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SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing

Zhifu Sun, Saurabh Baheti, Sumit Middha, Rahul Kanwar, Yuji Zhang, Xing Li, Andreas S. Beutler, Eric Klee, Yan W. Asmann, E. Aubrey Thompson, Jean-Pierre A. Kocher
2012 Computer applications in the biosciences : CABIOS  
To address this need, we have developed a Streamlined Analysis and Annotation Pipeline for RRBS data (SAAP-RRBS) that integrates read quality assessment/clean-up, alignment, methylation data extraction  ...  Reduced representation bisulfite sequencing (RRBS) is a cost-effective approach for genome-wide methylation pattern profiling.  ...  ACKNOWLEDGEMENT We are very grateful to Dr Yuanxin Xi at Baylor College of Medicine for his assistance to BSMAP/RRBSMAP.  ... 
doi:10.1093/bioinformatics/bts337 pmid:22689387 pmcid:PMC3413387 fatcat:jkfkosk3bnbddnabmvnpy2j62e

WBSA: Web Service for Bisulfite Sequencing Data Analysis

Fang Liang, Bixia Tang, Yanqing Wang, Jianfeng Wang, Caixia Yu, Xu Chen, Junwei Zhu, Jiangwei Yan, Wenming Zhao, Rujiao Li, Matteo Pellegrini
2014 PLoS ONE  
Whole-Genome Bisulfite Sequencing (WGBS) and genome-wide Reduced Representation Bisulfite Sequencing (RRBS) are widely used to study DNA methylation.  ...  To address these issues, we developed a convenient, stable, and efficient web service called Web Service for Bisulfite Sequencing Data Analysis (WBSA) to analyze bisulfate sequencing data.  ...  SAAP-RRBS [26] and RRBS-Analyser [27] integrated BSMAP as an alignment tool and acted as streamlined analysis and annotation pipelines.  ... 
doi:10.1371/journal.pone.0086707 pmid:24497972 pmcid:PMC3907392 fatcat:7lsiufdhrbgynf4msngslqyewi

Profiling genome-wide DNA methylation

Wai-Shin Yong, Fei-Man Hsu, Pao-Yang Chen
2016 Epigenetics & Chromatin  
Due to the increasing need to compute high-throughput epigenomic data, we interrogate the computational pipeline for bisulfite sequencing data and also discuss the concept of identifying differentially  ...  These profiling approaches vary in many aspects, such as DNA input, resolution, genomic region coverage, and bioinformatics analysis, and selecting a feasible method requires knowledge of these methods  ...  analyser, IGV integrative genomics viewer, SAAP-RRBS streamlined analysis and annotation pipeline for RRBS data, SMAP streamlined methylation analysis pipeline Function(s) Software Features References  ... 
doi:10.1186/s13072-016-0075-3 pmid:27358654 pmcid:PMC4926291 fatcat:vr2edm4eordavlqztcoh3eu5fa

Next-generation sequencing methylation profiling of subjects with obesity identifies novel gene changes

Samantha E. Day, Richard L. Coletta, Joon Young Kim, Latoya E. Campbell, Tonya R. Benjamin, Lori R. Roust, Elena A. De Filippis, Valentin Dinu, Gabriel Q. Shaibi, Lawrence J. Mandarino, Dawn K. Coletta
2016 Clinical Epigenetics  
We performed reduced representation bisulfite sequencing (RRBS) next-generation methylation and microarray analyses on DNA and RNA isolated from vastus lateralis muscle biopsies.  ...  The negative relationship observed between DNA methylation and gene expression for SORBS3 was validated by a site-specific sequencing approach, pyrosequencing, and qRT-PCR.  ...  We thank the Mayo Clinic Genotyping Shared Resource facility for the RRBS next generation methylation analysis. We thank Kara Peterson and Dr.  ... 
doi:10.1186/s13148-016-0246-x pmid:27437034 pmcid:PMC4950754 fatcat:shayyz7nujeufiirupmjgwmozi

Alterations of sorbin and SH3 domain containing 3 (SORBS3) in human skeletal muscle following Roux-en-Y gastric bypass surgery

