Genomics Resource Laboratory
Announcements
NextSeq 500 Services Discontinued
GRL will discontinue the NextSeq 500 related sequencing services and equipment support after 12/15/2023
Core Facilities Seminar
Rosha Poudyal, 10X Genomics–Biology at True Resolution: Resolve Biological Complexities with Single Cell and Spatial Solutions
Jennifer Rauch, Assistant Professor, Biochemistry & Molecular Biology and IALS–Introduction to the 10X Visium System and Applications
Located on the 3rd floor in the Morrill Science Center the Genomics Resource Laboratory (GRL) provides services and advanced instrumentation support for nucleic acid (DNA and RNA) analysis.
The GRL provides a suite of services to address your high-throughput next-generation sequencing, including solutions for sample processing such as nucleic-acid isolation, nucleic-acid quantitative and qualitative analysis, NGS library preparation, quantitative-PCR analysis, etc.
We provide a sample processing and library preparation such as whole genome sequencing, shotgun metagenomics, metatranscriptomics, targeted amplicon sequencing, RNA-Seq, ChIP-Seq, Exome Sequencing, Methyl-seq, Single Cell Genomics, etc., to address your NGS projects.
The facility accepts samples and will perform requested analysis. We offer training to users to conduct experimentation for use on a fee for service basis to both internal and external researchers, academic or industry based.
Following an initial consultation, covering experimental parameters training and access is arranged through the director.
What Makes Us Unique
- Library preparation
- Whole genome sequencing
- Shotgun metagenomics
- Metatranscriptomics
- 16S/18S rRNA amplicon library prep
- RNA-Seq
- ChIP-Seq
- Other library preps
- DNA and RNA isolation
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Illumina MiSeq Sequencing System
Mid-throughput sequencer, capable of generating up to 15 Gb data with 50 million paired-end sequencing reads with 300 bp read length. Applied for applications such as 16S rRNA amplicon sequencing, targeted gene sequencing, small genome sequencing and targeted gene expression.
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Bioruptor Pico Sonicator System
Sonication device for shearing DNA and RNA for NGS applications. Optimized for volumes of 20 - 100 μl.
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BluePippin, Sage Science
DNA size selection system, capable of selecting to 100 bp – 50 kb for NGS applications. Has integrated pulsed-field electrophoresis for resolving and collecting high molecular weight DNA for PacBio library prep as well.
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Agilent 2100 Bioanalyzer
Used for sizing, quantitation and quality control of DNA, RNA, and proteins.
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FastPrep-24 5G Sample Homogenizer (MP Biomedicals)
An advanced, high-speed benchtop homogenizer used for lysis of any type of cells, tissues, bacteria, fungi, plants, soil samples, etc.
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Thermo Scientific Savant DNA120 SpeedVac
High-performance concentrator for efficient concentration, and drying of small-volume DNA or RNA samples.
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Bio-RAD CFX96 Touch Real-Time PCR Detection System
The CFX96 Touch System is a powerful, precise, and flexible real-time PCR detection system. This six-channel (five colors and one FRET channel) real-time PCR instrument combines advanced optical technology with precise temperature control to deliver sensitive, reliable detection for singlexplex or multiplex reactions.
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10x Genomics Chromium Controller
The Chromium Controller uses advanced microfluidics to perform single cell partitioning and barcoding in a matter of minutes. Powered by Next GEM technology, the Chromium Controller enables integrated analysis of single cells at massive scale.
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Nexcelom Cellometer K2 Fluorescent Cell Counter
The Nexcelom Cellometer K2, powered by Matrix software, utilizes brightfield imaging and dual-fluorescence imaging to quickly and accurately identify and count individual cells. Cell count, concentration, diameter, and % viability are automatically calculated and reported.
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Qubit 4 Fluorometer
The Invitrogen Qubit 4 Fluorometer accurately and quickly measures the concentration of DNA, RNA, or protein in a single sample. It can also be used to assess RNA integrity and quality. The easy-to-use touchscreen menus make it easy to select and run the assays you need, with results displayed in just a few seconds.
Other Services
- GRL maintains NEB NEBnow Supply Center.
- GRL (Dr. Ranjan) also provides services and consultation for preparing plasmid constructs (eg., gene expression), Sanger-Seq design, qPCR project design, Bacterial and Mammalian Cloning, etc.
