The Internet Archive has a preservation copy of this work in our general collections.
The file type is application/pdf.
Filters
SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing
2012
Computer applications in the biosciences : CABIOS
Preserved Fulltext
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
2014
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2016
Epigenetics & Chromatin
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2016
Clinical Epigenetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2017
Clinical Epigenetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2017
Epigenetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2018
Clinical Cancer Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2015
Clinical Cancer Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2021
Clinical Epigenetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2021
Genome Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2016
Epigenetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2016
PLoS Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2018
Genome Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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