Samantha E. Day, Luis A. Garcia, Richard L. Coletta, Latoya E. Campbell, Tonya R. Benjamin, Elena A. De Filippis, James A. Madura, Lawrence J. Mandarino, Lori R. Roust, Dawn K. Coletta
2017 Clinical Epigenetics  
We identified 30 significantly altered promoter and untranslated region methylation sites in SORBS3 using reduced representation bisulfite sequencing (RRBS).  ...  Conclusions: These results demonstrate that SORBS3 methylation and gene expression are altered in obesity and restored to normal levels through weight loss induced by RYGB surgery.  ...  We thank the Mayo Clinic Genotyping Shared Resource facility for the RRBS next-generation methylation analysis. We thank Kara Peterson and Dr.  ... 
doi:10.1186/s13148-017-0396-5 pmid:28883895 pmcid:PMC5581422 fatcat:p3yupomsyze37dgcjbn4nxstq4

Potential epigenetic biomarkers of obesity-related insulin resistance in human whole-blood

Samantha E. Day, Richard L. Coletta, Joon Young Kim, Luis A. Garcia, Latoya E. Campbell, Tonya R. Benjamin, Lori R. Roust, Elena A. De Filippis, Lawrence J. Mandarino, Dawn K. Coletta
2017 Epigenetics  
We performed reduced representation bisulfite sequencing on genomic DNA isolated from the blood.  ...  Our findings demonstrate a new potential epigenetic biomarker, SLC19A1, for obesity and its underlying insulin resistance.  ...  We thank the Mayo Clinic Genotyping Shared Resource facility for the RRBS next generation methylation analysis. We thank Kara Peterson and Dr.  ... 
doi:10.1080/15592294.2017.1281501 pmid:28106509 pmcid:PMC5398771 fatcat:zv7k3b2735dkvivu75avyldicm

Detection of Gastric Cancer with Novel Methylated DNA Markers: Discovery, Tissue Validation, and Pilot Testing in Plasma

Bradley W Anderson, Yun-Suhk Suh, Boram Choi, Hyuk-Joon Lee, Tracy C Yab, William Taylor, Brian A Dukek, Calise K Berger, Xiaoming Cao, Patrick H Foote, Mary E Devens, Lisa A. Boardman (+8 others)
2018 Clinical Cancer Research  
SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinformatics 2012; 28(16):2180-1. 28.  ...  SAAP-RRBS (streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing) was used for sequence read assessment and clean-up, reference genome alignment, methylation status  ... 
doi:10.1158/1078-0432.ccr-17-3364 pmid:29844130 pmcid:PMC6239895 fatcat:rlp4qmuczfcfzk3z2mhc6sd43q

New DNA Methylation Markers for Pancreatic Cancer: Discovery, Tissue Validation, and Pilot Testing in Pancreatic Juice

J. B. Kisiel, M. Raimondo, W. R. Taylor, T. C. Yab, D. W. Mahoney, Z. Sun, S. Middha, S. Baheti, H. Zou, T. C. Smyrk, L. A. Boardman, G. M. Petersen (+1 others)
2015 Clinical Cancer Research  
Candidate markers were identified using variance-inflated logistic regression on reducedrepresentation bisulfite DNA sequencing results from matched pancreatic cancers, benign pancreas, and normal colon  ...  We sought to identify and validate methylated DNA markers for pancreatic cancer using next-generation sequencing unbiased by known targets.  ...  As described previously, (28) SAAP-RRBS, a streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing, was used for sequence alignment and methylation extraction.  ... 
doi:10.1158/1078-0432.ccr-14-2469 pmid:26023084 pmcid:PMC4592385 fatcat:phfdhvwvdjc3tnxssmdkthdyqi

Weight loss after Roux-En-Y gastric bypass surgery reveals skeletal muscle DNA methylation changes

Luis A Garcia, Samantha E Day, Richard L Coletta, Baltazar Campos, Tonya R Benjamin, Eleanna De Filippis, James A Madura, Lawrence J Mandarino, Lori R Roust, Dawn K Coletta
2021 Clinical Epigenetics  
We performed reduced representation bisulfite sequencing next generation methylation on DNA isolated from the vastus lateralis muscle biopsies.  ...  Transcription factor binding analysis for ITGB3 chr17.45,330,989 identified three putative transcription factor binding motifs; PAX-5, p53 and AP-2alphaA.  ...  We thank the Mayo Clinic Genotyping Shared Resource facility for the RRBS next generation methylation analysis.  ... 
doi:10.1186/s13148-021-01086-6 pmid:33933146 pmcid:PMC8088644 fatcat:uje5tk767namvprzxrumkkjtli

