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Transcriptome Analysis Of Cartilage


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Transcriptome Analysis Of Cartilage

  1. 1. Transcriptome Analysis Of Cartilage Using RNA-seq Yaobo Xu Institute of Cellular Medicine Provided by: Yaobo Xu
  2. 2. RNA-seq Bioinformatics Analysis Set of RNAs Fragments of uniform length Sequencing adaptors attached High-throughput sequencing Millions of short reads Mapped to the reference genome Provided by: Yaobo Xu
  3. 3. Cartilage samples Collected: •10 OA • 6 NOF (Neck of Femur fractures as controls) • Hip of Female patients only Sequencing: • Platform: Illumina Genome Analyzer II x. • 78-base pair-end sequencing • >50 Million Reads per sample • ~95% could be mapped to the Human reference genome Methods & Results Result 1: Differentially expressed (DE) genes (Absolute Fold Change ≥ 2 and P-value ≤ 0.05) In total 1777 DE genes 767 up-regulated 1010 down-regulated Result 2: Transcript Assembly & expression Result 3: Variant Detection Provided by: Yaobo Xu
  4. 4. RNA-seq has advantages in: • Expression Analysis: • More accurate expression • Higher Dynamic Range • Relatively simple normalization • Transcripts Assembly • Splicing patterns • Variants Detection Transcriptome comparison of OA/NOF • Differentially expressed genes • Transcripts expressed in Cartilage • Alternative splicing events in either OA or NOF • Allelic imbalance Summary Provided by: Yaobo Xu