|
| Status |
Public on Jun 17, 2019 |
| Title |
Scale dermis ventral Es19 |
| Sample type |
SRA |
| |
|
| Source name |
ventral skin
|
| Organism |
Alligator mississippiensis |
| Characteristics |
tissue: ventral skin
|
| Treatment protocol |
untreated
|
| Growth protocol |
fertilized eggs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Dissected tissue was extracted in Trizol reagent
Libraries were prepared using Illumina TruSeq RNA Sample Preparation V2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Read alignment was performed using Partek Flow version 3
We used Tophat2 2.1.0 to perform alignment
HTSeq-count was used for quantification.
TMM in edgeR was used for normalization
Genome_build: American alligator genome allMis1
Supplementary_files_format_and_content: Excel files include CPM value for each sample (Alligator skin samples-CPM)
|
| |
|
| Submission date |
Jun 18, 2018 |
| Last update date |
Jun 17, 2019 |
| Contact name |
Ping Wu |
| E-mail(s) |
pingwu@usc.edu
|
| Phone |
6264979629
|
| Organization name |
University of Southern California
|
| Department |
Pathology
|
| Street address |
2011 Zonal Ave HMR313A
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL24412 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN09445558 |
| SRA |
SRX4232785 |
