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| Status |
Public on Oct 22, 2020 |
| Title |
N1 |
| Sample type |
SRA |
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| Source name |
non-tumor
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| Organism |
Canis lupus familiaris |
| Characteristics |
tissue: Grossly non malignant bone
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| Extracted molecule |
total RNA |
| Extraction protocol |
OSA tumor and non-tumor tissue was obtained from a total four non-malignant bone and three osteosarcoma specimens via veterinary surgeons following amputation treatment or immediately following euthanasia. Confirmation of OSA was confirmed by pathologists via histopathological examination. A 1cm3 piece of tumor was extracted along with a 1cm3 piece of adjacent non-tumor affected bone tissue. These samples were placed directly into RNAlater® and shipped at room temperature and stored at -20°C. OSA tumor and matched adjacent non-tumor bone tissue samples were homogenized. and RNA extracted using Qiagen RNeasy Mini Kit (Qiagen, Germany) according to manufacturer’s instructions. The extracted RNA was stored at -80°C. RNA was quantified using both a NanoDrop 8000 (Thermo Fisher Scientific, USA), and an Agilent 2100 Bioanalyzer (Agilent, USA). RNAseq was completed at Edinburgh Genomics using an Illumina HiSeq platform. In all cases >20 million reads were obtained from all samples analysed.
Illumina TruSeq stranded library prepartion for paired end sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Quality control and base calling was completed using Illumina CASAVA.
Raw fastq reads were adapter trimmed and quality assessed using the Trimgalore wrapper for FastQC and Cutadapt. Reads with phred scores >30 were retained.
Reads were aligned to the canFam3.1 reference genome using Tophat and genes quantified and differential expression assessed using Cuffdiff.
Genome_build: canFam3.1
Supplementary_files_format_and_content: BAM alignment file
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| Submission date |
Aug 03, 2020 |
| Last update date |
Oct 22, 2020 |
| Contact name |
Nigel P Mongan |
| Organization name |
University of Nottingham
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| Department |
Biodiscovery Institute
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| Street address |
University Park
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| City |
Nottingham |
| ZIP/Postal code |
NG7 2RD |
| Country |
United Kingdom |
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| Platform ID |
GPL20988 |
| Series (1) |
| GSE155646 |
Transcriptomic profiling of canine osteosarcoma and non-malignant bone |
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| Relations |
| BioSample |
SAMN15717209 |
| SRA |
SRX8876221 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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