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

PRJNA481477: Single cell RNA-sequencing reveals the existence of naïve and primed pluripotency in pre-implantation rhesus monkey embryos [161 cells]

Source: NCBI / GSE117218
Submission Date: Jul 17 2018
Release Date: Aug 26 2018
Update Date: Aug 26 2018

Summary: To explore the dynamic change of transcriptome in pre-implantation of rhesus monkey, we collected single cells for RNA-sequencing.

Overall Design: We collected 161 ICM single cells from rhesus monkey early embryos encompassing the stages of early blastocyst, middle blastocyst, late blastocyst and hatching blastocyst.

GEN Datasets:
GEND000248
Strategy:
Species:
Healthy Condition:
Cell Type:
Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: To collect single blastomeres, embryos with good quality were transferred into 0.1% Pronase(Merck) in PBS to remove zona pellucida, followed by three washes in 0.05% PVP-PBS. To distinguish the outer and inner cells, embryos were incubated with PKH26 dye (Sigma) which labels the live outer cells with red fluorescence. After labeling, the embryos were washed for three times in PVP-PBS and cut off the blastocele with 1 mL syringe. Then the remaining embryo tissues were rinsed with Ca2+/Mg2+ free PVP-PBS and treated with 0.125% trypsin-EDTA for at least 5 min at 37℃ until the cell surface looks rough. Disaggregating was done by a mouth pipette aided by several finely pulled glass capillaries of different internal diameter. After most cells were separated apart, single cells were individually transferred into small droplets of 0.1% BSA-PBS and the inner/outer cell identity was identified by the fluorescent microscopy. Cells showing no fluorescence were inner cells, whereas those with red fluorescence were outer cells.
Library Construction Protocol: Briefly, single cells were washed three times in BSA-PBS and those with a clear round shape were added into cell lysis buffer, followed by First-strand cDNA synthesis and PCR amplification. PCR products were purified by Ampure XP beads and used for libraries construction.Libraries were deep sequenced on Illumina X-ten platform, using 150-bp paired-end strategy.
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina HiSeq X Ten
Strand-Specific: Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
Single-cell RNA-sequencing reveals the existence of naive and primed pluripotency in pre-implantation rhesus monkey embryos.
Genome research . 2018-08-28 [PMID: 30154223]