| Campus Users | External Academic | Industry | ||
| Tech Fee | hour | $86 | $99 | $111 |
| Bio-RAD CFX96 Touch Real-Time PCR Detection System Equipment Fee | hour | $15 | $18 | $20 |
| Eppendorf Mastercycler epGradient Equipment Fee | hour | $6 | $6 | $7 |
| Agilent 2100 Bioanalyzer Equipment Fee | hour | $21 | $24 | $27 |
| Agilent 2100 Bioanalyzer DNA HS assay | assay | $119 | $136 | $154 |
| Agilent 2100 Bioanalyzer DNA 7500 assay | assay | $93 | $107 | $121 |
| Agilent 2100 Bioanalyzer RNA 6000 Nano assay | assay | $102 | $117 | $133 |
| Agilent 2100 Bioanalyzer RNA 6000 Pico assay | assay | $130 | $147 | $166 |
| Syngene Ugenius Agarose GelDoc System Equipment Fee | 30 minutes | $4 | $5 | $6 |
| Agarose gel DNA analysis (DNA ladder, sample run + image), (minimum 5 sample rate), plus TechFee | sample | $5 | $5 | $6 |
| Qubit 4 Fluorometer Equipment Fee | 30 minutes | $5 | $5 | $6 |
| Qubit dsDNA BR, dsDNA HS, RNA BR, RNA HS Assays (minimum 2 sample rate) | sample | $5 | $6 | $6 |
| BluePippin Equipment Fee | hour | $21 | $24 | $27 |
| BluePippin sample prep (Minimum 2 sample rate, Additional 1 lane rate for external marker cassette). Only limited % gel assay) | sample | $76 | $87 | $98 |
| Bioruptor Pico Equipment Fee | hour | $21 | $24 | $27 |
| Bioruptor Pico sample processing (Minimum 8 sample rate) plus Tech and Machine fees | sample | $5 | $6 | $7 |
| Savant SpeedVac DNA120 Equipment Fee | hour | $11 | $12 | $14 |
| Fast Prep-24 5G Equipment Fee | hour | $20 | $23 | $26 |
| MiSeq Reagent Nano Kit v2 (300 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied) | assay | $648 | $746 | $843 |
| MiSeq Reagent Nano Kit v2 (500 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied) | assay | $862 | $991 | $1,120 |
| MiSeq Reagent Micro Kit v2 (300 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied) | assay | $862 | $991 | $1,120 |
| MiSeq Reagent kit v2 (50 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied) | assay | $1,373 | $1,579 | $1,785 |
| MiSeq Reagent kit v2 (300 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied) | assay | $1,680 | $1,932 | $2,184 |
| MiSeq Reagent kit v2 (500 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied) | assay | $1,986 | $2,284 | $2,582 |
| MiSeq Reagent Kit v3 (150 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied) | assay | $1,502 | $1,727 | $1,952 |
| MiSeq Reagent kit v3 (600 Cycle kit), (Note, additional fee for QC, pooling, custom primer, PhiX, sample sheet, may be applied) | assay | $2,588 | $2,977 | $3,365 |
| Illumina MiSeq Equipment Fee | 24 hours | $126 | $145 | $164 |
| Library Prep: DNA (Shotgun Metagenome / Genome, ChIP), (minimum 4 sample rate) | sample | $97 | $112 | $126 |
| Library Prep: Total RNA (no rRNA reduction and no poly(A), (minimum 4 sample rate) | sample | $111 | $128 | $145 |
| Library Prep: poly (A) mRNA, stranded, (minimum 4 sample rate) | sample | $127 | $146 | $165 |
| Library Prep: Targeted Amplicon Sequencing (16S, 18S rRNA), (minimum 10 sample rate), (custom primers addtional fee may be applied) | sample | $16 | $19 | $21 |
| Library Prep: Single Cell/Low Input RNA Library Prep for Illumina, (minimum 6 sample rate) | sample | $154 | $177 | $200 |
| NEBNext rRNA Depletion Kit (Human/Mouse/Rat), (minimum 4 sample rate) | sample | $78 | $89 | $101 |
| NGS Library QC (qPCR assay), (minimum 2 sample rate) | sample | $19 | $22 | $24 |
| DNA Isolation | sample | $16 | $19 | $21 |
| RNA Isolation | sample | $25 | $26 | $30 |
| Sample dilution/pooling | sample | $1 | $1 | $2 |
| PhiX Spike-in | sample | $16 | $18 | $21 |
| Custom Primer (Eg., 16S Seq by GRL) | assay | $31 | $35 | $40 |
| 10x Genomics Chromium Controller Equipment Fee | 24 hours | $87 | $100 | $113 |
| Library Prep: 10X Genomics Single Cell Gene Expression Profling Assay (3' RNA) | assay | $2,664 | $3,064 | $3,463 |
| Nexcelom Cellometer K2 Fluorescent Cell Counter Equipment Fee | 30 minutes | $6 | $6 | $7 |
| Note 1: Rates are inclusive of reagents. Vendors periodically adjust reagent cost. The cost will be adjusted accordingly. Rates are subject to change, contact facility to verify current fees. | ||||
| Note 2: GRL provides many other custom services, please contact facility staff. | ||||
| Note 3: For any failed unassisted/assisted runs, additional diagnostic fees may be applied. | ||||
| Note 4: Unassisted users for MiSeq. Due to limited budget, the sequencers are under Bronze service plan. Under this plan there is no reagent replacement. Any failed runs will be borne by user. | ||||
| Note 5: No show/ late cancellation for equipment reservation fees may be applied. No cancellation fees charged for cancellation before 48 h for MiSeq. No cancellation fees charged for cancellation before 24 h for other equipment) |
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| Note 6: Limited/restricted access for unassisted equipment use to external users. | ||||
| Note 7: *FY25 rates applicable as of April 1, 2024 | ||||
| Rates are subject to change, contact facility to verify current fees. | ||||
Services
Training
Training for new users consists of:
- lab safety training as mandated by UMass EH&S,
- operation of the instrument and associated software,
- use of data analysis software,
- exporting or presenting data,
- clean up and shutdown of the instrumentation.
