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Base editing reveals an essential role for NANOG in human embryo lineage specification.

GSE319780 Homo sapiens (human) RNA-seq (gene expression) 13 samples Submitted 2026/05/17 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 13 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
13 samples: 8 × Human NANOG Targeted Blastocyst Mosaic vs 3 × Human NANOG Targeted Blastocyst Homozygous vs 2 × Human AAVS1 Targeted BlastocystGroups 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.
Summary (written by the submitters)
Understanding the mechanisms that regulate how the first cell lineages in human development are specified and maintained is of fundamental importance and has clinical implications for regenerative medicine, infertility and pregnancy loss. Decades of research in mouse models have provided valuable insights into the role of transcription factors that regulate early development, however translating these findings to human embryos has been limited by ethical, technical and biological constraints.
Read the full summary ↓
Functional studies of key transcription factors in human embryos have been hindered by nuclease-based genome-editing approaches that often induce genotoxicity, such as aneuploidy1-3. To overcome this limitation, we applied adenine base editing (ABE8e)4,5 to efficiently and precisely target an exon splice donor site, resulting in a splicing defect and a functional knockout of the transcription factor NANOG. This work represents the first application of base editing to study a developmental regulator in human embryos. Importantly, we found this approach did not trigger genotoxicity. Loss of NANOG disrupts specification of the pluripotent epiblast and instead cells differentiate toward a yolk sac or placental-like transcriptional programme. The retention of yolk-sac progenitor cell differentiation in NANOG-edited human embryos reveals a functional compensation that is distinct from our observations in the mouse, underscoring the importance of direct investigation of human development. Altogether, our findings demonstrate an essential role for NANOG in human pluripotency and epiblast specification and highlights the utility of adenine base editing for precise functional interrogation of human development.
This dataset
Open GSE319780 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE319780_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1425079 and SRA study SRP677855. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
8 × Human NANOG Targeted Blastocyst Mosaic vs 3 × Human NANOG Targeted Blastocyst Homozygous vs 2 × Human AAVS1 Targeted Blastocyst

Supports a between-group comparison across 13 samples.

How we read this: 3 replicated groups read from 13 sample titles; they account for 13 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.

Samples in this study
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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.