KrasG12D induces changes in chromatin territories that differentially impact early nuclear reprogramming in pancreatic cells

Angela J. Mathison, Romica Kerketta, Thiago Milech de Assuncao, Elise Leverence, Atefeh Zeighami, Guillermo Urrutia, Timothy J. Stodola, Marina Pasca di Magliano, Juan L. Iovanna, Michael T. Zimmermann, Gwen Lomberk, Raul Urrutia
2021 Genome Biology  
Conclusions In summary, we report a comprehensive, time-dependent, and coordinated early epigenomic program for KrasG12D in pancreatic cells, which is mechanistically relevant to understanding chromatin  ...  remodeling events underlying transcriptional outcomes needed for the function of this oncogene.  ...  Raw data was further analyzed using SAAP-RRBS [80] , a streamlined analysis and annotation pipeline for RRBS.  ... 
doi:10.1186/s13059-021-02498-6 pmid:34649604 pmcid:PMC8518179 fatcat:xp34twgqjvgzjnywqgi64yzzz4

High fat diet and exercise lead to a disrupted and pathogenic DNA methylome in mouse liver

Dan Zhou, Ryan A. Hlady, Marissa J. Schafer, Thomas A. White, Chen Liu, Jeong-Hyeon Choi, Jordan D. Miller, Lewis R. Roberts, Nathan K. LeBrasseur, Keith D. Robertson
2016 Epigenetics  
To dissect the consequences of diet and exercise on the liver epigenome, we measured DNA methylation, using reduced representation bisulfite sequencing, and transcription, using RNA-seq, in mice maintained  ...  High-fat diet consumption and sedentary lifestyle elevates risk for obesity, non-alcoholic fatty liver disease, and cancer.  ...  , the Cancer Center, and the Center for Biomedical Discovery of Mayo Clinic, MN, and the Glenn Foundation for Medical Research.  ... 
doi:10.1080/15592294.2016.1261239 pmid:27858497 pmcid:PMC5270632 fatcat:qdhe4bq3ybhihestv44u2kt73i

Dnmt3a Is a Haploinsufficient Tumor Suppressor in CD8+ Peripheral T Cell Lymphoma

Staci L. Haney, G. Michael Upchurch, Jana Opavska, David Klinkebiel, Ryan A. Hlady, Sohini Roy, Samikshan Dutta, Kaustubh Datta, Rene Opavsky, Brian Huntly
2016 PLoS Genetics  
DNA methyltransferase 3a (DNMT3A) is one of the three catalytically active enzymes responsible for cytosine methylation and one of the most frequently mutated genes in myeloid and T cell malignancies.  ...  Hypomethylated promoters were enriched for binding sites of transcription factors AML1, NF-κB and OCT1, implying the transcription factors potential involvement in Dnmt3a-associated methylation.  ...  Keck Center for performing WGBS.  ... 
doi:10.1371/journal.pgen.1006334 pmid:27690235 pmcid:PMC5045215 fatcat:xu3d74st2bdwfdzzc4p7cvufuy

Distinctive epigenomes characterize glioma stem cells and their response to differentiation cues

Dan Zhou, Bonnie M. Alver, Shuang Li, Ryan A. Hlady, Joyce J. Thompson, Mark A. Schroeder, Jeong-Heon Lee, Jingxin Qiu, Philip H. Schwartz, Jann N. Sarkaria, Keith D. Robertson
2018 Genome Biology  
Our integrative study reveals that abnormal expression of ten-eleven-translocation (TET) family members correlates with global levels of 5mC and 5fC/5caC and may be responsible for the distinct levels  ...  Upon differentiation, glioma and neural stem cells exhibit distinct responses with regard to TET expression and DNA mark changes in the genome and GSCs fail to properly remodel their epigenome.  ...  Acknowledgements We kindly thank Yue Wang for developing phython programs for data analysis, Ann Tuma and Alissa Caron for GBM tissue samples, and Leonard Collins for conducting LC/MS-MS.  ... 
doi:10.1186/s13059-018-1420-6 pmid:29587824 pmcid:PMC5872397 fatcat:dgy6tgde2jh3pj3y4lbgxqjsk4