Synthetic microrna Reference Standards Genomics Research Group ABRF 2015
|
|
- Julia Manning
- 6 years ago
- Views:
Transcription
1 Synthetic microrna Reference Standards Genomics Research Group ABRF 2015 Don A. Baldwin, Ph.D.
2 Reference samples for Platform evaluation Protocol development Assay service improvement
3 Randomize Key Name CLUSTALW 1 hsa-mir-664*...acuggcuagggaaaaugauuggau... 2 hsa-mir uagauaaaauauugguaccug... 3 hsa-mir-576-3p...aagauguggaaaa.auuggaauc... 4 hsa-mir-208a...auaagacgagcaaaaagcuugu... 5 hsa-mir-208b...auaagacgaacaaaagguuugu... 6 hsa-mir uaaag.uaaauaugcaccaaaa... 7 hsa-mir-9*...auaaagcuagaua...accgaaagu... 8 hsa-mir-142-5p...cauaaag.uagaaa.gcacuacu... 9 hsa-mir ucaagagcaauaacgaaaaaugu hsa-mir auggagauagauauagaaau hsa-mir-516a-5p...uucucgaggaaagaagcacuuuc hsa-mir-516b...aucuggagguaagaagcacuuu hsa-mir-1255a...aggaugagcaaagaaaguagauu hsa-mir-1255b...cggaugagcaaagaaagugguu hsa-mir uggaggag.aaggaaggugaug hsa-mir-483-5p...aagacgggaggaaagaagggag hsa-mir-1...uggaauguaaagaaguauguau hsa-mir uggaauguaaggaagugugugg hsa-mir-452*...cucaucugcaaagaaguaagug hsa-mir ucugggcaacaaagugagaccu hsa-mir gggcgacaaagcaagacucuuucuu hsa-mir gggacccagggagagacguaag hsa-mir-423-5p...ugaggggcagagagcgagacuuu hsa-mir ugcaggaccaagaugagcccu hsa-mir-96*...aaucaugugcagugccaauaug hsa-mir ggcuagcaacagcgcuuaccu hsa-mir acucuagcugccaaaggcgcu... Design of Standards Random selection across range of composition Four pools of 16 Fifth pool of 829 Distribution of selected family members Many thanks to Life Technologies - AB
4 Name Sequence Pool hsa-mir-130b...cagugcaaugaugaaagggcau... 1 hsa-mir-130a...cagugcaauguuaaaagggcau... 2 hsa-mir-301b...cagugcaaugauauugucaaagc... 3 hsa-mir-301a...cagugcaauaguauugucaaagc... 4 hsa-mir-376a...aucauagaggaaaauccacgu... 1 hsa-mir-376c...aacauagaggaaauuccacgu... 2 hsa-mir-181d...aacauucauuguugucggugggu... 3 hsa-mir-181b...aacauucauugcugucggugggu... 4 hsa-let-7f...ugagguaguagauuguauaguu... 1 hsa-let-7a...ugagguaguagguuguauaguu... 2 hsa-let-7e...ugagguaggagguuguauaguu... 3 hsa-let-7b...ugagguaguagguugugugguu... 4 hsa-let-7c...ugagguaguagguuguaugguu... 1 hsa-mir-98...ugagguaguaaguuguauuguu... 2 hsa-let-7d...agagguaguagguugcauaguu... 3 hsa-let-7g...ugagguaguaguuuguacaguu... 4 hsa-let-7i...ugagguaguaguuugugcuguu... 1 hsa-mir-520b...aaagugcuuccuuuuagaggg... 2 hsa-mir-520c-3p...aaagugcuuccuuuuagagggu... 3 hsa-mir-520f...aagugcuuccuuuuagaggguu... 4 hsa-mir-15b...uagcagcacaucaugguuuaca... 1 hsa-mir-15a...uagcagcacauaaugguuugug... 2 hsa-mir-23a...aucacauugccagggauuucc... 3 hsa-mir-23b...aucacauugccagggauuacc... 4 Target discrimination Related sequences assigned to separate pools, should be measured at different abundances within a Standard
5 Preparation of Standards Request protocol from Don Request shipment of pools Send a prepaid shipping label, or your address and FedEx account number Mix pools to create Standards A-E Standard Pool 1 Pool 2 Pool 3 Pool 4 Pool 5 (majority) A B 0.5x C x D x 0. E x Total micrornas = 0.5 nm each mirna Each Standard contains 3 ng/ul
6 Affymetrix mirna GeneChip Sridar Chittur, SUNY Albany One chip per Standard RMA background correction No inter-chip normalization Calculate pool averages for each Standard Average signal Pool dilution
7 Affymetrix mirna GeneChip Discrimination of related mirnas Signal Standard Name Sequence Pool hsa-mir-130b...cagugcaaugaugaaagggcau... 1 hsa-mir-130a...cagugcaauguuaaaagggcau... 2 hsa-mir-301b...cagugcaaugauauugucaaagc... 3 hsa-mir-301a...cagugcaauaguauugucaaagc... 4
