File 5 MOUSE sequences used in target gene promoter regions to detect NFATc1 protein binding by ChIP.

Slides:

Advertisements

Similar presentations

20,000 GENES IN HUMAN GENOME; WHAT WOULD HAPPEN IF ALL THESE GENES WERE EXPRESSED IN EVERY CELL IN YOUR BODY? WHAT WOULD HAPPEN IF THEY WERE EXPRESSED.

Advertisements

Visualization of genomic data Genome browsers. UCSC browser Ensembl browser Others ? Survey.

Tutorial 7 Genome browser. Free, open source, on-line broswer for genomes Contains ~100 genomes, from nematodes to human. Many tools that can be used.

Visualization of genomic data Genome browsers. How many have used a genome browser ? UCSC browser ? Ensembl browser ? Others ? survey.

BME 130 – Genomes Lecture 14 Eukaryotic Genome Anatomy.

UCSC Archaeal genome browser Advanced browsing September 19, 2006 David Bernick, Aaron Cozen and Todd Lowe September 19, 2006 David Bernick, Aaron Cozen.

Lab 3.41 Demo: Exploiting the UCSC Genome Browser Stefanie Butland UBC Bioinformatics Centre

Genome Browsers Ensembl (EBI, UK) and UCSC (Santa Cruz, California)

Genomic Database - Ensembl Ka-Lok Ng Department of Bioinformatics Asia University.

Genome Browsing with the UCSC Genome Browser

UCSC Archaeal genome browser September 19, 2006 David Bernick, Aaron Cozen and Todd Lowe September 19, 2006 David Bernick, Aaron Cozen and Todd Lowe.

A Computational Analysis of the H Region of Mouse Olfactory Receptor Locus 28 Deanna Mendez SoCalBSI August 2004.

Gene Regulation: What it is, and how to detect it By Jordan, Jennifer, and Brian.

University of Oklahoma Genome Center4/14/12.

Doug Brutlag 2011 Genome Databases Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University School of Medicine Genomics, Bioinformatics.

RExPrimer Pongsakorn Wangkumhang, M.Sc. Biostatistics and Informatics Laboratory, Genome Institute, National Center for Genetic Engineering and Biotechnology.

Genomic walking (1) To start, you need: -the DNA sequence of a small region of the chromosome -An adaptor: a small piece of DNA, nucleotides long.

COURSE OF BIOINFORMATICS Exam_31/01/2014 A.

Browsing the Genome Using Genome Browsers to Visualize and Mine Data.

Runx1-VE+ Runx1+VE+CD41-Runx1+VE+CD41+Runx1+VE-CD41+ Supplementary Figure 1 Supplementary Figure 1: Validation of cell populations for gene expression.

RNA-Seq Primer Understanding the RNA-Seq evidence tracks on the GEP UCSC Genome Browser Wilson Leung08/2014.

Supplementary Table 1: Microarray datasets

How do we represent the position specific preference ? BID_MOUSE I A R H L A Q I G D E M BAD_MOUSE Y G R E L R R M S D E F BAK_MOUSE V G R Q L A L I G.

William S. Klug Michael R. Cummings Charlotte A. Spencer Concepts of Genetics Eighth Edition Chapter 21 Dissection of Gene Function: Mutational Analysis.

Cell Surface Targeting

.1Sources of DNA and Sequencing Methods.1Sources of DNA and Sequencing Methods 2 Genome Assembly Strategy and Characterization 2 Genome Assembly.

Accessing and visualizing genomics data

Genomes at NCBI. Database and Tool Explosion : 230 databases and tools 1996 : first annual compilation of databases and tools lists 57 databases.

Primers to map bsd deletion points on genomic DNA NameForwardReverse Amplicon size (base pairs) A15’-CCACGGATGGAGTGAGTTCT-3’5’-GCCCCCAAGATGAGGATTAT-3’931.

Quantitative Detection and Differentiation of Human Herpesvirus 6 Subtypes in Bone Marrow Transplant Patients by Using a Single Real-Time Polymerase Chain.

Supplementary file 1. Construct design of tagged Wnt proteins.

PCR Polymerase Chain Reaction

(B.P :51) ( B:P52 ).

Alu insert, PV92 locus, chromosome 16

Figure S1 A B The ratio of UMTs/CMTs by averaging every 100 peaks. A. Pol-II data, B. ER data. It showed the ratio is decreasing along the lower level.

Fig. S Fig. S2 Cre-mediated recombination in vivo. G2 mice displaying high levels of GFP were crossed.

5' breakpoint in intron 2 (chr19:1,219,187-1,219,238 shown)

TSS Annotation Workflow

Validation of a four-primer real-time PCR as a diagnostic tool for single and mixed Plasmodium infections L. Cnops, J. Jacobs, M. Van Esbroeck Clinical.

Access to Sequence Data and Related Information

Visualization of genomic data

Quantitative analysis of follistatin (FST) promoter methylation in peripheral blood of patients with polycystic ovary syndrome Qing Sang, Shaozhen Zhang,

Workflow of one-step integration into any potential chromosome location. Workflow of one-step integration into any potential chromosome location. (A) After.

