Microarray Agilent Microarray Total Solution
Agilent Microarray Total Solution 5 5 RNA-Seq 60 mer DNA in situ DNA 5 2 QC 4200 TapeStation 2100 / mirna CGHCGH+SNP ChIP-on-chip 2 mirna QC
RNA / mirna total RNA 10 ng 100 ng total RNA mirna 1.5 1 2 mirna 1 CGH/CGH+SNP CGH+SNP UPD Loss Of HeterozygosityLOH ChIP-on-chip / 8 x 60K 1 8 1 60K6 400K 1M 400K 180K 60K 60K 180K 60K 60K 180K 60K 60K 180K 60K 60K Agilent Agilent Agilent Agilent 1 x 1M 2 x 400K 4 x 180K 8 x 60K 105K 244K 105K 44K 15K 15K 44K 15K 15K 44K 15K 15K 44K 15K 15K Agilent Agilent Agilent Agilent 1 x 244K 2 x 105K 4 x 44K 8 x 15K / GeneSpring mirna CytoGenomics CGHCGH+SNP Agilent Genomic Workbench CGHCGH+SNP ChIP-on-chip AriaMx PCR 3
Agilent Microarray Total Solution mirna 5 RNA 5 5 DNA 1000 100 3 logs 5 logs Normalized Intensitylog scale 10 1 0.1 Human GE 8 x 60 K Ver 3.0 Log 2 Green Processed Signals 10 5 0 5 r=0.95 r 2 =0.966 5 0 5 10 15 Log 2 pmercc Mix 1 MCF7 / ERCC total RNA Human 8 x 60 K Ver 3.0 ERCC / ERCC long non coding RNA* 5 PCR mirna mirna PCR * Replicate 1 Replicate 1 Replicate 2 Replicate 2 long non coding RNA 4 Human 8 x 60 K Ver 3.0 log 10 60 mirna / PCR BMC Biotechnology 2008.8:69
2015 coding RNA non coding RNA Human 8 x 60 K Ver 3.0 coding RNABroad Institute lincrna/tucp catalog LNCipedia lncrnalong non coding RNA Human 8 x 60 K Ver 3.0 Mouse 8 x 60 K Ver 2.0 RefSeq Build 66 Unigene Build 236 LNCipedia Version 2.1 Ensemble Release 76 GenBankAug 2014 Broad Institute Human lincrna catalognov 2011 Broad Institute TUCP transcripts catalognov 2011 RefSeq Build 66 Unigene Build 236 RIKEN 3 Ensemble Release 76 GenBankAug 2014 26,083 Entrez Genes 30,606 lncrnas 27,122 Entrez Genes 4,578 lncrnas 60K 60K 60K 60K 60K 60K 60K 60K Rat 8 x 60 K Ver 2.0 RefSeq Build 66 Unigene Build 236 Ensemble Release 76 GenBankAug 2014 30,584 Entrez Gene Agilent 8 x 60K 44K 15K 15K 44K 15K 15K 44K 15K 15K 44K 15K 15K Agilent Agilent 4 x 44K 8 x 15K mirna mirna mirna mirbase 21 8 x 60K8 x 15K Total RNA mirna small RNA mirna probe extended hairpin hybridization sequence G C Cy mirna target 5 microarray surface truncated hybridization sequence G C probe-target interaction region 10 20 nts Cy microarray surface 5 mirna mirna 3' C 5' G mirna mirna 5
Agilent Microarray Total Solution 1 mirna earray earray 1 earray mirna mirbase 250 mirna earray RNA Web 1 earray 2 3 4 /mirna 1 Web CGH/CGH+SNP/ChIP-on-chip/ SureDesign 6
RNA polya 1 2 Volcano Plot 2 p 0.05 Gene Expression Profiling of Prokaryotic Samples using Low Input Quick Amp WT Kit5991-0879EN FFPE FFPE RNA RNA FFPE RNA FFPE total RNA RIN 14 2.4-2.7 3800 Reliable mrna Expression Profiles with FFPE Tissues Using the Agilent SurePrint G3 Human Gene Expression v2 8 x 60K Microarray5991-2385EN mirna mirna FFPE Fresh FrozenFF MicroRNA Analysis of Archival FFPE Samples by Microarray5990-4944EN N=3753 Volcano Plot 2 p 0.05 A Normal B Tumor R 2 =0.953 R 2 =0.948 mirna FFPE FFPE FF FF FFPE FF FFPE mirna FF A FF FFPE B FF FFPE mirna mirna mirna mirna 3 mirna 3 mirna 100 mirna mirna exosomal mirna 5991-7468JAJP Log10 signal intensity A A Log10 signal intensity 7
