product insert and an Assay Information File (AIF) that contains information
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- Beverly Kellie Simmons
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1 s Your Assays-by-Design SM order arrives with a CD-ROM. This CD-ROM contains a product insert and an Assay Information File (AIF) that contains information pertaining to your order and for configuring your LIMS system. The AIF can be automatically uploaded from the CD-ROM by your LIMS system. AIF File-Name Conventions The AIF in your CD-ROM is named so that your LIMS system will automatically upload it. AIF file-name conventions are summarized in the table below, where xx is the order number and is 10 characters; yy is the plate ID number and is 10 characters. Assay Assays by Design SM Service, Gene Expression Assays by Design SM Service, SNP Genotyping Assays on Demand TM Gene Expression Products Assays on Demand TM SNP Genotyping Products File-Name Convention AbD_GX_xx_yy.txt AbD_SNP_xx_yy.txt AoD_GX_xx_yy.txt AoD_SNP_xx_yy.txt Page 1 of 6
2 Understanding Your AIF The table below contains a list of all the different types of information (fields) in the AIF. The AIF on your CD-ROM will contain some, but not all, of the following information. To see which information is provided for your product, check the printed data sheet included in your shipment. AIF Field Explanation Example Customer Name The name of your organization or institution Company XYZ Order Number Your sales order number Ship Date Delivery Number Part Number Product Type Assay ID Lot Number The date that the product is packaged for shipment A unique number for shipment, see packing slip for details Product number used for ordering the The type of product, which is indicated by the part number A unique identifier for the A Unique identifier for the manufacturing batch 07-Nov-2002 See your packing slip Assays-on-Demand TM SNP Genotyping AoD-SNP: C xxxxxxxx_xx Aod-GX: Hsxxxxxxxx_xx AbD-SNP or AbD-GX: KR03TD-18T Plate Type 96-position tube rack v1 96-position tube rack v1 Plate ID 1D barcode ID of the plate in which the is shipped Page 2 of 6
3 Vial Type 10-digit 2D barcoded tube 10-digit barcoded tube Vial ID Well Location Assay Mix Conc. Forward Primer Name Forward Primer Seq. Forward Primer Conc. Reverse Primer Name Reverse Primer Seq. Reverse Primer Conc. Reporter 1 Name A unique 2D barcode of the tube The well location of the in the associated barcoded plate The concentration of the mix (primers and probe(s)) The name of the forward primer given by design software; F designates the forward primer The nucleotide sequence of the forward primer The concentration (in µm) of the forward primer The name of the reverse primer given by design software; R designates the reverse primer The nucleotide sequence of the reverse primer The concentration (in µm) of the reverse primer The name for the reporter 1 oligo (probe) given by design software; V1 indicates the dye label and the design strand B02 20X KR14TD-A22TF NNNNNNNNNNNNNNNN NNN 18 KR14TD-A22TR NNNNNNNNNNNNNNNN NNNNNN 18 KR14TD-A22TV1 Reporter 1 Dye The dye label for reporter 1 VIC Reporter 1 Sequence The nucleotide sequence of reporter 1 NNNNNNNNNNNNNN Reporter 1 Conc. The concentration (in µm) of reporter 1 8 Page 3 of 6
4 Reporter 1 Quencher Reporter 2 Name A quencher used for reporter 1 of the The Name for the reporter 2 oligo (probe) given by design software; M1 indicates the dye label and the design strand NFQ Reporter 2 Dye The dye label for reporter 2 FAM KR14TD-A22TM1 Reporter 2 Sequence Reporter 2 Conc. Reporter 2 Quencher Context Sequence Design Strand Category A nucleotide sequence of reporter 2 The Concentration (in µm) of reporter 2 A quencher used for reporter 2 of the The nucleotide sequence surrounding the probe For AbD-GX and AbD-SNP: Forward - the probe binds to the same strand as the forward primer, Reverse - the probe binds to the same strand as the reverse primer. For AoD-SNP: Forward -the probe contains the same sequence as the context sequence, Reverse - the probe contains the reverse complement sequence as the context sequence. Based on Celera Panther Protein Classification, Level 1 NNNNNNNNNNNNNNN 8 NFQ AoD-SNP:...NNNNNNNNN[A1/A2] NNNNNNNNN... (25 nucleotides on both sides of the SNP site) AoD-GX:...NNNNNNNNNNNNN... (25 nucleotides including the targeted exon(s)) Forward Chromosome 9 Page 4 of 6
5 Category ID 10-digit unique ID for the category name Chr9 Group Based on Celera Panther Protein Classification, Level 2 D9S1776-D9S1682 Group ID 10-digit unique ID for the group name D9S1776 Gene Symbol LocusLink symbol for associated gene C5 Gene Name LocusLink gene name complement component 5 Chromosome Chromosome on which gene/snp is found 9 Species Target Exons NCBI Gene Reference Genome against which the was designed The exon or exons (as referenced by the public accession number) that are spanned by the probe. For s that are appended with _m1, the target exons are the exon displayed and the adjacent 3' exon. For an with _s1, the target exon in this example would be 2. For an with _m1, the target exons would be exons 2 and 3 (the probe would span the 2-3 junction site). NCBI transcript ID that is detected by the Homo_sapiens 2 NM_ NCBI SNP Reference Reference ID from NCBI-dbSNP database rs17611 Medline Reference PubMed references for gene Celera ID Unique ID in Celera Discovery System (CDS) hcv Page 5 of 6
6 Cytogenetic Band SNP Type Caucasian African-American Chromosomal band location of gene (if not available, then chromosome number will be given) Type of SNP (based upon Celera Assembly); Acceptor Splice Site, Donor Splice Site, Intergenic/Unknown, Intron, Mis-sense Mutation, Nonsense Mutation, Putative UTR 5', Silent Mutation, UTR 3', UTR 5' Applied Biosystems Caucasian population Applied Biosystems - African-American population 9q34 Mis-sense Mutation Japanese Chinese Celera Build Assembly Number Applied Biosystems Japanese population Applied Biosystems Chinese population Version of the Celera assembly from which the coordinate position is taken R26 Location on Celera Assembly Nucleotide location on the Celera human genome assembly (as referenced) Note: Sequence information will be shown as NNNNNNN, except where a SNP is designated as [A1/A2] Note: AbD-GX refers to Assays-by-Design SM Service, Gene Expression AbD-SNP refers to Assays-by-Design SM Service, SNP Genotyping AoD-GX refers to Assays-on-Demand TM Gene Expression Products AoD-SNP refers to Assays-on-Demand TM SNP Genotyping Products Page 6 of 6
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