Once the training is complete, researchers may schedule their experiments through the director of the GRL (Ravi Ranjan).
Genomics Resource Facility: The facility provides as suite of services, including, but not limited to - Next-Generation Sequencing services (whole genome, shotgun metagenome, metatranscriptome, amplicon, exome sequencing, etc), quantitative-PCR analysis, nucleic-acid isolation, quantitative and qualitative analysis. To provide these services, the facility is equipped with Illumina MiSeq Sequencing System, 10x Genomics Chromium Controller, Nexcelom Cellometer K2 Fluorescent Cell Counter, Bioruptor Pico Sonicator System (Diagenode), BluePippin (Sage Science), Agilent 2100 Bioanalyzer system, FastPrep-24 5G Sample Homogenizer (MP Biomedicals), Qubit 4.0 Fluorometer (Life Technologies), Bio-RAD CFX96 Touch Real-Time PCR Detection System, Thermo Scientific Savant DNA120 SpeedVac, One Eppendorf Mastercycler epGradient and Two BioRad T100 thermal cycler (PCR), Gel electrophoresis system (Denville Scientific) and Gel-Documentation system (Model UGenius, Syngene).
CORUM (access and reservations)
Ravi Ranjan, MSc, PhD, MB(ASCP)CM
Ravi joined IALS in 2017, as the Director of the Genomics Resource Laboratory at UMass Amherst. He supervises the Genomics Facility, providing Next-Generation Sequencing (NGS) services, from sample preparation, NGS library preparation to generation of high throughput sequencing data and data analysis. He provides instrumentation training, NGS project consultation, single cell genomics project consultation, technical assistance, documentation for grants application and manuscripts. Ravi also assists with any genomics or molecular biology projects that falls within his realm of expertise and interest. His research interests are in the field of Molecular Microbiology and Microbiome research. He is interested to introduce new technologies and develop new SOPs related to NGS and genomics research.
Ravi Ranjan Publications: https://scholar.google.com/citations?user=G7hUmMEAAAAJ&hl=en
Ravi Ranjan LinkedIn: linkedin.com/in/ravichicago
GRL maintains only the NEB Freezer (NEBnow) program (https://www.neb.com/en-us/nebnow/university-of-massachusetts-amherst-nebnow)
Below are instructions for access to the NEB "NEBnow" Supply center:
- New account set-up: Walk to NEB Freezer (Morrill 1, N328), Create “New Account” using touchscreen,
or create your account online at http://go.neb.com/nebnowumassamherst - You will receive Notification on the registered email for next steps.
- Call NEB (at the phone number provided in notification email) and provide your ProCard (Credit card) Information.
- After approval from NEB (usually very quick, same day), you are all set.
- You will get a PIN on the registered email, and you are ready to access the freezer.
- Log on the NEB Freezer, using your credentials for access to the freezer.
- For stocked items, user MUST scan barcode and before taking items. ProCard (credit card) is charged automatically. GRL will not send any invoice to the user.
- For non-stocked items, user can place “special order’ through the Kiosk. Use Special order Tab and place your order. Orders placed before or on Tuesday, are delivered same week Thursday ONLY. Special order placed after Tuesday are delivered following week Thursday. The Kiosk is stocked on/after Thursday after noon ( ~ 3 PM).
Note: Deliveries and restocking can be delayed due to inclement weather, non-availability of staff, campus closure, etc.
Special order: -20°C reagents are stored in the NEB Freezer in the “Special Order” Bin. Check your order and name on the package. No need to scan the special order, as it is already charged on the ProCard.
Special order: 4°C, Room Temp, and -80°C are stored at GRL (Morrill1, N330). Call at 7-4501 or 7-4502 to schedule pick-up.
2024
- Zintel, T.M., Pizzollo, J., Claypool, C.G., & Babbitt, C.C. (2024). Astrocytes Drive Divergent Metabolic Gene Expression in Humans and Chimpanzees. Genome Biology and Evolution, 16(1), evad239. doi: 10.1093/gbe/evad239
- Rickelton, K., Zintel, T.M., Pizzollo, J., Miller, E., Ely, J.J., Raghanti, M.A., Hopkins, W.D., Hof, P.R., Sherwood, C.C., Bauernfeind, A.L., et al. (2024). Tempo and mode of gene expression evolution in the brain across primates. eLife, 13, e70276. doi: 10.7554/eLife.70276
- He, X.D., Phillips, S., Hioki, K., Majhi, P.D., Babbitt, C., Tremblay, K.D., Pobezinsky, L.A., & Mager, J. (2024). TATA-binding associated factors have distinct roles during early mammalian development. Developmental Biology, 511, 53-62. doi: https://doi.org/10.1016/j.ydbio.2024.04.002
- Satbhai K, Marques E, Ranjan R, Timme-Laragy A. 2024. Single-cell RNA sequencing to evaluate tissue-specific transcriptomic changes induced by perfluorooctanesulfonic acid (PFOS) in the embryonic zebrafish (Danio rerio). The Toxicologist, a Supplement to Toxicological Sciences, Abstract #4087.
