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Model : ABI 3130 Genetic Analyzer
Make : M/s. Applied Biosystems, USA
Location : Genomics Lab.
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Applications:

  • DNA Sequencing
  • Fragment Analysis (Genotyping)
  • Mutation/Heterozgote Identification.
  • SNP validation
  • Microbial Identification
  • AFLP / RFLP Analysis
  • HIV-1 Drug Resistant Genotyping
  • Microsatellite Analysis
  • Forensic Identification
  • SAGE (Serial Analysis of Gene Expression)

The ABI 3130 Genetic Analyzer will be used for high class molecular biology research work to meet the DNA Sequencing and Fragment Analysis needs for various applications in the field of Human Genetics, Cancer Research, Microbial Identification and Human Identification

Overview of the Genetic Analyzer :

This laser based 4 capillary Genetic Analyzer can sequence 96 samples / day without any operator intervention, The Automated Polymer Delivery System eliminates manual washing and filling of polymer syringes, significantly reducing the time required for instrument setup and maintenance. All steps are automated, including polymer loading, sample injection, separation and detection, and data analysis.

Both DNA Sequencing and Fragment Analysis can be performed on the POP7 polymer using a 50 cm capillary array. Data is collected by a high resolution CCD camera during the run and analyzed. The analyzed files are then available for direct transfer to a database for further post analysis using specific software’s for identification and reporting.

Genetic Analyzer Software :

  1. Data Collection v 3.0 : Interface between the Genetic Analyzer and the Data station, which controls the Genetic Analyzer. The run modules and plate setup is performed using this Data collection software and to monitor the run progress.
  2. Sequencing Analysis Software v 5.2—designed to analyze, display, edit, save, and print sequencing data. Generation of quality values provides accurate basecall information for pure and mixed base calls.
  3. SeqScape® Software v.2.5—used for mutation detection and profiling. Basecalling algorithms seek out mixed bases for comparative sequencing, SNP discovery, and validation. With comparisons to a reference sequence, many samples can be analyzed and assembled simultaneously for fast and accurate determination of mutations.
  4. GeneMapper® Software v.4.0 —the most comprehensive fragment analysis software available. Multiple application features make it an ideal tool for genotyping, allele calling, fragment sizing, and SNP analysis. Quality Values (QV) are assigned to each fragment analyzed for easy automation and throughput, and questionable fragments are easily identified. Applications include Microsatellite analysis (diploid and polyploid), linkage mapping, SNP analysis (including SNaPshot® Kits), AFLP, relative fluorescent quantitation including loss of heterozygosity, and conformational sizing.

List of Reagents for ABI 3130 Genetic Analzyer

Applications

De-novo Sequencing

Item Description Part # Rxns
ABI PRISM BigDye Terminator v3.1 Ready Reaction Cycle Sequencing Kit
(standard run upto 600 bases)
4337454 24
4337455 100
Sequencing Primers (coupled with M13 Forward & M13 Reverse) 500
3130 POP-7 TM Performance Optimized Polymer - 7 mL 4352759 750
Genetic Analyzer 10X Running Buffer with EDTA - 25 mL 402824 1000
Hi-Di TM Formamide, Genetic Analysis Grade 4311320 1000
BigDye® XTerminator TM Purification Kit 4376486 2 mL

Sequencing of PCR Products ‎

Item Description Part # Rxns
ABI PRISM BigDye Terminator v3.1 Ready Reaction Cycle Sequencing Kit
(standard run upto 600 bases)
4337454 24
4337455 100
3130 POP-7 TM Performance Optimized Polymer - 7 mL 4352759 750
Genetic Analyzer 10X Running Buffer with EDTA - 25 mL 402824 1000
Hi-Di TM Formamide, Genetic Analysis Grade 4311320 1000
BigDye® XTerminator TM Purification Kit 4376486 2 mL

Mitochondrial DNA Sequencing Products

This PCR based resequencing system identifies human mitochondrial genetic variations.

Item Description Part # Rxns
MitoSEQr Resequencing System for the entire mitochondrial genome
with 46 resequencing amplicon
4348846 500
MitoSEQr Resequencing System for the entire mitochondrial control region
with 9 resequencing amplicon
4348809 500
ABI PRISM BigDye Terminator v3.1 Ready Reaction Cycle Sequencing Kit
(standard run upto 600 bases).
4337454 24
4337455 100
3130 POP-7 TM Performance Optimized Polymer - 7 mL 4352759 750
Genetic Analyzer 10X Running Buffer with EDTA - 25 mL 402824 1000
Hi-Di TM Formamide, Genetic Analysis Grade 4311320 1000
BigDye® XTerminator TM Purification Kit 4376486 2 mL
M13 Forward and M13 reverse for Variant Resequencing System 500

VariantSEQr ReSequencing System

Primer sets formulated at working concentrations for hundreds of disease-related human genetic variants. Reference sequences for all amplicons provided for auto analysis.

