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| Status |
Public on Mar 01, 2019 |
| Title |
A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We sequence the transcriptomes of 86,024 single cells from C. elegans embryos, spanning from gastrulation to the beginning of cuticle synthesis. We identify the lineage (from the invariant C. elegans cell lineage) and approximate developmental age of each cell in the single cell data. Using these annotations, we investigate the competing influences of cell lineage and cell fate on gene expression.
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| Overall design |
Single cell RNA-seq profiles of cells from C. elegans embryos at varying developmental stages (~100-650 minutes post first cleavage).
Please note that the GSM2599701 (in GSE98561) raw data was re-analyzed and the resulting (processed) data is linked to the GSM4318946 records, which is duplicated sample record of GSM2599701 (with the re-analysis details) for the convenient retrieval of the complete raw data from SRA.
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| Contributor(s) |
Packer JS, Zhu Q, Huynh C, Sivaramakrishnan P, Preston E, Dueck H, Stefanik D, Tan K, Trapnell C, Kim J, Waterston RH, Murray JI |
| Citation(s) |
31488706 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| U41 HG007355 |
Creating Comprehensive Maps of Worm and Fly Transcription Factor Binding Sites |
UNIVERSITY OF WASHINGTON |
ROBERT H WATERSTON |
| R01 GM072675 |
Automated single cell expression analysis in C. elegans |
UNIVERSITY OF WASHINGTON |
ROBERT H WATERSTON |
| R35 GM127093 |
Decoding lineage and fate specification in the C. elegans embryo |
UNIVERSITY OF PENNSYLVANIA |
JOHN Isaac MURRAY |
| R21 HD085201 |
Single cell reconstruction of lineages and variability in C. elegans embryos |
UNIVERSITY OF PENNSYLVANIA |
JOHN Isaac MURRAY |
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| Submission date |
Feb 22, 2019 |
| Last update date |
Feb 22, 2020 |
| Contact name |
Junhyong Kim |
| Organization name |
University of Pennsylvania
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| Department |
Biology
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| Lab |
Junhyong Kim
|
| Street address |
433 S University Avenue
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (1) |
| GPL19757 |
Illumina NextSeq 500 (Caenorhabditis elegans) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA523834 |
| SRA |
SRP186643 |
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