Gene Expression & Genotyping

Sample Requirements
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Sample Requirements

10X Genomics Single Cell Analysis

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

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

For Single Cell Linked-reads, and Single Cell ATAC-Seq, please contact NextGen Core Director at moraga@ufl.edu.

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

RNA Sample Submission for RNA-Seq, Microarray and Gene Expression Study

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.

Request Type RNA Type Input amount Recommended Minimum Volume Maximum Volume Recommended Amount
Stranded mRNA-Seq Total RNA 100 ng – 4 ug   RIN ≥ 7 20 µl 50 µl ≥ 500 ng
Stranded Total RNA-Seq with Ribo-zero Total RNA 100 ng – 1 ug   RIN <7 is acceptable 10 µl 10 µl ≥ 500 ng
Low RNA input RNA-Seq – not stranded Total RNA 10pg – 10ng     RIN ≥ 7 10 µl 10 µl ≥ 10 ng
Blood mRNA-seq Total RNA from blood 10 ng – 1 ug     RIN ≥ 7 10 µl 50 µl ≥ 500ng
Affimetrix Array/Micro Array (GeneChip WT) Total RNA 100 ng – 500 ng   RIN ≥ 7 10 µl 20 µl ≥ 500 ng

For RNAseq frequently asked questions RNA Seq_FAQ.

16S Metagenomics Sample Submission

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

For 16S metagenomics frequently asked questions, Click Here

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.

Droplet Digital PCR

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.

For Droplet Digital PCR frequently asked questions ddPCR FAQs

Fragment Analysis

Ready-to-run samples should be submitted in a 96-well plate with 10ul for each sample.  Sample position in plate should be correlated with the position listed in the excel template. Please fill out the excel template and submit electronically with your iLab submission.

For Fragment Analysis frequently asked questions, Fragment FAQs

Cell-Line Authentication / STR

For Cell-Line Authentication and STR analysis, we can start with either a cell pellet or extracted gDNA. For extracted gDNA please submit 10 uL of your samples at a concentration above 10 ng/uL.  For cell pellet, please submit 5×105 cells in 100 uL of 1x PBS thawed on ice or frozen at -20C.  Samples should be submitted in 1.5 mL microcentrifuge tube if <8 samples, for 8 or more samples please submit in 8-tube strips. For Cell-Line Authentication or STR frequently asked questions Cell Line FAQs.

Tapestation

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:

Bioanalzyer
Assay Size Range Quantitative Range Qualitative Range
High Sensivitiy DNA 50 – 7000 bp 5 – 500 pg/uL
D1000 25 – 1000 bp 0.5 – 50 ng/uL
Nano, Total RNA 25 – 500 ng/uL 5 – 500 ng/uL
Nano, mRNA 25 – 250 ng/uL 25 – 250 ng/uL
Pico, Total RNA 200 – 5000 pg/uL 50 – 5000 pg/uL
Pico, mRNA 500 – 5000 pg/uL 250 – 5000 pg/uL
Small RNA 6-150 nt 50 – 2000 pg/uL

For Tapestation frequently asked questions Bioanalyzer-TapeStation FAQs

Bioanalyzer

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:

Bioanalzyer
Assay Size Range Quantitative Range Qualitative Range
High Sensivitiy DNA 50 – 7000 bp 5 – 500 pg/uL
D1000 25 – 1000 bp 0.5 – 50 ng/uL
Nano, Total RNA 25 – 500 ng/uL 5 – 500 ng/uL
Nano, mRNA 25 – 250 ng/uL 25 – 250 ng/uL
Pico, Total RNA 200 – 5000 pg/uL 50 – 5000 pg/uL
Pico, mRNA 500 – 5000 pg/uL 250 – 5000 pg/uL
Small RNA 6-150 nt 50 – 2000 pg/uL

For Tapestation frequently asked questions Bioanalyzer-TapeStation FAQs

Qubit

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:

Bioanalzyer
Assay Size Range Quantitative Range Qualitative Range
High Sensivitiy DNA 50 – 7000 bp 5 – 500 pg/uL
D1000 25 – 1000 bp 0.5 – 50 ng/uL
Nano, Total RNA 25 – 500 ng/uL 5 – 500 ng/uL
Nano, mRNA 25 – 250 ng/uL 25 – 250 ng/uL
Pico, Total RNA 200 – 5000 pg/uL 50 – 5000 pg/uL
Pico, mRNA 500 – 5000 pg/uL 250 – 5000 pg/uL
Small RNA 6-150 nt 50 – 2000 pg/uL

For Tapestation frequently asked questions Bioanalyzer-TapeStation FAQs

PicoGreen

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.