Sushmita Singh N ABRF 2010 · 1 Consultation Based on application-specific project goals and...
Transcript of Sushmita Singh N ABRF 2010 · 1 Consultation Based on application-specific project goals and...
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454 Sample Prep / Workflowat the
BioMedical Genomics Center (BMGC)University of Minnesota
Sushmita Singh
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Sample Prep (client)
Sample Prep (Core)
Sequencing
Consultation
Data QC
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3
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Consultation1
Based on application-specific project goalsand various other factors, help client developsuitable experimental design, - sequencing type: genomic / amplicon - coverage: what size regions / plates
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Provide detailed information on sample prep and samplesubmission requirements,
- during consultation- providing information through brochures- through links on BMGC website
• Genomic DNA
• cDNA (total RNA)
• Amplicon (PCR product)
Sample Prep (client)2
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Sample Prep (client)2
Client is provided with detailed sample submissionspecifications in terms of quality and quantity
At time of submission client is required to submit asample submission form which queries user oninformation on sample and basic protocol used
Genomic DNA
Check:
• Gel picture
• OD values
• Quantization data
BMGC: Quantifies sample using Nanodrop spec analysisand PicoGreenTM assay (these numbers are used in core)
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cDNA (now total RNA)Sample Prep (client)2
Client is provided with detailed sample submissionspecifications in terms of quality and quantity
At time of submission client will be required to submit asample submission form which queries user oninformation on sample and basic protocol used
Check:
• Quantization data
• Agilent profile (gel picture)
BMGC: Ethanol precipitate out RNA, quantify sampleusing Nanodrop spec analysis and run Agilent analysisto check quality
Under Construction!
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Amplicon (PCR product)Sample Prep (client)2
Client is provided with detailed sample preparationand submission specifications
At time of submission client is required to submit asample submission form which queries user oninformation on sample
Check:
• Quantization data
• Agilent profile, if available
BMGC: Quantifies sample using PicoGreen assayand runs an Agilent profile
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For the most part, vendor specified protocols arefollowed - A detailed review of the protocol wasconducted and a workflow generated to,
- optimize efficiency- minimize human error- record detailed information
• Genomic DNA
• cDNA (total RNA)
• Amplicon (PCR product)
Sample Prep (Core)3
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Project list:
Project detail:
Preliminary LIMS system (FM Pro)
A very basic LIMS system in place
Looking into possibilities with commercial NGSdata handling software for future tech adaptations
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Genomic DNA Sample Prep: QC & Library Preparation
Genomic DNA received
Submissions checked forgiven specifications
Samples quantified at core
Project opened
Library prep initiated usingvendor specified protocols
Library Preparation1. Quantify sample2. Nebulization3. Fragment end polishing4. Adaptor ligation5. Library immobilization6. Fill in reaction7. sstDNA lib preparation8. sstDNA lib assessment9. Labeling and storage of
library
• Rapid library prep method
• MID library prep protocol
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cDNA Sample Prep: QC & Library Preparation
Total RNA received
Submissions checked forgiven specifications
Samples quantified at core
Project opened
Total RNA quality checkedusing Agilent RNA Nano
Library Preparation1. Quantify sample2. RNA fragmentation3. lib assessment4. Labeling and storage of library
mRNA isolated using acommercial kit
Library prep initiated usingvendor specified protocols
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Amplicon Sample Prep: QC and Dilution
Amplicon sample received
Samples quantified at core
Project opened
Amplicon quality checkedusing Agilent DNA 1000
Dilution prepared based onquantization data
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All samples: enrichment titration and emPCR
A bead enrichment titration assay conducted ascertain the best ‘molecules perbead’ (mpb) ratio for each library to ensure maximal output from emPCR reaction
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Default filtering parameters used(reanalysis with variant filter parameter usedin special cases only)
Control sequences generated are prettygood indicators of the sequencing run quality
Close attention paid to machine functioningby checking for any leakage etc.Maintenance washes are conductedfrequently and volume tests are conductedperiodically
Sequencing
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Data QC4
Summary file generatedused to evaluate run
Contamination checksfor the run conducted to
detect cross-contamination
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Raw well numbers
Passed filter wells
Keypass numbers
For Control:
% Dot + Mixed% Short quality primer
For Sample:
% Dot + Mixed% Short quality primer
Summary Report
Check:
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We are currently in the process of obtaining anIllumina system
Let the games begin….. again!….
Thank you for your attention!