8 Affymetrix mirna GeneChip Cross-hybridization of related mirnas Signal Standard Name Sequence Pool hsa-mir-520b...aaagugcuuccuuuuagaggg... 2 hsa-mir-520c-3p...aaagugcuuccuuuuagagggu... 3 hsa-mir-520f...aagugcuuccuuuuagaggguu... 4
9 HTG Molecular Bruce Seligmann Debrah Thompson HTG EdgeSeq Standards spiked into yeast trna, 75 pg input Nuclease protection assay Quantitation by probe sequencing Bowtie2 alignment to mirbase mature mirnas in probe panel
10 ABRF reference mirna Latin Square Test 0.5x 0.5x 0.5x x mirbase 19 assay
11 Specificity differentiating between closely-related mirnas Pool-specific signals (using all probes) 1-base difference 2-base difference 6862 total counts total counts Pool 3 Pool 4 mir-301a-3p 30 mir-301b hsa-mir-301b CAGUGCAAUGAUAUUGUCAAAGC hsa-mir-301a CAGUGCAAUAGUAUUGUCAAAGC Pool 2 Pool 3 let-7e-5p let-7a-5p hsa-let-7a UGAGGUAGUAGGUUGUAUAGUU hsa-let-7e UGAGGUAGGAGGUUGUAUAGUU EdgeSeq differentiates between closely-related mirnas (1 or 2 base differences) in different pools, even within a complex background.
12 Illumina Small RNA Sequencing Catharine Aquino Hubert Rehrauer Functional Genomics Center Zurich Standards only, no background TruSeq Small RNA Library Prep Kit HiSeq 2500 Alternative library production Adam Morris Bioo Scientific No 5 phosphates on the oligomers
13 Illumina Small RNA Sequencing
14 Illumina Small RNA Sequencing Read count Mapped length
15 Illumina Small RNA Sequencing Read count Mapped length
16 Illumina Small RNA Sequencing Read count Mapped length
17 Work to be done Phosphorylate the pools by kinase reactions Repeat TruSeq Small RNA sequencing Quantitative PCR TaqMan Array MicroRNA Card, Nadereh Jafari
mirna Whole Transcriptome Assay
mirna Whole Transcriptome Assay HTG EdgeSeq mirna Whole Transciptome Assay The HTG EdgeSeq mirna Whole Transcriptome Assay (WTA) is a next generation sequencing (NGS) application that measures the expression
More informationSupplementary Figure 1
Supplementary Figure 1 a Location of GUUUCA motif relative to RNA position 4e+05 3e+05 Reads 2e+05 1e+05 0e+00 35 40 45 50 55 60 65 Distance upstream b 1: Egg 2: L3 3: Adult 4: HES 4e+05 3e+05 2e+05 start
More informationBenchmark study: Exiqon mircury LNA microrna arrays vs. Supplier A s DNA based capture probes. Includes comparison of:
Benchmark study: Exiqon mircury LNA microrna arrays vs. Supplier A s DNA based capture probes Includes comparison of: I. II. III. Signal levels Relative quantification False differences For complete experimental
More informationSC-L-H shared(37) Specific (1)
A. Brain (total 2) Tissue-specific (2) Brain-heart shared (8) Specific (2) CNS-heart shared(68) Specific () Heart (total 4) Tissue-specific () B-L-H shared (37) specific () B. Brain (total 2) Tissue-specific
More informationObstacles and challenges in the analysis of microrna sequencing data
Obstacles and challenges in the analysis of microrna sequencing data (mirna-seq) David Humphreys Genomics core Dr Victor Chang AC 1936-1991, Pioneering Cardiothoracic Surgeon and Humanitarian The ABCs
More informationAdvance Your Genomic Research Using Targeted Resequencing with SeqCap EZ Library
Advance Your Genomic Research Using Targeted Resequencing with SeqCap EZ Library Marilou Wijdicks International Product Manager Research For Life Science Research Only. Not for Use in Diagnostic Procedures.
