E-MTAB-3112
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-3112 | ExpressionAtlas | 2014-11-21
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description: Not available
| S-BSST1361 | biostudies-other
Project description:Raw data from E-MTAB-1585 was normalized by using reads per million. https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585/ Strand specific RNA-Seq data E-MTAB-1585 was normalized and subtracted control from knockdown to generate tracks that more clearly displayed the unusual pattern of RNA expression caused by knockdown of 7SK. The following wig files were generated from multiple samples (i.e.raw data files), as indicated in the 'readme.txt' file. 7sk_3p_KD_norm.wig: 7SK 3P Knockdown normalized 7sk_3p_KDF_norm.wig: 7SK 3P Knockdown normalized (Forward) 7sk_3p_KDR_norm.wig: 7SK 3P Knockdown normalized (Reverse) 7sk_5p_KD_norm.wig: 7SK 5P Knockdown normalized 7sk_5p_KDF_norm.wig: 7SK 5P Knockdown normalized (Forward) 7sk_5p_KDR_norm.wig: 7SK 5P Knockdown normalized (Reverse) 7sk_Control_norm.wig: 7SK Control normalized 7sk_ControlF_norm.wig: 7SK Control normalized (Forward) 7sk_ControlR_norm.wig: 7SK Control normalized (Reverse) 7sk_3p_KDF-ControlF.wig: 7SK 3P Knockdown-Control (Forward) 7sk_3p_KDR-ControlR.wig: 7SK 3P Knockdown-Control (Reverse) 7sk_5p_KDF-ControlF.wig: 7SK 5P Knockdown-Control (Forward) 7sk_5p_KDR-ControlR.wig: 7SK 5P Knockdown-Control (Reverse)
2013-09-19 | E-GEOD-50860 | biostudies-arrayexpress
Project description:WARNING: This library was yield low amount of material and it was over-amplified by PCR. This libraries are used study the robustness of several statitical methods against PCR artifacts. ChIP experiments were performed on Arabidopsis wildtype inflorescences using an antibody raised against a C-terminal peptide of SEP3. ArrayExpress Release Date: 2011-04-27 Publication Title: ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions Publication Author List: Jose M. Muino, Kerstin Kaufmann, Roeland C. H. J. van Ham, Gerco C. Angenent, and Pawel Krajewski Person Roles: submitter Person Last Name: Muino Person First Name: Jose Person Mid Initials: M. Person Email: jose.muino@wur.nl Person Phone: 0317-481122 Person Address: Droevendaalsesteeg 1, P.O. Box 16, 6700 AA Wageningen, The Netherlands Person Affiliation: Plant Research International B.V.
2011-07-14 | GSE30616 | GEO
Project description:Abstract: Paired-end sequence data has been generated using polyA selected RNA from a range of zebrafish tissues using the Illumina Genome Analyzer. Study description: Zebrafish total RNA was extracted from adult tissue, then polyA selected. After fragmentation and reverse transcription Illumina sequencing libraries were prepared. Paired-end sequence runs were performed with 76 base reads on the Illumina Genome Analyzer. ArrayExpress Release Date: 2011-01-28 Person Roles: submitter Person Last Name: Service Person First Name: Submission Person Mid Initials: Person Email: datahose@sanger.ac.uk Person Phone: Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom Person Affiliation: Wellcome Trust Sanger Institute
2011-07-14 | GSE30608 | GEO
Project description:Sequencing the transcriptome of DBAxC57BL/6J mice. To study the regulation of transcription, splicing and RNA turnover we have sequenced the transcriptomes of tissues collected DBAxC57BL/6J mice. We strongly encourage researchers to contact us if there is any queries about referencing or publishing analysis based on pre-publication data. This data is part of a pre-publication release. For information on use of the data and the data release policy please see: http://www.sanger.ac.uk/resources/mouse/genomes/datarelease.html ArrayExpress Release Date: 2011-04-09 Publication Title: Sequence variation amongst 17 classical and wild-derived mouse genomes and its effect on gene regulation and phenotypic variation. Publication Author List: Thomas M. Keane, Petr Daneck, Leo Goodstadt, Bret Payseur, Michael White, Kim Wong, Binnaz Yalcin, Andreas Heger, Avi Agam, Guy Slater, Martin Goodson, Nick Furotte, Eleazar Eskin, Christoffer Nellaker, Helen Whitley, James Cleak, Deborah Janowitz, Polinka Hernandez-Pliego, Amartjit Bhomra, Jerome Nicod, Xiangchao Gan, Wei Yuan, Louise van der Weyden, Sendu Bala, Allan Bradley, Jim Stalker, Richard Mott, Richard Durbin, Ian Jackson, Laura Reinholdt, Chris P. Ponting, Ewan Birney, Jonathan Flint, David J. Adams Person Roles: submitter Person Last Name: Service Person First Name: Submission Person Mid Initials: Person Email: datahose@sanger.ac.uk Person Phone: Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom Person Affiliation: Wellcome Trust Sanger Institute Person Roles: project owner Person Last Name: Adams Person First Name: David Person Mid Initials: Person Email: da1@sanger.ac.uk Person Phone: Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom Person Affiliation: Wellcome Trust Sanger Institute
