Transcriptome analysis of OA and Homeostasis cartilage using RNA ...

clumpfrustratedΒιοτεχνολογία

2 Οκτ 2013 (πριν από 3 χρόνια και 8 μήνες)

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Transcriptome Analysis Of Cartilage

Using RNA
-
seq

Yaobo Xu

Institute of Cellular Medicine

Provided by:
Yaobo Xu

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

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
u
p
-
regulated

1010
d
own
-
regulated


Result 2: Transcript Assembly & expression

Result 3: Variant Detection

Provided by:
Yaobo Xu

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