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MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing

Krishna R Kalari, Asha A Nair, Jaysheel D Bhavsar, Daniel R O'Brien, Jaime I Davila, Matthew A Bockol, Jinfu Nie, Xiaojia Tang, Saurabh Baheti, Jay B Doughty, Sumit Middha, Hugues Sicotte (+3 others)
2014 BMC Bioinformatics  
Several clinical and research projects at the Mayo Clinic have applied the MAP-RSeq workflow for RNA-Seq studies.  ...  Although the costs of next generation sequencing technology have decreased over the past years, there is still a lack of simple-to-use applications, for a comprehensive analysis of RNA sequencing data.  ...  Acknowledgements This work is supported by the Mayo Clinic Center for Individualized Medicine (CIM). KRK is supported by CIM and Eveleigh family career Development award.  ... 
doi:10.1186/1471-2105-15-224 pmid:24972667 pmcid:PMC4228501 fatcat:q5u5p7x5u5eztpwippd7bqyeom

BBBomics-Human Blood Brain Barrier Transcriptomics Hub

Krishna R. Kalari, Kevin J. Thompson, Asha A. Nair, Xiaojia Tang, Matthew A. Bockol, Navya Jhawar, Suresh K. Swaminathan, Val J. Lowe, Karunya K. Kandimalla
2016 Frontiers in Neuroscience  
ACKNOWLEDGMENTS The authors would like to acknowledge the following people for their assistance with sequencing Bruce Eckloff, Chris Kolbert, and Jin Jen.  ...  College of Pharmacy, University of Minnesota, Minneapolis, MN) and meritorious research awards (KRK) provided by the Division of Biostatistics and Informatics, Department of Health Sciences Research (Mayo  ...  Gene Expression Analysis Gene expression counts were obtained using HT-Seq module http://www-huber.embl.de/users/anders/HTSeq/doc/count. html from MAP-RSeq (Kalari et al., 2014) pipeline for eight hCMEC  ... 
doi:10.3389/fnins.2016.00071 pmid:26973449 pmcid:PMC4771746 fatcat:olouith5svfnzmdqkl2tv7li6u

Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine

Naresh Prodduturi, Aditya Bhagwate, Jean-Pierre A. Kocher, Zhifu Sun
2018 BMC Medical Genomics  
RNA-seq is the most commonly used sequencing application.  ...  Methods: The pipeline incorporates most sensitive aligners for Indels in RNA-Seq, the best practice for data preprocessing and variant calling, and STAR-fusion is for chimeric transcripts.  ...  Funding This work was supported by the Mayo Clinic Center for Individualized Medicine, which also provided the cost of publication. Availability of data and materials  ... 
doi:10.1186/s12920-018-0391-5 fatcat:ijf3zz65ybflndl7awsi6rehiq

Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts

Yuanhang Liu, Pritha Chanana, Jaime I. Davila, Xiaonan Hou, Valentina Zanfagnin, Cordelia D. McGehee, Ellen L. Goode, Eric C. Polley, Paul Haluska, S. John Weroha, Chen Wang
2019 Scientific Reports  
As patient derived xenograft (PDX) models are increasingly used for preclinical drug development, strategies to account for the nonhuman component of PDX RNA expression data are critical to its interpretation  ...  A bioinformatics pipeline to separate donor tumor and mouse stroma transcriptome profiles was devised and tested.  ...  Acknowledgements This research was supported by a career enhancement award from the Mayo Clinic Ovarian Cancer SPORE (P50 CA136393) and R01 CA184502 from the National Institutes of Health, Ovarian Cancer  ... 
doi:10.1038/s41598-019-42680-2 pmid:31004097 pmcid:PMC6474864 fatcat:mb6fvglunrhtvg6yyjziukhhz4

Mutational Landscapes of Sequential Prostate Metastases and Matched Patient Derived Xenografts during Enzalutamide Therapy

