|
| Status |
Public on Jun 05, 2017 |
| Title |
Awake rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Retina
|
| Organism |
Ictidomys tridecemlineatus |
| Characteristics |
tissue: retina
condition: awake in summer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Retinas of active and hibernating ground squirrels were collected in July and August, and January and February, respectively. Total RNAs were extracted by TRIzol (Thermo Fisher Scientific)
the TruSeq stranded total RNA sample preparation kit (Illumina) were used for RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Awake rep4
|
| Data processing |
bcl2fastq was used for base calling.
All the reads were trimmed to be 50nt of length. Trimmed reads were aligned to Ictidomys tridecemlineatus genome reference (Ensembl spetri2) with Tophat v2.0.11. The parameter options applied in alignment were -r 200, -g 20, -p 8, --no-coverage-search, --library-type fr-firststrand and -G corresponding GTF file.
Rsubread was used for gene feature count
Genome_build: spetri2
Supplementary_files_format_and_content: tab-delimited text files include raw count values of genes for each Sample
|
| |
|
| Submission date |
Jan 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yizhao Luan |
| E-mail(s) |
luanyz_leo@163.com
|
| Organization name |
Sun Yat-sen university
|
| Department |
Zhongshan Ophthalmic Center
|
| Street address |
Xianlie South Rd. 54, Yuexiu Dist
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510060 |
| Country |
China |
| |
|
| Platform ID |
GPL22929 |
| Series (1) |
| GSE93685 |
Transcriptomics analysis reveals adaptive changes of hibernating retinas in 13-lined ground squirrel |
|
| Relations |
| BioSample |
SAMN06234886 |
| SRA |
SRX2496657 |
