Nuclear actin structure regulates chromatin accessibility [RNA-seq]
RNA-seq (gene expression) · mouse · 18 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
- 18 samples: 18 samples, each with a distinct title — no replicated groupsGroups 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
- Nuclear actin structure regulates chromatin accessibilityNature communications · 2024
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 GSE242943_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 PRJNA1015598 and SRA study SRP459900. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 18 sample titles: 18 distinct titles with little repetition. 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.
- GSM7775376 MSC, CK666, replicate1, RNA-seq
- GSM7775377 MSC, CK666, replicate2, RNA-seq
- GSM7775378 MSC, CK666, replicate3, RNA-seq
- GSM7775379 MSC, CytoD, replicate1, RNA-seq
- GSM7775380 MSC, CytoD, replicate2, RNA-seq
- GSM7775381 MSC, CytoD, replicate3, RNA-seq
- GSM7775382 MSC, control, replicate1, RNA-seq
- GSM7775383 MSC, control, replicate2, RNA-seq
- GSM7775384 MSC, control, replicate3, RNA-seq
- GSM7775385 MSC, siRNA Arp4, replicate1, RNA-seq
- GSM7775386 MSC, siRNA Arp4, replicate2, RNA-seq
- GSM7775387 MSC, siRNA Arp4, replicate3, RNA-seq
- GSM7775388 MSC, siRNA Arp4 plus CK666, replicate1, RNA-seq
- GSM7775389 MSC, siRNA Arp4 plus CK666, replicate2, RNA-seq
- GSM7775390 MSC, siRNA Arp4 plus CK666, replicate3, RNA-seq
- GSM7775391 MSC, siRNA control, replicate1, RNA-seq
- GSM7775392 MSC, siRNA control, replicate2, RNA-seq
- GSM7775393 MSC, siRNA control, replicate3, RNA-seq
- GSE166225 Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates [RNA-seq] 288 samples shares chromatin, rna-seq
- GSE290224 Intermittent Fasting Reprograms Chromatin Accessibility to Modulate Gene Expression in Brain and Muscle 96 samples shares accessibility, chromatin
- GSE241587 Pervasive nuclear envelope ruptures precede ECM signaling and disease onset without activating cGAS-STING in Lamin cardiomyopathy mice [sci-RNA-seq] 96 samples shares nuclear, rna-seq
- GSE299114 Endothelial Cells retain inflammatory memory through chromatin remodeling [RNA-Seq 2] 53 samples shares chromatin, rna-seq
- GSE327304 Transcriptomic characterization of Wild type mouse Embryonic Stem Cells (mESCs), β-actin Knock out mESC and upon rescue with a nuclear localization signal β-actin 45 samples shares nuclear, actin
- GSE234248 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [RNA-seq] 24 samples shares accessibility, rna-seq
- GSE320350 Nuclear class 3 PI3K co-activates fasting-specific chromatin remodeling 12 samples shares chromatin, nuclear
- GSE269808 The antiviral nuclear body protein SP140 represses Ifnb1 transcript stabilization by the novel regulator RESIST [WT and SP140 KO RNA-seq] 12 samples shares nuclear, 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.