In vitro cultured H7 human embryonic stem cells (WiCell) and H7-derived downstream early mesoderm progenitors
Single-cell RNA-seq · human · 12 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
- 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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.
Read the full summary ↓
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 GSE85066_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 PRJNA319573 and SRA study SRP073808. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 distinct titles with little repetition. 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.
- GSM2257291 H7_hESC_ATAC-seq
- GSM2257292 H7_derived_APS_ATAC-seq
- GSM2257293 H7_derived_MPS_ATAC-seq
- GSM2257294 H7_derived_DLL1pPXM_ATAC-seq
- GSM2257295 H7_derived_ESMT_ATAC-seq
- GSM2257296 H7_derived_Sclrtm_ATAC-seq
- GSM2257297 H7_D5CntrlDrmmtm_ATAC-seq
- GSM2257298 H7_D2LtM_ATAC-seq
- GSM2257299 H7_D3GARPpCrdcM_ATAC-seq
- GSM2257300 H7_dreived_D2.25_Smtmrs_ATAC-seq
- GSM2257301 All_samples_bulk_RNA-seq_TPM
- GSM2257302 All_samples_single-cell_RNA-seq_TPM
- GSE271234 Generation of self-renewing neuromesodermal progenitors with neuronal and skeletal muscle bipotential from human embryonic stem cells 15 samples shares progenitors, embryonic, mesoderm
- GSE277202 Comprehensive Transcriptomic and Translational Profiling of Human Embryonic Stem Cell Differentiation to Definitive Endoderm and Pancreatic Progenitors via RNA-seq and Ribo-seq 14 samples shares progenitors, embryonic
- GSE305132 Single-Cell Multiomic Atlas of Human Cortical Development in Down Syndrome - Neural Progenitors in vitro - Treatment with Antisense Oligonucleotides for PKNOX1, BACH1 and GABPA (Bulk RNA-seq Dataset) 68 samples shares progenitors, vitro
- GSE275739 CHD7 Regulates Definitive Endodermal and Mesodermal Development from Human Embryonic Stem Cells [ATACseq] 10 samples shares embryonic, mesoderm
- GSE284370 Feeder-free culture of naive human PSCs preserving embryonic, extraembryonic and blastoid potential 57 samples shares embryonic
- GSE270174 Trajectory modeling of first trimester placenta highlight differences between cytotrophoblast progenitors and trophoblast stem cells 50 samples shares progenitors
- GSE310173 Embryonic stem cell factors DPPA2/4 amplify active H3K4me3-H2AK119ub chromatin domains in non-small cell lung cancer 300 samples shares embryonic
- GSE201709 Multiomic profiling of vascular endothelial cell differentiation from human embryonic stem cells 130 samples shares embryonic
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.