Manish Kohli, Liguo Wang, Fang Xie, Hugues Sicotte, Ping Yin, Scott M. Dehm, Steven N. Hart, Peter T. Vedell, Poulami Barman, Rui Qin, Douglas W. Mahoney, Rachel E. Carlson (+10 others)
2015 PLoS ONE  
Tissue biopsies from a metastatic rib lesion were obtained for sequencing before and after initiating enzalutamide treatment over a twelve-week period and also implanted subcutaneously as well as under  ...  for delivery of precision medicine.  ...  Acknowledgments The study is supported by the Mayo Clinic Centre for Individualized Medicine and the Pharmacogenomics Research Network (PGRN).  ... 
doi:10.1371/journal.pone.0145176 pmid:26695660 pmcid:PMC4687867 fatcat:7v7dcytlynaxbpa5izfwjvgshi

Transcriptomic and Immunohistochemical Profiling of SLC6A14 in Pancreatic Ductal Adenocarcinoma

Alan R. Penheiter, Sibel Erdogan, Stephen J. Murphy, Steven N. Hart, Joema Felipe Lima, Fariborz Rakhshan Rohakhtar, Daniel R. O'Brien, William R. Bamlet, Ryan E. Wuertz, Thomas C. Smyrk, Fergus J. Couch, George Vasmatzis (+2 others)
2015 BioMed Research International  
We used a target-centric strategy to identify transporter proteins upregulated in pancreatic ductal adenocarcinoma (PDAC) as potential targets for a functional imaging probe to complement existing anatomical  ...  Very little is known about the role of SLC6A14 in PDAC and our results demonstrate that this target merits further investigation as a candidate transporter for functional imaging of PDAC.  ...  P50CA102701 (Mayo Clinic SPORE in Pancreatic Cancer)), the Imaging Biomarker Program within the Center for Individualized Medicine at Mayo Clinic, and the Minnesota Partnership for Biotechnology and Medical  ... 
doi:10.1155/2015/593572 pmid:26106611 pmcid:PMC4461733 fatcat:6epuhfbuofc5ze6soenswazy7a

Comparative evaluation of cDNA library construction approaches for RNA-Seq analysis from low RNA-content human specimens

T L Masters, C A Hilker, P R Jeraldo, A V Bhagwate, K E Greenwood-Quaintance, B W Eckloff, N Chia, A D Hanssen, M P Abdel, J Z Yao, J Jen, R Patel
2018 Journal of Microbiological Methods  
The Ovation SoLo RNA-Seq System provided more useful transcriptomic data for the infecting bacterium, whereas the TruSeq Stranded Total RNA kit provided more useful human transcriptomic data.  ...  With the emergence of RNA sequencing technologies, metatranscriptomic studies are rapidly gaining attention as they simultaneously provide insight into gene expression profiles and therefore disease association  ...  Acknowledgements We thank the Mayo Clinic Medical Genome Facility for assistance with library preparation and sequencing, and the Mayo Clinic Center for Individualized Medicine for assisting with transcriptomic  ... 
doi:10.1016/j.mimet.2018.10.008 pmid:30332617 pmcid:PMC6242773 fatcat:odtd653vbbfafc6srgcr6kdipi

Transcriptomic signatures reveal immune dysregulation in human diabetic and idiopathic gastroparesis

Madhusudan Grover, Simon J. Gibbons, Asha A. Nair, Cheryl E. Bernard, Adeel S. Zubair, Seth T. Eisenman, Laura A. Wilson, Laura Miriel, Pankaj J. Pasricha, Henry P. Parkman, Irene Sarosiek, Richard W. McCallum (+11 others)
2018 BMC Medical Genomics  
Deep RNA sequencing was performed and pathway analysis of differentially expressed transcripts was done using Ingenuity®.  ...  Cellular changes described in human gastroparesis have revealed a role for immune dysregulation, however, a mechanistic understanding of human gastroparesis and the signaling pathways involved are still  ...  Kristy Zodrow for administrative assistance.  ... 
doi:10.1186/s12920-018-0379-1 pmid:30086735 pmcid:PMC6081936 fatcat:mwjhi7d5yngdtpfpgygyb2yucm

