Cardiac fibroblast deletion of PTBP1 modulates the profibrotic response by alternative splicing.
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 × control, untreated, biol vs 3 × control, TGFb treated, biol vs 3 × PTBP1 KO, untreated, biol vs 3 × PTBP1 KO, TGFb, 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.
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 GSE287133_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 PRJNA1211157 and SRA study SRP557654. 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.
- GSM8739243 control, untreated, biol rep 1 control, untreated, biol
- GSM8739244 control, untreated, biol rep 2 control, untreated, biol
- GSM8739245 control, untreated, biol rep 3 control, untreated, biol
- GSM8739246 control, TGFb treated, biol rep 1 control, TGFb treated, …
- GSM8739247 control, TGFb treated, biol rep 2 control, TGFb treated, …
- GSM8739248 control, TGFb treated, biol rep 3 control, TGFb treated, …
- GSM8739249 PTBP1 KO, untreated, biol rep 1 PTBP1 KO, untreated, bi…
- GSM8739250 PTBP1 KO, untreated, biol rep 2 PTBP1 KO, untreated, bi…
- GSM8739251 PTBP1 KO, untreated, biol rep 3 PTBP1 KO, untreated, bi…
- GSM8739252 PTBP1 KO, TGFb, biol rep 1 PTBP1 KO, TGFb, biol
- GSM8739253 PTBP1 KO, TGFb, biol rep 2 PTBP1 KO, TGFb, biol
- GSM8739254 PTBP1 KO, TGFb, biol rep 3 PTBP1 KO, TGFb, biol
- GSE336247 Cardiac fibroblast deletion of PTBP1 modulates the profibrotic response by alternative splicing II 36 samples shares ptbp1, profibrotic, alternative, fibroblast, modulates, deletion, splicing, cardiac
- GSE248443 RNA helicase DDX5 maintains cardiac function by regulating CamkIIδ alternative splicing [RNA-seq] 12 samples shares alternative, splicing, cardiac
- GSE286904 Persistent large-scale changes in alternative splicing in prefrontal cortical neuron types following psychedelic exposure 118 samples shares alternative, splicing
- GSE328655 A high-resolution, sex-stratified atlas of transcriptional and alternative splicing dynamics in the fasting mouse liver. 80 samples shares alternative, splicing
- GSE242179 Role of the histone variant H2A.Z.1 in memory, transcription, and alternative splicing is mediated by lysine modification 40 samples shares alternative, splicing
- GSE228599 High-throughput sensitive screening of small molecule modulators of microexon alternative splicing using dual Nano and Firefly luciferase reporters 34 samples shares alternative, splicing
- GSE279927 RNA next-generation sequencing of cardiac fibroblasts isolated from young and old mice 7 days post-MI 25 samples shares fibroblast, cardiac
- GSE319401 Exercise Mitigates Cardiac Dysfunction Post-MI in Ovariectomized Mice via miR-21/Sox7-Mediated Suppression of Cardiac Fibroblast Activation 24 samples shares fibroblast, cardiac
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.