Gene expression in Phf6-deleted and Phf6-intact foetal mouse cortical neurons and foetal mouse cortex assessed by RNA-seq
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: 5 × Cortex Phf6 knock-out vs 4 × Cultured cortical neurons Phf6 knock-out vs 3 × Cortex wild type vs 3 × Cultured cortical neurons wild typeGroups 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.
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 GSE275729_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 PRJNA1152848 and SRA study SRP528814. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 4 replicated groups read from 15 sample titles; they account for 15 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.
- GSM8483583 Cortex wild type replicate 1 Cortex wild type
- GSM8483584 Cortex wild type replicate 2 Cortex wild type
- GSM8483585 Cortex wild type replicate 3 Cortex wild type
- GSM8483586 Cortex Phf6 knock-out replicate 1 Cortex Phf6 knock-out
- GSM8483587 Cortex Phf6 knock-out replicate 2 Cortex Phf6 knock-out
- GSM8483588 Cortex Phf6 knock-out replicate 3 Cortex Phf6 knock-out
- GSM8483589 Cortex Phf6 knock-out replicate 4 Cortex Phf6 knock-out
- GSM8483590 Cortex Phf6 knock-out replicate 5 Cortex Phf6 knock-out
- GSM8483591 Cultured cortical neurons wild type replicate 1 Cultured cortical neuro…
- GSM8483592 Cultured cortical neurons wild type replicate 2 Cultured cortical neuro…
- GSM8483593 Cultured cortical neurons wild type replicate 3 Cultured cortical neuro…
- GSM8483594 Cultured cortical neurons Phf6 knock-out replicate 1 Cultured cortical neuro…
- GSM8483595 Cultured cortical neurons Phf6 knock-out replicate 2 Cultured cortical neuro…
- GSM8483596 Cultured cortical neurons Phf6 knock-out replicate 3 Cultured cortical neuro…
- GSM8483597 Cultured cortical neurons Phf6 knock-out replicate 4 Cultured cortical neuro…
- GSE335970 KMT2C catalytic activity regulates enhancer H3K4me1 and synaptic gene expression in cortical excitatory neurons [RNA-Seq] 39 samples shares cortical, neurons, rna-seq
- GSE213012 Total and dendritic RNA-sequencing from primary mouse cortical neurons 32 samples shares cortical, neurons, rna-seq
- GSE262872 Mouse cortex PV interneuron transcriptome changes assessed with FACS-assisted bulk RNA-seq 16 samples shares assessed, rna-seq, cortex
- GSE68715 Global transcriptional analysis of mouse fibroblasts, chemically-induced neurons (neuron-like cells) from mouse fibroblasts and mouse primary cortical neurons by RNA-seq 15 samples shares cortical, neurons, rna-seq
- GSE246688 CUT&Tag, ATAC-seq, bulk RNA-seq and single-nucleus RNA-seq analysis of histone variant H2BE in cortical neurons 67 samples shares cortical, neurons, rna-seq
- GSE279677 Single cell deletion of the transcription factors Sox9 and Trps1 reveals novel functions in adult cortical astrocytes [RNA-seq] 289 samples shares cortical, rna-seq
- GSE246589 Organization of Corticocortical and Thalamocortical Top-down Inputs in the Primary Visual Cortex 91 samples shares cortical, cortex
- GSE278199 Microglia regulate cortical remyelination via ΤNFR1-dependent phenotypic polarization [scRNA-Seq] 45 samples shares cortical, rna-seq
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.