- Pavon, N., Diep, K., Yang, F., Sebastian, R., Martinez-Martin, B., Ranjan, R., Sun, Y., & Pak, C. (2024). Patterning ganglionic eminences in developing human brain organoids using a morphogen-gradient-inducing device. Cell Reports Methods, 4(1), 100689. doi: https://doi.org/10.1016/j.crmeth.2023.100689
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10831957/ - McCullough AK, Ranjan R. Do kinematic features of human movement correlate with telomere length? A pilot study. Poster No.42, presented at the Translational Science 2024 Conference, April 3 – 5, 2024, Las Vegas, USA, organized by Association for Clinical and Translational Science, Washington, DC.
- Kennard, A.S., Velle, K.B., Ranjan, R., Schulz, D., & Fritz-Laylin, L.K. (2024). An internally controlled system to study microtubule network diversification links tubulin evolution to the use of distinct microtubule regulators. bioRxiv, 2024.2001.2008.573270. doi: 10.1101/2024.01.08.573270
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802493/ - Bechtold Emily, K., Wanek, W., Nuesslein, B., DaCosta, M., & Nüsslein, K. (2024). Successional changes in bacterial phyllosphere communities are plant-host species dependent. Applied and Environmental Microbiology, 90(3), e01750-01723. doi: 10.1128/aem.01750-23
- Kennard, A.S., Velle, K.B., Ranjan, R., Schulz, D., & Fritz-Laylin, L.K. (2024). An internally controlled system to study microtubule network diversification links tubulin evolution to the use of distinct microtubule regulators. bioRxiv, 2024.2001.2008.573270. doi: 10.1101/2024.01.08.573270
- Ranjan R. Genomics Resource Laboratory, UMass Amherst Genomics Core Facility: Capabilities and Resources, at UMass Interdisciplinary Neurosciences Conference 2024. Held on 05/30/2024.
- Ranjan R. User Experience: NEBNext UltraExpress RNA Library Prep Kit, hosted by New England Biolabs, at Advances in Genome Biology and Technology (AGBT) 2024, General Meeting, Orlando, FL, USA.
- Srinivasan, S., He, X., Mirza, S., & Mager, J. (2024). Exosome complex components 1 and 2 are vital for early mammalian development. Gene Expression Patterns, 51, 119346. doi: 10.1016/j.gep.2023.119346
https://pubmed.ncbi.nlm.nih.gov/37940010/
2023
- Jessica, A.G., Robin, A.R., Neville, F.T., Rose, A.F., Seth, R.B., Kevin, M., Mark Allan, C.J., Carl, W., Park, M., Grant, O.B., et al. (2023). A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes. bioRxiv, 2023.2008.2004.552006. doi: 10.1101/2023.08.04.552006
- Hioki, K.A., Ryan, D.J., Thesmar, I., Lynch, A.C., Pobezinsky, L.A., & Pobezinskaya, E.L. (2023). The mosquito effect: regulatory and effector T cells acquire cytoplasmic material from tumor cells through intercellular transfer. Frontiers in Immunology, 14.
- Shinfuku, M., S., Domeignoz-Horta, L., A., Choudoir, M., J., Frey, S., D., & DeAngelis, K., M. (2023). Season, not long-term warming, affects the relationship between ecosystem function and microbial diversity. bioRxiv, 2023.2008.2014.553264. doi: 10.1101/2023.08.14.553264
https://www.biorxiv.org/content/10.1101/2023.08.14.553264v1 - Kado, T., Akbary, Z., Motooka, D., Sparks, I.L., Melzer, E.S., Nakamura, S., Rojas, E.R., Morita, Y.S., & Siegrist, M.S. (2023). A cell wall synthase accelerates plasma membrane partitioning in mycobacteria. Elife, 12. doi: 10.7554/eLife.81924.
https://pubmed.ncbi.nlm.nih.gov/37665120/ - Li, S., You, X., Rani, A., Özcan, E., & Sela, D.A. (2023). Bifidobacterium infantis utilizes N-acetylglucosamine-containing human milk oligosaccharides as a nitrogen source. Gut Microbes, 15(2), 2244721. doi: 10.1080/19490976.2023.2244721
https://pubmed.ncbi.nlm.nih.gov/37609905/ - Satbhai, K., Marques, E., Ranjan, R., & Timme-Laragy, A. (2023). Single-cell RNA sequencing to evaluate tissue-specific transcriptomic changes induced by perfluorooctanesulfonic acid (PFOS) in the embryonic zebrafish (Danio rerio). Paper presented at the Gordon Research Conference - Cellular and Molecular Mechanisms of Toxicity.
