Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons
RNA-seq (gene expression) · mouse · 19 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
- 19 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.
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 GSE48895_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 PRJNA212143 and SRA study SRP027411. 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.
+ 19 more — browse all 19 samples with per-sample file links →
- GSE237916 Regulation of T helper cell differentiation by the interplay between histone modification and chromatin interaction 197 samples shares interplay, chromatin
- GSE200323 Establishment of chromatin architecture interplays with embryo hypertranscription 158 samples shares interplay, chromatin
- GSE314917 FACT maintains nucleosomes around promoters and opposes to the spreading of chromatin factors, thereby playing a major role in chromatin architecture 115 samples shares chromatin, promoter
- GSE264193 H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [ChIP-seq] 57 samples shares chromatin, dynamics
- GSE283958 Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators 47 samples shares chromatin, promoter
- GSE233975 DOT1L activity limits transcription elongation velocity and favors RNAPII pausing to facilitate mutagenesis by AID 45 samples shares elongation, pausing
- GSE234065 Unexpected nuclear hormone receptor and chromatin dynamics regulate estrous cycle dependent gene expression 32 samples shares chromatin, dynamics
- GSE295991 Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at meiotic promoters in mice 32 samples shares chromatin, promoter
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.