overview of sample management · dna assays quantifluor dsdna system (0.4-20ng, 2-200ng) rna assays...
TRANSCRIPT
![Page 1: Overview of Sample Management · DNA assays Quantifluor dsDNA system (0.4-20ng, 2-200ng) RNA assays ... Check Quantity Quality Purity . New Technology 4/8/15 13 Instrument & Method](https://reader034.vdocuments.us/reader034/viewer/2022042322/5f0c20f27e708231d433e151/html5/thumbnails/1.jpg)
Overview of Sample Management
Mansi Chovatia March 24, 2015
![Page 2: Overview of Sample Management · DNA assays Quantifluor dsDNA system (0.4-20ng, 2-200ng) RNA assays ... Check Quantity Quality Purity . New Technology 4/8/15 13 Instrument & Method](https://reader034.vdocuments.us/reader034/viewer/2022042322/5f0c20f27e708231d433e151/html5/thumbnails/2.jpg)
Functions
• Sample Receipt
• Sample Tracking/Inventory
• Sample Quantification & Quality Assessment
• Sample Aliquots
• Technical Support
4/8/15 2
![Page 3: Overview of Sample Management · DNA assays Quantifluor dsDNA system (0.4-20ng, 2-200ng) RNA assays ... Check Quantity Quality Purity . New Technology 4/8/15 13 Instrument & Method](https://reader034.vdocuments.us/reader034/viewer/2022042322/5f0c20f27e708231d433e151/html5/thumbnails/3.jpg)
Operation
4/8/15 3
Sample Storage
Sample QC
Sample Aliquot
![Page 4: Overview of Sample Management · DNA assays Quantifluor dsDNA system (0.4-20ng, 2-200ng) RNA assays ... Check Quantity Quality Purity . New Technology 4/8/15 13 Instrument & Method](https://reader034.vdocuments.us/reader034/viewer/2022042322/5f0c20f27e708231d433e151/html5/thumbnails/4.jpg)
Sample Storage
4/8/15 4
Sample Management
Project Manager
Supply Chain Manager
JGI Users
-User Agreements -Project initiation -Sample metadata -Project tracking
-Coordinates shipping schedule -Ships out prelabled containers
Sample Return & Disposal -Completed projects returned to users or discarded -Tracked in JIRA tickets
Sample Receipt -Receive packages -Barcode association -Log sample into GLS
![Page 5: Overview of Sample Management · DNA assays Quantifluor dsDNA system (0.4-20ng, 2-200ng) RNA assays ... Check Quantity Quality Purity . New Technology 4/8/15 13 Instrument & Method](https://reader034.vdocuments.us/reader034/viewer/2022042322/5f0c20f27e708231d433e151/html5/thumbnails/5.jpg)
Sample QC
• Measure sample volume • Top-off low volume samples
• Quantify samples using fluorometric dyes
• Assess sample quality based on scope of work (SOW)
• Record measurements and analysis in LIMS
4/8/15 5
![Page 6: Overview of Sample Management · DNA assays Quantifluor dsDNA system (0.4-20ng, 2-200ng) RNA assays ... Check Quantity Quality Purity . New Technology 4/8/15 13 Instrument & Method](https://reader034.vdocuments.us/reader034/viewer/2022042322/5f0c20f27e708231d433e151/html5/thumbnails/6.jpg)
Sample Aliquot
• Transfer required amount for library construction
• Top-off low volumes to required amount
• Create intermediate dilution for highly concentrated samples
• Re-array partial plates and tubes into a single final destination plate for library construction
• Record sample transfer information in LIMS
4/8/15 6
![Page 7: Overview of Sample Management · DNA assays Quantifluor dsDNA system (0.4-20ng, 2-200ng) RNA assays ... Check Quantity Quality Purity . New Technology 4/8/15 13 Instrument & Method](https://reader034.vdocuments.us/reader034/viewer/2022042322/5f0c20f27e708231d433e151/html5/thumbnails/7.jpg)
Throughput
4/8/15 7
![Page 8: Overview of Sample Management · DNA assays Quantifluor dsDNA system (0.4-20ng, 2-200ng) RNA assays ... Check Quantity Quality Purity . New Technology 4/8/15 13 Instrument & Method](https://reader034.vdocuments.us/reader034/viewer/2022042322/5f0c20f27e708231d433e151/html5/thumbnails/8.jpg)
Automation
4/8/15 8
Storage Volume Check QC Aliquot
• Sample archival • Manage in-progress
containers • Houses a total of 532
plates and 11,320 tubes.
