Gene Expression
Nebulas
Gene Expression NebulasSummary: Abstract from Vermillion et al: During vertebrate development, progenitor cells give rise to tissues and organs through a complex choreography that commences at gastrulation. A hallmark event of gastrulation is the formation of the primitive streak, a linear assembly of cells along the anterior-posterior (AP) axis of the developing organism. To examine the primitive streak at a single-cell resolution, we measured the transcriptomes of individual chick cells from the streak or the surrounding tissue (the rest of the area pellucida) in Hamburger-Hamilton stage 4 embryos. The single-cell transcriptomes were then ordered by the statistical method Wave-Crest to deduce both the relative position along the AP axis and the prospective lineage of single cells. The ordered transcriptomes reveal intricate patterns of gene expression along the primitive streak.
Overall Design: Examination of single-cells of stage 4 chicken embryos.
| Strategy: |
|
| Species: |
|
| Healthy Condition: |
|
| Cell Type: |
|
| Development Stage: |
|
| Growth Protocol: | - |
| Treatment Protocol: | - |
| Extract Protocol: | Hamburger-Hamilton Stage 4 chicken embryos were collected in Ringer's solution. The primitive streak was dissected out using a fine tungsten needle, and the remaining surrounding tissue (rest of the area pellucida) was collected separately. |
| Library Construction Protocol: | iluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina).scRNA-seq with ~40x multiplexing |
| 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 |
|---|