Accelerated evolution in the human lineage led to gain and loss of transcriptional enhancers in the RBFOX1 locus [midbrain]
RNA-seq (gene expression) · mouse · 10 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
- 10 samples: 5 × Midbrain-321-WT vs 5 × Midbrain-321-KOGroups 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
- Accelerated evolution in the human lineage led to gain and loss of transcriptional enhancers in the RBFOX1 locusScience advances · 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 GSE242502_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 PRJNA1013592 and SRA study SRP458881. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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.
- GSM7764679 Midbrain-321-WT1 Midbrain-321-WT
- GSM7764680 Midbrain-321-WT2 Midbrain-321-WT
- GSM7764681 Midbrain-321-WT4 Midbrain-321-WT
- GSM7764682 Midbrain-321-WT5 Midbrain-321-WT
- GSM7764683 Midbrain-321-WT6 Midbrain-321-WT
- GSM7764684 Midbrain-321-KO2 Midbrain-321-KO
- GSM7764685 Midbrain-321-KO3 Midbrain-321-KO
- GSM7764686 Midbrain-321-KO4 Midbrain-321-KO
- GSM7764687 Midbrain-321-KO5 Midbrain-321-KO
- GSM7764688 Midbrain-321-KO6 Midbrain-321-KO
- GSE312828 Integrated stress response couples mitochondrial fitness with lineage reprogramming to drive cancer evolution. [RNA-Seq] 24 samples shares evolution, lineage
- GSE287513 Integrated stress response couples mitochondrial fitness with lineage reprogramming to drive cancer evolution. 15 samples shares evolution, lineage
- GSE218155 ILC2 development requires GATA3-related super-enhancers after lineage commitment 17 samples shares enhancers, lineage
- GSE283469 Cell-Type-Specific Splicing of Transcription Regulators and Ptbp1 by Rbfox1/2/3 in the Developing Neocortex 25 samples shares rbfox1
- GSE264344 Early spatiotemporal evolution of the immune response elicited by adenovirus vector vaccination 195 samples shares evolution
- GSE215960 Subclonal evolution revealed by single-cell profiles of expressed mutations identifies adaptation mechanisms to immunotherapy in melanoma [scRNA-seq] 192 samples shares evolution
- GSE307881 Mouse Offspring Conceived by In Vitro Fertilization Exhibit Accelerated Reproductive Aging Through Early Ovarian Failure 151 samples shares accelerated
- GSE277241 Evaluation of the evolution of aged vs young lung tumor cells derived from ex vivo transformation 80 samples shares evolution
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.