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[E-MTAB-189] Genomewide Analysis of Histone Modifications in Normal Human Islets

ABSTRACT: This experiment used ChIP-seq technology to create a genome-wide profile of histone marks in normal human pancreatic islets. In the current work we analyzed two histone marks associated with gene expression (H3K4me3, H3K4me1) and marks associated with gene repression (H3K27me3). Each mark was anayzed using samples obtained from four donors (n=4). Chromatin Immunoprecipitations (ChIPs) for histone marks were performed using specific anti-histone antibodies. Enrichment of each sample was calulated with respect to its individual input using qPCR. Samples were sequenced with Solexa and sequenced DNA from both Input (n=4) and ChIP (n = 4) samples were aligned to the NCBI Genome Build 36.1 Hg18 to determine regions that were enriched for binding by modified histones. ArrayExpress Release Date: 2010-02-17 Publication Title: Genome-wide analysis of histone modifications in human pancreatic islets Publication Author List: Bhandare R, Schug J, Le Lay J, Fox A, Smirnova O, Liu C, Naji A, Kaestner KH Person Roles: submitter Person Last Name: Bhandare Person First Name: Reena Person Email: bhandare@mail.med.upenn.edu Person Phone: Person Address: 771 Clinical Research Building, 415 Curie Blvd, Philadelphia, PA, 19104 Person Affiliation: Department of Genetics, University of Pennsylvania

ORGANISM(S): Homo sapiens

PROVIDER: GSE25126 | GEO | 2011/02/05

SECONDARY ACCESSION(S): PRJNA134577

REPOSITORIES: GEO

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ChIP-Seq of human normal pancreatic islets with anti-histone antibodies to analyse histone modifications

Project description:This experiment used ChIP-seq technology to create a genome-wide profile of histone marks in normal human pancreatic islets. In the current work we analyzed two histone marks associated with gene expression (H3K4me3, H3K4me1) and marks associated with gene repression(H3K27me3). Each mark was anayzed using samples obtained from four donors (n=4). Chromatin Immunoprecipitations (ChIPs) for histone marks were performed using specific anti-histone antibodies. Enrichment of each sample was calulated with respect to its individual input using qPCR. Samples were sequenced with Solexa and sequenced DNA from both Input (n=4) and ChIP (n = 4) samples were aligned to the NCBI Genome Build 36.1 Ð Hg18 to determine regions that were enriched for binding by modified histones.

2010-02-18 | E-MTAB-189 | biostudies-arrayexpress

ChIP profiling by array of histone modifications in normal human islets

2010-02-18 | E-MTAB-191 | biostudies-arrayexpress

[E-MTAB-442] ChIP-seq of mouse liver with no antibody to provide input sequences for ChIP experiments on C57BJ/6J mice

Project description:Odom_mouse_C57BL6J_input This experiment provides chromatin immunoprecipitation input sequences (i.e. no antibody was added during the ChIP protocol), suitable for use as input for ChIP experiments on C57BJ/6J mice. ArrayExpress Release Date: 2011-03-01 Publication Title: Pol III occupancy of tRNA genes is highly divergent between loci but highly conserved by amino acid isotypes Publication Author List: Claudia Kutter; Gordon D. Brown; Stephen Watt; Michael D. Wilson; Angela Goncalves; Robert J. White, Duncan T. Odom Person Roles: submitter Person Last Name: Brown Person First Name: Gordon Person Mid Initials: D Person Email: gordon.brown@cancer.org.uk Person Phone: +44(0)1223404275 Person Address: Cancer Research UK, Robinson Way, Cambridge, CB2 0RE, UK Person Affiliation: CRUK-CRI

2011-07-14 | GSE30604 | GEO

[E-MTAB-445] Transcription profiling by high throughput sequencing of blackface sheep infected with the gastrointestinal helminth Teladorsagia circumcincta to analyse resistance to infection

Project description:Blackface Teladorsagia Solexa Analysis of resistance to Teladosagia ArrayExpress Release Date: 2010-12-08 Publication Author List: Pemberton, J.; Beraldi, D.; Craig, B. and Hopkins, J. Publication Title: Digital gene expression analysis of gastrointestinal helminth resistance in Scottish blackface lambs Publication Author List: Sylvain Aubry, Mali Salmon, Kim M Rutherford, Paul Bertone, Andrea Brautigam, Andreas PM Weber, Krystyna A Kelly, Julian M Hibberd Publication Title: De novo transcriptome assembly enables quantitative expression analysis in non-sequenced model organisms Person Roles: submitter Person Last Name: Hopkins Person First Name: John Person Mid Initials: Person Email: john.hopkins@ed.ac.uk Person Phone: 44 131 650 6160 Person Address: Roslin Institute, Summerhall, Edinburgh. EH9 1QH. UK Person Affiliation: University of Edinburgh

2011-07-14 | GSE30606 | GEO

[E-MTAB-214] ChiP-seq profiling of Drosophila melanogaster salivary glands to identify targets for NSL1 and MCRS2.

