Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJNA153427: Tracing pluripotency of human early embryos and embryonic stem cells by single cell RNA-seq

Source: NCBI / GSE36552
Submission Date: Mar 16 2012
Release Date: Aug 10 2013
Update Date: May 15 2019

Summary: Find the casual relationship between gene expression network and cellular phenotype at single cell resolution. We collected donated human pre-implatation embryos; and the embryonic stem cells derived from them; isolate individual cells; prepared single cell cDNAs; and sequenced them by HiSeq2000. Then we analyzed the expression of known RefSeq genes.

Overall Design: Development and applications of single-cell transcriptome analysis. Nat Meth 8; S6-S11.

GEN Datasets:
GEND000355
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Cell Line:
Development Stage:
Protocol
Growth Protocol: Donated human preplantation embryos were dissociated into individual blastmeres and were separately amplied to set up single cell cDNA libraries.
Treatment Protocol: -
Extract Protocol: Amplied single cell cDNAs were further amplied for another ten cycles of PCR. Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manufacturer suggestion protocol
Library Construction Protocol: Amplied single cell cDNAs were further amplied for another ten cycles of PCR. Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manufacturer suggestion protocol
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: SINGLE
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2000
Strand-Specific: Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Publications
Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells.
Nature structural & molecular biology . 2013-08-11 [PMID: 23934149]