Gene Expression
Nebulas
Gene Expression NebulasSummary: Time series of single cell transcriptome measurements can reveal dynamic features of cell differentiation pathways. From measurements of whole frog embryos spanning zygotic genome activation through early organogenesis we derived a detailed catalog of cell states in vertebrate development and a map of differentiation across all lineages over time. The inferred map recapitulates most if not all developmental relationships, and associates new regulators and marker genes with each cell state. We find that many embryonic cell states appear earlier than previously appreciated. We also assess conflicting models of neural crest development. Incorporating a matched time series of zebrafish development from a companion paper, we reveal conserved and divergent features of vertebrate early developmental gene expression programs.
Overall Design: 136,966 single cell transcriptomes were profiled from whole Xenopus tropicalis embryos at ten timepoints during the first 24 hours of its embryonic development. The data includes 75 total single cell RNA sequencing libraries, collected in 2 replicate timeseries. 4 of the 75 libraries focussed on dissected neural plate border tissue. The counts data for all pass filter cells are available in a single matrix (see "Corrected_combined.annotated_counts.tsv.gz" and "Raw_combined.annotated_counts.tsv.gz"). Alternatively, raw FASTQ or unfiltered counts files are also available for each individual library.
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| Growth Protocol: | - |
| Treatment Protocol: | - |
| Extract Protocol: | 5-15 healthy embryos at each desired developmental stage were collected, devitellinized using Pronase (1mg/mL in 1X MMR), dissociated to single cells (as described in Briggs et al., 2018), washed using a density gradient media replacement approach (on ice), and finally resuspended in cold PBS-/- with 0.5mg/mL BSA for scRNA-seq analysis by InDrops. Embryos were processed rapidly to minimize potential artifactual transcriptional changes in response to dissociation. Cells were generally ready for InDrops encapsulation within 1hr of starting Pronase treatment, and kept on ice from the washing steps onwards. |
| Library Construction Protocol: | Cells were encapsulated using the inDrops platform, into droplets on ice and lysed in the 3 nL microfluidic droplets using a final concentration of 0.4% w/v Igepal-CA630. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015 and Zilionis et al., Nat. Protoc. 2017). Libraries were prepared as in Zilionis et al., Nat. Protoc. 2017, with primer modifications for v3 libraries as summarized in supplement of the associated manuscript (Briggs et al., 2018)). |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | Forward |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina NextSeq 500 |
| Strand-Specific: | Specific |
| 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 |
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