Agilent Microarray Total Solution 5 40 80 Million Colon TumorRNA-Seq 40 80 M= 4,000 8,000 5 Refseq gene RNA-Seq Refseq gene 5 5 log 10 log 10 150 ng total RNAColon Tumor Human 8 x 60 K Ver 2.0 1 µg total RNAColon Tumor Illumina Genome Analyzer II2 x 76 bp reads Colon Tumor 40 80 M RNA-Seq 4 1 18201 4 4 16906 8
RNA-Seq ENCODE ENCODE 2 x 76 bp 100 200 M = 1 2 10 20 M = 1,000 2,000 40 80M 10 M 40 80 M 100 M ENCODEhttp://genome.ucsc.edu/ENCODE/protocols/dataStandards/ENCODE_RNAseq_Standards_V1.0.pdf dt 1 IVT 10 ng total RNA crna Total RNA 1 1.5 2 3 Quality Check 1 2 3 RNA-Seq Quality Check PC 9
Agilent Microarray Total Solution CGH Comparative Genomic HybridizationCGH2 DNA CGH DNA A B CGH Cancer DNA % 0 5.2 11.4 16.2 34.5 49.1 73.0 100 DNA DNA CRL-5929 A1 1 B15 29 kb CGH CGH+SNP UPD Loss Of HeterozygosityLOH FFPE 1 CGH CGH 5991-5989JAJP ChIP-on-chip DNA ChIP-on-chip/ ChIP-on-chip Agilent Genomic Workbench CGH/CGH+SNPChIP-on-chip 3 CytoGenomics CytoGenomics CGH CGH+SNP 10
/ SureScan 5 mirna 5 SureScan 20 bit 1 5 5 20 bit 1 3 25 75 mm 2 µm3 µm QC H42 W43 D67 cm Feature Extraction 1 S/N Feature Extraction 2 QC QC / 5 70 5 20 rpm 11
Agilent Microarray Total Solution GeneSpring GX GeneSpring GX GeneSpring GX 20,000 3 AgilentAffymetrixIllumina mirna Agilent mirna mirna Exon SNP/CNV/CGH PCR Wikipathways 2D- 12 Venn Diagram 4 ANDOR NOT Volcano Plot T-test p-value Fold change GO Gene Ontology
AriaMx PCR AriaMx PCR AriaMx PCR 96 SYBR Green I AriaMx LED 2 43 AriaMx Brilliant III Ultra-FAST QPCR master mix SYBR Green I 40 43 2 10 qpcr Brilliant Ultra-Fast QPCR Master Mix 13
Agilent Microarray Total Solution QC RNA Agilent 2100 RNA PCR RNA RNA 1 µl RNA RNA RNA 1 µl50 pg total RNA RINrRNA DNA RNA RNA Integrity NumberRIN RIN RNA Total RNA RNA 1 10 RIN Schroeder et al.,bmc Molecular Biology 2006, 73 Agilent 2100 RIN 9.7 total RNA RNA RIN 6.7, 2.3 PCR RNA RIN Total RNA 1 10 TotalRNA RIN 9.7 RIN 6.7 RIN 2.3 RIN 9.7 RIN 9.7 RIN 9.7 RNA RIN 9.7Intact RIN 6.7Partial Degradation RIN 2.3Severe Degradation RNA MVP Total RNA, Human MDA-MB+453 Cells Agilent 4200 TapeStation 14 Agilent 4200 TapeStation ScreenTape 96 1 TapeStation RIN RIN e RNA Integrity Number equivalent RNA DNA CGH QC
CGH mirna https://www.chem-agilent.com/customertr/?cat=17 GeneSpring GX GeneSpring GX Q&A GeneSpring GX Presentation GeneSpring GX 2 GeneSpring GX Basic 1 GeneSpring GX Advanced 1 GeneSpring GX mirna http://www.digital-biology.co.jp/j_workshop DNA Agilent 2100 9 12 13 18 0120-477-111 email_japan@agilent.com GeneSpring GeneSpring 10 17 genespring_jp_support@agilent.com URL https://www.chem-agilent.com/form_earray.php Agilent 4200 TapeStaion AriaMx PCR 15
/ 192-8510 9-1 0120-477-111 mailemail_japan@agilent.com http://agilentgenomics.jp Agilent Technologies, Inc. 2017 Printed in Japan, Aug. 25, 2017 5991-8338JAJP