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| Status |
Public on Dec 31, 2021 |
| Title |
HDAC Inhibitor Titration of Transcription and Axolotl Tail Regeneration |
| Organism |
Ambystoma mexicanum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
10X transcriptome sequencing of control and romidepsin treated embryonic tail regenerates.
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| Overall design |
To map transcripts to axolotl cell types, single-nuclei RNA-Seq was performed. Embryos were administered 2 mm distal tail amputations and either treated in Axololt Rearing Water (N = 100) or 10 uM romidepsin (N=100). At 6 HPA, 1 mm of distal tail tip tissue was collected and pooled for nuclei isolation and 10x single nuclei RNA-Seq. Nuclei isolation, library preparation, and next generation sequencing were performed by Singulomics. The resulting data were mapped to an axolotl transcript assembly as described previously (Rodgers et al., 2020), analyzed using Cell Ranger, and visualized using 10x visualization software (Loupe version 5.0). Default graph-based clustering was used to identify distinct clusters of cells and enriched genes were used to manually identify and differentiate among cell types.
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| Contributor(s) |
Voss SR, Smith JJ, Timoshevskaya N, Ponomareva LV, Thorson JS, Veliz-Cuba A, Murrugarra D |
| Citation(s) |
35036404 |
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| Submission date |
Sep 07, 2021 |
| Last update date |
Jan 20, 2022 |
| Contact name |
Jeramiah James Smith |
| E-mail(s) |
jjsmit3@uky.edu
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| Phone |
(859)948-3674
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| Organization name |
University of Kentucky
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| Department |
Biology
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| Street address |
101 Morgan Building
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| City |
Lexington |
| State/province |
KY |
| ZIP/Postal code |
40506 |
| Country |
USA |
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| Platforms (1) |
| GPL27159 |
Illumina NovaSeq 6000 (Ambystoma mexicanum) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA761455 |
| SRA |
SRP342567 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE183645_Merged_filtered_feature_bc_matrix.h5 |
89.6 Mb |
(ftp)(http) |
H5 |
| GSE183645_RAW.tar |
367.1 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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