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Getting Started Guide
The Genome Center
To other GC Cores -> Bioinformatics, Metabolomics, Proteomics, ...
Bioinformatics Core
Proteomics Core
Metabolomics Core
Tilling Core
To important UC Cores -> Sample preps, 16S, qPCR, Flow Sorting, ...
Host Microbe Systems Core -- 16S
RT-qPCR Core — DNA/RNA extractions, Taqman
Sanger Sequencing Core
Cancer Center Shared Genomics Resource
Flow Cytometry & Sorting
Getting Started
Getting Started Guide
Sample and Library Requirements
Sample Submission and Shipping
Intro: Illumina Sequencing
Intro: Element Biosciences AVITI Sequencing
Intro: Pacbio Sequencing
Intro: Nanopore Sequencing
Services
Short-Read Sequencing Services – Illumina & Element Bio AVITI
DNA Sequencing (whole-genome shotgun, targeted, amplicon, exome, ChIP, reduced-representation, Methyl, …)
RNA-Sequencing (high-throughput mRNA-Seq, total RNA-seq, 3'-Tag-Seq, miRNA-seq, ... )
Gene Expression Profiling with 3' Tag-Seq
Nanopore Sequencing – PromethION
PacBio Revio and Sequel II Library Prep & Sequencing
Linked Read Sequencing – 10X Genomics Chromium Technology
High Molecular Weight DNA Isolation (HMW-DNA)
Illumina & Aviti Sample and Library Requirements
DNA/RNA Quantification & Library QC
DNA and RNA Extraction
Single Cell Expression Profiling & Genomics (10X Genomics, SPLiT-Seq & Plate-based scRNA-Seq)
Spatial Transcriptomics
Genotyping – Illumina Infinium, Fluidigm EP1
Infinium Genotyping
Fluidigm EP1
Consultations
Bioinformatics
Sequencing Data Download & Access
Genotyping Data
Sample Submission & Forms
Sample Submission & Shipping
Illumina & Aviti Sample and Library Requirements
Downloads/Forms
Prices
UC Rates -- UC Davis and other UC campuses
Academic/Non-Profit Rates
Industry Rates
FAQs
Shared Equipment
Booking Shared Instruments - Equipment Calendar
Equipment Training & Use
Agilent Bioanalyzer 2100
FilterMax F5 Plate Reader
Qubit Fluorometer
LabChip GX Touch HT (High-Throughput Bioanalyzer)
Nanodrop Spectrophotometer
Sonicators
BluePippin and Pippin HT
Robotic Liquid Handlers
Fluidigm C1 – Single Cell Genomics
Fluidigm Access Array
News & Workshops
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Accounts & Calendars
Booking Shared Instruments & Training – PPMS Equipment Calendar
Submission System
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SLIMS Account Login
Sequencing Calendar & Queue
Free Consultations
Downloading Your Bioanalyzer & Plate Reader Data
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FAQs
Breadcrumb
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FAQs
01 General Information
Can I use Core facility equipment?
Do you archive submitted samples? Do you return samples?
Do you ask for co-authorships?
Do you provide Bioinformatics help?
Do you support pilot projects with Seed Grants?
How do I acknowledge your services?
How Do I Contact You?
How do I get into the Genome Center Building?
How do I get started working with the Core facilities? How do I set up an account with the Genome Center?
How do I make an appointment for a consultation?
How do I set up an account in the PPMS ordering and instrument reservation system?
How do I submit samples or libraries?
How do I subscribe to your newsletter or listserv?
How do you assure the quality of your sequencing data?
RNA-seq recommendations?
What happened to the BGI@UC DAVIS ?
What Information Do You Require About My Project?
When can I visit you / reach you?
Where are you located?
Which impact has the RNA quality on RNA-seq?
Who do I ask for administrative/billing questions?
02 Prices and Recharge Rates
How and when will I be invoiced?
What are the prices associated with genotyping and sequencing?
What is a Purchase Order? How do I create a PO?
Which recharge-rate scale (price scale) will apply to my project?
03 Sample Preparation & Sample Requirements
Can I submit samples of lower integrity than recommended?
