AP-3-84 effects on gene expression in thioglycollate-induced, ID8 ascites or bone-marrow derived macrophages
RNA-seq (gene expression) · mouse · 48 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 48 samples: 12 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Targeting LxCxE Cleft Pocket of Retinoblastoma Protein in Immunosuppressive Macrophages Inhibits Ovarian Cancer ProgressionCancer immunology research · 2025
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE239479_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA999363 and SRA study SRP451833. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 36 samples.
How we read this: 12 replicated groups read from 48 sample titles; they account for 36 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM7665945 1.Ascites_control_replicate1
- GSM7665946 2.Ascites_control_replicate2
- GSM7665947 3.Ascites_control_replicate3
- GSM7665948 4.Ascites_AP3-84_replicate1
- GSM7665949 5.Ascites_AP3-84_replicate2
- GSM7665950 6.Ascites_AP3-84_replicate3
- GSM7665951 7.Thio-Macs_control_replicate1
- GSM7665952 8.Thio-Macs_control_replicate2
- GSM7665953 9.Thio-Macs_control_replicate3
- GSM7665954 10.Thio-Macs_AP3-84_replicate1
- GSM7665955 11.Thio-Macs_AP3-84_replicate2
- GSM7665956 12.Thio-Macs_AP3-84_replicate3
- GSM7665957 WT.M0.D.1 WT.M0.D
- GSM7665958 WT.M0.D.2 WT.M0.D
- GSM7665959 WT.M0.D.3 WT.M0.D
- GSM7665960 WT.M0.A.1 WT.M0.A
- GSM7665961 WT.M0.A.2 WT.M0.A
- GSM7665962 WT.M0.A.3 WT.M0.A
- GSM7665963 WT.M1.D.1 WT.M1.D
- GSM7665964 WT.M1.D.2 WT.M1.D
- GSM7665965 WT.M1.D.3 WT.M1.D
- GSM7665966 WT.M1.A.1 WT.M1.A
- GSM7665967 WT.M1.A.2 WT.M1.A
- GSM7665968 WT.M1.A.3 WT.M1.A
- GSM7665969 WT.M2.D.1 WT.M2.D
- GSM7665970 WT.M2.D.2 WT.M2.D
- GSM7665971 WT.M2.D.3 WT.M2.D
- GSM7665972 WT.M2.A.1 WT.M2.A
- GSM7665973 WT.M2.A.2 WT.M2.A
- GSM7665974 WT.M2.A.3 WT.M2.A
- GSM7665975 KO.M0.D.1 KO.M0.D
- GSM7665976 KO.M0.D.2 KO.M0.D
- GSM7665977 KO.M0.D.3 KO.M0.D
- GSM7665978 KO.M0.A.1 KO.M0.A
- GSM7665979 KO.M0.A.2 KO.M0.A
- GSM7665980 KO.M0.A.3 KO.M0.A
- GSM7665981 KO.M1.D.1 KO.M1.D
- GSM7665982 KO.M1.D.2 KO.M1.D
- GSM7665983 KO.M1.D.3 KO.M1.D
- GSM7665984 KO.M1.A.1 KO.M1.A
+ 8 more — browse all 48 samples with per-sample file links →
- GSE254137 Immunomodulatory effects of glucocorticoid-induced leucine zipper (GILZ) expression in murine bone-marrow derived macrophages. 18 samples shares bone-marrow, macrophages, derived
- GSE290443 Effects of WDFY3 overexpression on the transcriptomic profile of murine bone-marrow derived macrophages. 10 samples shares bone-marrow, macrophages, derived
- GSE78849 Investigation of the effect of succinate and dimethyl malonate on murine bone-marrow derived macrophages (BMDMs) treated with or without LPS 21 samples shares bone-marrow, macrophages, derived
- GSE166050 RNA sequencing to profile transcriptomes in murine bone-marrow-derived macrophages upon infection with Leptospira spp. 18 samples shares bone-marrow, macrophages, derived
- GSE301317 Differentially expressed genes in Bone-Marrow Derived Macrophages (M0) from DKO (Cdk8 flox/flox Vav-iCre Cdk19null) or VavCre control 8 samples shares bone-marrow, macrophages, derived
- GSE217269 RNA-seq analysis of Wild Type (WT) and Mettl3-/- (KO) BMDMs (bone-marrow-derived macrophages) Transcriptomes 6 samples shares bone-marrow, macrophages, derived
- GSE337254 Transcriptomic analysis of bone-marrow-derived macrophages treated with extracellular vesicles (EVs) from Aspergillus flavus 6 samples shares bone-marrow, macrophages, derived
- GSE336549 Effect of intravenous poly(lactide-co-glycolide) nanoparticles on M2-polarized bone-marrow derived macrophages 6 samples shares bone-marrow, macrophages, derived
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.