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Building a Custom RT2 Profiler PCR Array in GeneGlobe

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Custom Builder enables you to create the arrays/plates or assays/tubes you need for your research. Simply provide QIAGEN with a list of identifiers for your genes or proteins (name, RefSeq ID, catalog number, genomic coordinates, etc.), decide your plate's layout (for arrays) and QIAGEN will create a product customized just for you! With Custom Builder, you can create customized products for mRNA expression, NGS targeted sequencing, ELISA protein analysis and analysis of siRNA and miRNA mimics and inhibitors. Start building your custom product today!

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Building a Custom RT2 Profiler PCR Array in GeneGlobe

  1. 1. Sample to Insight Building a Custom RT2 Profiler PCR Array in GeneGlobe Samuel Rulli Global Product Manager – RT2 Profiler PCR Arrays Samuel.rulli@qiagen.com Title, Location, Date 1
  2. 2. Sample to Insight How to build a custom array for RNA-seq validation Title, Location, Date 2 Gene Transcript Fold Change p-val q-val IL12B NM_002187 Infinity 4.97E-04 1.20E-03 TNFSF14 NM_172014 129 8.99E-55 1.49E-52 CXCL2 NM_002089 110 3.26E-30 1.08E-28 IL1RN NM_173843 102 7.30E-51 6.06E-49 C3 NM_000064 82.4 1.66E-18 2.13E-17 CXCL9 NM_002416 47.1 5.51E-39 3.05E-37 FASLG NM_000639 35.1 2.33E-22 3.86E-21 CCL11 NM_002986 35 4.86E-11 2.99E-10 SELE NM_000450 26.5 1.22E-27 2.52E-26 TNFSF10 NM_003810 23.3 2.24E-29 5.31E-28 CD27 NM_001242 19.5 1.09E-17 1.21E-16 CCL5 NM_002985 18.6 2.53E-27 4.67E-26 SELP NM_003005 17.3 6.77E-18 8.02E-17 CD80 NM_005191 12.7 2.28E-17 2.36E-16 CASP8 NM_033355 11.3 2.76E-17 2.69E-16 IFNG NM_000619 10.8 8.81E-07 3.18E-06 IL1R1 NM_000877 9.9 1.64E-16 1.43E-15 CXCL10 NM_001565 9 4.80E-15 3.46E-14 BCL3 NM_005178 8.9 1.33E-19 1.84E-18 CCL22 NM_002990 8 3.69E-04 9.01E-04 CCNB2 NM_004701 7.7 2.10E-12 1.40E-11 MYD88 NM_002468 7.7 3.00E-17 2.77E-16 IL2 NM_000586 7.3 3.24E-03 6.47E-03 HMOX1 NM_002133 6.8 2.86E-15 2.16E-14 TNFRSF10B NM_147187 6.5 1.93E-11 1.23E-10 LTBR NM_002342 6.2 1.02E-13 7.09E-13 VCAM1 NM_001199834 5.6 2.66E-10 1.52E-09 CD69 NM_001781 5.3 1.88E-07 7.24E-07 TLR9 NM_017442 -5.00 4.57E-08 1.95E-07 CD83 NM_004233 -13.33 1.61E-21 2.44E-20 CCNE1 NM_001238 -14.93 5.97E-16 4.96E-15 CCNG2 NM_004354 -15.15 7.87E-31 3.27E-29 CCND2 NM_001759 -17.54 8.22E-30 2.27E-28 IFNA1 NM_024013 -128.21 2.76E-15 2.16E-14 52 samples with 48 genes 34 genes +/- 5 fold change 5 normalization genes Controls for RT, PCR and gDNA contamination n=1 qPCR assays per sample Biorad CFX96 instrument 26 total plates
  3. 3. Sample to Insight How to Find the Custom RT2 PCR Array builder Title, Location, Date 3 1.) www.qiagen.com/MyPCRArray (capitalization not important) 2.) Navigate from QIAGEN.com homepage
  4. 4. Sample to Insight Genes to upload Title, Location, Date 4 IL12B,TNFSF14,CXCL2,IL1RN,C3,CXCL9,FASLG,CCL11,SELE,TNFSF10,CD27,C CL5,SELP,CD80,CASP8,IFNG,IL1R1,CXCL10,BCL3,CCL22,CCNB2,MYD88,IL2,H MOX1,TNFRSF10B,LTBR,VCAM1,CD69,TLR9,CD83,CCNE1,CCNG2,CCND2,IFN A1 AIRN,BANCR,FAS-AS1,PCAT1,TUG1,XIST
  5. 5. Sample to Insight Title, Location, Date 5
  6. 6. Sample to Insight Title, Location, Date 6
  7. 7. Sample to Insight Title, Location, Date 7 Type in NCBI GeneSymbol, Entrez GeneIDs, NCBI Transcript Refseq IDs. SangerIDs, Sanger Accessions GeneGlobe Catalog Numbers
  8. 8. Sample to Insight Title, Location, Date 8
  9. 9. Sample to Insight Confirm gene list Title, Location, Date 9 Confirm gene list
  10. 10. Sample to Insight Title, Location, Date 10 Configure Product Select instrument Choose plate
  11. 11. Sample to Insight Add controls and normalization genes Title, Location, Date 11 ! Select RT2 for only mRNA applications. Select RT2 lncRNA for lncRNA applications. Select both to have option of mRNA or lncRNA from same gene locus.
  12. 12. Sample to Insight Configure Plate (add, move or delete genes) Title, Location, Date 12
  13. 13. Sample to Insight I added some controls and normalization genes Title, Location, Date 13 Price is for minimal # plates Add to cart to assign Custom catalog number
  14. 14. Sample to Insight How many plates do I need? 15 (and I can order exactly 15!) Title, Location, Date 14 Material # 330171 Material # 330181
  15. 15. Sample to Insight My shopping cart. Order online or call customer care. Title, Location, Date 15 To order online: press “Checkout” and follow ordering process (credit card or PO) To order using customer care, call and mention product 330171. Quantity 1. CLAH20268. 12 plates Product 330181. Quantity 3. CLAH20268 Forward cart to procurement
  16. 16. Sample to Insight Ordering process for 330171/330181 Title, Location, Date 16 Ordering online: Customer or procurement can use credit card or PO. Once order is placed it automatically enters SAP and once order has cleared SAP it enters production. Calling customer care: Customer must supply custom array number and total number of plates. Custom Array numbers Will start with CLA[SPECIES] ##### (5 unique numbers). One gene list to one unique catalog number Any changes to gene list generates new unique catalog number Customer’s orders and gene lists will be saved online for future re-orders

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