HCA Data Explorer

Transcriptomes of 1,529 individual cells from 88 human preimplantation embryos

Updated January 19, 2022

Mouse studies have been instrumental in forming our current understanding of early cell-lineage decisions; however, similar insights into the early human development are severely limited. Here, we present a comprehensive transcriptional map of human embryo development, including the sequenced transcriptomes of 1,529 individual cells from 88 human preimplantation embryos. These data show that cells undergo an intermediate state of co-expression of lineage-specific genes, followed by a concurrent establishment of the trophectoderm, epiblast, and primitive endoderm lineages, which coincide with blastocyst formation. Female cells of all three lineages achieve dosage compensation of X chromosome RNA levels prior to implantation. However, in contrast to the mouse, XIST is transcribed from both alleles throughout the progression of this expression dampening, and X chromosome genes maintain biallelic expression while dosage compensation proceeds. We envision broad utility of this transcriptional atlas in future studies on human development as well as in stem cell research.

Sandberg RickardKarolinska Instituetrickard.sandberg@ki.se
Sandberg Rickard (Principal Investigator)1
Lanner Frederik (Principal Investigator)1
Vibranovski D Maria (Principal Investigator)2
1Karolinska Instituet
2University of São Paulo
Schwartz Rachel

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/03c6fce7-789e-4e78-a27a-664d562bb738
None
Array Express Accessions:

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Analysis Portals

UCSC Cell BrowserUCSC Cell Browser

Project Label

humanPreimplantationEmbryos

Species

Homo sapiens

Sample Type

specimens

Anatomical Entity

embryo

Organ Part

Unspecified

Selected Cell Types

2 cell types

Disease Status (Specimen)

normal

Disease Status (Donor)

normal

Development Stage

human adult stage

Library Construction Method

Smart-seq2

Nucleic Acid Source

single cell

Paired End

false

Analysis Protocol

MultiSampleSmartSeq2_v2.2.6, SmartSeq2SingleSample_v5.1.5

File Format

5 file formats

Cell Count Estimate

1.5k

Donor Count

88
bai1,529 file(s)bam1,529 file(s)fastq.gz1,529 file(s)loom1 file(s)zip4 file(s)