More informationSelective depletion of abundant RNAs to enable transcriptome analysis of lowinput and highly-degraded RNA from FFPE breast cancer samples
DNA CLONING DNA AMPLIFICATION & PCR EPIGENETICS RNA ANALYSIS Selective depletion of abundant RNAs to enable transcriptome analysis of lowinput and highly-degraded RNA from FFPE breast cancer samples LIBRARY
More informationSimple, rapid, and reliable RNA sequencing
Simple, rapid, and reliable RNA sequencing RNA sequencing applications RNA sequencing provides fundamental insights into how genomes are organized and regulated, giving us valuable information about the
More informationVantage Diabetes Panel 1
Catalog No. AM100050 50 Reactions To be used in conjunction with the Vantage microrna Detection Kit, catalog number AM100091 (50 reactions) or AM100092 (200 reactions). Components included in this kit:
More informationSmall RNA Sequencing. Project Workflow. Service Description. Sequencing Service Specification BGISEQ-500 SERVICE OVERVIEW SAMPLE PREPARATION
BGISEQ-500 SERVICE OVERVIEW Small RNA Sequencing Service Description Small RNAs are a type of non-coding RNA (ncrna) molecules that are less than 200nt in length. They are often involved in gene silencing
More informationPatnaik SK, et al. MicroRNAs to accurately histotype NSCLC biopsies
Patnaik SK, et al. MicroRNAs to accurately histotype NSCLC biopsies. 2014. Supplemental Digital Content 1. Appendix 1. External data-sets used for associating microrna expression with lung squamous cell
More informationHuman breast milk mirna, maternal probiotic supplementation and atopic dermatitis in offsrping
Human breast milk mirna, maternal probiotic supplementation and atopic dermatitis in offsrping Melanie Rae Simpson PhD candidate Department of Public Health and General Practice Norwegian University of
More informationA two-microrna signature in urinary exosomes for diagnosis of prostate cancer
Poster # B4 A two-microrna signature in urinary exosomes for diagnosis of prostate cancer Anne Karin Ildor Rasmussen 1, Peter Mouritzen 1, Karina Dalsgaard Sørensen 3, Thorarinn Blondal 1, Jörg Krummheuer
More informationRNA-Seq Preparation Comparision Summary: Lexogen, Standard, NEB
RNA-Seq Preparation Comparision Summary: Lexogen, Standard, NEB CSF-NGS January 22, 214 Contents 1 Introduction 1 2 Experimental Details 1 3 Results And Discussion 1 3.1 ERCC spike ins............................................
More informationWe used the kanamycin-resistant pneumococcal strain S. pneumoniae Xen10
Supplementary Methods Bacterial strain We used the kanamycin-resistant pneumococcal strain S. pneumoniae Xen (Caliper Life Sciences, Waltham, MA) derived from the wild type strain A66., which expresses
More informationAssaying micrornas in biofluids for detection of drug induced cardiac injury. HESI Annual Meeting State of the Science Session June 8, 2011
Assaying micrornas in biofluids for detection of drug induced cardiac injury HESI Annual Meeting State of the Science Session June 8, 2011 Karol Thompson, PhD Center for Drug Evaluation & Research US Food
More informationSUPPLEMENTAY FIGURES AND TABLES
SUPPLEMENTAY FIGURES AND TABLES Supplementary Figure S1: Validation of mir expression by quantitative real-time PCR and time course studies on mir- 29a-3p and mir-210-3p. A. The graphs illustrate the expression
More informationCirculating Microrna Expression As A Biomarker For Early Diagnosis Of Severity In Spinal Cord Injury
Circulating Microrna Expression As A Biomarker For Early Diagnosis Of Severity In Spinal Cord Injury Susumu Hachisuka 1, Naosuke Kamei, MD, PhD 2, Satoshi Ujigo 3, Shigeru Miyaki 3, Mitsuo Ochi 3. 1 Hiroshima
More informationAnalysis of small RNAs from Drosophila Schneider cells using the Small RNA assay on the Agilent 2100 bioanalyzer. Application Note
Analysis of small RNAs from Drosophila Schneider cells using the Small RNA assay on the Agilent 2100 bioanalyzer Application Note Odile Sismeiro, Jean-Yves Coppée, Christophe Antoniewski, and Hélène Thomassin
More informationmicrornas (mirna) and Biomarkers
micrornas (mirna) and Biomarkers Small RNAs Make Big Splash mirnas & Genome Function Biomarkers in Cancer Future Prospects Javed Khan M.D. National Cancer Institute EORTC-NCI-ASCO November 2007 The Human
More informationWHITE PAPER. Increasing Ligation Efficiency and Discovery of mirnas for Small RNA NGS Sequencing Library Prep with Plant Samples
WHITE PPER Increasing Ligation Efficiency and iscovery of mirns for Small RN NGS Sequencing Library Prep with Plant Samples ioo Scientific White Paper May 2017 bstract MicroRNs (mirns) are 18-22 nucleotide
More informationomiras: MicroRNA regulation of gene expression
omiras: MicroRNA regulation of gene expression Sören Müller, Goethe University of Frankfurt am Main Molecular Bioinformatics Group, Institute of Computer Science Plant Molecular Biology Group, Institute
More informationmicrorna analysis Merete Molton Worren Ståle Nygård
microrna analysis Merete Molton Worren Ståle Nygård Help personnel: Daniel Vodak Background Dysregulation of mirna expression has been connected to progression and development of atherosclerosis The hypothesis:
More informationArabidopsis thaliana small RNA Sequencing. Report
Arabidopsis thaliana small RNA Sequencing Report September 2015 Project Information Client Name Client Company / Institution Macrogen Order Number Order ID Species Arabidopsis thaliana Reference UCSC hg19
More informationOncology Biomarker Panel
Oncology Biomarker Panel HTG EdgeSeq Oncology Biomarker Panel The HTG EdgeSeq Oncology Biomarker Panel profiles tumor samples in order to identify therapeutic targets and drug response markers using an
More informationSupplementary materials and methods.
