|
| Status |
Public on Aug 29, 2024 |
| Title |
Regenerating mandible, 5 dpi, An2 (Replicate 2) |
| Sample type |
SRA |
| |
|
| Source name |
Regenerating mandible
|
| Organism |
Ambystoma mexicanum |
| Characteristics |
tissue: Regenerating mandible
time point: 5 days post-injury
size: 12 cm snout-to-tail (ST)
genotype: DD
treatment: Paramedial mandible resection (5 mm)
|
| Treatment protocol |
The mandible (lower jaw) of 12 cm ST long juvenile d/d axolotls was resected to create a 5 mm defect in the paramedial left side. Tissue was collected at intact (0 dpa)5-, 14-, and 35 days post-amputation (dpa). 2 mandibles (biological replicates) were used per time point for sequencing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using RNAeasy Mini Kit according to the manufacturer's instructions. Samples were disrupted and homogenized using the NG010 Tissue Grinder Mixy Professional (NIPPON Genetics) in 600 µl of RLT Buffer containing β-mercaptoethanol (M625, Sigma). Extracted RNA was stored at -80 until processed for sequencing.
RNA sequencing libraries were prepared using NEBNext Ultra II Directional RNA Lib Prep (Biomek i7) with estimated fragment sizes of 300 - 400 bp. Poly-dT pull down enrichment of mRNA was performed before sequencing 101 bp paired-end reads on an Illumina NovaSeq 6000 (Illumina), generating between 37 and 57 million read pairs per sample.
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| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Generated lower jaw reads and the downloaded limb fastq files were trimmed of adapter sequences and low quality bases via the programs cutadapt (https://journal.embnet.org/index.php/embnetjournal/article/view/200) and fastq_quality_filter from the FASTX-Toolkit (Hannon, G.J. (2010) FASTX-Toolkit. http://hannonlab.cshl.edu/fastx_toolkit), respectively. The reads were then mapped against the current axolotl reference genome (www.axolotl-omics.org, AmexG_v6.0-DD), using HISAT2 ver. 2.2.1 (Pertea et al., 2015) with standard parameters and a known-splicesite-infile created from the current axolotl annotation file (AmexT_v47-AmexG_v6.0-DD.gtf) via the hisat2_extract_splice_sites.py command. Reads aligned with an average mapping rate of 96.02% for the jaw and 78.06% for the limb. Transcript quantification was then conducted using StringTie (Pertea et al., 2015) with standard parameters and the option of assembling novel transcripts. Finally, normalized CPM values for each sample were calculated using the Bioconductor package edgeR (Robinson et al., 2009) for R.
Assembly: AmexG_v6_DD
Supplementary files format and content: tab-delimited text files include CPM values for each sample
Supplementary files format and content: tab-delimited text files include raw count values for each sample
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| |
|
| Submission date |
Jun 28, 2024 |
| Last update date |
Aug 29, 2024 |
| Contact name |
Tatiana Sandoval-Guzmán |
| E-mail(s) |
tatiana.sandoval_guzman@tu-dresden.de
|
| Organization name |
Technische Universität Dresden
|
| Department |
Department of Internal Medicine III, Center for Healthy Aging, Medical Faculty Carl Gustav Carus
|
| Lab |
Vertebrate Tissue Repair and Regeneration
|
| Street address |
Fetscherstrasse 74
|
| City |
Dresden |
| State/province |
Saxony |
| ZIP/Postal code |
01307 |
| Country |
Germany |
| |
|
| Platform ID |
GPL27159 |
| Series (1) |
| GSE271056 |
Axolotl mandible regeneration occurs through mechanical gap closure and a shared regenerative program with the limb |
|
| Relations |
| BioSample |
SAMN42159253 |
| SRA |
SRX25145901 |
