|
| Status |
Public on Feb 16, 2024 |
| Title |
S16-0779 |
| Sample type |
SRA |
| |
|
| Source name |
Meningioma
|
| Organism |
Canis lupus familiaris |
| Characteristics |
library name: S16-0779
survival: 561
treatment: Sx (lost to follow-up)
breed: Rat Terrier
Sex: Male
neuter.status: Neutered
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue samples from canines with spontaneous meningioma were acquired as surgical biopsies or from immediate post-mortem necropsies and archived as formalin-fixed, paraffin-embedded (FFPE) samples at Texas A&M University between 2011 and 2022. Following histopathological diagnosis, 5-10 25um thickness scrolls were collected from each meningioma for RNA sequencing. Scrolls were deparaffinized with xylene at room temperature, re-hydrated with an ethanol series, and subject to total RNA extraction using TRIzol reagent (Thermofisher, manufacturer’s instructions). RNA quantity and quality was evaluated on a TapeStation and all samples with a concentration of 10 ng/µl between 200-1,000nts were used for library preparation (n=62). Illumina library preparation was performed to manufacturer’s specification and 150 nt paired-end sequencing was performed.
RNA libraries were prepared for sequencing using standard Illumina protocols.Paired-end RNA sequencing was performed.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
S16-0779_R1_001.fastq.gz_Aligned.sortedByCoord.out.bam
|
| Data processing |
Raw reads from the RNA-seq data were processed using an in-house pipeline that uses STAR for read alignment and FeatureCount for expression count.The reads were aligned to CanFam3 reference genome and mapping to the canine transcriptome annotations. We then normalized the RNA-seq read counts for genes, applied a variance stabilizing transformation, and identified differentially expressed genes using the DESeq2 package. Differential gene expression determined by a false discovery rate cutoff of 0.05.
Assembly: canFam3
Supplementary files format and content: raw expression count matrix
|
| |
|
| Submission date |
Dec 15, 2023 |
| Last update date |
Feb 16, 2024 |
| Contact name |
Akdes Serin Harmanci |
| E-mail(s) |
akdes.serinharmanci@bcm.edu
|
| Organization name |
Baylor College of Medicine
|
| Street address |
One Baylor Plaza
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL27015 |
| Series (1) |
| GSE250310 |
Aggressive human MenG C meningiomas have a molecular counterpart in canines |
|
| Relations |
| BioSample |
SAMN38858355 |
| SRA |
SRX22904579 |