Supplementary materials and methods. Microarray printing and data analysis. The LNA-modified oligonucleotide probe set for all annotated mirnas from mouse (Mus musculus) and human (Homo sapiens) in the
More informationTranscriptome Analysis
Transcriptome Analysis Data Preprocessing Sample Preparation Illumina Sequencing Demultiplexing Raw FastQ Reference Genome (fasta) Reference Annotation (GTF) Reference Genome Analysis Tophat Accepted hits
More informationCellecta Overview. Started Operations in 2007 Headquarters: Mountain View, CA
Cellecta Overview Started Operations in 2007 Headquarters: Mountain View, CA Focus: Development of flexible, scalable, and broadly parallel genetic screening assays to expedite the discovery and characterization
More informationBiopharma and HTG Molecular Diagnostics Sample Sensitivity Data
Biopharma and HTG Molecular Diagnostics Sample Sensitivity Data Accelerating your success. Working in harmony with next-generation sequencing (NGS) platforms, HTG s patented chemistry, multiplexed assays
More informationCONTRACTING ORGANIZATION: Joan & Sanford I. Weill Medical College of Cornell University New York, NY 10065
AWARD NUMBER: W81XWH-14-1-0263 TITLE: Early Detection of NSCLC Using Stromal Markers in Peripheral Blood PRINCIPAL INVESTIGATOR: Dingcheng Gao CONTRACTING ORGANIZATION: Joan & Sanford I. Weill Medical
More informationmirna seq of mouse brain regions
mirna seq of mouse brain regions Iiris Hovatta, PhD University of Helsinki Research Program of Molecular Neurology and Department of Medical Genetics, Faculty of Medicine i National Network of Molecular
More informationEukaryotic small RNA Small RNAseq data analysis for mirna identification
Eukaryotic small RNA Small RNAseq data analysis for mirna identification P. Bardou, C. Gaspin, S. Maman, J. Mariette, O. Rué, M. Zytnicki INRA Sigenae Toulouse INRA MIA Toulouse GenoToul Bioinfo INRA MaIAGE
More informationSupplemental Figure 1. Small RNA size distribution from different soybean tissues.
Supplemental Figure 1. Small RNA size distribution from different soybean tissues. The size of small RNAs was plotted versus frequency (percentage) among total sequences (A, C, E and G) or distinct sequences
More informationChip Seq Peak Calling in Galaxy
Chip Seq Peak Calling in Galaxy Chris Seward PowerPoint by Pei-Chen Peng Chip-Seq Peak Calling in Galaxy Chris Seward 2018 1 Introduction This goals of the lab are as follows: 1. Gain experience using
More informationSet the stage: Genomics technology. Jos Kleinjans Dept of Toxicogenomics Maastricht University, the Netherlands
Set the stage: Genomics technology Jos Kleinjans Dept of Toxicogenomics Maastricht University, the Netherlands Amendment to the latest consolidated version of the REACH legislation REACH Regulation 1907/2006:
More informationHEK293FT cells were transiently transfected with reporters, N3-ICD construct and
Supplementary Information Luciferase reporter assay HEK293FT cells were transiently transfected with reporters, N3-ICD construct and increased amounts of wild type or kinase inactive EGFR. Transfections
More informationA Hepatocyte Growth Factor Receptor (Met) Insulin Receptor hybrid governs hepatic glucose metabolism SUPPLEMENTARY FIGURES, LEGENDS AND METHODS
A Hepatocyte Growth Factor Receptor (Met) Insulin Receptor hybrid governs hepatic glucose metabolism Arlee Fafalios, Jihong Ma, Xinping Tan, John Stoops, Jianhua Luo, Marie C. DeFrances and Reza Zarnegar
More informationOn the Reproducibility of TCGA Ovarian Cancer MicroRNA Profiles
On the Reproducibility of TCGA Ovarian Cancer MicroRNA Profiles Ying-Wooi Wan 1,2,4, Claire M. Mach 2,3, Genevera I. Allen 1,7,8, Matthew L. Anderson 2,4,5 *, Zhandong Liu 1,5,6,7 * 1 Departments of Pediatrics
More informationParasite-Derived MicroRNAs in Host Serum As Novel Biomarkers of Helminth Infection
Parasite-Derived MicroRNAs in Host Serum As Novel Biomarkers of Helminth Infection Anna M. Hoy 1, Rachel J. Lundie 2, Alasdair Ivens 1, Juan F. Quintana 1, Norman Nausch 1, Thorsten Forster 3, Frances
More informationsirna count per 50 kb small RNAs matching the direct strand Repeat length (bp) per 50 kb repeats in the chromosome
Qi et al. 26-3-2564C Qi et al., Figure S1 sirna count per 5 kb small RNAs matching the direct strand sirna count per 5 kb small RNAs matching the complementary strand Repeat length (bp) per 5 kb repeats
More informationRNA-Seq profiling of circular RNAs in human colorectal Cancer liver metastasis and the potential biomarkers
Xu et al. Molecular Cancer (2019) 18:8 https://doi.org/10.1186/s12943-018-0932-8 LETTER TO THE EDITOR RNA-Seq profiling of circular RNAs in human colorectal Cancer liver metastasis and the potential biomarkers
More informationExoQuick Exosome Isolation and RNA Purification Kits
ExoQuick Exosome Isolation and RNA Purification Kits Cat # EQ806A-1, EQ806TC-1, EQ808A-1 User Manual Storage: Please see individual components Version 2 8/14/2018 A limited-use label license covers this
More informationLentiviral Delivery of Combinatorial mirna Expression Constructs Provides Efficient Target Gene Repression.