https://www.grc.org/cellular-and-molecular-mechanisms-of-toxicity-confer... - Leonard, E.R., Marques, E.S., Roy, M.A., Conlin, S.M., Ranjan, R., & Timme-Laragy, A.R. (2023). Dietary exposure to the food preservative tert-Butylhydroquinone (tBHQ) impairs zebrafish (Danio rerio) survival, growth, organ development, and gene expression in Nrf2a-dependent and independent ways. Food and Chemical Toxicology, 176, 113788. doi: 10.1016/j.fct.2023.113788
https://doi.org/10.1016/j.fct.2023.113788 - Dedon, L.R., Hilliard, M.A., Rani, A., Daza-Merchan, Z.T., Story, G., Briere, C.E., & Sela, D.A. (2023). Fucosylated Human Milk Oligosaccharides Drive Structure-Specific Syntrophy between Bifidobacterium infantis and Eubacterium hallii within a Modeled Infant Gut Microbiome. Molecular Nutrition & Food Research, 67(11), e2200851. doi: 10.1002/mnfr.202200851
https://pubmed.ncbi.nlm.nih.gov/36938958/ - Bermudez, Y., Miles, J., & Muller, M. (2023). Nonstructural protein 1 widespread RNA decay phenotype varies among coronaviruses. iScience, 26(1), 105887. doi: 10.1016/j.isci.2022.105887
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9794394/ - You, X., Rani, A., Özcan, E., Lyu, Y., & Sela, D.A. (2023). Bifidobacterium longum subsp. infantis utilizes human milk urea to recycle nitrogen within the infant gut microbiome. Gut Microbes, 15(1), 2192546. doi: 10.1080/19490976.2023.2192546
https://pubmed.ncbi.nlm.nih.gov/36967532/ - Edwards, M., Lam, S., Ranjan, R., Pereira, M., Babbitt, C., & Lacreuse, A. (2023). Letrozole treatment alters hippocampal gene expression in common marmosets (Callithrix jacchus). Hormones and Behavior, 147, 105281. doi: 10.1016/j.yhbeh.2022.105281
https://pubmed.ncbi.nlm.nih.gov/36434852/ - Kim, M., Swenson, J., McLoughlin, F., & Vierling, E. (2023). Mutation of the polyadenylation complex subunit CstF77 reveals that mRNA 3' end formation and HSP101 levels are critical for a robust heat stress response. Plant Cell, 35(2), 924-941. doi: 10.1093/plcell/koac351
https://academic.oup.com/plcell/article/35/2/924/6874267 - Rani, A., Ranjan, R., Bonina, S.M.C., Izadmehr, M., Giesy, J.P., Li, A., Sturchio, N.C., & Rockne, K.J. (2023). Aqueous Geochemical Controls on the Sestonic Microbial Community in Lakes Michigan and Superior. Microorganisms, 11(2). doi: 10.3390/microorganisms11020504
https://pubmed.ncbi.nlm.nih.gov/36838469/ - Prithviraj, M., Kado, T., Mayfield, J.A., Young, D.C., Huang, A.D., Motooka, D., Nakamura, S., Siegrist, M.S., Moody, D.B., & Morita, Y.S. (2023). Tuberculostearic Acid Controls Mycobacterial Membrane Compartmentalization. mBio, 14(2), e0339622. doi: 10.1128/mbio.03396-22
https://pubmed.ncbi.nlm.nih.gov/36976029/ - Ranjan, R. (2023). Poster No.25. Genomics Resource Laboratory, UMass Amherst: Capabilities and Resources. Paper presented at the 2023 Interdisciplinary Neurosciences Conference.
https://sites.google.com/view/umassneuroscience2023/abstracts2023 - Pak, C., Pavon, N., Diep, K., Yang, F., Sebastian, R., Martinez-Martin, B., Ranjan, R., & Sun, Y. (2023). Patterning ganglionic eminences in developing human brain organoids using morphogen gradient inducing device. bioRxiv, 2023.2006.2020.545705. doi: 10.1101/2023.06.20.545705
https://www.biorxiv.org/content/10.1101/2023.06.20.545705v1 - Barnett, J.R., Sharma, R., Buonauro, G., Gillis, I.M., Rashidzade, M., & Caicedo, A.L. (2023). Evidence of fruit syndromes in the recently diverged wild tomato clade opens new possibilities for the study of fleshy fruit evolution. Plants, People, Planet. doi: 10.1002/ppp3.10399
https://nph.onlinelibrary.wiley.com/doi/10.1002/ppp3.10399 - Velle, K.B., Kennard, A.S., Trupinić, M., Ivec, A., Swafford, A.J.M., Nolton, E., Rice, L.M., Tolić, I.M., Fritz-Laylin, L.K., & Wadsworth, P. (2022). Naegleria's mitotic spindles are built from unique tubulins and highlight core spindle features. Current Biology, 32(6), 1247-1261.e1246. doi: 10.1016/j.cub.2022.01.034
https://www.sciencedirect.com/science/article/pii/S0960982222000458?via%...
2022
- Pizzollo, J., Zintel, T.M., & Babbitt, C.C. (2022). Differentially Active and Conserved Neural Enhancers Define Two Forms of Adaptive Noncoding Evolution in Humans. Genome Biology and Evolution, 14(8), evac108. doi: 10.1093/gbe/evac108
- Mahmoud, S.A., Aldikacti, B., & Chien, P. (2022). ATP hydrolysis tunes specificity of a AAA+ protease. Cell Reports, 40(12), 111405. doi: https://doi.org/10.1016/j.celrep.2022.111405
Petreš, M., Hrustić, J., Vučinić, N., Ma, L.-J., Ayhan, Dilay H., & Grahovac, M. (2022). Genome Sequence Resource of Fusarium graminearum TaB10 and Fusarium avenaceum KA13, Causal Agents of Stored Apple Rot. Molecular Plant-Microbe Interactions®, 36(1), 64-67. doi: 10.1094/MPMI-03-22-0069-A - Bechtold, E. (2022). Community Assembly and Stress Response of Grassland Phyllosphere Bacteria. (Doctor of Philosophy (PhD)), The University of Massachusetts Amherst, https://hdl.handle.net/20.500.14394/18795.
