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| Status |
Public on Jan 21, 2017 |
| Title |
Transcriptomic, Proteomic, and Metabolomic Landscape of Positional Memory in the Caudal Fin of Zebrafish |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules, few of which have been identified. Here, we quantified the global abundance of transcripts, proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach, we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions, including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover, 32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus, the identification of proximodistal differences in levels of RNAs, proteins, and metabolites will facilitate future functional studies of positional memory during appendage regeneration.
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| Overall design |
RNA-seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal, middle and distal (15 total samples). Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.
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| Contributor(s) |
Rabinowitz JS |
| Citation(s) |
28096348 |
| Submission date |
Dec 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeremy Rabinowitz |
| E-mail(s) |
jsr2137@gmail.com
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| Organization name |
University of Washington
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| Street address |
850 Republican St
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platforms (1) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA358533 |
| SRA |
SRP095533 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE92760_DESeq_distal_vs_middle.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE92760_DESeq_distal_vs_proximal.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE92760_DESeq_middle_vs_proximal.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE92760_monotonic_genes_v2.txt.gz |
129.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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