Shared Resource

Analytical & Translational Genomics

The Analytical and Translational Genomics (ATG) Shared Resource is essential for advancing basic, clinical, and population-based cancer research. It offers UNMCCC members and non-members cost-effective and comprehensive genomic analysis services, including next-generation sequencing (NGS), single-cell RNA sequencing (scRNA-seq), spatial genomics, initial data analysis, and support for functional genomics assays
and other genomics-related technologies.

The Shared Resource is funded by the UNM Comprehensive Cancer Center through the CCSG core grant P30CA118100 and additional funding, as well as funds from the state of NM and user fees.

The knowledgeable staff is available for consultations to assist users in creating the best possible experiments and optimizing the quality of the data generated.

Genomics lab group — The Genomics Lab Team: Funmi (now in BDS), Maggie, Charlie, Kel, and Dr. Palanisamy

Faculty Director

Viswanathan Palanisamy, PhD
Professor, Internal Medicine/Molecular Medicine
Tel:(505) 272-0652

Technical Director / Bioinformatics

Kathryn (Charlie) Brayer, PhD | CRF G22A

Senior Technical Staff

Kel Cook, PhD | CRF 118, Tel: (505) 272-5564

Magdalena (Maggie) Cyphery | CRF 119, Tel: (505) 272-5564

Analytical and Translational Genomics

The ATG is accessible to all researchers at the University of New Mexico (UNM) and its related institutions. Nevertheless, it is essential for you to provide a citation for the P30CA118100 and also mention ATG, along with other UNMCCC shared resources that were used to produce the data.

To give credit to our contributions, we kindly request that you include the following text in the acknowledgment section of your manuscripts:

This study received partial funding from the UNM Comprehensive Cancer Center Support Grant NCI P30CA118100 and utilized the Analytical and Translational Genomics Shared Resource.

Key Services, Technologies, & Equipment

High-throughput DNA-seq and RNA-seq. ATG offers whole-genome sequencing, bulk RNA-seq, ChIP-seq, RIP-seq, exome, and small RNA analysis using the Singular Genomics G4 sequencer. Starting material can include cells, saliva, blood, and FFPE or fresh-frozen pathology samples.

10x Genomics single-cell sequencing. Using the 10x Genomics Chromium controller, together with a Countess II Automated Cell Counter and a Miltenyi gentleMACS Octo Dissociator to create single-cell suspensions, ATG staff prepare the samples and construct the NGS libraries for NGS of DNA and RNA.

10x Visium-HD and Xenium in situ for whole-transcriptome and targeted gene expression analysis. In partnership with the Human Tissue Repository & Tissue Analysis (HTR-TA) Shared Resource, the ATG offers spatial whole transcriptome analysis of fresh-frozen and FFPE tissues using the Visium-HD and Xenium in situ spatial gene expression technologies from 10x Genomics. Visium HD spatial gene expression delineates the complete transcriptome of entire tissue sections, providing morphological context and high cellular resolution. Xenium in situ enables the high-throughput subcellular mapping of up to 5,000 genes alongside multiplexed proteins within the same tissue segment, obtained in collaboration with the HTR-TA for sample preparation.

NGS data analysis, scRNA-seq, and interactions with the Biostatistics and Bioinformatics & Data Science (BDS) Shared Resources. The ATG coordinates with the Biostatistics and BDS Shared Resources to establish quality control analytics and develop data analysis pipelines for the G4-Singular data, including single-nucleotide variant (SNV) detection from DNA samples, gene expression analysis, variant analysis from RNA, scRNA-seq data, detection of fusion transcripts from RNA-seq, and copy number variant (CNV) analysis. The processed files are stored in our secure AWS cloud account and used for downstream analyses by ATG staff or the BDS, utilizing customized R scripts. ATG Technical Director Brayer serves a dual role as a senior bioinformatician and a liaison with the Biostatistics and BDS Shared Resources to facilitate study design and data analysis.

