The long noncoding RNA Peanut promotes neurogenesis and rod photoreceptor differentiation during postnatal retinal development.
RNA-seq (gene expression) · mouse · 14 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
- 14 samples: 4 × P0 Peanut Heterozygote vs 4 × P0 Peanut Knockout vs 4 × P22 Peanut Knockout vs 2 × P22 Peanut HeterozygoteGroups 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.
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 GSE310182_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 PRJNA1365243 and SRA study SRP645447. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 4 replicated groups read from 14 sample titles; they account for 14 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.
- GSM9290656 P0 Peanut Heterozygote 1 P0 Peanut Heterozygote
- GSM9290657 P0 Peanut Heterozygote 2 P0 Peanut Heterozygote
- GSM9290658 P0 Peanut Heterozygote 3 P0 Peanut Heterozygote
- GSM9290659 P0 Peanut Heterozygote 4 P0 Peanut Heterozygote
- GSM9290660 P0 Peanut Knockout 1 P0 Peanut Knockout
- GSM9290661 P0 Peanut Knockout 2 P0 Peanut Knockout
- GSM9290662 P0 Peanut Knockout 3 P0 Peanut Knockout
- GSM9290663 P0 Peanut Knockout 4 P0 Peanut Knockout
- GSM9290664 P22 Peanut Heterozygote 1 P22 Peanut Heterozygote
- GSM9290665 P22 Peanut Heterozygote 2 P22 Peanut Heterozygote
- GSM9290666 P22 Peanut Knockout 1 P22 Peanut Knockout
- GSM9290667 P22 Peanut Knockout 2 P22 Peanut Knockout
- GSM9290668 P22 Peanut Knockout 3 P22 Peanut Knockout
- GSM9290669 P22 Peanut Knockout 4 P22 Peanut Knockout
- GSE283880 Sox15 is a novel retinal developmental gene that promotes cone photoreceptor differentiation through inhibition of alternative rod photoreceptor fates 33 samples shares photoreceptor, promotes, retinal
- GSE248780 ZFP57 is a regulator of postnatal growth and life-long health 120 samples shares postnatal, long
- GSE328562 Histone Demethylase KDM6B Promotes Postnatal Oligodendrocyte Development and Cortical Myelination 24 samples shares postnatal, promotes
- GSE296005 Chronic HIF1A activity in rod photoreceptors causes type 3 neovascularization and retinal atrophy 18 samples shares photoreceptor, retinal
- GSE269514 Age-Related Retinal Degeneration Resulting from the Deletion of Shp2 Tyrosine Phosphatase in Photoreceptor 12 samples shares photoreceptor, retinal
- GSE310313 The long noncoding RNA Malat1 contains an internal ribosome entry site mediating micropeptide translation 12 samples shares noncoding, long
- GSE327434 Halofantrine protects photoreceptors in multiple models of retinal degeneration [rd10] 10 samples shares photoreceptor, retinal
- GSE342498 Developmental Synchrony of Retinal Waves, Apoptosis, and Angiogenesis in Postnatal Retina 1 samples shares postnatal, retinal
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.