Pathogenicity of genomic duplications is determined by formation of novel chromatin domains (neo-TADs) (RNA-seq)
RNA-seq (gene expression) · mouse · 17 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
- 17 samples
- 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 GSE78105_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 PRJNA312623 and SRA study SRP070571. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 17 more — browse all 17 samples with per-sample file links →
- GSE291987 Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [RNA-Seq] 23 samples shares formation, chromatin, rna-seq
- GSE273306 Chromatin remodeler CHD4 establishes chromatin states required for ovarian reserve formation, maintenance, and germ cell survival [RNA-seq] 20 samples shares formation, chromatin, rna-seq
- GSE313112 Inhibition of METTL3 by STC-15 induces RNA misprocessing that results in dsRNA formation and activates innate immunity [RNA-Seq MC38] 69 samples shares formation, rna-seq
- GSE293599 The Polycomb Protein EED Constrains the SCLC Neuroendocrine Phenotype and Drives Lung Cancer Histological Transformation [Bulk RNA-seq] 50 samples shares formation, rna-seq
- GSE293374 An extracellular matrix niche secreted by epithelial cells drives intestinal organoid formation (RNA-seq) 44 samples shares formation, rna-seq
- GSE295772 Mechanisms governing interaction of the chromosomal protein SMCHD1 with chromatin determined by live-cell and single molecule imaging 36 samples shares determined, chromatin
- GSE261166 Transcription factor 21 regulates cardiac myofibroblast formation and fibrosis [RNA-Seq] 16 samples shares formation, rna-seq
- GSE215759 Mettl3-dependent m6A modification is essential for effector differentiation and memory formation of CD8+ T cells [RNA-seq] 15 samples shares formation, 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.