Age-Related Retinal Degeneration Resulting from the Deletion of Shp2 Tyrosine Phosphatase in Photoreceptor
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 × ko_bead vs 3 × wt_bead vs 3 × ko_input vs 3 × wt_inputGroups 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.
- Paper
- Age-related retinal degeneration resulting from the deletion of Shp2 tyrosine phosphatase in photoreceptor neuronsCell death & disease · 2024
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 GSE269514_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 PRJNA1122170 and SRA study SRP513044. 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.
- GSM8317905 ko_bead_1 ko_bead
- GSM8317906 ko_bead_2 ko_bead
- GSM8317907 ko_bead_3 ko_bead
- GSM8317908 wt_bead_1 wt_bead
- GSM8317909 wt_bead_2 wt_bead
- GSM8317910 wt_bead_3 wt_bead
- GSM8317911 ko_input_1 ko_input
- GSM8317912 ko_input_2 ko_input
- GSM8317913 ko_input_3 ko_input
- GSM8317914 wt_input_1 wt_input
- GSM8317915 wt_input_2 wt_input
- GSM8317916 wt_input_3 wt_input
- GSE271791 Intermittent fasting alleviates photoreceptor degeneration and retina inflammation in oxidative stress-induced model of Age-Related Macular Degeneration 12 samples shares photoreceptor, degeneration, age-related
- GSE307127 Immune Receptor Lag3 Deletion Alleviates Neurodegeneration Phenotypes in a Mouse Model of Alzheimer’s Disease 36 samples shares degeneration, deletion
- GSE247436 Deletion of Gba in neurons, but not microglia, causes neurodegeneration in a Gaucher mouse model 32 samples shares degeneration, deletion
- GSE271038 Natural killer cells cooperate with neutrophils to suppress pathological angiogenesis in neovascular age-related macular degeneration 22 samples shares degeneration, age-related
- GSE291600 Complement C3aR deletion does not attenuate neurodegeneration in a tauopathy model or alter acute inflammation-induced gene expression changes in the brain 20 samples shares degeneration, deletion
- GSE272674 An in vitro high-content screening unveils miR-429 as a protective molecule in photoreceptor degeneration models 18 samples shares photoreceptor, degeneration
- GSE288035 Smoking aggravates neovascular age-related macular degeneration via Sema4D-PlexinB1 axis-mediated activation of pericytes [bulk RNA-seq] 16 samples shares degeneration, age-related
- GSE305276 Osteocyte-specific deletion of Gasdermin D drives osteoarthritis cartilage degeneration by promoting inflammation and remodeling in subchondral bone 9 samples shares degeneration, deletion
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.