|
| Status |
Public on Jun 02, 2021 |
| Title |
WE with MS-275 at D3 (rep1) |
| Sample type |
SRA |
| |
|
| Source name |
Wound epidermis
|
| Organism |
Ambystoma mexicanum |
| Characteristics |
treatment: MS-275
tissue: Wound epidermis
days after amuptation: 3
|
| Treatment protocol |
Two microliters of 25 mM MS-275 (Selleckchem, Houston, TX, USA) was injected into the stumps immediately beneath the WE of juveniles every other day after amputation.
|
| Growth protocol |
All the axolotls were kept in modified Holtfreter's solution.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues from axolotls were subjected to total RNA extraction using TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions. RNA samples were purified using a RNeasy Mini Kit (Qiagen, Hilden, Germany), then quantified on a Qubit 4 fluorometer (Invitrogen, CA, USA) and Qsep100 capillary gel electrophoresis (BiOptic, New Taipei City, Taiwan).
Libraries were constructed uing SureSelect Strand Specific RNA Library kit according to the manufacturers
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WE with MS-275 at D3
D3-WE-M1
|
| Data processing |
Adaptor trimming by cutadapt
Alignment by bowtie2
Expression quantification by RSEM
Genome_build: Am_3.4
Supplementary_files_format_and_content: Tab-delimited text file includes transcript expression level represented by TPM
|
| |
|
| Submission date |
Sep 09, 2020 |
| Last update date |
Jun 02, 2021 |
| Contact name |
Chia-Lang Hsu |
| E-mail(s) |
chialanghsu@ntuh.gov.tw
|
| Organization name |
National Taiwan University Hospital
|
| Department |
Department of Medical Research
|
| Street address |
No. 7, Zhongshan S. Rd.
|
| City |
Taipei |
| ZIP/Postal code |
100 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL27159 |
| Series (1) |
| GSE157716 |
HDAC1 paces the temporal expression of morphogenic genes during axolotl limb regeneration |
|
| Relations |
| BioSample |
SAMN16088191 |
| SRA |
SRX9099865 |
