|
| Status |
Public on Jul 25, 2024 |
| Title |
dog 18-7, macular RPE/choroid |
| Sample type |
SRA |
| |
|
| Source name |
macular RPE/choroid
|
| Organism |
Canis lupus familiaris |
| Characteristics |
tissue: macular RPE/choroid
Sex: female
estimated age: 3-5 years
estimated breed: pitbull mixed breed
eye (right_or_left): Right
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini kit with on column DNAse digestion (Qiagen).A minimum of 1ug of total RNA was used as template for library preparation
RNA libraries for RNA-seq were prepared using Illumina directional library kit following manufacturer guidelines.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
trimmed Illumina adaptor and 5’- end 12 bases with trimmomatic v0.39
QC tirimmed sequences with FastQC v0.11.8
mapped sequences with HISAT2 v2.1.0
sorted by chromosome with samtools sort v 1.9
marked up duplicated reads by MarkDuplicate version 2.20.1
count mapped sequences with featureCounts v2.0.0
Assembly: CanFam 3.1
Supplementary files format and content: tab delimited files containing raw counts
|
| |
|
| Submission date |
Mar 17, 2023 |
| Last update date |
Jul 25, 2024 |
| Contact name |
Freya Mowat |
| E-mail(s) |
mowat@wisc.edu
|
| Organization name |
University of Wisconsin-Madison
|
| Department |
Ophthalmology and Visual Sciences
|
| Street address |
1300 University Avenue
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706-1510 |
| Country |
USA |
| |
|
| Platform ID |
GPL20988 |
| Series (1) |
| GSE227619 |
Analysis of gene expression in the dog macular retina and supporting tissues: comparison with human macular gene expression profiles |
|
| Relations |
| BioSample |
SAMN33798907 |
| SRA |
SRX19704872 |