• Barcode association Retrieves upon command
• Improved tracking • Provides security • Eliminates the human
error
• Sonic pulses • Non-contact
measurement • Compatible with
plates and tubes
• Microplate reader for quantification
• NanoDrop for the purity
• Agarose gels for DNA quality
• 2 LabChips for RNA sample quality
• 2 STARlets in production
• Main workforce for both sample QC and aliquots
• Integrated tube decapper
• Re-array capability • High consistency • Reduces ergonomic
issues
![Page 9: Overview of Sample Management · DNA assays Quantifluor dsDNA system (0.4-20ng, 2-200ng) RNA assays ... Check Quantity Quality Purity . New Technology 4/8/15 13 Instrument & Method](https://reader034.vdocuments.us/reader034/viewer/2022042322/5f0c20f27e708231d433e151/html5/thumbnails/9.jpg)
Sample Receipt
4/8/15 9
Common concerns: Ø Packaging Ø Dry ice
Ø Secondary containers Ø Container seals
Ø Labels/documents
![Page 10: Overview of Sample Management · DNA assays Quantifluor dsDNA system (0.4-20ng, 2-200ng) RNA assays ... Check Quantity Quality Purity . New Technology 4/8/15 13 Instrument & Method](https://reader034.vdocuments.us/reader034/viewer/2022042322/5f0c20f27e708231d433e151/html5/thumbnails/10.jpg)
Sample Quantity
4/8/15 10
DNA assays Quantifluor dsDNA system
(0.4-20ng, 2-200ng)
RNA assays Quant-iT RNA BR kit (50-1000ng)
Quantifluor RNA system (1.5-80ng)
Common cause for discrepancy: Ø Pipetting errors Ø Calibration curve Ø Contaminants Ø Assays/kits Ø Standards
y = 9.6749x - 44.49 R² = 0.99957
0
2000
4000
6000
8000
10000
12000
0 200 400 600 800 1000 1200
RFU
RNA (ng)
Calibration Curve
![Page 11: Overview of Sample Management · DNA assays Quantifluor dsDNA system (0.4-20ng, 2-200ng) RNA assays ... Check Quantity Quality Purity . New Technology 4/8/15 13 Instrument & Method](https://reader034.vdocuments.us/reader034/viewer/2022042322/5f0c20f27e708231d433e151/html5/thumbnails/11.jpg)
Sample Quality
4/8/15 11
![Page 12: Overview of Sample Management · DNA assays Quantifluor dsDNA system (0.4-20ng, 2-200ng) RNA assays ... Check Quantity Quality Purity . New Technology 4/8/15 13 Instrument & Method](https://reader034.vdocuments.us/reader034/viewer/2022042322/5f0c20f27e708231d433e151/html5/thumbnails/12.jpg)
Sample QC Requirements per Library
4/8/15 12
LMP Ø 8kb CLRS Ø 4kb CLRS Ø 2.5kb CLRS Ø Nextera LMP PacBio Long reads Stranded RNA-seq Ø Poly A selection Ø rRNA depletion Ø FFPE/LCM smRNA Ø Eukaryote Ø Prokaryote Full length Ø Iso-seq
All library types except: Amplicon sequencing Ø Ribosomal iTags
All library types Long reads Ø PacBio 20kb Ø PacBio >10kb Ø PacBio 3kb Ø PacBio 2kb
Relaxed Stringent
Volume Check Quantity Quality Purity
![Page 13: Overview of Sample Management · DNA assays Quantifluor dsDNA system (0.4-20ng, 2-200ng) RNA assays ... Check Quantity Quality Purity . New Technology 4/8/15 13 Instrument & Method](https://reader034.vdocuments.us/reader034/viewer/2022042322/5f0c20f27e708231d433e151/html5/thumbnails/13.jpg)
New Technology
4/8/15 13
Instrument & Method
Evaluation
• Advanced Analytical Fragment Analyzer
• Agilent Tape Station • Biotek Synergy • STARlet method validation • SAM validation
Optimization
• Chlamy DNA/RNA sample prep
• Microbial DNA sample prep • Biomatrica RNAstable &
DNAstable • Promega Quantifluor DNA &
RNA systems
Technical Guidance
• Genomic DNA QC protocol • Total RNA QC protocol • Chlamydomonas RNA
extraction • Etc…
![Page 14: Overview of Sample Management · DNA assays Quantifluor dsDNA system (0.4-20ng, 2-200ng) RNA assays ... Check Quantity Quality Purity . New Technology 4/8/15 13 Instrument & Method](https://reader034.vdocuments.us/reader034/viewer/2022042322/5f0c20f27e708231d433e151/html5/thumbnails/14.jpg)
Sample Management Team
4/8/15 14
Kathleen Lail
Juying Yan
Mansi Chovatia
Aditi Sharma
Tim Williams
How may we assist you?