A Missense Mutation (R565W) in Cirhin (FLJ14728) in North American Indian Childhood Cirrhosis Pierre Chagnon, Jacques Michaud, Grant Mitchell, Jocelyne.

High-Resolution Profiling of Histone Methylations in the Human Genome

Strategy for CRISPR/Cas9-mediated genome editing in ΔEx50 mice

Fragile X Syndrome The Journal of Molecular Diagnostics

Rotation review Gaurav Moghe Genetics Program

Kimberly A. Aldinger, Stephen J. Mosca, Martine Tétreault, Jennifer C

SeqSharp The Journal of Molecular Diagnostics

The ETS-CRE array identifies genomic sequences specifically cobound by CREB1 and GABPα. The ETS-CRE array identifies genomic sequences specifically cobound.

Differentiation-induced changes in Tfam mRNA stability (A) The nt sequence corresponding to the 3′-UTR of mouse Tfam is illustrated. Differentiation-induced.

High-Resolution Profiling of Histone Methylations in the Human Genome

Gene Safari (Biological Databases)

.1Sources of DNA and Sequencing Methods 2 Genome Assembly Strategy and Characterization 3 Gene Prediction and Annotation 4 Genome Structure 5 Genome.

APOE Gene Targeting (A) Schematic representation of the endogenous APOE locus, the gene targeting vector and the targeted APOE locus. The exons of the.

Diagram of fusion primers and dual-indexing approach for library construction. Diagram of fusion primers and dual-indexing approach for library construction.

Genetic mapping and epigenetic landscape of RUNX3 locus overlapping rs

Fig. 1. Generation of WNK3 knockout mice

Fig. 4 Gene disruption via chip.

Fig. 4 p100/TSN enables E2F1 to interact with alternatively spliced transcripts. p100/TSN enables E2F1 to interact with alternatively spliced transcripts.

Transcription-mediated amplification (TMA).

Thomas J Cradick, Peng Qiu, Ciaran M Lee, Eli J Fine, Gang Bao

ITS rRNA gene locus. ITS rRNA gene locus. Schematic of the eukaryotic ribosomal gene cluster. The SILVA database contains sequences of the 18S gene, while.

Sox11's partner proteins and targets in differentiated neurons.

Target versatility. Target versatility. (A) Δctl0063, Δctl0064, Δctl0065, ΔtrpA, and wild-type C. trachomatis were analyzed by PCR with primers immediately.

Interaction of MAPJD with E-box sequence of the RIOK1 gene.

Figure Genetic characterization of the novel GYG1 gene mutation (A) GYG1_cDNA sequence and position of primers used. Genetic characterization of the novel.

Polymerase Chain Reaction (PCR)

Fig. 3 Genome editing of the MSTN gene.

Presentation transcript:

File 5 MOUSE sequences used in target gene promoter regions to detect NFATc1 protein binding by ChIP

ANGPTL2 (324 bp amplicon) UCSC Genome Browser on Mouse Dec 2011 (GRCm38/mm10) Assembly ACGTCAGCCTTCAGGGAGTGGAGCAGGCTGGTGAGCCAGGAGCAGAGCTGGCCAGCCTTCCTGTG CCAAAGAAGGAGGGGGCCCCGCCCAGGCCGCCAAAGCAGGCAGGAGGGGCTGGGCCAGCTGGG GCTGGAGCTAGTGTGACATCACCAGGCGGCCCGCCCCTGTCTGGAGCTGAGGGGAGGCCCAGAGC TTTTCTGGGGCCTGGGGGATCCTCTTGCACTGGTGGGCGGAGAGAAGTGCCTGCAGCCAACCAGG GTCAGGCTGTGCTCACAGTTTCCTCTGGCGGCACGTAAAGGCTCCACAAAGGACCTGGGAGTTCAA >chr2: FR Forward Primer Reverse Primer

ASPN (367 bp amplicon) UCSC Genome Browser on Mouse Dec 2011 (GRCm38/mm10) Assembly Forward Primer Reverse Primer GGCTTGATTTGTGCCATTTCTTTGCGGTGGGAACCATAGATGATACTTTTTGACTGGAGAAACTAGA TTTCTGCTAACTCACTAGATACCTTCTGTACCAACTGAGTATTTCCCCTTAGGGTCAATAAACCGCCC GTTCTTACAGGATTCTGTGCTTCAAGGATGTGGGGCTGGGTAATCTCTTGGAGTGGAAAGGGGGA AATGATTTTCTTCTTGAAGAATGGCATCTCTTGAACACTAGTGAGAAGGGAGCTGAGACTCTTGCA GAGGAAAGGTGGAGTTACCTGACTCTGCTTAGTTATCTGTACCACAACAGACGCAGGCCCAGGAA GAGTTTAAAGGGCCTGGCTTGCAGTTCCCAAAGAAG >chr13: F R

