Transcriptomics of BMDM treated with PTEN in the presence or absence of STAT1 inhibitors
RNA-seq (gene expression) · mouse · 16 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
- 16 samples: 4 × CON_CON vs 4 × CON_PTEN vs 4 × F_CON vs 4 × F_PTENGroups 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
- Secreted PTEN binds PLXDC2 on macrophages to drive antitumor immunity and tumor suppressionDevelopmental cell · 2024
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 GSE249265_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 PRJNA1048390 and SRA study SRP475674. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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.
- GSM7932570 CON_CON_1 CON_CON
- GSM7932571 CON_CON_2 CON_CON
- GSM7932572 CON_CON_3 CON_CON
- GSM7932573 CON_CON_4 CON_CON
- GSM7932574 CON_PTEN_1 CON_PTEN
- GSM7932575 CON_PTEN_2 CON_PTEN
- GSM7932576 CON_PTEN_3 CON_PTEN
- GSM7932577 CON_PTEN_4 CON_PTEN
- GSM7932578 F_CON_1 F_CON
- GSM7932579 F_CON_2 F_CON
- GSM7932580 F_CON_3 F_CON
- GSM7932581 F_CON_4 F_CON
- GSM7932582 F_PTEN_1 F_PTEN
- GSM7932583 F_PTEN_2 F_PTEN
- GSM7932584 F_PTEN_3 F_PTEN
- GSM7932585 F_PTEN_4 F_PTEN
- GSE276416 Data Mining of IFNgamma-induced macrophage and Atherosclerotic Plaque Transcriptomes predicts a macrophage-specific role of STAT1 in human atherosclerosis [BMDM] 18 samples shares stat1, bmdm
- GSE293700 Transcriptome analysis in the prefrontal cortex of PTEN KI heterozygous mice treated with drug 60 samples shares pten, treated
- GSE279654 BMDM from Young and Aged Mice Treated with β-glucan 42 samples shares bmdm, treated
- GSE319618 Prefrontal cortex bulk RNA-seq analysis of drug-treated PTEN KI heterozygous mice at P40 30 samples shares pten, treated
- GSE196249 Secondary LPS stimulation of BMDMs differentiated from bone marrow of C57B/6J mice treated with 4xLPS, 1xLPS or PBS 18 samples shares bmdm, treated
- GSE298720 Global gene expression profiles were compared among IL1B-treated, Ad-OSCAR-treated, and control mice, with or without subsequent treatment with OSCAR inhibitors (Brivudine or Adefovir). 35 samples shares inhibitors, treated
- GSE201128 The response to lipopolysaccharide (LPS) of bone marrow derived macrophages treated with oxysterol binding protein (OSBP) inhibitors 30 samples shares inhibitors, treated
- GSE211774 RNA-seq of bilateral frontal cortex tissues in mice treated with HDAC complex inhibitors 22 samples shares inhibitors, treated
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.