DERC/IDOM FGC Sample Submission Form

1

Fill out the form below as well as you can to submit samples for analysis at the DERC/IDOM FGC.

When estimating the total cost, make sure you choose your affiliation correctly.

Click the Submit button (upper right corner of the page) to send the form to the FGC staff. We will review the submission and contact you regrarding any additional information required.

Click the Save button (upper right corner of the page) to save your entries for later editing or submission.

Once you have saved or submitted your form, it will have an ID, e.g., FGC:20101010123456. You can retrieve a form for review, modification, and/or resubmission by filling in the form ID and clicking Recall.

2

For additional information or to set up an initial consultation, please contact:

Jonathan Schug, Ph.D.
Department of Genetics, IDOM
12-156 Translational Research Center
3400 Civic Center Blvd Bldg 421
Philadelphia, PA 19104-5156

    Phone: +1 (215) 898-0773
      Fax: +1 (215) 573-2326
   E-mail: jschug@mail.med.upenn.edu
3

When shipping samples to us, be sure to use plenty of dry ice, ship overnight, but do not send on Friday. The shipping address is:

Alan Fox or Olga Smirnova
Department of Genetics, IDOM
12-160 Translational Research Center
3400 Civic Center Blvd Bldg 421
Philadelphia, PA 19104-5156

     Phone: +1 (215) 898-0772
    E-mail: foxaj@mail.med.upenn.edu
            smirnova@mail.med.upenn.edu
4

Checks should be made payable to "The Trustees of the University of Pennsylvania" and mailed to:

Tom Hoffman
DERC and IDOM
12-153 Translational Research Center
3400 Civic Center Blvd Bldg 421
Philadelphia, PA 19104-6145

Phone: (215) 898-5362
  Fax: (215) 573-5809
Email: lhoffmant@mail.med.upenn.edu
5

The Functional Genomics Core is supported by the United States National Institute of Diabetes & Digestive & Kidney Diseases of the National Institutes of Health.

Please acknowledge the IDOM, the DERC grant (P30DK19525), and the services of the Functional Genomics Core in any research publications deriving from this work.

Form Info

Sample Submission Form ID  
FGC Experiment ID   FGC staff will enter this once it has been assigned.
Comments or questions for FGC staff  

Investigator Information

Name and Contact
Last Name First Name Email Phone Fax
Experimenter
Principle Investigator
Billing
Address
Organization  
  Investigators Billing
Department
Address 1
Address 2
City
State
ZIP/Postal Code
Country
Date of Submission  
UPenn Client Payment Information
UPenn Grant Transfer Code
cnac org bc fund obj program cref exp
Outside Client Payment Information
Purchase Order/Requisition #  
Check #  

Experiment Information

Title  
Summary  
Species
Number of Test Conditions  

Charge Information

Affiliation   Affiliation determines the price. "Genetics" is UPenn Genetics Department.
Estimated Total
Sample Preparation
RNA/DNA quality assessment @ /sample = Quality assessment of RNA or DNA using the Agilent Bioanalyzer. Required for most types of experiments.
RNA preparation @ /sample = Extraction of RNA from < 100 mg of tissue.
Islet purity matching @ /sample = "For experiments involving islets, these must be matched for purity using Q-PCR with four markers to control the bad effects of mis-matched islet purity."
Gene Expression Analysis
Agilent Expression Analysis - Single Color @ /sample = Global gene expression analysis using the Agilent Whole Genome Arrays. Use for experiments with 3 or more groups.
Agilent Expression Analysis - Dual Color @ /sample = Global gene expression analysis using the Agilent Whole Genome Arrays. Use for experiments with 2 groups.
Library Preparation for Illumina Sequencing
ChIP-Seq Library Reagents @ /sample = Reagent costs for library preparation. Add labor costs below.
Genomic-Seq Library Reagents @ /sample = Reagent costs for library preparation. Add labor costs below.
ChIP-Seq or Genomic-Seq Library Labor @ /day = Sample preparation and training. Client should be present. Add sample count above. 6 samples max per day.
mRNA-Seq Library Reagents @ /sample = Reagent costs for library preparation. Add labor costs below.
mRNA-Seq Library Labor @ /day = Sample preparation and training. Client should be present. Add sample count above. 6 samples max per day.
Small RNA-Seq Library Reagents @ /sample = Reagent costs for library preparation. Add labor costs below.
Small RNA-Seq Library Labor @ /day = Sample preparation and training. Client should be present. Add sample count above. 6 samples max per day.
Illumina Oligos @ /vial = Oligos for 10 reactions.
Single-End Sequencing on Illiumina GA-IIx
36bp Single End @ /lane = "Single-end sequencing to a length of 36bp. This is suitable for ChIP-seq, miRNA, or HITS-CLIP experiments."
72bp Single End @ /lane = Single-end sequencing to a length of 72bp. This is suitable for HITS-CLIP or RNA-Seq experiments.
100bp Single End @ /lane = Single-end sequencing to a length of 100-120bp. This is suitable for RNA-Seq or (targeted) genome sequencing.
150bp Single End @ /lane = Single-end sequencing up to a length of 150bp. This is suitable for RNA-Seq or (targeted) genome sequencing.
Paired-End Sequencing on Illiumina GA-IIx
36bp Paired End @ /lane = Paired-end sequencing to a length of 36bp on each end
72bp Paired End @ /lane = Paired-end sequencing to a length of 72bp on each end
100bp Paired End @ /lane = Paired-end sequencing to a length of 100-120bp on each end
150bp Paired End @ /lane = Paired-end sequencing up to a length of 150bp on each end. This is suitable for RNA-Seq or (targeted) genome sequencing.
Single-End Sequencing on Illiumina hiSeq2000
50bp Single End @ /lane = "Single-end sequencing to a length of 50bp. This will generally yield 187 million raw sequences. This is suitable for multiplexed ChIP-seq, miRNA-seq, or HITS-CLIP experiments."
100bp Single End @ /lane = "Single-end sequencing to a length of 100bp. This will generally yield 187 million raw sequences. This is suitable for RNA-Seq, (targetted) genome sequencing experiments."
Paired-End Sequencing on Illiumina hiSeq2000
50bp Paired End @ /lane = Paired-end sequencing to a length of 36bp on each end.
100bp Paired End @ /lane = "Paired-end sequencing to a length of 100bp on each end. This will generally yield 187 million raw pairs of sequences. This is suitable for RNA-Seq, (targetted) genome sequencing experiments."
Multiplexing
Barcode Sequencing @ /unit = Sequencing barcode information. This is minimum charge when all lanes have bar codes. We may charge additional units to cover costs if not all lanes are barcoded.
Analysis
Pathway analysis @ /comparison = "Analysis of biological pathways using (for example) DAVID, or GSEA."
Advanced Custom Analysis @ /hour = Hourly rate for additional custom analysis beyond basic service
Submission to Public Repository @ /experiment = "Formatting and upload of data to public repository - GEO, SRA, or ArrayExpress, as appropriate."
Promoter Occupancy Analysis (ChIP-On-Chip)
Agilent Promoter Analysis @ /sample = "ChIP-on-Chip analysis of 17,000 transcripts represented by 488,000 60 bp promoter tiles."
Comparative Genomic Hybridization
Agilent Medium Density CGH @ /sample = Comparative Genomic Hybridization for genome-wide analyses of chromosomal changes. 105K elements.
Agilent High Density CGH @ /sample = Comparative Genomic Hybridization for genome-wide analyses of chromosomal changes. 244K elements.