UCSC Genome Browser on Mouse Dec 2011 (GRCm38/mm10) Assembly Col3A1 (278 bp amplicon) CGGAGAATGGGAGTCAAAACACTTTTTCAAATTCAGACAGTTTTTACTGTTTCAGA GGGAAATTTAAAAACACACAAACAATTGTTGTAGGCTATCACAAAGCACATTCCTAT GTGTTTCTGTCATGCAAATATGTATTTAAGACTAATGCATGTTATAAACATATGCATAG GCTGATGTACACATGCTCCAGATGTGCTGTTTCTGTGTCTGTGGGTTGTGTCCTCTAC ACACAGGGAAAAATATATTAATCATTGCTTTTACTGCTGAGGGGATGG >chr1: F R Forward Primer Reverse Primer

UCSC Genome Browser on Mouse Dec 2011 (GRCm38/mm10) Assembly FAP (286 bp amplicon) AGCTGGAGCTCATGGAGGTATTTCCCCAACTGAAGCTCCCTTCTCTGTGATAACTCCAGCC TGTGTCAAGTTGACACACAAAACCAACCAGTACAAACTTGGACTTTAAACCCATCTGATTAT AGAGGCTGAGTACATTACCATTATTGTTTAACATGAAAGCACACTTGTAGTAAAACAATAAC AAATATAAAAACTAGAGCAAGAACCAAACAACACACAACACGTAGAAAAGTTATGCTTCAA AGCATAGATGATAAGAAAAGAAAGAAATCTGAGCTGCTTG Forward Primer Reverse Primer >chr2: FR

UCSC Genome Browser on Mouse Dec 2011 (GRCm38/mm10) Assembly MGP (230 bp amplicon) TGATCATGGAAACAGGGAAGACTACTTCGTGGTACTTTGGCTTGTAATAGAGAA CGGGAAAGATGAGGAAGAAGGGGAGAGAGACAGTGAGGAGCGTGAAGGGA AGTCCAAGGTAGGGAGGGAAAACCCACAGACAGCAGGGAGAGAGGTTTCTCA CCGTAGCACAGGGTTGCCACGGCCAGCGCAGCCAGGATGGCCAGAGGGAGCA GGCTCTTCATGGTGTCTCGGGT >chr6: F R Forward Primer Reverse Primer

UCSC Genome Browser on Mouse Dec 2011 (GRCm38/mm10) Assembly MRC2 (239 bp amplicon) ACTGGCCACCTGAGTCAGTCGCGCATCCCATCCTTCGGCTGGCCAGGCCTCGCAGCAGCCCAG GCTTCGCCACGCGGTGAAGTTCTGCGGAAAGTTTTGCAGTTGCTTCGCCTCTCGCGCCAGCA GGAGAAGCTGTGACGCAGCGTCTGGGGCTCCAGGCCCGGTCTGAAAAGAGAGGGTAGACAA GGCGGGAAGGAATTAAGAAGCAGAATAGGGGAAGATAAAGAGCGCACACTGGG Forward Primer Reverse Primer >chr11: F R

UCSC Genome Browser on Mouse Dec 2011 (GRCm38/mm10) Assembly PTRF (263 bp amplicon) GACTGGGGCAGAGGAATGTGAGCTGCGGAAAGGAATTAGGTCTTCGGAGTGTG CTCTACTCTTTCTCTTTCCTCACCCACAAACCCACTCCAGCCTTTTAAGATCAAGCTG AGGTCCAAATGGCGCGTGAATTGGGTGTAAACGAGTAGTTTGTGTCTATGCCTCAT GTCCTTGGAGGATCCTTGCCCTATACAATCTTTTTCAAAGATTTGGGGGTCTGCCCC CATCGTCTATCTATACACTGAGTTACCACTGTCCCCCAA Forward Primer Reverse Primer >chr11: FR

UCSC Genome Browser on Mouse Dec 2011 (GRCm38/mm10) Assembly TWIST1 (223 bp amplicon) CAGGTCGGTTTTGAATGGTTCGCAGGACGAATTGTTAGACCCCGAGCAAGGGGGGAGGGGG CGAGGGAGGGGGGCTGGAAAGAGGAAACTTTCCTATAAAACTTCGAAAAGTCCCTCCTCCCC ACGTCAGGCCAATGACACCGCTGCCCCCAAACTTTCCGCCCGCACGGAGGTATAAGAGCCGCC AAGTCCACAGCCCGCGCCCAACTCTCAGACACCTCGC Forward Primer Reverse Primer >chr12: F R

IL2 (249 bp amplicon) UCSC Genome Browser on Mouse Dec 2011 (GRCm38/mm10) Assembly GTCGGGTTAGCCCACACTTAGGTGGCAGTTTTAATTCATACAATGAACGCCTT CTGTATGAAACAAATTTTCCTCTTTGGGGTGGAGACACAAAAGTAACTCATG AAAATGTTCTCTTTGTCAAAACCATCCTGAACCTGTAAGCAGCCTGTTGTGGT GGACAAACGCAAGAGGAGATAGATGAAAAGAATAAATCTTTTAGATTTGTTG ATTAGACAGGAAGGATATTGGTTTCCTGTTTCAAGATGG Forward Primer Reverse Primer >chr3: FR