Data storage and computing. The ATG maintains a secure, HIPAA-compliant, and IRB-approved AWS account where large datasets can be stored and analyzed. All data are de-identified, encrypted in transit, and stored. Only authorized users have access, which requires two-factor authentication. For the security of genomic data, the ATG adheres to the policies outlined in the NIH Security Best Practices for Controlled-Access Data, Subject to the NIH Genomic Data Sharing Policy.

Other services. The ATG has an Agilent BioAnalyzer, Qubit fluorometer, a Miltenyi gentleMACs Octo Dissociator with heaters (for generating single-cell suspensions from tissue), a Countess II automated cell counter, and ThermoFisher QuantStudio 6 Pro Q-PCR, which are available for use by UNMCCC members. A Qiagen EZ2 DNA/RNA extraction robot is available for high-volume, automated nucleic acid extraction.

ATG can sequence the following types:

Detection of mutations or gene variants. This could involve assessing the level of genetic mutations in a tumor, analyzing specific genetic variations in a particular cancer or disease, or evaluating how cells respond to DNA damage after injury or treatment. Typically, this is achieved by using targeted gene panel sequencing to analyze genes linked to cancer or certain diseases.
Gene expression studies. Transcriptional profiling of cells, tissue, organoids, or patient samples, either as individual cells or in larger quantities.
A range of chromatin state analysis assays, from DNA methylation studies to ATAC assays to ChIP-seq, are available.
Studying non-coding RNAs such as ncRNAs, lincRNAs, miRNAs, and tRNAs.

Please contact either Kel Cook (kelcook@salud.unm.edu) or Kathryn Brayer (kbrayer@salud.unm.edu) to schedule a consultation.

ATG uses iLab for billing.

For questions regarding iLabs or for account/PR set-up for use in the shared resource, please email Palakshi Reddy Bandapalli or call 505-272-4539.

Analytical and Translational Genomics

Acknowledge

To give credit to our contributions, we kindly request that you include the following text in the acknowledgment section of your manuscripts:

This study received partial funding from the UNM Comprehensive Cancer Center Support Grant NCI P30CA118100 and utilized the Analytical and Translational Genomics Shared Resource.

Services

Key Services, Technologies, & Equipment

Applications

ATG can sequence the following types:

Detection of mutations or gene variants. This could involve assessing the level of genetic mutations in a tumor, analyzing specific genetic variations in a particular cancer or disease, or evaluating how cells respond to DNA damage after injury or treatment. Typically, this is achieved by using targeted gene panel sequencing to analyze genes linked to cancer or certain diseases.
Gene expression studies. Transcriptional profiling of cells, tissue, organoids, or patient samples, either as individual cells or in larger quantities.
A range of chromatin state analysis assays, from DNA methylation studies to ATAC assays to ChIP-seq, are available.
Studying non-coding RNAs such as ncRNAs, lincRNAs, miRNAs, and tRNAs.

Start a Project

Please contact either Kel Cook (kelcook@salud.unm.edu) or Kathryn Brayer (kbrayer@salud.unm.edu) to schedule a consultation.

iLab

ATG uses iLab for billing.

For questions regarding iLabs or for account/PR set-up for use in the shared resource, please email Palakshi Reddy Bandapalli or call 505-272-4539.

Genomics Instruments

The Singular Genomics G4 sequencer

Flexible and fast paired-end sequencer
Capable of producing up to 1.6 billion 2 x 150 bp reads in 24 hours
Can be configured for a variety of read lengths
Compatible with almost all libraries that can be sequenced on Illumina instruments.

For more information: https://www.singulargenomics.com/

The 10x Genomics Chromium iX

Partitions cells or nuclei for single-cell sequencing
Captures RNA, protein, and/or chromatin
Assay gene expression, immune cell repertoire, chromatin accessibility, CRISPR perturbations
Inputs vary with assay, but include live cell suspensions, nuclei, fixed cells, frozen tissue, and FFPE blocks. Species agnostic assays available

For more information: https://www.10xgenomics.com/instruments/chromium-x-series

The 10x Genomics Xenium Analyzer

Spatial transcriptomics imaging platform
Sub-cellular resolution
Capable of capturing up to 5,000 genes
Multiple pre-designed gene panels that can be further customized (https://www.10xgenomics.com/products/xenium-panels)