Project description:ChiP-seq profiling of Drosophila melanogaster salivary glands to identify targets for NSL1 and MCRS2. ArrayExpress Release Date: 2010-04-16 Publication Title: The Nonspecific Lethal Complex Is a Transcriptional Regulator in Drosophila Publication Author List: Raja SJ, Charapitsa I, Conrad T, Vaquerizas JM, Gebhardt P, Holz H, Kadlec J, Fraterman S, Luscombe NM, Akhtar A. Person Roles: submitter Person Last Name: Vaquerizas Person First Name: Juan Person Mid Initials: M Person Email: jvaquerizas@ebi.ac.uk Person Phone: Person Address: Person Affiliation: EBI

2010-12-04 | GSE25709 | GEO

[E-MTAB-607] Transcription profiling by high throughput sequencing of the planarian Schmidtea mediterranea during head regeneration

Project description:The head-regeneration transcriptome of the planarian Schmidtea mediterranea ArrayExpress Release Date: 2011-07-15 Publication Title: The head-regeneration transcriptome of the planarian Schmidtea mediterranea Publication Author List: Thomas Sandmann, Matthias C. Vogg, Suthira Owlarn, Michael Boutros, and Kerstin Bartscherer Person Roles: submitter Person Last Name: Sandmann Person First Name: Thomas Person Mid Initials: Person Email: t.sandmann@dkfz.de Person Phone: +49 6221 42 1954 Person Address: Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany Person Affiliation: German Cancer Research Center

2012-01-20 | GSE30996 | GEO

[E-MTAB-533] GENCODE Targeted Sequencing Batch III

Project description:As part of the RNASeq Genome Annotation Assessment Project (RGASP) selected novel gene model predictions were analysed with RT-PCR-Seq. ArrayExpress Release Date: 2011-03-01 Publication Title: GENCODE: producing a reference annotation for ENCODE Publication Author List: Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R Person Roles: submitter Person Last Name: Kokocinski Person First Name: Felix Person Mid Initials: Person Email: fsk@sanger.ac.uk Person Phone: -498006 Person Address: Wellcome Trust Genome Campus, Hinxton, UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: investigator Person Last Name: Hubbard Person First Name: Tim Person Mid Initials: Person Email: th@sanger.ac.uk Person Phone: -498055 Person Address: Wellcome Trust Genome Campus, Hinxton, UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: investigator Person Last Name: Reymond Person First Name: Alexandre Person Mid Initials: Person Email: Alexandre.Reymond@unil.ch Person Phone: Person Address: Lausanne, Switzerland Person Affiliation: University of Lausanne For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

2011-07-14 | GSE30612 | GEO

[E-MTAB-197] CEU_RNASEQ60, Transcription profiling by high throughput sequencing of 60 HapMap CEU population individuals

Project description:RNA-sequencing of 60 HapMap CEU individuals ArrayExpress Release Date: 2010-03-04 Publication Title: Transcriptome genetics using second generation sequencing in a Caucasian population Publication Author List: Stephen B. Montgomery, Micha Sammeth, Maria Gutierrez-Arcelus, Radoslaw P. Lach, Catherine Ingle, James Nisbett, Roderic Guigo, Emmanouil T. Dermitzakis Person Roles: submitter Person Last Name: Montgomery Person First Name: Stephen Person Mid Initials: B Person Email: stephen.montgomery@unige.ch Person Phone: +41 (0) 22 379 5483 Person Address: 1 Rue Michel Servet, Geneva, Switzerland, 1211 Person Affiliation: University of Geneva Medical School

2010-12-04 | GSE25030 | GEO

[E-MTAB-610] Tag profiling of genes from two Pachycladon species

Project description:Tag profiling and expression analysis of genes from Pachycladon enysii and Pachycladon fastigiatum. ArrayExpress Release Date: 2011-06-01 Publication Title: Short read expression profiling in a non-model allopolyploid plant Publication Author List: Voelckel, C, Gruenheit, N, Biggs, P, Deusch, O, Lockhart, PJ Person Roles: submitter Person Last Name: Voelckel Person First Name: Claudia Person Mid Initials: Person Email: c.voelckel@massey.ac.nz Person Phone: Person Address: Institute of Molecular Biosciences, Private Bag 11 222, Palmerston North 4442 Person Affiliation: Institute of Molecular Biosciences, Allan Wilson Centre for Molecular Ecology and Evolution

2011-07-14 | GSE30618 | GEO

[E-MTAB-75] Cryptic unstable transcripts in yeast

Project description:Poly(A) and CUT RNA fractions are compared using 3 'Long-SAGE deep-sequencing. ArrayExpress Release Date: 2008-12-19 Publication Title: Widespread bidirectional promoters are the major source of cryptic transcripts in yeast Publication Author List: Helen Neil, Christophe Malabat, Yves d'Aubenton-Carafa, Zhenyu Xu, Lars M. Steinmetz and Alain Jacquier Person Roles: submitter Person Last Name: Malabat Person First Name: Christophe Person Mid Initials: Person Email: christophe.malabat@pasteur.fr Person Phone: Person Address: Unité de Génétique des Interactions Macromoléculaires; CNRS, URA2171,F-75015, Paris, France Person Affiliation: Institut Pasteur

2011-02-05 | GSE25132 | GEO

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