Chromoanasynthesis is a common mechanism that leads to ERBB2 amplifications in a cohort of early stage HER2+ breast cancer samples

George Vasmatzis, Xue Wang, James B. Smadbeck, Stephen J. Murphy, Katherine B. Geiersbach, Sarah H. Johnson, Athanasios G. Gaitatzes, Yan W. Asmann, Farhad Kosari, Mitesh J. Borad, Daniel J. Serie, Sarah A. McLaughlin (+3 others)
2018 BMC Cancer  
Methods: We interrogated the genomic structure of 18 clinically-defined HER2+ breast tumors through integrated analysis of whole genome and transcriptome sequencing, coupled with clinical information.  ...  The RNA-Seq Paired end sequence data were reran using MAP-RSeq version 3.0.0 [36] , an integrated RNA-Seq bioinformatics pipeline developed at the Mayo Clinic for comprehensive analysis of raw RNA sequencing  ...  MAP-RSeq employs the very fast, accurate and splice-aware aligner, STAR [37] , to align reads to the reference human genome, build hg38.  ... 
doi:10.1186/s12885-018-4594-0 pmid:30005627 pmcid:PMC6045826 fatcat:fvhfwtow4rhujjil6ncuon4k4m

Clustering-based time series analysis on insulin response in the blood-brain barrier [article]

Krishna Rani Kalari, Zengtao Wang, Xiaojia Tang, Suresh Kumar Swaminathan, Karunya Kumar Kandimalla
2021 bioRxiv   pre-print
Methods: RNA-Sequencing (RNA-Seq) was performed on hCMEC/D3 cell monolayers with and without insulin treatment at various time points.  ...  Functional annotation and pathway analysis of the genes from top clusters were conducted using the Webgestalt and Ingenuity Pathway Analysis (IPA) software, respectively.  ...  The main goal of the MAP-RSeq pipeline is to obtain multiple genomic features, such as gene expression, exon counts, fusion transcripts from RNA-Seq data.  ... 
doi:10.1101/2021.03.07.434315 fatcat:ql3ak653lnfpjnxzszusr6f6j4

Gene Expression and Missplicing in the Corneal Endothelium of Patients With a TCF4 Trinucleotide Repeat Expansion Without Fuchs' Endothelial Corneal Dystrophy

Eric D. Wieben, Keith H. Baratz, Ross A. Aleff, Krishna R. Kalari, Xiaojia Tang, Leo J. Maguire, Sanjay V. Patel, Michael P. Fautsch
2019 Investigative Ophthalmology and Visual Science  
To understand events leading from TCF4 TNR expansion to disease phenotype, we characterized splicing, gene expression, and exon sequence changes in a rare cohort of patients with TNR expansions but no  ...  Analysis of Differentially Spliced Genes RNASeq datasets were analyzed using MAP-RSeq 10 and MISO (Mixture of Isoforms) 11 software as previously described. 6 MAP-RSeq was utilized to obtain in-depth  ...  RNA Library Preparation and RNA Sequencing Three corneal endothelial samples were collected over a 5-year period (2013-2017) , and processed for RNASeq as described previously. 5, 6, 9 Briefly, total  ... 
doi:10.1167/iovs.19-27689 pmid:31469403 pmcid:PMC6716950 fatcat:vx2qjndyyzh2lli5dey5agwyza

RNA-Sequencing Analysis of Messenger RNA/MicroRNA in a Rabbit Aneurysm Model Identifies Pathways and Genes of Interest