Item Description Part # Rxns
Variant Resequencing Set with one Amplicon 4348601 250
Variant Resequencing Set with five Amplicon 4348605 250
Variant Resequencing Set with Ten Amplicon 4348610 250
ABI PRISM BigDye Terminator v3.1 Ready Reaction Cycle Sequencing Kit
(standard run upto 600 bases).
4337454 24
4337455 100
3130 POP-7 TM Performance Optimized Polymer - 7 mL 4352759 750
Genetic Analyzer 10X Running Buffer with EDTA - 25 mL 402824 1000
Hi-Di TM Formamide, Genetic Analysis Grade 4311320 1000
BigDye® XTerminator TM Purification Kit 4376486 2 mL
M13 Forward and M13 reverse for Variant Resequencing System 500

Microbial Identification

The MicroSeq® Microbial Identification System is a complete solution for all eubacteria, yeasts, and filamentous fungi. It rapidly identifies slow-growers and non-fermenters (in less than 24 hours) that are often impossible to identify with conventional systems. No prior knowledge of the organism is required since the system uses universal, domain-level primers.

Item Description Part # Rxns
MicroSeq 500 16S rDNA PCR Kit with Protocol 4348229 50
MicroSeq 500 16S rDNA Sequencing Kit 4346480 50
Genetic Analyzer 10X Running Buffer with EDTA - 25mL 4352759 1000
3130 POP-7 TM Performance Optimized Polymer - 7 mL 4352759 750
Hi-Di TM Formamide, Genetic Analysis Grade 4311320 1000
BigDye® XTerminator TM Purification Kit 4376486 2 mL

Fragment Analysis

Microsatellite Analysis (LOH & MIN)

Microsatellites, also known as short tandem repeats (STRs), are polymorphic DNA loci that contain a repeat sequence of 2–7 nucleotides. The number of repeats for a given locus may vary, resulting in alleles of differing lengths.

Item Description Part # Rxns
ABI Prism Primers for Fragment Analysis (Custom design) -
Primers are labeled for Allelic sizing (Dyes range from 6FAM, TET, VIC, NED & TET)
450056 500
AmpliTaq Gold PCR Master Mix -5 mL 4318739 200
GeneScan-500 LIZ Size Standard 4322682 800
Genetic Analyzer 10X Running Buffer with EDTA - 25 mL 4352759 1000
3130 POP-7 TM Performance Optimized Polymer - 7 mL 4352759 750
Hi-Di TM Formamide, Genetic Analysis Grade 4311320 1000

SNaPshot Multiplex System

SNaPshot Multiplex System is a primer extension based method that enables multiplexing to 10 SNPs. Interrogate multiple SNPs regardless of chromosome position. Could be used ‎to screen and confirm SNP, assess DNA methylation, finger print BACs.

Item Description Part # Rxns
ABI Prism Snapshot Multiplex Kit 4323159 100
AmpliTaq Gold PCR Master Mix -5 mL 4318739 200
GeneScan-120 LIZ ® Size Standard (SNPlex system only) 4324287 800
Genetic Analyzer 10X Running Buffer with EDTA - 25 mL 4352759 1000
3130 POP-7 TM Performance Optimized Polymer - 7 mL 4352759 750
Hi-Di TM Formamide, Genetic Analysis Grade 4311320 1000

Human Linkage Mapping System

ABI Prism Linkage Mapping set v2.5 consists of fluorescently labeled PCR primers selected to amplify highly informative di-repeat Microsatellite loci from Genethon human linkage map.

Item Description Part # Rxns
Linkage Mapping Set v2.5 MD10 (400 markers of 10-cM set) 4329185 300
Linkage Mapping Set v2.5 HD 5 (411 markers of 5-cM plus addition to MD10) 4329189 300
AmpliTaq Gold PCR Master Mix -5mL 4318739 200
GeneScan-400HD ROX Size Standard 402985 800
Genetic Analyzer 10X Running Buffer with EDTA - 25 mL 4352759 1000
3130 POP-7 TM Performance Optimized Polymer - 7 mL 4352759 750
Hi-Di TM Formamide, Genetic Analysis Grade 4311320 1000

Human Identification (Forensic application)

Fluorescent STR-based assay for human identification applications. The AmpFlSTR Identifiler PCR Amplification Kit simultaneously amplifies 15 STR loci plus the Amelogenin gender-determining marker in a single, robust PCR. The widely accepted ‎tetranucleotide loci co-amplified in the Identifiler Kit include the thirteen core STR loci as ‎required for sample entry into CODIS (Combined DNA Index System):

Item Description Part # Rxns
AmpFISTR Identifiler PCR Amplification Kit 4322288 200
GeneScanTM-500 LIZ® Size Standard 4322682 800
Genetic Analyzer 10X Running Buffer with EDTA - 25 mL 4352759 1000
3130 POP-4 TM Performance Optimized Polymer 4352755 750
Hi-Di TM Formamide, Genetic Analysis Grade 4311320 1000

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