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| Status |
Public on Jul 22, 2019 |
| Title |
RNA-seq data of canine mammary tumors and normal samples |
| Organism |
Canis lupus familiaris |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Canine mammary gland tumors (CMTs) have been suggested as promising cancer models to human breast cancer due to their many biological and clinical similarities. Here, we collected 222 samples consist of 158 tumor samples and 64 matched normal samples of CMTs. Fresh tissue samples were transferred in to RNAlater, and refrigerated overnight at 4°C and then stored at -80°C. Total RNA was extracted from tissues using RNeasy mini kit. We aligned RNA-Seq raw data from 222 samples to canine reference genome CanFam3.1 using Tophat. We assembled transcript and calculated FPKM values using Cufflinks. All tumor samples were evaluated by histopathological characteristics including histopathological subtype, grade, and lymphatic invasion, and annotated with corresponding sequencing data. The histopathological classification and the histological grading system of CMTs were adopted from those of human breast cancer. In addition, immunohistochemical evaluation was performed in samples for estrogen receptor (ER) and human epidermal growth factor receptor 2 (HER2) status.
DISCLAIMER: Using this dataset became freely available on Jul 22, 2019. On the other hand, we are now preparing a key paper about comparative analysis of canine and human breast cancer based on this dataset. If you plan to submit a similar paper using this dataset before the main paper is published, please feel free to contact the submitter (swkim@yuhs.ac) to coordinate submission.
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| Overall design |
RNA-seq of 158 canine mammary gland tumors and 64 matched normal samples.
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| Contributor(s) |
Kim KK, Seung BJ, Kim D, Park HM, Song DW, Cheong JH, Nam H, Sur JH, Kim S |
| Citation(s) |
32680987 |
| BioProject |
PRJNA489087 |
| |
| Submission date |
Sep 11, 2018 |
| Last update date |
Aug 20, 2020 |
| Contact name |
Sangwoo Kim |
| E-mail(s) |
swkim@yuhs.ac
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| Organization name |
Yonsei University College of Medicine
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| Department |
Dept. of Biomedical Systems Informatics
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| Lab |
Translational Genome Informatics Lab
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| Street address |
50-1 Yonsei-ro, Seodaemun-gu
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| City |
Seoul |
| State/province |
State... |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
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| Platforms (1) |
| GPL20988 |
Illumina HiSeq 2500 (Canis lupus familiaris) |
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| Samples (222)
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| Relations |
| SRA |
SRP159466 |
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