Supplementary Figure 1 Lentiviral Delivery of Combinatorial mirna Expression Constructs Provides Efficient Target Gene Repression. a, Design for lentiviral combinatorial mirna expression and sensor constructs.
More informationAVENIO family of NGS oncology assays ctdna and Tumor Tissue Analysis Kits
AVENIO family of NGS oncology assays ctdna and Tumor Tissue Analysis Kits Accelerating clinical research Next-generation sequencing (NGS) has the ability to interrogate many different genes and detect
More informationab FirePlex mirna Panel Kidney Toxicity
Version 1 Last updated 30 May 2017 ab219508 FirePlex mirna Panel Kidney Toxicity This product is for research use only and is not intended for diagnostic use. Copyright 2017 Abcam. All rights reserved.
More informationDiscovery of mirna cancer biomarkers
1 Discovery of mirna cancer biomarkers Thomas Litman, Ph.D. Head of Biomarker Discovery www.exiqon.com June 7 2007 Agenda 2 micrornas Biogenesis Function LNA Applications in mirna detection CASE STUDIES
More informationProfiles of gene expression & diagnosis/prognosis of cancer. MCs in Advanced Genetics Ainoa Planas Riverola
Profiles of gene expression & diagnosis/prognosis of cancer MCs in Advanced Genetics Ainoa Planas Riverola Gene expression profiles Gene expression profiling Used in molecular biology, it measures the
More informationMicroRNAs: novel regulators in skin research
MicroRNAs: novel regulators in skin research Eniko Sonkoly, Andor Pivarcsi KI, Department of Medicine, Unit of Dermatology and Venerology What are micrornas? Small, ~21-mer RNAs 1993: The first mirna discovered,
More informationmedoct group, Medical University Vienna, Jack Ballantyne, PhD National Center for Forensic Science, Orlando, FL USA
medoct group, Medical University Vienna, Jack Ballantyne, PhD National Center for Forensic Science, Orlando, FL USA Association of Forensic DNA Analysts and Administrators San Antonio, TX June 2012 Perceived
More informationFigure S1: Heat map based on the relative expression of genes and mirnas in human
Figure S1: Heat map based on the relative expression of genes and mirnas in human prostate tissue. Columns represent genes and mirnas; rows represent prostate tissue samples (red squares: Tu samples, green
More informationPhosphate buffered saline (PBS) for washing the cells TE buffer (nuclease-free) ph 7.5 for use with the PrimePCR Reverse Transcription Control Assay
Catalog # Description 172-5080 SingleShot Cell Lysis Kit, 100 x 50 µl reactions 172-5081 SingleShot Cell Lysis Kit, 500 x 50 µl reactions For research purposes only. Introduction The SingleShot Cell Lysis
More informationBi 8 Lecture 17. interference. Ellen Rothenberg 1 March 2016
Bi 8 Lecture 17 REGulation by RNA interference Ellen Rothenberg 1 March 2016 Protein is not the only regulatory molecule affecting gene expression: RNA itself can be negative regulator RNA does not need
More informationmirnas as Biomarkers for Drug-Induced Liver Injury and as Predictors in Clinical Trials
mirnas as Biomarkers for Drug-Induced Liver Injury and as Predictors in Clinical Trials Herbert L. Bonkovsky, M.D. Professor of Medicine Wake Forest University School of Medicine Chief of Hepatology, NC
More informationSupplementary information
Supplementary information Human Cytomegalovirus MicroRNA mir-us4-1 Inhibits CD8 + T Cell Response by Targeting ERAP1 Sungchul Kim, Sanghyun Lee, Jinwook Shin, Youngkyun Kim, Irini Evnouchidou, Donghyun
More informationBest practice DNA prep for SMRT. Olga Vinnere Pettersson, PhD Project coordinator NGI-Sweden / SciLifeLab (UU)
Best practice DNA prep for SMRT Olga Vinnere Pettersson, PhD Project coordinator NGI-Sweden / SciLifeLab (UU) National Genomics Infrastructure - Sweden NGI Stockholm NGI Uppsala NGI staff: 60-70 FTE, including
More informationHigh AU content: a signature of upregulated mirna in cardiac diseases
https://helda.helsinki.fi High AU content: a signature of upregulated mirna in cardiac diseases Gupta, Richa 2010-09-20 Gupta, R, Soni, N, Patnaik, P, Sood, I, Singh, R, Rawal, K & Rani, V 2010, ' High
More informationAnalysis of Massively Parallel Sequencing Data Application of Illumina Sequencing to the Genetics of Human Cancers
