O-GlcNAcase Regulates Pluripotency States of Human Embryonic Stem Cells
RNA-seq (gene expression) · human · 12 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
- Homo sapiens (human)
- Samples
- 12 samples: 3 × PXGL_siNC vs 3 × PXGL_siOGA vs 3 × PXGL_siP300 vs 3 × siP300+OGAGroups 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
- O-GlcNAcase regulates pluripotency states of human embryonic stem cellsStem cell reports · 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 GSE256456_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 PRJNA1079719 and SRA study SRP491352. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8098723 PXGL_siNC_1 PXGL_siNC
- GSM8098724 PXGL_siNC_2 PXGL_siNC
- GSM8098725 PXGL_siNC_3 PXGL_siNC
- GSM8098726 PXGL_siOGA_1 PXGL_siOGA
- GSM8098727 PXGL_siOGA_2 PXGL_siOGA
- GSM8098728 PXGL_siOGA_3 PXGL_siOGA
- GSM8098729 PXGL_siP300_1 PXGL_siP300
- GSM8098730 PXGL_siP300_2 PXGL_siP300
- GSM8098731 PXGL_siP300_3 PXGL_siP300
- GSM8098732 siP300+OGA_1 siP300+OGA
- GSM8098733 siP300+OGA_2 siP300+OGA
- GSM8098734 siP300+OGA_3 siP300+OGA
- GSE182804 DDX18 coordinates nucleolus phase separation and chromatin organization to control the pluripotency of human embryonic stem cells. 10 samples shares pluripotency, embryonic, stem
- GSE249035 Sex-biased Gene Expression During Neural Differentiation of Human Embryonic Stem Cells 72 samples shares embryonic, stem
- GSE274217 METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [RNA-Seq] 28 samples shares pluripotency, stem
- GSE216593 Generation of megakaryocytes and functional platelets from human embryonic stem cells 18 samples shares embryonic, stem
- GSE245986 Profiling circular RNAs across human embryonic stem cell differentiation identifies the role of circACVR2A(4-6) in neuroectoderm lineage differentiation. 54 samples shares embryonic, stem
- GSE274620 Temporal multiomics gene expression data across human embryonic stem cell derived cardiomyocyte differentiation [RNA-seq] 20 samples shares embryonic, stem
- GSE305933 Temporal multi-omics gene expression data across human embryonic stem cell-derived polyhormonal cell differentiation [RNA-seq] 20 samples shares embryonic, stem
- GSE245984 Profiling circular RNAs across human embryonic stem cell differentiation identifies the role of circACVR2A(4-6) in neuroectoderm lineage differentiation [Total_circACRVA] 18 samples shares embryonic, stem
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.