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Human trophectoderm becomes multi-layered by internalization at the polar region

GSE244721 Homo sapiens (human) Single-cell RNA-seq 268 samples Submitted 2024/05/14 Platform GPL11154
At a glance

Single-cell RNA-seq · human · 268 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
Homo sapiens (human)
Samples
268 samples: 25 conditions, mostly with about 10 replicates eachGroups 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
Human trophectoderm becomes multi-layered by internalization at the polar regionDevelopmental cell · 2024
Summary (written by the submitters)
The human blastocyst is composed of outer trophectoderm and an inner cell mass, which segregates into epiblast and hypoblast. scRNA sequencing of human blastocyst cells was performed to identify subpopulations following immunosurgery to remove outer cells.
Published in
Human trophectoderm becomes multi-layered by internalization at the polar region
Corujo-Simon E, Bates LE, Yanagida A et al. · Developmental cell 2024 · PMID 38889726 · doi:10.1016/j.devcel.2024.05.028
This dataset
Open GSE244721 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 GSE244721_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: 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 PRJNA1024446 and SRA study SRP464809. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38889726) ↗
Study design
25 conditions, mostly with about 10 replicates each
embryo13_cell ×37 embryo19_cell ×18 embryo15_cell ×17 embryo4_cell ×16 embryo21_cell ×14 embryo25_cell ×14 embryo23_cell ×13 embryo16_cell ×12 +17 more

Supports a between-group comparison across 268 samples.

How we read this: 25 replicated groups read from 268 sample titles; they account for 268 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

+ 228 more — browse all 268 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

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.