Genome-wide transcriptome analysis of whole brain (Except for the cerebellum and olfactory bulb) in CBA/N mouse (Mus musculus)
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 3 × 1 vs 3 × 2 vs 3 × 7 vs 3 × 8Groups 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 GSE278078_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 PRJNA1165650 and SRA study SRP534958. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8539300 1-1 1
- GSM8539301 1-2 1
- GSM8539302 1-3 1
- GSM8539303 2-1 2
- GSM8539304 2-2 2
- GSM8539305 2-3 2
- GSM8539306 7-1 7
- GSM8539307 7-2 7
- GSM8539308 7-3 7
- GSM8539309 8-1 8
- GSM8539310 8-2 8
- GSM8539311 8-3 8
- GSE253581 Transcriptional profiling of CD11b+ microglia isolated from cerebellum and olfactory bulb-removed brains of K18-seeded P301L, PBS-injected P301L and PBS-injected FVB at 1-week, 1-month, and 3-months post-injection. 27 samples shares cerebellum, olfactory, brain
- GSE253582 Transcriptional profiling of CD11b+ microglia isolated from cerebellum and olfactory bulb-removed brains of SAMP8 and SAMR1 mice at 2, 5, and 9 months of age. 18 samples shares cerebellum, olfactory, brain
- GSE307546 Transcriptomics Analysis of bulk RNA from dissected brain regions (medial prefrontal cortex, cerebellum, and hippocampus) from 129/Sv-Cyp2e1tm1Gonz/J (CYP2E1-KO) and 129S1/SvImJ (WT) mice 48 samples shares cerebellum, brain
- GSE274703 Smug1 DNA glycosylase modulates the perception of smell in mouse brain through downregulation of olfactory receptor genes 30 samples shares olfactory, brain
- GSE243373 Genome-wide 5mC and 5hmC patterns determine unique transcriptional signatures,regulators and exon inclusion of neural cell types in mouse brain [RNA-Seq] 15 samples shares genome-wide, brain
- GSE244256 Genome-wide 5mC and 5hmC patterns determine unique transcriptional signatures,regulators and exon inclusion of neural cell types in mouse brain 24 samples shares genome-wide, brain
- GSE169312 Next-generation sequencing Facilitates Quantitative Analysis of Wild Type and EED-/- mice cerebellum Transcriptomes and Genome-wide maps of chromatin state in Wild Type and EED-/- mice cerebellum 12 samples shares genome-wide, cerebellum
- GSE283534 scRNA-seq transcriptomic profiles of cochlear and vestibular hair cells from adult mice [10_weeks_CBAJ] 10 samples shares cba
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.