Gene Expression
Nebulas
Gene Expression NebulasSummary: To explore the dynamic change of transcriptome in pre-implantation of rhesus monkey, we collected single cells for RNA-sequencing.
Overall Design: We collected 95 single cells from rhesus monkey early embryos encompassing the stages of 16-cell, early morula, late morula, early blastocyst, middle blastocyst, late blastocyst and hatched blastocyst. 95 single cells were sequenced in total.
| Strategy: |
|
| Species: |
|
| Healthy Condition: |
|
| Cell Type: |
|
| Growth Protocol: | - |
| Treatment Protocol: | - |
| Extract Protocol: | To collect single blastomeres, embryos with good quality were transferred into 0.5% Pronase in TL-HEPES to remove zona pellucida, followed by three washes in PVP-BSA. To distinguish the outer and inner cells, embryos were incubated with PKH2 dye (Sigma) which labels the live outer cells with red fluorescence. After labeling, embryos 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 PVP-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. |
| Molecule Type: | poly(A)+ RNA |
| Library Source: | |
| Library Layout: | SINGLE |
| Library Strand: | - |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2500 |
| Strand-Specific: | Unspecific |
| 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 |
|---|