RNAseq of SMAD2/3DKO and Smad4KO in pluripotent mESC and EBs
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: 6 conditions, mostly in duplicateGroups 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
- A stepwise mode of TGFβ-SMAD signaling and DNA methylation regulates naïve-to-primed pluripotency and differentiationNature communications · 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 GSE240785_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 PRJNA1005247 and SRA study SRP454916. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 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.
- GSM7709274 WT_D0_Rep1 WT_D0
- GSM7709275 WT_D0_Rep2 WT_D0
- GSM7709276 WT_D4_Rep1 WT_D4
- GSM7709277 WT_D4_Rep2 WT_D4
- GSM7709278 S2/3DKO_D0_Rep1 S2/3DKO_D0
- GSM7709279 S2/3DKO_D0_Rep2 S2/3DKO_D0
- GSM7709280 S2/3DKO_D4_Rep1 S2/3DKO_D4
- GSM7709281 S2/3DKO_D4_Rep2 S2/3DKO_D4
- GSM7709282 S4KO_D0_Rep1 S4KO_D0
- GSM7709283 S4KO_D0_Rep2 S4KO_D0
- GSM7709284 S4KO_D4_Rep1 S4KO_D4
- GSM7709285 S4KO_D4_Rep2 S4KO_D4
- GSE240786 The binding sites of SMAD2/3, Dnmt3a and Dnmt3b in pluripotent mESC, EBs and ME when Smad4 is lost with or without Dnmt3b knockdown 22 samples shares smad2, pluripotent, mesc
- GSE300213 Comparing gene expression effects of Hnrnpf knockout in mESCs while they are pluripotent vs. after they have been differentiating for 4 days due to LIF removal [RNA-seq] 6 samples shares pluripotent, mesc
- GSE303716 Nodal/Smad2 signaling sustains developmental pausing by repressing Pparg -mediated lipid metabolism [RNA-Seq] 24 samples shares smad2
- GSE256393 Protogenin Facilitates Trunk-to-Tail HOX Code Transition via Modulating GDF11/SMAD2 Signaling in Mammalian Embryos 8 samples shares smad2
- GSE299451 Cardiomyocyte-Specific Smad7 protects the pressure-overloaded heart, inhibiting the TbR1/Smad2/3 cascade [Smad7 knockout] 8 samples shares smad2
- GSE101772 Fibroblast-specific genetic dissection of TGFβ-Smad2/3 signaling in cardiac fibrosis 8 samples shares smad2
- GSE299359 Cardiomyocyte-Specific Smad7 protects the pressure-overloaded heart, inhibiting the TbR1/Smad2/3 cascade 8 samples shares smad2
- GSE168855 Transcriptional profiling of microglia lacking Smad2/3 8 samples shares smad2
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.