 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 07, 2024 |
| Title |
Feline thyroid, hyperthyroid, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Thyroid
|
| Organism |
Felis catus |
| Characteristics |
tissue: Thyroid
Sex: Female
breed: Domestic short hair
thyroid status: Hyperthyroid
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A 3-4 mm3 sample of each thyroid was dissected with scissors and washed with PBS prior to lysis in TRIzol reagent (Invitrogen). Where a distinct nodule or nodules were present in hyperthyroid cats, this area of tissue was prioritised for RNA-Seq. Phenol-chloroform extraction was used to isolate nucleic acids from the lysate, and RNA was purified from the resulting aqueous phase using a RNeasy Micro kit (Qiagen) with on-column DNase treatment to digest genomic DNA. Pure RNA was eluted with RNase-free water, and cleaned up using an RNA Clean & Concentrator-25 kit (Zymo Research). RNA integrity and concentration were determined using a Tapestation 4200 (Agilent) and Nanodrop ND-1000 (Thermo Scientific), respectively
RNA-seq libraries were prepared from total RNA by Oxford Genomics Centre (Wellcome Centre for Human Genetics, University of Oxford). Following ribodepletion with the NEBNext rRNA Depletion Kit v2 (NEB) to remove abundant rRNA species, stranded libraries were generated using a TruSeq Stranded Total RNA kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
HT03
|
| Data processing |
Adapters were trimmed from raw reads using PEAT v1.2.4.
Trimmed reads were aligned to the felCat9 reference genome (GCA_000181335.4) using STAR v2.6.0c.
Alignments were filtered to retain only uniquely mapped, properly paired reads using Samtools v1.9.
Gene-level read counts were obtained using featureCounts (from Rsubread v2.12.3) in R, and raw counts were TMM normalised and analysed with edgeR v3.40.2.
Assembly: Felis_catus_9.0 (GCA_000181335.4)
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
|
| |
|
| Submission date |
Sep 03, 2024 |
| Last update date |
Sep 07, 2024 |
| Contact name |
Lucy Davison |
| E-mail(s) |
ldavison@RVC.AC.UK
|
| Organization name |
Royal Veterinary College
|
| Department |
CSS
|
| Lab |
MFG
|
| Street address |
Hawkshead Lane
|
| City |
Hatfield |
| ZIP/Postal code |
AL97TA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL28702 |
| Series (1) |
| GSE276271 |
Transcriptomic analysis reveals a critical role for activating GsĪ± mutations in spontaneous feline hyperthyroidism |
|
| Relations |
| BioSample |
SAMN43485339 |
| SRA |
SRX25958288 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