- Hila, S., Mallory, J.C., Vedang, D., John Stoffolano, Jr., & Kristen, M.D. (2022). Chitosan diet alters the microbiome of adult house flies. bioRxiv, 2022.2008.2031.502951. doi: 10.1101/2022.08.31.502951
https://www.biorxiv.org/content/10.1101/2022.08.31.502951v1 - Sarsani, V., Aldikacti, B., He, S., Zeinert, R., Chien, P., & Flaherty, P. (2022). Model-based identification of conditionally-essential genes from transposon-insertion sequencing data. PLoS Computational Biology, 18(3), e1009273. doi: 10.1371/journal.pcbi.1009273
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1... - Ranjan, R. (2022). Poster No.1. UMass Amherst Genomics Core Facility: Capabilities and Resources. Paper presented at the UMass 2022 Interdisciplinary Neurosciences Conference (05/26/2022).
https://sites.google.com/view/umass-neurosciences/abstracts - Kitrinos, C., Bell, R.B., Bradley, B.J., & Kamilar, J.M. (2022). Hair Microbiome Diversity within and across Primate Species. mSystems, 7(4), e0047822. doi: 10.1128/msystems.00478-22
https://pubmed.ncbi.nlm.nih.gov/35876529/ - Roy, M.A., Gridley, C.K., Li, S., Park, Y., & Timme-Laragy, A.R. (2022). Nrf2a dependent and independent effects of early life exposure to 3,3'-dichlorobiphenyl (PCB-11) in zebrafish (Danio rerio). Aquatic Toxicology, 249, 106219. doi: 10.1016/j.aquatox.2022.106219
https://pubmed.ncbi.nlm.nih.gov/35700651/ - Moore, K.J.M., Cahill, J., Aidelberg, G., Aronoff, R., Bektaş, A., Bezdan, D., Butler, D.J., Chittur, S.V., Codyre, M., Federici, F., Ranjan, R, et al. (2021). Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications. Journal of Biomolecular Techniques, 32(3), 228-275. doi: 10.7171/jbt.21-3203-017
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8802757/
2021
- Atwood, T.P., Radik, M., & Seifried, R.M. (2021). Supporting Big Data Research at the University of Massachusetts Amherst. University Libraries Working Papers and Reports. doi: https://doi.org/10.7275/jsr0-2n21
- Bechtold Emily, K., Ryan, S., Moughan Sarah, E., Ranjan, R., & Nüsslein, K. (2021). Phyllosphere Community Assembly and Response to Drought Stress on Common Tropical and Temperate Forage Grasses. Applied and Environmental Microbiology, 87(17), e00895-00821. doi: 10.1128/AEM.00895-21
- Özcan, E., Rozycki, M.R., & Sela, D.A. (2021). Cranberry Proanthocyanidins and Dietary Oligosaccharides Synergistically Modulate Lactobacillus plantarum Physiology. Microorganisms, 9(3). doi: 10.3390/microorganisms9030656
https://www.mdpi.com/2076-2607/9/3/656/htm - Öztürk, A.B., Ranjan, R., Rani, A., Yazıcı, D., & Bavbek, S. (2021). Microbiota - The Unseen Players in Adult Asthmatic Airways. Turk Thorac J, 22(1), 75-82. doi: 10.5152/TurkThoracJ.2020.19085
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7919442/ - Kim, M., Schulz, V., Brings, L., Schoeller, T., Kühn, K., & Vierling, E. (2021). mTERF18 and ATAD3 are required for mitochondrial nucleoid structure and their disruption confers heat tolerance in Arabidopsis thaliana. New Phytologist, 232(5), 2026-2042. doi: 10.1111/nph.17717
https://pubmed.ncbi.nlm.nih.gov/34482561/ - Schwartz, A.D., Adusei, A., Tsegaye, S., Moskaluk, C.A., Schneider, S.S., Platt, M.O., Seifu, D., Peyton, S.R., & Babbitt, C.C. (2021). Genetic Mutations Associated with Hormone-Positive Breast Cancer in a Small Cohort of Ethiopian Women. Annals of Biomedical Engineering, 49(8), 1900-1908. doi: 10.1007/s10439-021-02800-4
https://link.springer.com/article/10.1007%2Fs10439-021-02800-4 - Nie, Y., Nirujogi, T.S., Ranjan, R., Reader, B.F., Chung, S., Ballinger, M.N., Englert, J.A., Christman, J.W., & Karpurapu, M. (2021). PolyADP-Ribosylation of NFATc3 and NF-κB Transcription Factors Modulate Macrophage Inflammatory Gene Expression in LPS-Induced Acute Lung Injury. Journal of Innate Immunity, 13(2), 83-93. doi: 10.1159/000510269
https://pubmed.ncbi.nlm.nih.gov/33045713/ - Minsoo, K., John, S., Fionn, M., & Elizabeth, V. (2021). A temperature sensitive mutation in the CstF77 subunit of the polyadenylation complex reveals the critical function of mRNA 3’ end formation for a robust heat stress response in plants. bioRxiv, 2021.2010.2031.466691. doi: 10.1101/2021.10.31.466691
