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| Status |
Public on Feb 04, 2022 |
| Title |
Cell type specific transcriptome profiling reveals a role for thioredoxin in neutrophils and tumor initiation |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We report the application of Translating Ribosomal Affinity Purification (TRAP) seq for identifying cell type specific gene expression in the zebrafish larvae. Using cell specific promoters to drive an EGFP-tagged ribosomal subunit, we were able to identify translating mRNA transcripts in keratinocytes (krt4), neutrophils (lyz) and macrophages (mpeg) during early cancer transformation. In our zebrafish model of HRasG12V -transformed keratinocytes, we identified 56 differentially expressed genes in keratinocytes, 53 genes in neutrophils, and no differentially expressed genes found in macrophages, compared to control. These data indicate activation of gene expression pathways in distinct cell types following early keratinocyte transformation and validate the use of TRAPseq in the zebrafish model system.
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| Overall design |
Comparison of TRAP-seq gene expression data in a HRasG12V-transformed keratinocyte Zebrafish model in 3 different cells types
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| Contributor(s) |
Ben K, Morgan G, Gayathri R, Stella M, David B, Julie R, Colin D, Anna H |
| Citation(s) |
35250998 |
| Submission date |
Jan 13, 2022 |
| Last update date |
May 06, 2022 |
| Contact name |
Colin Dewey |
| Organization name |
University of Wisconsin-Madison
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| Street address |
425 Henry Mall, 5420 Genetics/Biotechnology Center
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| City |
Madison |
| ZIP/Postal code |
53706 |
| Country |
USA |
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| Platforms (1) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA796794 |
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