PBRM1 RNA-seq [4T1]
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 3 × 4T1_control_0h_biol vs 3 × 4T1_control_TGF_biol vs 3 × 4T1_PBRM1_KO_0h_biol vs 3 × 4T1_PBRM1_KO_TGF_biolGroups 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.
Read the full summary ↓
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 GSE327926_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 PRJNA1452994 and SRA study SRP691562. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9668747 4T1_control_0h_biol rep1 4T1_control_0h_biol
- GSM9668748 4T1_control_0h_biol rep2 4T1_control_0h_biol
- GSM9668749 4T1_control_0h_biol rep3 4T1_control_0h_biol
- GSM9668750 4T1_control_TGF_biol rep1 4T1_control_TGF_biol
- GSM9668751 4T1_control_TGF_biol rep2 4T1_control_TGF_biol
- GSM9668752 4T1_control_TGF_biol rep3 4T1_control_TGF_biol
- GSM9668753 4T1_PBRM1_KO_0h_biol rep1 4T1_PBRM1_KO_0h_biol
- GSM9668754 4T1_PBRM1_KO_0h_biol rep2 4T1_PBRM1_KO_0h_biol
- GSM9668755 4T1_PBRM1_KO_0h_biol rep3 4T1_PBRM1_KO_0h_biol
- GSM9668756 4T1_PBRM1_KO_TGF_biol rep1 4T1_PBRM1_KO_TGF_biol
- GSM9668757 4T1_PBRM1_KO_TGF_biol rep2 4T1_PBRM1_KO_TGF_biol
- GSM9668758 4T1_PBRM1_KO_TGF_biol rep3 4T1_PBRM1_KO_TGF_biol
- GSE312302 NMuMG PBRM1 RNA-seq, ATAC-seq, and ChIP-seq 171 samples shares pbrm1, rna-seq
- GSE241165 Characterizing the gene expression profiles of 4T1 and 4T1.2 cells at different stages of bone metastsis using SMART-Seq2 technology 1248 samples shares 4t1
- GSE298752 NMuMG PBRM1 ATAC-seq 24 samples shares pbrm1
- GSE264105 Plate-based scRNA-seq of plasma-positive microglia and plasma-negative microglia in young mice 1111 samples shares rna-seq
- GSE326100 scRNA-seq of mouse cochlea organoid cells 768 samples shares rna-seq
- GSE311449 Single cell RNA-seq of mouse brain vascular cells with Smart-seq2 method 391 samples shares rna-seq
- GSE319614 Bulk RNA-seq transcriptome profiling of hippocampus across 17 autism spectrum disorder mouse models 269 samples shares rna-seq
- GSE326452 Bulk RNA-seq of mouse brain following closed head injury: role of IL-1R1 signaling 200 samples shares rna-seq
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.