https://www.biorxiv.org/content/10.1101/2021.10.31.466691v1 - Kimura, Y., Ranjan, R., Raghuraman, N., & Srimathveeravalli, G. (2021). Abstract No. 85. Electric pulse assisted transcriptomic and proteomic profiling of tumors. Journal of Vascular and Interventional Radiology, 32(5), Supplement, S37-S38. doi: 10.1016/j.jvir.2021.03.509
https://www.jvir.org/article/S1051-0443(21)00898-8/fulltext - Reinhart, P., Ranjan, R., Moineau, A., Poulin, E., Ngom, P.T., Burnside, A., Rinaldi, A., & Johari, V. (2021). Abstract No. 94. Validation study: Evaluation of dry anterior nasal swabs for collection and transport of specimens to the testing laboratory for the SARS-CoV-2-RT-PCR (COVID-19) assay. Archives of Pathology and Laboratory Medicine, 145(9), e2-e194. doi: 10.5858/arpa.2021-0267-AB
https://meridian.allenpress.com/aplm/article/145/9/e2/469635/Abstracts-a... - Katrina, B.V., Monika, T., Arian, I., Andrew, S., Emily, N., Luke, R., Iva, M.T., Lillian, K.F.-L., & Patricia, W. (2021). Naegleria’s mitotic spindles are built from unique tubulins and highlight core spindle features. bioRxiv, 2021.2002.2023.432318. doi: 10.1101/2021.02.23.432318
https://www.biorxiv.org/content/10.1101/2021.02.23.432318v1.full.pdf
2020
- Zeinert, R.D., Baniasadi, H., Tu, B.P., & Chien, P. (2020). The Lon Protease Links Nucleotide Metabolism with Proteotoxic Stress. Molecular Cell, 79(5), 758-767.e756. doi: https://doi.org/10.1016/j.molcel.2020.07.011
- Ranjan, R. (2020). BREAKOUTS SESSION (10:00-11:00 AM, Core facility pandemic perspectives and preparations). Setting up a COVID-19 Testing Lab in Challenging Times. Paper presented at the The Northeast Regional Laboratory Staff & Core Directors (NERLSCD) 2020 Conference, ABRF, Virtual.
https://nerlscd.abrf.org/program-2020/ - Abraham-Juárez, M.J., Schrager-Lavelle, A., Man, J., Whipple, C., Handakumbura, P., Babbitt, C., & Bartlett, M. (2020). Evolutionary Variation in MADS Box Dimerization Affects Floral Development and Protein Abundance in Maize. Plant Cell, 32(11), 3408-3424. doi: 10.1105/tpc.20.00300
https://pubmed.ncbi.nlm.nih.gov/32873631/ - Adams, B.M., Canniff, N.P., Guay, K.P., Larsen, I.S.B., & Hebert, D.N. (2020). Quantitative glycoproteomics reveals cellular substrate selectivity of the ER protein quality control sensors UGGT1 and UGGT2. Elife, 9. doi: 10.7554/eLife.63997
https://elifesciences.org/articles/63997 - Ranjan, R., Green, S.J., Mason, C., Butler, D., Vinas, N.R., Hsu, C.Y., Wagner, N., Thomas, W.K., Simpson, S., Bivens, N., et al. (2020). Methods to preserve individual bacteria and microbiome samples for nucleic acid analyses without altering cellular structure or integrity. Journal of Biomolecular Techniques, 31(Suppl), S16.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7424855/ - Metwally, A.A., Ascoli, C., Turturice, B., Rani, A., Ranjan, R., Chen, Y., Schott, C., Faro, A., Ferkol, T.W., Finn, P.W., et al. (2020). Pediatric lung transplantation: Dynamics of the microbiome and bronchiolitis obliterans in cystic fibrosis. Journal of Heart and Lung Transplantation, 39(8), 824-834. doi: 10.1016/j.healun.2020.04.016
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7437357/ - Yu, H., Ayhan, D.H., Diener, A.C., & Ma, L.J. (2020). Genome Sequence of Fusarium oxysporum f. sp. matthiolae, a Brassicaceae Pathogen. Molecular Plant-Microbe Interactions, 33(4), 569-572. doi: 10.1094/mpmi-11-19-0324-a
https://www.ncbi.nlm.nih.gov/pubmed/31967942 - Zhang, Y., Yang, H., Turra, D., Zhou, S., Ayhan, D.H., DeIulio, G.A., Guo, L., Broz, K., Wiederhold, N., Coleman, J.J., et al. (2020). The genome of opportunistic fungal pathogen Fusarium oxysporum carries a unique set of lineage-specific chromosomes. Communications Biology, 3(1), 50. doi: 10.1038/s42003-020-0770-2
https://www.nature.com/articles/s42003-020-0770-2?proof=true - Woldemeskel, S.A., Daitch, A.K., Alvarez, L., Panis, G., Zeinert, R., Gonzalez, D., Smith, E., Collier, J., Chien, P., Cava, F., et al. (2020). The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter. PLoS Genetics, 16(1), e1008591. doi: 10.1371/journal.pgen.1008591
