Novel culture systems for naive human embryonic stem cells based on chemical molecule screening [RNA-seq]
RNA-seq (gene expression) · human · 16 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
- 16 samples: 7 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
- Optimized derivation and culture system of human naïve pluripotent stem cells with enhanced DNA methylation status and genomic stabilityProtein & cell · 2025
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 GSE252312_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 PRJNA1059627 and SRA study SRP480814. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 7 replicated groups read from 16 sample titles; they account for 14 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.
- GSM7999319 LAY_replicate1 LAY
- GSM7999320 LAY_replicate2 LAY
- GSM7999321 LADY_replicate1
- GSM7999322 LADY_replicate2.
- GSM7999323 LUDY_replicate1 LUDY
- GSM7999324 LUDY_replicate2 LUDY
- GSM7999325 LKPY_replicate1 LKPY
- GSM7999326 LKPY_replicate2 LKPY
- GSM7999327 prolong_LAY_replicate1 prolong_LAY
- GSM7999328 prolong_LAY_replicate2 prolong_LAY
- GSM7999329 prolong_LADY_replicate1 prolong_LADY
- GSM7999330 prolong_LADY_replicate2 prolong_LADY
- GSM7999331 prolong_LUDY_replicate1 prolong_LUDY
- GSM7999332 prolong_LUDY_replicate2 prolong_LUDY
- GSM7999333 prolong_LKPY_replicate1 prolong_LKPY
- GSM7999334 prolong_LKPY_replicate2 prolong_LKPY
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- GSE298209 Chemical reprogramming of human blood cells into hCiPS cells [bulk RNA-seq] 62 samples shares chemical, rna-seq
- GSE298471 A combinatorial transcription factor screening platform for immune cell reprogramming [scRNA-seq] 46 samples shares screening, rna-seq
- GSE285009 Mechanistic Investigation of Five Small-Molecule Inhibitors in the Treatment of Pemphigus Vulgaris via RNA-Seq Analysis 34 samples shares molecule, rna-seq
- GSE274620 Temporal multiomics gene expression data across human embryonic stem cell derived cardiomyocyte differentiation [RNA-seq] 20 samples shares embryonic, rna-seq
- GSE305933 Temporal multi-omics gene expression data across human embryonic stem cell-derived polyhormonal cell differentiation [RNA-seq] 20 samples shares embryonic, rna-seq
- GSE283776 Human stem cell-derived GABAergic interneuron development reveals early emergence of subtype diversity followed by gradual electrochemical maturation [snRNA-seq] 19 samples shares chemical, rna-seq
- GSE327354 Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells [RNA-seq Exp3] 18 samples shares screening, 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.