Nuclear-localized HDAC4 promotes neuroprotection of retinal ganglion cells after optic nerve injury
Single-cell RNA-seq · mouse · 12 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Mus musculus (mouse)
- Samples
- 12 samples: 6 conditions, mostly in duplicateGroups 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 GSE252860_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1062840 and SRA study SRP482787. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 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.
- GSM8008996 HDAC4NT_rep1 HDAC4NT
- GSM8008997 HDAC4NT_rep2 HDAC4NT
- GSM8008998 HDAC4NT_1dpc_rep1 HDAC4NT_1dpc
- GSM8008999 HDAC4NT_1dpc_rep2 HDAC4NT_1dpc
- GSM8009000 HDAC43SA_rep1 HDAC43SA
- GSM8009001 HDAC43SA_rep2 HDAC43SA
- GSM8009002 HDAC43SA_1dpc_rep1 HDAC43SA_1dpc
- GSM8009003 HDAC43SA_1dpc_rep2 HDAC43SA_1dpc
- GSM8009004 Control_rep1 Control
- GSM8009005 Control_rep2 Control
- GSM8009006 Control_1dpc_rep1 Control_1dpc
- GSM8009007 Control_1dpc_rep2 Control_1dpc
- GSE261492 Hypertension Promotes Neuroinflammation, Brain Injury and Cognitive Impairment 48 samples shares promotes, injury
- GSE254704 Skeletal muscle cystathionine γ-lyase deficiency promotes obesity and insulin resistance and results in hyperglycemia and skeletal muscle injury upon HFD in mice 32 samples shares promotes, injury
- GSE232327 Activation of imprinted gene Pw1 promotes cardiac fibrosis after ischemic injury 41 samples shares promotes, injury
- GSE287148 Catalytic activity of nuclear METTL3 promotes functional m6A modifications that drive retinal development 6 samples shares promotes, retinal
- GSE228457 IL-7 mediated immunoregulatory feedback loop promotes dampening of immune effector functions by hypoinflammatory monocytes. 305 samples shares promotes
- GSE218178 Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance 183 samples shares promotes
- GSE303699 Autoimmune Disease Risk Gene ANKRD55 Promotes Th17 Effector Function Through Metabolic Modulation [RNA-Seq] 60 samples shares promotes
- GSE318897 L-DOPA treatment promotes sustained neurovascular and synaptic homeostasis in the diabetic retina 53 samples shares promotes
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.