Gene Expression & Genotyping Resources

FAQs Bioanalyzer-TapeStation

FAQs Digital PCR

FAQs Visium HD

FAQs Single Cell RNA-seq

FAQs Short Read RNA-seq

FAQs DNA Sequencing

FAQs_16s Sequencing

Bioanlayzer/TapeStation Rerun policy

We reserve the right to fill out partial bioanalyzer chips with internal ICBR Gene Expression & Genotyping samples. ICBR will bear responsibility for the run if failure is determined to be due to bad kits, bad runs, bad reactions, or issues with the instruments. However, the client is responsible for payment of services due to incorrect concentration for the specific chosen assay even if results are not as expected or desired. ICBR cannot accept responsibility for delays in completion of projects or data delivery due to unpredictable reasons such as but not limited to: instrument failures, unavailability of vendor supplies, or university closures due to weekends, holidays or natural calamities.

Sample replacement policy

It is the customers’ responsibility for the QC payment for the replaced samples.

Sample return policy

Samples are stored for up to six months following the completion of the project. It is the customers’ responsibility to retrieve the extra samples during this six month period. An intention to pick up samples may be communicated through the “notes” section of the CrossLab (iLab) submission form. We cannot guarantee samples can be returned following this six month period.

Authorship credit should be given if members of the UF ICBR Gene Expression & Genotyping staff have provided services or expertise that is critical to a manuscript. Note: Visit ‘Acknowledging UF ICBR’ to see how proper acknowledgments are easier than ever!

Although other circumstances may warrant authorship, authors are those that meet the items below:

• Agrees to be accountable for accuracy and/or integrity of the work and expertise. (In all our work the person executing the work takes the fullest degree of responsibility for accuracy and integrity.)
• Provides substantial contributions to the experimental design, acquisition, and analysis/interpretation of the work.
• Provides input on drafting of the work (often figures) and approves of the work to be submitted/published. (If a member of the facility has made substantial contributions it is expected that s/he will be given the opportunity to review drafts of manuscripts for accuracy/fidelity and should indicate agreement before a draft is moved forward to publication.)

If a member of UF ICBR Gene Expression & Genotyping has contributed work to a manuscript, but does not meet the criteria for authorship, the corresponding author should acknowledge the UF ICBR Gene Expression & Genotyping staff member who provided the data and their contributions should be specified.

These authorship expectations were developed in accordance with several other documents that outline criteria for authorship:

https://oir.nih.gov/sites/default/files/uploads/sourcebook/documents/ethical_conduct/guidelines-conduct_research.pdf

http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html

The Gene Expression & Genotyping core provides a variety of services related to Affymetrix and Agilent array process, including whole genomic-wide gene expression arrays, miRNA arrays, DNA arrays, and Gene Regulation Analysis arrays. GE also offers RNA-Seq, SAGE, small RNA and Sequence Capture libraries construction, and cDNA normalization service for different NextGen Platforms. In addition, DNA and RNA quality assessment services are offered using an Agilent Bioanalyzer.

The core also provides a variety of basic molecular biology services such as DNA isolations, PCR reactions, and PCR purifications for sequencing. We also set up most types of fragments for analysis on the AB3730xl automated sequencer; providing the buffers and size standards. The AdvanCE FS96 is a 96 capillary instrument used to analyze fragments with greater than trinucleotide repeats. In addition, the Genotyping core designs, characterizes, and processes microsatellite loci used for individual identification, population studies, and geneflow. The core has an Illumina BeadArray Reader used to analyze SNP and gene expression samples in a high-throughput fashion.

We also provide real-time PCR services by utilizing Applied Biosystems (ABI) 7500 FAST, ABI 7900HT, and BioRad CFX96. We support both SybrGreen and TaqMan reaction chemistries. Our 7900HT system is equipped with both 96- and 384-well blocks to facilitate high-throughput analysis. Applications include quantitative gene expression analysis, pathogen detection/quantification, and allelic discrimination (SNP detection). Our walk-up self service on the AB 7500 FAST allows researchers to set-up and run their own plates, but not purchase their own machine. The QUANTSTUDIO 3d DPCR SYSTEM allows customer to do absolute quantification, rare allele detection, quantification using TaqMan SNP array, and CNV (Copy Number Variation) in a more sensitive, specific, and precise way.

Sample submission for single cell study differs from project to project. Please start a consultation meeting with ICBR Core Directors to plan your experiment.

For Single Cell RNA-Seq, Single Cell V(D)J, Single Cell Feature barcoding, Single Cell CRISPR Screening, and Spatial Gene Expression, please contact GE Core Direct at yanp@ufl.edu.

For basic knowledge of 10X Single Cell Analysis, please visit their website: https://www.10xgenomics.com/.

