Effect of depletion of Nsd1 or Ezh2 on gene expression during pluripotency transition
Single-cell RNA-seq · mouse · 8 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Mus musculus (mouse)
- Samples
- 8 samples: 2 × CTRL-P vs 2 × Nsd1 KO vs 2 × CTRL-E vs 2 × Ezh2 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.
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 GSE334791_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1476514 and SRA study SRP707990. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 8 sample titles; they account for 8 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.
- GSM9797105 CTRL-P_1 CTRL-P
- GSM9797106 CTRL-P_2 CTRL-P
- GSM9797107 Nsd1 KO1 Nsd1 KO
- GSM9797108 Nsd1 KO2 Nsd1 KO
- GSM9797109 CTRL-E_1 CTRL-E
- GSM9797110 CTRL-E_2 CTRL-E
- GSM9797111 Ezh2 KO1 Ezh2 KO
- GSM9797112 Ezh2 KO2 Ezh2 KO
- GSE294457 TCA cycle rewiring underpins histone acetylation sourcing and cell-fate transitions during exit from naive pluripotency 12 samples shares pluripotency, transition
- GSE252224 Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition [RNA-Seq 1] 18 samples shares pluripotency, transition
- GSE293593 Slow RNAPII elongation facilitates early pluripotency cell transitions without reducing replication fork rates 17 samples shares pluripotency, transition
- GSE253147 Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition 33 samples shares pluripotency, transition
- GSE264171 Effects at the transcriptomic level after knockout of Eed, Ezh2, Brd8 or Nr6a1 in spinal cord neural progenitor differentiation [bulkRNAseq] 41 samples shares ezh2
- GSE279346 Ezh2 Delays Activation of Differentiation Genes During Normal Cerebellar Granule Neuron Development and in Medulloblastoma [RNA-seq] 15 samples shares ezh2
- GSE297143 EZH2 alters aggressive variant prostate cancer subtype evolution, but is not required for neuroendocrine prostate cancer [RNAseq] 54 samples shares ezh2
- GSE291454 A conserved function of EZH2-PRC2 in the repression of primitive endoderm cell fate [RNA-Seq - mouse] 22 samples shares ezh2
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.