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.
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| 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 |
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| Library Layout: | SINGLE |
| Library Strand: | - |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2500 |
| Strand-Specific: | Unspecific |