Next generation sequencing facilliates quantitative analysis of Wild type and KitW/Wv Smooth muscle cells transcriptomes
RNA-seq (gene expression) · mouse · 10 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
- 10 samples: 5 × Wild type SMC vs 5 × WWv SMCGroups 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.
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 GSE168110_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 PRJNA706029 and SRA study SRP308920. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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.
- GSM5129118 Wild type SMC 1 Wild type SMC
- GSM5129119 Wild type SMC 2 Wild type SMC
- GSM5129120 Wild type SMC 3 Wild type SMC
- GSM5129121 Wild type SMC 4 Wild type SMC
- GSM5129122 Wild type SMC 5 Wild type SMC
- GSM5129123 WWv SMC 1 WWv SMC
- GSM5129124 WWv SMC 2 WWv SMC
- GSM5129125 WWv SMC 3 WWv SMC
- GSM5129126 WWv SMC 4 WWv SMC
- GSM5129127 WWv SMC 5 WWv SMC
- GSE183318 Next-Generation Sequencing to compare RNA transcripts between Adam19 wildtype and knockout mice 12 samples shares generation, next, wild
- GSE279927 RNA next-generation sequencing of cardiac fibroblasts isolated from young and old mice 7 days post-MI 25 samples shares generation, next
- GSE306935 The Integrated Stress Response Pathway Improves Aged Murine Muscle Stem Cell Activation and in vivo Regeneration 12 samples shares generation, muscle
- GSE329069 Deletion of P311 enhances regeneration in aged skeletal muscle 9 samples shares generation, muscle
- GSE248916 Metabolic Promotion of Adult and Aging Skeletal Muscle Regeneration by the Serine Biosynthesis Pathway 30 samples shares generation, muscle
- GSE254129 Macrophage histone lactylation during ischemia induced-muscle regeneration [CUT&Tag] 16 samples shares generation, muscle
- GSE98816 Single cell RNA-seq of mouse brain vascular transcriptomes 3186 samples shares transcriptomes
- GSE267938 Functional optic tract rewiring via subtype- and target-specific axonal regeneration and presynaptic activity enhancement 256 samples shares generation
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.