Transcriptomic profiling of long non-coding RNAs identifies circRmst as a regulator of midbrain dopamine neuron migration
RNA-seq (gene expression) · mouse · 21 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
- 21 samples: 17 distinct titles, 2 of them repeatedGroups 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
- Circular RNAs regulate neuron size and migration of midbrain dopamine neurons during developmentNature communications · 2024
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 GSE229488_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 PRJNA954734 and SRA study SRP432164. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 21 sample titles: 17 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.
- GSM7164231 E14 GFP negative1
- GSM7164232 E14 GFP negative2
- GSM7164233 E14 GFP negative3
- GSM7164234 E14 GFP positive1
- GSM7164235 E14 GFP positive2
- GSM7164236 E14 GFP positive3
- GSM7164237 E14 GFP positive1 timeseries
- GSM7164238 E14 GFP positive2 timeseries
- GSM7164239 E14 GFP positive3 timeseries
- GSM7164240 E16 GFP positive1 timeseries
- GSM7164241 E16 GFP positive2 timeseries
- GSM7164242 E16 GFP positive3 timeseries
- GSM7164243 P0 GFP positive1 timeseries
- GSM7164244 P0 GFP positive2 timeseries
- GSM7164245 P0 GFP positive3 timeseries
- GSM7164480 Scramble Control_1 (104494-001-001)
- GSM7164481 Scramble Control_2 (104494-001-002)
- GSM7164482 Scramble Control_3 (104494-001-003)
- GSM7164483 circRMST KD_1 (104494-001-004)
- GSM7164484 circRMST KD_2 (104494-001-005)
- GSM7164485 circRMST KD_3 (104494-001-006)
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- GSE325852 Translatome profiling reveals opposing alterations in inhibitory and excitatory neurons of Fragile X mice and identifies EPAC2 as a therapeutic target 69 samples shares identifies, neuron
- GSE302682 Sleeping Beauty mutagenesis identifies BACH2 and other regulators promoting CD8+ T cell persistence and effector function under tumor-associated chronic antigen stimulation - RNAseq 66 samples shares identifies, regulator
- GSE254090 A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders 87 samples shares non-coding, regulator
- GSE249978 Egr1 is a sex-specific regulator of neuronal chromatin, synaptic plasticity, and behaviour 52 samples shares regulator, neuron
- GSE334890 Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors 48 samples shares identifies, regulator
- GSE241378 Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of embryonic stem cell maintenance and neuronal differentiation. 36 samples shares regulator, neuron
- GSE331248 Hepatic translation rewiring in insulin deficiency identifies Reg3α as an insulin-independent glucoregulatory factor [RNA_Ribo_Seq: ID_Healthy] 20 samples shares identifies, regulator
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.