Cell-Type-Specific Splicing of Transcription Regulators and Ptbp1 by Rbfox1/2/3 in the Developing Neocortex
RNA-seq (gene expression) · mouse · 25 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
- 25 samples: 8 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.
- Paper
- Cell-Type-Specific Splicing of Transcription Regulators and Ptbp1 by Rbfox1/2/3 in the Developing NeocortexThe Journal of neuroscience : the official journal of the Society for Neuroscience · 2025
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 GSE283469_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 PRJNA1000980 and SRA study SRP452539. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 22 samples.
How we read this: 8 replicated groups read from 25 sample titles; they account for 22 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.
- GSM8662990 IUE_PCIG_E13_to_E14_replicate_1 IUE_PCIG_E13_to_E14
- GSM8662991 IUE_PCIG_E13_to_E14_replicate_2 IUE_PCIG_E13_to_E14
- GSM8662992 IUE_Rbfox3_E13_to_E14_replicate_1 IUE_Rbfox3_E13_to_E14
- GSM8662993 IUE_Rbfox3_E13_to_E14_replicate_2 IUE_Rbfox3_E13_to_E14
- GSM8662994 E14_Tbr2_GFP_positive_replicate_1 E14_Tbr2_GFP_positive
- GSM8662995 E14_Tbr2_GFP_positive_replicate_2 E14_Tbr2_GFP_positive
- GSM8662996 E14_Tbr2_GFP_negative_replicate_1 E14_Tbr2_GFP_negative
- GSM8662997 E14_Tbr2_GFP_negative_replicate_2 E14_Tbr2_GFP_negative
- GSM8662998 E14_Tubb3_GFP_positive_replicate_1 E14_Tubb3_GFP_positive
- GSM8662999 E14_Tubb3_GFP_positive_replicate_2 E14_Tubb3_GFP_positive
- GSM8663000 Neuro2a_Control_replicate_1 Neuro2a_Control
- GSM8663001 Neuro2a_Control_replicate_2 Neuro2a_Control
- GSM8663002 Neuro2a_Control_replicate_3 Neuro2a_Control
- GSM8663003 Neuro2a_Control_replicate_4 Neuro2a_Control
- GSM8663004 Neuro2a_Meis2_Neuron_replicate_1 Neuro2a_Meis2_Neuron
- GSM8663005 Neuro2a_Meis2_Neuron_replicate_2 Neuro2a_Meis2_Neuron
- GSM8663006 Neuro2a_Meis2_Neuron_replicate_3 Neuro2a_Meis2_Neuron
- GSM8663007 Neuro2a_Meis2_Neuron_replicate_4 Neuro2a_Meis2_Neuron
- GSM8663008 Neuro2a_Meis2_RGC_replicate_1 Neuro2a_Meis2_RGC
- GSM8663009 Neuro2a_Meis2_RGC_replicate_2 Neuro2a_Meis2_RGC
- GSM8663010 Neuro2a_Meis2_RGC_replicate_3 Neuro2a_Meis2_RGC
- GSM8663011 Neuro2a_Meis2_RGC_replicate_4 Neuro2a_Meis2_RGC
- GSM8663012 Pacbio_E14.RGC
- GSM8663013 Pacbio_E14.IPC
- GSM8663014 Pacbio_E14.neuron
- GSE336247 Cardiac fibroblast deletion of PTBP1 modulates the profibrotic response by alternative splicing II 36 samples shares ptbp1, splicing
- GSE287133 Cardiac fibroblast deletion of PTBP1 modulates the profibrotic response by alternative splicing. 12 samples shares ptbp1, splicing
- GSE282096 Diminished transcriptional activity and splicing changes drive gene length-biased rewiring in the aging transcriptome (RNA-Seq) 94 samples shares transcription, splicing
- GSE242179 Role of the histone variant H2A.Z.1 in memory, transcription, and alternative splicing is mediated by lysine modification 40 samples shares transcription, splicing
- GSE282097 Diminished transcriptional activity and splicing changes drive gene length-biased rewiring in the aging transcriptome 116 samples shares transcription, splicing
- GSE283958 Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators 47 samples shares transcription, regulators
- GSE241378 Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of embryonic stem cell maintenance and neuronal differentiation. 36 samples shares transcription, splicing
- 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.