Analysis of Massively Parallel Sequencing Data Application of Illumina Sequencing to the Genetics of Human Cancers Gordon Blackshields Senior Bioinformatician Source BioScience 1 To Cancer Genetics Studies
More informationSTAT1 regulates microrna transcription in interferon γ stimulated HeLa cells
CAMDA 2009 October 5, 2009 STAT1 regulates microrna transcription in interferon γ stimulated HeLa cells Guohua Wang 1, Yadong Wang 1, Denan Zhang 1, Mingxiang Teng 1,2, Lang Li 2, and Yunlong Liu 2 Harbin
More informationAccurate detection for a wide range of mutation and editing sites of micrornas from small RNA high-throughput sequencing profiles
Published online 26 May 2016 Nucleic Acids Research, 2016, Vol. 44, No. 14 e123 doi: 10.1093/nar/gkw471 Accurate detection for a wide range of mutation and editing sites of micrornas from small RNA high-throughput
More informationmicrorna Presented for: Presented by: Date:
microrna Presented for: Presented by: Date: 2 micrornas Non protein coding, endogenous RNAs of 21-22nt length Evolutionarily conserved Regulate gene expression by binding complementary regions at 3 regions
More informationA Statistical Framework for Classification of Tumor Type from microrna Data
DEGREE PROJECT IN MATHEMATICS, SECOND CYCLE, 30 CREDITS STOCKHOLM, SWEDEN 2016 A Statistical Framework for Classification of Tumor Type from microrna Data JOSEFINE RÖHSS KTH ROYAL INSTITUTE OF TECHNOLOGY
More informationMusculoskeletal Diseases
microrna Biomarkers of Bone Quality Neurodegenerative Diseases Cardiovascular Diseases Musculoskeletal Diseases a simple and standardized kit qpcr analysis of validated microrna bone biomarkers The osteomirtm
More informationGene-microRNA network module analysis for ovarian cancer
Gene-microRNA network module analysis for ovarian cancer Shuqin Zhang School of Mathematical Sciences Fudan University Oct. 4, 2016 Outline Introduction Materials and Methods Results Conclusions Introduction
More informationNational Disease Research Interchange Annual Progress Report: 2010 Formula Grant
National Disease Research Interchange Annual Progress Report: 2010 Formula Grant Reporting Period July 1, 2012 June 30, 2013 Formula Grant Overview The National Disease Research Interchange received $62,393
More informationChIP-seq hands-on. Iros Barozzi, Campus IFOM-IEO (Milan) Saverio Minucci, Gioacchino Natoli Labs
ChIP-seq hands-on Iros Barozzi, Campus IFOM-IEO (Milan) Saverio Minucci, Gioacchino Natoli Labs Main goals Becoming familiar with essential tools and formats Visualizing and contextualizing raw data Understand
More informationSupplementary Materials for
www.sciencesignaling.org/cgi/content/full/7/310/ra11/dc1 Supplementary Materials for STAT3 Induction of mir-146b Forms a Feedback Loop to Inhibit the NF-κB to IL-6 Signaling Axis and STAT3-Driven Cancer
More informationHigh Throughput TruSeq Stranded mrna Library Construction on the Biomek FX P
High Throughput TruSeq Stranded mrna Library Construction on the Biomek FX P Zach Smith and Scott D. Michaels The Center for Genomics and Bioinformatics Indiana University Bloomington, IN USA Mary Blair
More informationMusculoskeletal Diseases
Neurodegenerative Diseases Cardiovascular Diseases Musculoskeletal Diseases a simple and standardized kit qpcr analysis of circulating micrornas for fracture risk analysis stability for life. stability
More informationmirna-guided regulation at the molecular level
molecular level Hervé Seitz IGH du CNRS, Montpellier, France March 3, 2016 microrna target prediction . microrna target prediction mirna: target: 2 7 5 N NNNNNNNNNNNNNN 3 NNNNNN the seed microrna target
More informationSignatures (of Response) to Environmental Exposures
Gene-expression Profiles as Signatures (of Response) to Environmental Exposures Smoking and the airway field of injury as a novel paradigm for the exposome Avrum Spira, M.D., M.Sc. Section of Computational
More informationSerum mirna expression profile as a prognostic biomarker of stage II/III
Serum mirna expression profile as a prognostic biomarker of stage II/III colorectal adenocarcinoma Jialu Li a,b,, Yang Liu c,, Cheng Wang d,, Ting Deng a,, Hongwei Liang b, Yifei Wang e, Dingzhi Huang
More informationSupplementary methods:
