Ngn family transcription factors reprogram mouse embryonic fibroblasts into neuron-like cells
RNA-seq (gene expression) · mouse · 15 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
- 15 samples: 15 samples, each with a distinct title — no replicated groupsGroups 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
- Retinal Ganglion Cell Fate Induction by Ngn-Family Transcription FactorsInvestigative ophthalmology & visual science · 2023
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 GSE234613_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 PRJNA982132 and SRA study SRP442194. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 15 sample titles: 15 distinct titles with little repetition. 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.
- GSM7471897 Ctrl_a
- GSM7471898 Ctrl_b
- GSM7471899 Ctrl_c
- GSM7471900 D1_Ngn1_a
- GSM7471901 D1_Ngn1_b
- GSM7471902 D1_Ngn1_c
- GSM7471903 D1_Ngn3_a
- GSM7471904 D1_Ngn3_b
- GSM7471905 D1_Ngn3_c
- GSM7471906 D13_Ngn1_a
- GSM7471907 D13_Ngn1_b
- GSM7471908 D13_Ngn1_c
- GSM7471909 D13_Ngn3_a
- GSM7471910 D13_Ngn3_b
- GSM7471911 D13_Ngn3_c
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- GSE283382 N6-methyladenosine modulate second cell fate decision by enhancing mRNA stability of pivotal transcription factors during primitive endoderm development [TBLC_RNAseq] 98 samples shares transcription, factors
- GSE282280 DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation. 93 samples shares transcription, factors
- GSE268172 Stable maintenance of MERVL-positive embryonic stem cells reveals sustained transcriptional programs and enhancer remodeling 45 samples shares transcription, embryonic
- GSE243165 Signal-responsive transcription factors cooperate to establish alveolar macrophage identity 42 samples shares transcription, factors
- GSE326173 Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by regulating expression of AP-1 transcription factors and their target genes [ChIP-seq] 42 samples shares transcription, factors
- GSE281941 Klf5 functions as a multi-lineage reprogramming transcription factor 30 samples shares transcription, reprogram
- GSE284504 Transcriptional profiling of brain from a zQ175 KI mouse model of Huntington's disease 335 samples shares transcription
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.