|
| Status |
Public on May 24, 2023 |
| Title |
case16, FCGS |
| Sample type |
SRA |
| |
|
| Source name |
Oral mucosa
|
| Organism |
Felis catus |
| Characteristics |
tissue: Oral mucosa
disease: Feline chronic gingivostomatitis (FCGS)
Sex: Female
neutered status: Spayed
age (years): 2
breed: Domestic Shorthair (DSH)
|
| Treatment protocol |
none
|
| Growth protocol |
none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue samples were homogenized in Trizol and RNA was extracted from the aqueous phase using the Quick-RNA Prep Kit (Zymo Research). Samples were treated with DNase on an RNA Clean & Concentrator column (Zymo Research) if high molecular weight material was observed on a Fragment Analyzer trace.
Ribosomal RNA was depleted with the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat; New England Biolabs) using 500 ng input total RNA and RNA-seq libraries were generated with the NEBNext Ultra II Directional library prep kit (New England Biolabs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
case16_FCGS
Cat
Sex type: FS
|
| Data processing |
Illumina pipeline software was used for base calling.
Sequenced reads were trimmed for 3' adaptor sequence and low-quality sequence and filtered to remove reads < 50nt with TrimGalore/cutadapt.
Processed reads were mapped to the reference genome/transcriptome with STAR using --quantMode GeneCounts to generate raw counts per gene.
Raw counts were analyzed in R with DEseq2.
Assembly: FelCat9 (Ensembl gene build)
Supplementary files format and content: AllSamples_rawCounts.txt: Matrix table with raw gene counts for every gene and every sample.
|
| |
|
| Submission date |
Apr 24, 2023 |
| Last update date |
May 24, 2023 |
| Contact name |
Jennifer K Grenier |
| Organization name |
Cornell University
|
| Department |
Biomedical Sciences
|
| Lab |
Biotechnology Building rm 333
|
| Street address |
526 Campus Rd
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL28702 |
| Series (1) |
| GSE230491 |
Transcriptomic signatures of feline chronic gingivostomatitis are influenced by upregulated IL6 |
|
| Relations |
| BioSample |
SAMN34356180 |
| SRA |
SRX20088421 |