Supplementary methods: Primers sequences used in real-time PCR analyses: β-actin F: GACCTCTATGCCAACACAGT β-actin [11] R: AGTACTTGCGCTCAGGAGGA MMP13 F: TTCTGGTCTTCTGGCACACGCTTT MMP13 R: CCAAGCTCATGGGCAGCAACAATA
More informationdeveloping new tools for diagnostics Join forces with IMGM Laboratories to make your mirna project a success
micrornas developing new tools for diagnostics Join forces with IMGM Laboratories to make your mirna project a success Dr. Carola Wagner IMGM Laboratories GmbH Martinsried, Germany qpcr 2009 Symposium
More informationProfiling of MicroRNA Expression in Obese and Diabetic-Induced Mice for Biomarker Discovery
Transactions on Science and Technology Vol. 4, No. 3-3, 391-395, 2017 Profiling of MicroRNA Expression in Obese and Diabetic-Induced Mice for Biomarker Discovery Janan N. Hadi, Mohammad Iqbal, Vijay Kumar
More informationCancer Problems in Indonesia
mirna and Cancer : mirna as a Key Regulator in Cancer Sofia Mubarika 2 nd Symposium Biomolecular Update in Cancer PERABOI Padang 18 Mei 2013 Cancer Problems in Indonesia 1. Chemoresistency / recurrency
More informationhe micrornas of Caenorhabditis elegans (Lim et al. Genes & Development 2003)
MicroRNAs: Genomics, Biogenesis, Mechanism, and Function (D. Bartel Cell 2004) he micrornas of Caenorhabditis elegans (Lim et al. Genes & Development 2003) Vertebrate MicroRNA Genes (Lim et al. Science
More informationP. Mathijs Voorhoeve, Carlos le Sage, Mariette Schrier, Ad J.M. Gillis, Hans Stoop,
Supplemental Data A Genetic Screen Implicates mirna-372 and mirna-373 As Oncogenes in Testicular Germ Cell Tumors P. Mathijs Voorhoeve, Carlos le Sage, Mariette Schrier, Ad J.M. Gillis, Hans Stoop, Remco
More informationEXOSOMES & MICROVESICLES
The Sample Preparation Experts EXOSOMES & MICROVESICLES The New Standard in Exosome Purification and RNA Isolation Best-in-Class, Pure & Simple Exosome Purification, Fractionation of Exosomal Free & Circulating
More informationSupplementary Figure 1 (Related with Figure 4). Molecular consequences of Eed deletion. (a) ChIP analysis identifies 3925 genes that are associated
Supplementary Figure 1 (Related with Figure 4). Molecular consequences of Eed deletion. (a) ChIP analysis identifies 3925 genes that are associated with the H3K27me3 mark in chondrocytes (see Table S1,
More informationNature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1. Differential expression of mirnas from the pri-mir-17-92a locus.
Supplementary Figure 1 Differential expression of mirnas from the pri-mir-17-92a locus. (a) The mir-17-92a expression unit in the third intron of the host mir-17hg transcript. (b,c) Impact of knockdown
More informationSupplementary Fig. 1. Delivery of mirnas via Red Fluorescent Protein.
prfp-vector RFP Exon1 Intron RFP Exon2 prfp-mir-124 mir-93/124 RFP Exon1 Intron RFP Exon2 Untransfected prfp-vector prfp-mir-93 prfp-mir-124 Supplementary Fig. 1. Delivery of mirnas via Red Fluorescent
More informationPREPARED FOR: U.S. Army Medical Research and Materiel Command Fort Detrick, Maryland
AD Award Number: W81XWH-10-1-1029 TITLE: PRINCIPAL INVESTIGATOR: Mu-Shui Dai, M.D., Ph.D. CONTRACTING ORGANIZATION: Oregon Health Science niversity, Portland, Oregon 97239 REPORT DATE: October 2013 TYPE
More informationBhatnagar et al, 2010 Cell Death and Disease Manuscript # CDDIS T
Bhatnagar et al, Cell Death and Disease Manuscript # CDDIS--98-T Supplemental Materials. Supplemental Figure Legends Supplemental Figure (A) WPE-NA and WPE-NB6 cells were treated with 4 nm of Docetaxel
More informationNot IN Our Genes - A Different Kind of Inheritance.! Christopher Phiel, Ph.D. University of Colorado Denver Mini-STEM School February 4, 2014
Not IN Our Genes - A Different Kind of Inheritance! Christopher Phiel, Ph.D. University of Colorado Denver Mini-STEM School February 4, 2014 Epigenetics in Mainstream Media Epigenetics *Current definition:
More information# of Normal brain # of controls Upregulated Downregulated Normalizer # of mirnas in Platform profile
Profiling studies comparing mirna expression in glioblastoma or glioblastoma cell lines to normal brain. MiRNAs were only included if fold change was greater than or equal to twofold Author Year Type of
More informationP. Tang ( 鄧致剛 ); PJ Huang ( 黄栢榕 ) g( 鄧致剛 ); g ( 黄栢榕 ) Bioinformatics Center, Chang Gung University.