We recommend incorporating an on-column DNAase I treatment during the RNA extraction and measuring the OD 260/280 and 260/230 ratios. OD 260/230 should be higher than 1.6. Sample concentration of 40-100ng/ul by Qubit (in ddH2O) is prefered. If possible, we also recommend checking the integrity of total RNA using a Bioanalyzer RNA assay.

Please use RNase/DNase-free 1.5 mL microcentrifuge tubes or RNase/DNase-free 8-tube strips tubes and label it clearly (less than 5 characters is preferred), samples must be on ice or dry ice while transporting from lab to drop off in GE. Samples should be put into an appropriate sized box or zip-lock bag labelled with Submission ID (GE#), PI’s Name, Researcher’s Name, and date of submission. Please provide the inputs RNA listed below with extra 4 uL of each sample for QC.

RNA- and protein-free double strand gDNA with OD260/280 ratio of approximately 1.8 to 2.0 are requested. Concentration should be measured by Qubit.  We prefer the samples be submitted in RNAase DNAase-free 8-strips PCR tubes or 96-well plate

Note: Full-length 16S Metagenomics sequencing is also supported on the PacBio. Please contact us as ICBR-NextGen@ad.ufl.edu to discuss your project.

For ddPCR we can use gDNA, cDNA, plasmids, or viruses. 8 or less samples should be submitted in 1.5mL microcentrifuge tubes. 8 or more samples may be submitted in either 8-tube strips or 96-well plates. The detailed sample requirement, please visit ddPCR FAQ or contact the core: ICBR-GeneExpression@ad.ufl.edu.

Please provide at least 4 uL of each sample.  For less than 8 samples, submit samples in RNase/DNase-free 1.5 mL microcentrifuge tubes. For 8 or more samples, submit samples in RNase/DNase-free 8-tube strips.  Please label samples with their ID#.  Samples should be put into an appropriately sized zip-lock bag labelled with GE#, PI’s Name, Researcher’s Name, and date of submission.  Samples must be submitted at concentrations appropriate for the assay chosen. Assay Acceptable Concentration Ranges:

For Tapestation frequently asked questions Bioanalyzer-TapeStation FAQs

Please provide at least 4 uL of each sample.  For less than 8 samples, submit samples in RNase/DNase-free 1.5 mL microcentrifuge tubes. For 8 or more samples, submit samples in RNase/DNase-free 8-tube strips.  Please label samples with their ID#.  Samples should be put into an appropriately sized zip-lock bag labelled with GE#, PI’s Name, Researcher’s Name, and date of submission.  Samples must be submitted at concentrations appropriate for the assay chosen. Assay Acceptable Concentration Ranges:

For Tapestation frequently asked questions Bioanalyzer-TapeStation FAQs

Please provide at least 4 uL of each sample.  For less than 8 samples, submit samples in RNase/DNase-free 1.5 mL microcentrifuge tubes. For 8 or more samples, submit samples in RNase/DNase-free 8-tube strips.  Please label samples with their ID#.  Samples should be put into an appropriately sized zip-lock bag labelled with GE#, PI’s Name, Researcher’s Name, and date of submission.  Samples must be submitted at concentrations appropriate for the assay chosen. Assay Acceptable Concentration Ranges:

For Tapestation frequently asked questions Bioanalyzer-TapeStation FAQs

PicoGreen can be used to quantify double-stranded DNA. Please provide exactly 3 uL of each sample.  Samples should be submitted in RNase/DNase-free 8-tube strips (0.2 mL).  Please label samples with their ID#.  Samples should be put into an appropriate sized zip-lock bag labelled with GE#, PI’s Name, Researcher’s Name, and date of submission.  Samples must be submitted at concentrations appropriate for the assay chosen.

When samples are submitted they should be labeled with Sample IDs. These Sample IDs are associated with their sample names listed on the excel sample information sheet.

Please submit the samples in RNAase DNAase-free 8-tube strips or 96-well plate if you have more than 16 samples..

If you have less than 8 samples, you can submit in RNAase DNAase-free 1.5 ml microfuge tubes having numerical ID (e.g., 1, 2, 3….)

10X Genomics Single Cell: Scheduling is needed. We are not able to process if it is not scheduled. We prefer to receive samples in morning time/as early as possible so that we can complete certain process to a ‘save stop’ point in the same day.

RNA-Seq, Microarray and 16s Metogenomics: Room 178B (In person or shipment on dry ice)

DNA RNA QC: please drop off in the refrigerator in ICBR hallway (please fill out the submission sheet next to the refrigerator)

Fragment Analysis: Drop off in refrigerator in 185 or ship with ice pack (please fill out the submission sheet next to the refrigerator)