For more information: https://www.10xgenomics.com/platforms/xenium

The 10x Genomics CytAssist

Facilitates Visium and Visium HD spatial transcriptomics assays
Start from FFPE blocks or pre-cut FFPE and fresh-frozen sections
Compatible with H&E or immunofluorescence stained sections

For more information: https://www.10xgenomics.com/instruments/visium-cytassist

Agilent Bioanalyzer: Analyze DNA and RNA quality/quantity using minimal inputs. (https://www.agilent.com/en/product/automated-electrophoresis/bioanalyzer-systems/bioanalyzer-instrument)
Qubit II Fluorometer: DNA and RNA quantification.
ThermoFisher/Invitrogen Countess II: Count cells and quantify proportion of live cells in a sample.

Miltenyi Biotec gentle MACS Octo Dissociator with Heaters: Dissociate tissue samples prior to single-cell sequencing.
Qiagen EZ2: Automated DNA and RNA extraction.
ThermoFisher QuantStudio 6 Pro Q-PCR. Real-time PCR system with both 96- and 384-well blocks to allow flexibility and ease in gene expression analyses.

ThermoFisher QuantStudio 6 Pro Q-PCR

Select instruments are available for use by qualified and trained members of the UNM community. Shared instruments are available during regular working hours and at other times by special arrangement. Please get in touch with the ATG Facility staff for more information about assays and pricing.

Genomics Instruments

Singular Genomics G4 sequencer

The Singular Genomics G4 sequencer

Flexible and fast paired-end sequencer
Capable of producing up to 1.6 billion 2 x 150 bp reads in 24 hours
Can be configured for a variety of read lengths
Compatible with almost all libraries that can be sequenced on Illumina instruments.

For more information: https://www.singulargenomics.com/

Chromium iX

The 10x Genomics Chromium iX

Partitions cells or nuclei for single-cell sequencing
Captures RNA, protein, and/or chromatin
Assay gene expression, immune cell repertoire, chromatin accessibility, CRISPR perturbations
Inputs vary with assay, but include live cell suspensions, nuclei, fixed cells, frozen tissue, and FFPE blocks. Species agnostic assays available

For more information: https://www.10xgenomics.com/instruments/chromium-x-series

Xenium Analyzer

The 10x Genomics Xenium Analyzer

Spatial transcriptomics imaging platform
Sub-cellular resolution
Capable of capturing up to 5,000 genes
Multiple pre-designed gene panels that can be further customized (https://www.10xgenomics.com/products/xenium-panels)

For more information: https://www.10xgenomics.com/platforms/xenium

Visium CytAssist

The 10x Genomics CytAssist

Facilitates Visium and Visium HD spatial transcriptomics assays
Start from FFPE blocks or pre-cut FFPE and fresh-frozen sections
Compatible with H&E or immunofluorescence stained sections

For more information: https://www.10xgenomics.com/instruments/visium-cytassist

Additional Instruments

Agilent Bioanalyzer: Analyze DNA and RNA quality/quantity using minimal inputs. (https://www.agilent.com/en/product/automated-electrophoresis/bioanalyzer-systems/bioanalyzer-instrument)
Qubit II Fluorometer: DNA and RNA quantification.
ThermoFisher/Invitrogen Countess II: Count cells and quantify proportion of live cells in a sample.

Miltenyi Biotec gentle MACS Octo Dissociator with Heaters: Dissociate tissue samples prior to single-cell sequencing.
Qiagen EZ2: Automated DNA and RNA extraction.
ThermoFisher QuantStudio 6 Pro Q-PCR. Real-time PCR system with both 96- and 384-well blocks to allow flexibility and ease in gene expression analyses.

ATG FAQs

Before You Begin, Schedule an Appointment

These are guidelines for researchers contemplating the use of Next-Generation Sequencing (NGS) services from the ATG Shared Resource. All researchers are urged to consult with the ATG staff before beginning to prepare or analyze samples. We can assist with experimental design and, if necessary, put you in touch with expert biostatisticians who can help with experimental design. It is very important to consider the experimental design before beginning NGS experiments, which can be quite expensive.

