|
| Status |
Public on Sep 15, 2020 |
| Title |
C497A |
| Sample type |
SRA |
| |
|
| Source name |
longissimus dorsi muscle, early molt
|
| Organism |
Mirounga angustirostris |
| Characteristics |
Stage: early molt
tissue: skeletal muscle
developmental stage: adult
Sex: female
|
| Treatment protocol |
Skeletal muscle biopsies were taken from adult female northern elephant seals within 5 days of arrival on the beach for the annual molt. Muscle biopsies were taken again (not exclusively paired to the same animals) after an average of 34 days of molt before returning to sea. Samples were preserved in chilled RNAlater for 24 hours before freezing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were blotted free of RNAlater, flash-frozen in liquid nitrogen and pulverized using a mortar and pestle before mechanical homogenization with a rotary tissue grinder using an RNAqueous Total RNA Isolation Kit.
Poly-A plus RNA was enriched from ~0.1 ug of total RNA and used to generate libraries using the Illumina TruSeq RNA kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Base calling was using Illumina's bcl2fastq2-v2.20 converter
A genome index was built with STAR (v2.5.3amod) from the NCBI Hawaiian Monk Seal genome and corresponding annotation release 100.
Reads were aligned to the seal reference using the STAR software version 2.5.3amod with the parameters recommended for the ENCODE consortium.
Read counts per gene were produced with the --quantMode GeneCounts function of STAR
Differential gene expression was analyzed with the R (version 3.4.3) software DESeq2 (version 1.18.1)
Genome_build: GCF_002201575.1
Supplementary_files_format_and_content: Tab delimited table of raw read counts per gene
|
| |
|
| Submission date |
May 31, 2020 |
| Last update date |
Sep 15, 2020 |
| Contact name |
Traver Wright |
| E-mail(s) |
traywright@gmail.com
|
| Phone |
4096924120
|
| Organization name |
Texas A&M University
|
| Department |
Health and Kinesiology
|
| Street address |
675 John Kimbrough Blvd., TAMU 4253
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77843 |
| Country |
USA |
| |
|
| Platform ID |
GPL28602 |
| Series (1) |
| GSE151509 |
Changes in Northern Elephant Seal Skeletal Muscle Following Thirty Days of Fasting and Reduced Activity |
|
| Relations |
| BioSample |
SAMN15065693 |
| SRA |
SRX8432404 |