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1... - Rani, A., Ranjan, R., Metwally, A.A., Brennan, D.C., Finn, P.W., & Perkins, D.L. (2020). Abundance of Multidrug Resistance Efflux Pumps in the Urinary Metagenome of Kidney Transplant Patients. BioMed Research International, 2020, 5421269. doi: 10.1155/2020/5421269
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7093903/ - Dedon, L.R., Özcan, E., Rani, A., & Sela, D.A. (2020). Bifidobacterium infantis Metabolizes 2'Fucosyllactose-Derived and Free Fucose Through a Common Catabolic Pathway Resulting in 1,2-Propanediol Secretion. Frontiers in Nutrition, 7, 583397. doi: 10.3389/fnut.2020.583397
https://www.frontiersin.org/articles/10.3389/fnut.2020.583397/full#T2 - Albert, K., Rani, A., & Sela, D.A. (2020). Comparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum. Microorganisms, 8(1). doi: 10.3390/microorganisms8010007
https://www.mdpi.com/2076-2607/8/1/7
2019
- Roy, M.A., Sant, K.E., Venezia, O.L., Shipman, A.B., McCormick, S.D., Saktrakulkla, P., Hornbuckle, K.C., & Timme-Laragy, A.R. (2019). The emerging contaminant 3,3′-dichlorobiphenyl (PCB-11) impedes Ahr activation and Cyp1a activity to modify embryotoxicity of Ahr ligands in the zebrafish embryo model (Danio rerio). Environmental Pollution, 254, 113027.https://pubmed.ncbi.nlm.nih.gov/31421573/
https://pubmed.ncbi.nlm.nih.gov/31421573/ - Sant, K.E., Venezia, O.L., Sinno, P.P., & Timme-Laragy, A.R. (2019). Perfluorobutanesulfonic Acid Disrupts Pancreatic Organogenesis and Regulation of Lipid Metabolism in the Zebrafish, Danio rerio. Toxicological Sciences, 167(1), 258-268. doi: 10.1093/toxsci/kfy237
https://academic.oup.com/toxsci/article/167/1/258/5098224
2018
- Ranjan, R., Yadav, M.K., Suneja, G., & Sharma, R. (2018). Discovery of a diverse set of esterases from hot spring microbial mat and sea sediment metagenomes. International Journal of Biological Macromolecules, 119, 572-581. doi: 10.1016/j.ijbiomac.2018.07.170
https://pubmed.ncbi.nlm.nih.gov/30059741/ - Abrha, A., & Suvorov, A. (2018). Transcriptomic Analysis of Gonadal Adipose Tissue in Male Mice Exposed Perinatally to 2,2',4,4'-Tetrabromodiphenyl Ether (BDE-47). Toxics, 6(2). doi: 10.3390/toxics6020021
https://pubmed.ncbi.nlm.nih.gov/29596321/ - Ranjan, R., Rani, A., Finn, P.W., & Perkins, D.L. (2018). Multiomic Strategies Reveal Diversity and Important Functional Aspects of Human Gut Microbiome. BioMed Research International, 2018, 6074918. doi: 10.1155/2018/6074918
https://pubmed.ncbi.nlm.nih.gov/30584534/ - Khalil, A., Cevik, S.E., Hung, S., Kolla, S., Roy, M.A., & Suvorov, A. (2018). Developmental Exposure to 2,2′,4,4′-Tetrabromodiphenyl Ether Permanently Alters Blood-Liver Balance of Lipids in Male Mice. Frontiers in Endocrinology, 9.
https://www.frontiersin.org/articles/10.3389/fendo.2018.00548/full - Einson Jonah, E., Rani, A., You, X., Rodriguez Allison, A., Randell Clifton, L., Barnaba, T., Mammel Mark, K., Kotewicz Michael, L., Elkins Christopher, A., & Sela David, A. (2018). A Vegetable Fermentation Facility Hosts Distinct Microbiomes Reflecting the Production Environment. Applied and Environmental Microbiology, 84(22), e01680-01618. doi: 10.1128/AEM.01680-18
https://pubmed.ncbi.nlm.nih.gov/30171008/
2017
- Zhanayeva, A. (2017). Comparative Transcriptome Analysis of Wild Tomato Species during Fruit Development. (MASTER OF SCIENCE), University of Massachusetts Amherst.
The genomics services were performed at the Genomics Resource Laboratory (RRID:SCR_017907), Institute for Applied Life Sciences, University of Massachusetts Amherst, MA.
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Training
The facility accepts samples and will perform requested analysis. We offer training to users to conduct experimentation for use on a fee for service basis to both internal and external researchers, academic or industry based. Following an initial consultation, covering experimental parameters training and access is arranged through the director, Ravi Ranjan at ranjan@umass.edu.
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