Impact of ribosomal depletion, PCR ramp rate, and fragment length on RNA-seq
RNA-seq (gene expression) · mouse · 34 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
- 34 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.
- Paper
- Sources of non-uniform coverage in short-read RNA-Seq databioRxiv : the preprint server for biology · 2025
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 GSE288460_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 PRJNA1217800 and SRA study SRP560888. 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.
+ 34 more — browse all 34 samples with per-sample file links →
- GSE288300 Postmitotic transcription and 3D regulation show locus-specific and differentiation-specific sensitivity to cohesin depletion [RNA-seq] 27 samples shares depletion, rna-seq
- GSE248755 RNA-seq of V-SZV derived aNS cells with siRNA mediated depletion of Pbx1, Tcf3 and Tcf4 21 samples shares depletion, rna-seq
- GSE291043 PUS10-induced tRNA fragmentation impacts retrotransposon-driven inflammation [Polysome profiling] 18 samples shares fragment, impact
- GSE254077 Effect of depletion of NR4A3 on vascular calcification [RNA-seq] 12 samples shares depletion, rna-seq
- GSE271355 Galectin 3-binding protein (Lgals3bp) depletion attenuates hepatic fibrosis by reducing transforming growth factor-β1 (TGF-β1) availability and inhibits hepatocarcinogenesis [PH RNA-seq] 12 samples shares depletion, rna-seq
- GSE287164 Effect of depletion of ISG20 on gene expression in EMT6 mouse breast cancer cells with RNA-Seq. 12 samples shares depletion, rna-seq
- GSE327297 Ribo-Tweezer: rapid removal of ribosomal proteins reveals new layers of post-transcriptional gene-regulation [RNA-Seq] 12 samples shares ribosomal, rna-seq
- GSE313643 Single cell RNA-seq of mouse brain microvascular fragments with Smart-seq2 method 9 samples shares fragment, 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.