How much RNA do I need?

Bulk RNA-seq can be successfully performed with minimal amounts of RNA, as little as 1ng of mRNA. ATG checks their integrity (RIN) upon receiving RNAs, using the Agilent Bioanalyzer. Suggested inputs for RNA-seq are 150 ng of total RNA for high-quality RNAs and 250 ng for degraded RNAs (e.g. FFPE RNA). RNAs are then ribodepleted to remove unwanted rRNA, which makes up ~90% of RNA in cells.

How much will an NGS experiment cost?

NGS experiments can be expensive, and the costs vary depending on the assay in question. Additionally, the total cost depends on the kit being used to construct the libraries and the sequencing depth required. Please get in touch with the staff to get more information and to get a quote.

How will the data be analyzed?

NGS assays produce extensive, complex data sets that contain enormous amounts of information but can also be challenging to analyze. The ATG Shared Resource provides the first level of analysis, including analysis of quality control parameters, alignment of the reads to the appropriate genome, identifying sequence variants or feature counts, as appropriate.

ATG Shared Resource has a team of bioinformatics experts who will perform the initial data analysis and who will manage and back-up the data. They can perform most straightforward types of analyses (e.g. gene expression from RNA-seq). More in depth analysis, such as correlating results to patient information, should be performed with the input from the Bioinformatics Shared Resource or the Biostatistics Shared Resource. The ATG staff can help set up interactions with the appropriate experts, who should be involved from the beginning to help with experimental design and quality control. Please discuss your analysis needs with staff members.

How can I verify my NGS results?

Verification is an integral part of each NGS experiment, and the requirements vary depending on the type of experiment. Please get in touch with the ATG staff to discuss options for verifying NGS results.

What information should I include in my grant application?

The facility Director, Viswanathan Palanisamy, Ph.D., can provide letters of support and advice about describing the ATG Shared Resource and potential NGS experiments in grant applications. Dr. Palanisamy has served on numerous NIH, ACS, and DOD study sections and reviewed many grant applications, including NGS experiments. His own funded grants have NGS experiments in them. He can help with writing sections of your grant regarding NGS experiments and point out potential pitfalls and things to avoid.

Things to avoid in grants containing NGS experiments:

The easiest way to criticize an NGS experiment is to describe it as a fishing expedition. Here are some things you should definitely avoid.

Do not propose to characterize genes that you have not yet identified. If you have no preliminary data, you don't know what genes or how many genes you will find. However, they will likely number in the hundreds. Simply saying that you will pick some interesting genes to study is a quick way to get a bad score on your grant. If possible, your experiment should test a hypothesis. For example, you might hypothesize that certain genes (e.g. apoptosis genes) will get induced. Then you can propose to use NGS assays to test that (and propose real-time PCR as a back-up approach). That way you can test a hypothesis, propose expected outcomes and controls (e.g. genes that should go up and down), which is a much better way of doing an NGS experiment (or any other experiment). Simply going fishing for genes is a bad approach and always draws the ire of the review committee.
Simply saying that you will use some software program to analyze the data or group the genes into pathways is also going to get you in trouble. NGS data can be extremely complex, and will require statistical methods for analysis. The pathway data that is known is woefully incomplete. Most genes are not in the pathways, anyway. You will need a well-planned approach for analyzing the data. You should have a way of telling whether the experiment worked or not (e.g. did the expected apoptosis genes get activated?).
The NGS experiment should not be merely a paragraph at the end of one of your aims. Whatever you do, absolutely do not add an NGS experiment to the end of a grant application as something that you "will also do". NGS experiments are big, expensive and complicated and they can't be done as an afterthought. Many, many grants have a one-paragraph description of an NGS experiment that the researchers will also do. That is a lightning rod for criticism from the reviewers.
If you are looking for genes, you should be looking for them for a reason. Don't just propose to look for regulated genes without proposing to do something with them. Finding the genes that go up and down is not a significant enough goal. You need to be looking for genes with some purpose in mind (e.g. some hypothesis to be tested).