively, the immune-regulatory functions of TAMs remained JUN-independent. JUN was required for the specification and maintenance of pro-tumoral TAMs that support blood vessel maturation and tumor growth. Single-cell transcriptomics analysis uncovered the alternative fates for tumor-infiltrating monocytes and the development of distinct TAM states associated with trophic functions and immune-regulation. These studies demonstrate an important role for JUN in the specification of pro-tumoral monocyte-derived TAMs that could offer opportunities for selective TAM-targeted therapies for cancer.","dates":{"release":"2026-05-24T00:00:00Z","modification":"2026-05-26T20:15:26.304Z","creation":"2026-05-14T10:42:52.153Z"},"accession":"E-MTAB-17032","cross_references":{"ENA":["ERP193383"],"Biostudies":["E-MTAB-13634"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}