Small RNA High Throughput Sequencing Analysis I P. Tang ( 鄧致剛 ); PJ Huang ( 黄栢榕 ) g( 鄧致剛 ); g ( 黄栢榕 ) Bioinformatics Center, Chang Gung University. Prominent members of the RNA family Classic RNAs mediating
More informationAre microbes the missing piece of the gut comfort puzzle?
Priority Research Programme Foods for improving gut function and comfort Are microbes the missing piece of the gut comfort puzzle? Wayne Young Senior Scientist, AgResearch Host institution Foods for gut
More informationScreening for novel oncology biomarker panels using both DNA and protein microarrays. John Anson, PhD VP Biomarker Discovery
Screening for novel oncology biomarker panels using both DNA and protein microarrays John Anson, PhD VP Biomarker Discovery Outline of presentation Introduction to OGT and our approach to biomarker studies
More informationTechnical Bulletin No. 161
CPAL Central Pennsylvania Alliance Laboratory Technical Bulletin No. 161 cobas 6800 HIV-1 Viral Load Assay - New Platform - June 1, 2017 Contact: Heather Habig, MLS (ASCP) CM, MB CM, 717-851-1422 Operations
More informationSupplementary Appendix
Supplementary Appendix This appendix has been provided by the authors to give readers additional information about their work. Supplement to: Choi YL, Soda M, Yamashita Y, et al. EML4-ALK mutations in
More informationDNA-seq Bioinformatics Analysis: Copy Number Variation
DNA-seq Bioinformatics Analysis: Copy Number Variation Elodie Girard elodie.girard@curie.fr U900 institut Curie, INSERM, Mines ParisTech, PSL Research University Paris, France NGS Applications 5C HiC DNA-seq
More informationClinical Study MicroRNA Expression Profile in CAD Patients and the Impact of ACEI/ARB
SAGE-Hindawi Access to Research Cardiology Research and Practice Volume 20, Article ID 53295, 5 pages doi:0.406/20/53295 Clinical Study MicroRNA Expression Profile in CAD Patients and the Impact of ACEI/ARB
More informationSUPPLEMENTARY INFORMATION
DOI:.38/ncb3399 a b c d FSP DAPI 5mm mm 5mm 5mm e Correspond to melanoma in-situ Figure a DCT FSP- f MITF mm mm MlanaA melanoma in-situ DCT 5mm FSP- mm mm mm mm mm g melanoma in-situ MITF MlanaA mm mm
More informationSmall RNA-Seq and profiling
Small RNA-Seq and profiling Y. Hoogstrate 1,2 1 Department of Bioinformatics & Department of Urology ErasmusMC, Rotterdam 2 CTMM Translational Research IT (TraIT) BioSB: 5th RNA-seq data analysis course,
More informationA novel and universal method for microrna RT-qPCR data normalization
A novel and universal method for microrna RT-qPCR data normalization Jo Vandesompele professor, Ghent University co-founder and CEO, Biogazelle 4 th International qpcr Symposium Weihenstephan, March 1,
More informationAssessing intercomponent. heterogeneity of biphasic uterine carcinosarcoma. December 7, 2018
December 7, 2018 Assessing intercomponent heterogeneity of biphasic uterine carcinosarcoma Research Grand Rounds 2018 Avera McKennan Hospital Presented by Erik Ehli, PhD Research Grand Rounds Brief Outline:
More informationSupplementary information for: Human micrornas co-silence in well-separated groups and have different essentialities
Supplementary information for: Human micrornas co-silence in well-separated groups and have different essentialities Gábor Boross,2, Katalin Orosz,2 and Illés J. Farkas 2, Department of Biological Physics,
More informationResults and discussion
Supplementary Figure 1. Assessment of the cross-talk between FuraPE3 and D4ER fluorescent spectra. Cells were perifused with 15 mmol/l glucose (G15) in the presence of 250 µmol/l of the KATP channel opener
More informationRoles of microrna-mediated Drug Resistance in Tumor Stem Cells of Small Cell Lung Carcinoma
AD Award Number: W81XWH-12-1-0479 TITLE: Roles of microrna-mediated Drug Resistance in Tumor Stem Cells of Small Cell Lung Carcinoma PRINCIPAL INVESTIGATOR: Kounosuke Watabe, Ph.D. CONTRACTING ORGANIZATION:
More informationGene expression analysis. Roadmap. Microarray technology: how it work Applications: what can we do with it Preprocessing: Classification Clustering
Gene expression analysis Roadmap Microarray technology: how it work Applications: what can we do with it Preprocessing: Image processing Data normalization Classification Clustering Biclustering 1 Gene
More information