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Published byDaisy Fulford Modified over 9 years ago
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Francois Vigneault Church Lab CEGS meeting Oct 16th 2008
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How to clone miRNAs? X 3’ 3’-OH5’ PO 4 5’ PO 4 5’ PO 4 + X 3’ + T4 RNA ligase ATP
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How to capture miRNAs? X 3’ 3’-OH5’ PO 4 5’ App 5’ PO 4 + X 3’ + T4 RNA ligase ATP X 3’5’ PO 4
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How does one make app-Oligo Lau et al. Science 2001 (Bartel lab) Yield 10-20% IDT (5 nmole $ 595)
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Enzymatic adenylation X 5’ PO 4 3’ 5’ 3’ App T4 DNA Ligase. ATP
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Pre-adenylation
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3’adapter ligation
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5’ adapter ligation
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High-throughput sequencing Illumina ~5 000 000 reads/track for 1200$ Less than ~1000 miRNAs in human cells Multiplexing up to 50 samples per track (100 fold dynamic range) bring cost per samples to 24$
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Bar-coded adenylation 3’ GCGC X 5’ PO 4 CCAA X 5’ PO 4 3’ TAGC X 5’ PO 4 3’ ATAT X 5’ PO 4 3’ NNNN 5’ 3’ NNNN 5’ 3’ NNNN 5’ 3’ NNNN 5’ 3’ App T4 DNA Ligase.
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Bar-coded adenylation 3’ GCGC X 5’ CCAA X 5’3’ TAGC X 5’3’ ATAT X 5’3’ App
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miRNAs ligation 3’ GCGC X 5’ CCAA X 5’3’ TAGC X 5’3’ ATAT X 5’3’ App 3’-OH5’ PO 4 3’-OH5’ PO 4 3’-OH5’ PO 4 3’-OH5’ PO 4 T4 DNA Ligase
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miRNAs ligation 3’ GCGC X CCAA X 3’ TAGC X 3’ X ATAT 3’ 5’ PO 4 5’ PO 4 5’ PO 4 5’ PO 4 T4 DNA Ligase
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5’adapter ligation 3’ NNNN X 5’ PO 4 5’3’-OH T4 DNA Ligase
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5’adapter ligation 3’ NNNN X 5’ T4 DNA Ligase.
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RT-PCR 3’ NNNN X 5’ RT pol TAQ pol
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Sequencing miRNAbarcode
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Sequencing
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ATC TGAATCACG GCC TCA AAT GTG GGG ATAT GCGC TAGC CCAA TTG… GTC TTC CCA ATC TCA AAT GGG TTG… ATC TGA GCC GTG ATC TCA AAT GGGATC TGA GCC GTGATCTGA GCC GTG Sequencing.
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TGAATCACGGCGCAATTTG…ATC GGGATC GCCGGGTAGCTTCATCTTG…TGAGTGATCTGA ATCAATATATTTG…CCATCAGCCAATTGAGCC TCAGTGCCAAGTCGGGTTG…GTGTCAGCCGTG Analysis
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Expression levels miRNA sequences miRNA profiling TGAATCACGGCGCAATTTG…ATC GGGATCGCCGGGTAGCTTCATCTTG…TGAGTGATCTGA TCAGTG CCAA GTCGGG TTG… GTG TCAGCCGTG Analysis ATCAATATATTTG…CCATCAGCCAATTGAGCC ATCAATATATTTG…CCATCAGCCAATTGAGCC ATCAATATATTTG…CCATCAGCCAATTGAGCC ATCAATATATTTG…CCATCAGCCAATTGAGCC TGAATCACGGCGCAATTTG…ATC GGGATC TGAATCACGGCGCAATTTG…ATC GGGATC TGAATCACGGCGCAATTTG…ATC GGGATC GCCGGGTAGCTTCATCTTG…TGAGTGATCTGA GCCGGGTAGCTTCATCTTG…TGAGTGATCTGA TCAGTG CCAA GTCGGG TTG…GTGTCAGCCGTG TCAGTG CCAA GTCGGG TTG…GTGTCAGCCGTG TCAGTGCCAAGTCGGGTTG…GTGTCAGCCGTG TCAGTGCCAAGTCGGGTTG…GTGTCAGCCGTG Sample1Sample2Sample3Sample4.
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Projections Personal Genome Project (PGP) Induced pluripotent stem cells (iPS) VDJ-ome
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VDJ-ome
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Acknowledgment George M Church Michael Sismour Greg Porreca Andrew Z Fire and lab All Church lab members…
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