|
| Status |
Public on Sep 12, 2016 |
| Title |
Ground Squirrel Eye 3 |
| Sample type |
SRA |
| |
|
| Source name |
Ground Squirrel Eye tissue
|
| Organism |
Ictidomys tridecemlineatus |
| Characteristics |
strain: WT
tissue: Eye
genotype: Wild Type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Each rodent species-specific library preparation was pooled from multiple RNA samples: 4 ground squirrels for Ictidomys tridecemlineatus.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Isolated eye mRNA
GSq_eye_expression_with_topblast
|
| Data processing |
Transcriptomes of Arivacanthis niloticus and Ictidomys tridecemlineatus were assembled de novo. The processed reads were assembled using velvet, oases, and Trinity with multiple k-mers ranging from 21 to 67 with an increment of 2 whereas reads assembled with ABYSS and trans-ABYSS were done with multiple k-mers ranging from 40 to 78 with an increment of 2. The assemblies were combined and the duplicated transcripts were collapsed together to remove redundancy. Transcriptome annotation was done by first searching against the SWISS-PROT database using the BLASTx algorithm and an E value cutoff of 1e-5. Transcripts with the best matches to proteins from viruses and bacteria were considered as potential contaminants and thus were removed from further analysis. The resulting filtered BLASTx results were then used for Gene Ontology analysis with the blast2GO program. Protein domains were predicted for all such transcripts by searching the PFAM database with the HMMER program. The expression value for each transcript was calculated by aligning the original Illumina reads to the transcriptome using the Bowtie program, with all mapping reads reported. The expression value for each transcript was calculated as RPKM using a customized Perl script.
Genome_build: de novo assembly
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each eye tissue sample
|
| |
|
| Submission date |
Jul 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaodong Bai |
| Organization name |
Case Western Reserve University
|
| Department |
Center for RNA Molecular Biology
|
| Street address |
10900 Euclid Avenue
|
| City |
Cleveland |
| ZIP/Postal code |
44212 |
| Country |
USA |
| |
|
| Platform ID |
GPL22249 |
| Series (1) |
| GSE84931 |
RNA-Seq of eye tissues from Ground Squirrel eye and retina samples |
|
| Relations |
| BioSample |
SAMN05449772 |
| SRA |
SRX1981364 |
