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MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing
2014
BMC Bioinformatics
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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
2016
Frontiers in Neuroscience
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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
2018
BMC Medical Genomics
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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
2019
Scientific Reports
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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
2015
PLoS ONE
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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
2015
BioMed Research International
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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
2018
Journal of Microbiological Methods
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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
2018
BMC Medical Genomics
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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
2018
BMC Cancer
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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]
2021
bioRxiv
pre-print
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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
2019
Investigative Ophthalmology and Visual Science
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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
2015
American Journal of Neuroradiology
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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
2017
Neurology: Genetics
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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
2021
Stem Cell Research & Therapy
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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
2015
American Journal of Neuroradiology
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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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