M. Holcomb, Y.-H. Ding, D. Dai, R.J. McDonald, J.S. McDonald, D.F. Kallmes, R. Kadirvel
2015 American Journal of Neuroradiology  
The results from RNA sequencing were analyzed by using the Ingenuity Pathway Analysis tool.  ...  CONCLUSIONS: RNA-sequencing analysis of rabbit aneurysms revealed differential regulation of some key pathways, including inflammation and antigen presentation.  ...  Schultz, and Christopher Kolbert (Gene Expression Core) and Jared Evans, Daniel O'Brien, and Jamie Davila (Division of Biomedical Statistics and Informatics, Mayo Clinic).  ... 
doi:10.3174/ajnr.a4390 pmid:26228879 pmcid:PMC4924589 fatcat:evorpfilznfqln5onmhpvdzlaa

ABCA7loss-of-function variants, expression, and neurologic disease risk

Mariet Allen, Sarah J. Lincoln, Morgane Corda, Jens O. Watzlawik, Minerva M. Carrasquillo, Joseph S. Reddy, Jeremy D. Burgess, Thuy Nguyen, Kimberly Malphrus, Ronald C. Petersen, Neill R. Graff-Radford, Dennis W. Dickson (+1 others)
2017 Neurology: Genetics  
We measured brain ABCA7 protein and messenger RNA (mRNA) levels using Western blot and quantitative PCR, respectively, in 11 carriers of the 3 most common variants, and sequenced all 47 ABCA7 exons in  ...  these participants to screen for other coding variants.  ...  . ; has received research support from the National Institute on Aging; and has served on a data safety monitoring committee for Pfizer and Janssen Alzheimer Immunotherapy. Dr.  ... 
doi:10.1212/nxg.0000000000000126 pmid:28097223 pmcid:PMC5217615 fatcat:o2343g74trfenouewktmbrgyta

Alterations of mesenchymal stromal cells in cerebrospinal fluid: insights from transcriptomics and an ALS clinical trial

Ashley A. Krull, Deborah O. Setter, Tania F. Gendron, Sybil C. L. Hrstka, Michael J. Polzin, Joseph Hart, Amel Dudakovic, Nicolas N. Madigan, Allan B. Dietz, Anthony J. Windebank, Andre J. van Wijnen, Nathan P. Staff
2021 Stem Cell Research & Therapy  
Large-scale transcriptomic analysis of MSCs revealed a distinct gene expression profile for cells cultured in aCSF.  ...  As MSCs are used for diverse applications, it is important to appreciate how specific physiological environments may stimulate changes that alter the phenotype of the cells.  ...  We thank the staff of the Mayo Clinic Genome Analysis Core and Bioinformatics Core for performing the transcriptomic analyses and preliminary data processing.  ... 
doi:10.1186/s13287-021-02241-9 pmid:33736701 fatcat:iiydqky33ba7jngfvyizux5f4i

Differential Gene Expression in Coiled versus Flow-Diverter-Treated Aneurysms: RNA Sequencing Analysis in a Rabbit Aneurysm Model

A. Rouchaud, C. Johnson, E. Thielen, D. Schroeder, Y.-H. Ding, D. Dai, W. Brinjikji, J. Cebral, D.F. Kallmes, R. Kadirvel
2015 American Journal of Neuroradiology  
RNA samples were processed by using RNA-sequencing technology and were analyzed by using the Ingenuity Pathway Analysis tool.  ...  RESULTS: With RNA sequencing for coiled versus untreated aneurysms, 464/9990 genes (4.6%) were differentially expressed (58 downregulated, 406 up-regulated).  ...  RNA Sequencing Bioinformatics Analysis The processing of the mRNA and microRNA data was performed by using MAP-RSeq (Version 1.2.1.3). 21 MAP-RSeq consists of the following steps: alignment, quality  ... 
doi:10.3174/ajnr.a4648 pmid:26721773 pmcid:PMC4907800 fatcat:kgoebis4gjb3zgogkyeodcoh7u
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