Can you run samples with less than the recommended input material?
Do you have recommendations for the isolation of plant total RNA samples?
Do you offer DNA isolations and RNA isolations as a service?
How do I prepare DNA samples for RR-Seq (reduced representation sequencing)
How do I ship RNA samples? How do I ship RNA samples if the transport will take a long time?
How should I purify my samples? How should I remove DNA or RNA contamination?
How should I QC my genomic DNA samples before sequencing?
How to prepare samples for multiplexed amplicon sequencing on Illumina systems?
How to prepare samples for multiplexed amplicon sequencing on the PacBio Sequel?
How to purify DNA samples for long-read sequencing (PacBio, Nanopore)? How to remove polysaccharides?
How to submit samples for Labchip GX RNA-QC and fragment analysis?
What are the sample requirements for DNA and RNA samples or for sequencing libraries ?
What type of samples are recommended for RNA isolations for gene annotations?
What type of samples are recommended for the isolation of HMW-DNA? (for Long-Read Sequencing)
When is a genome suitable for Bionano Optical Genome Mapping?
Which DNA isolation protocols do you recommend for Illumina sequencing?
Which orientation should the index sequences have? (barcode sequences)
Which protocols or kits do you recommend for RNA isolations from human and animal samples? How many cells will I need?
04 Library Preparation and QC
Do you recommend PCR-free sequencing library preparations?
How do I amplify Illumina sequencing libraries?
How do I pool sequencing libraries? Can you pool them for me?
How do I remove long fragments from a library?
How do I size select libraries for the HiSeq 4000 with beads?
How many indexes are available for my libraries?
How should I prepare and sequence samples for ChIP-seq?
How to remove primer contamination from sequencing libraries? (free primers)
My libraries show peaks larger than expected. Can I still sequence these PCR-bubbles?
My PCR-free libraries do not look as expected on the Bioanalyzer. How should I QC PCR-free libraries?
Suboptimal RNA samples - How much RNA sample to start with?
What are the sample requirements for DNA and RNA samples or for sequencing libraries ?
When do you recommend 3'-Tag RNA-seq?
Which indexing scheme should I use for Illumina sequencing to prevent index hopping? (UDI adapter)
Which strand is sequenced for my strand-specific RNA-seq data?
Why should I avoid technical replicates and pseudoreplicates?
05 Sequencing
Can I reserve a spot in the queue?
Can I submit a library I made?
Can I use custom sequencing primers? What melting temperatures should these have?
Do you offer 16S sequencing and 18S sequencing?
Do you store samples and sequencing libraries?
How should I prepare and sequence samples for ChIP-seq?
How should I sequence ATAC-seq libraries?
How should I submit the barcode sequence information? In which direction will they be sequenced?
In which form will I receive the data?
My libraries show peaks larger than expected. Can I still sequence these PCR-bubbles?
Sanger DNA sequencing and other services at UC Davis
What are UMIs and why are they used in high-throughput sequencing?
What read numbers/yields can I expect from Illumina sequencing?
What type of library services are available through the Core?
When can I expect to get my data?
Where can I find a tutorial on Illumina and NGS sequencing?
Which indexing scheme should I use for Illumina sequencing to prevent index hopping? (UDI adapter)
06 Sequencing Data
Do you archive the sequencing data?
Do you de-multiplex the sequencing data?
How do I download my sequencing data?
How should the miRNA/small-RNA data be trimmed?
My FASTQ file contains some "N"s. Is there a problem with my data?
Should I remove PCR duplicates from my RNA-seq data?
What data will I receive for Illumina sequencing? Demultiplexing, Trimming, Filtering
When should I trim my Illumina reads and how should I do it?
Where and how can I get my data?
Where can I find the UMIs in the Tag-Seq data? When and how should I trim my Tag-Seq data? What is the low complexity stretch in the Tag-Seq data?
Which data will I receive from the PacBio Sequel II sequencer? Will they have quality scores?
Which strand is sequenced for my strand-specific RNA-seq data?
Why does FASTQC show unexpectedly high sequence duplication levels (PCR-duplicates)?