2011-07-14 | GSE30617 | GEO
Project description:Recent advances in high throughput sequencing methodologies allow the opportunity to probe in depth the transcriptomes of organisms including N. caninum. In this project, we are using Illumina sequencing technology to analyze the transcriptome (RNA-Seq) of experimentally accessible stages (e.g. tachyzoites at different times points) of N. caninum NCLiv. The aim is to make transcriptional landscape maps at different time points at different life cycle stages of N. caninum and compare it with equivalent datasets from the closely related parasite Toxoplasma gondii. ArrayExpress Release Date: 2011-02-08 Person Roles: submitter Person Last Name: Service Person First Name: Submission Person Mid Initials: Person Email: datahose@sanger.ac.uk Person Phone: Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom Person Affiliation: Wellcome Trust Sanger Institute Person Roles: Investigator Person Last Name: Reid Person First Name: Adam Person Mid Initials: Person Email: ar11@sanger.ac.uk Person Phone: 01223 834244 Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: Project Coordinator Person Last Name: Sanders Person First Name: Mandy Person Mid Initials: J Person Email: mjs@sanger.ac.uk Person Phone: 01223 834244 Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK Person Affiliation: Wellcome Trust Sanger Institute
2011-07-14 | GSE30613 | GEO
Project description:Recent advances in high throughput sequencing methodologies allow the opportunity to probe in depth the transcriptomes of organisms including N. caninum and Toxoplasma gondii. In this project, we are using Illumina sequencing technology to analyze the transcriptome (RNA-Seq) of experimentally accessible stages (e.g. tachyzoites at different times points) of T. gondii VEG strain. The aim is to make comparative transcriptional landscape maps of Neospora and Toxoplasma at different time points at different life cycle stages and compare levels of expression of orthologous genes in these two organisms. ArrayExpress Release Date: 2011-02-08 Person Roles: submitter Person Last Name: Service Person First Name: Submission Person Mid Initials: Person Email: datahose@sanger.ac.uk Person Phone: Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom Person Affiliation: Wellcome Trust Sanger Institute Person Roles: Investigator Person Last Name: Reid Person First Name: Adam Person Mid Initials: Person Email: ar11@sanger.ac.uk Person Phone: 01223 834244 Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: Project Coordinator Person Last Name: Sanders Person First Name: Mandy Person Mid Initials: J Person Email: mjs@sanger.ac.uk Person Phone: 01223 834244 Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK Person Affiliation: Wellcome Trust Sanger Institute
2011-07-14 | GSE30614 | GEO
Project description:Raw data from E-MTAB-1585 was normalized by using reads per million. https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1585/
2013-09-19 | GSE50860 | GEO
Project description:The centromere-specific Histone H3-variant CENH3 (also known as CENP-A) is considered to be an epigenetic mark for establishment and propagation of centromere identity. Pulse-induction of CENH3 (Drosophila CID) in Schneider S2 cells incorporates into noncentromeric regions and generates CID islands that resist clearing from chromosome arms for multiple cell generations. We demonstrate that CID islands represent functional ectopic kinetochores, which are non-randomly distributed on the chromosome and display a preferential localization near telomeres and pericentric heterochromatin in transcriptionally silent, intergenic chromatin domains. Although overexpression of heterochromatin protein 1 (HP1) or increasing Histone acetylation interferes with CID islands formation on a global scale, induction of a locally defined region of synthetic heterochromatin by targeting HP1-LacI fusions to stably integrated Lac Operator arrays produces a proximal hotspot for CID islands formation. These data suggest that the characteristics of regions bordering heterochromatin promote de novo kinetochore assembly and thereby contribute to centromere identity. ArrayExpress Release Date: 2011-07-15 Person Roles: submitter Person Last Name: Diehl Person First Name: Sarah Person Mid Initials: Person Email: diehl@immunbio.mpg.de Person Phone: (+49) 761 5108 795 Person Address: Stuebeweg 51, 79108 Freiburg im Breisgau, Germany Person Affiliation: Max-Planck-Institute for Immunobiology and Epigenetics Person Roles: investigator Person Last Name: Heun Person First Name: Patrick Person Mid Initials: Person Email: heun@immunbio.mpg.de Person Phone: (+49) 761 5108 717 Person Address: Stuebeweg 51, 79108 Freiburg im Breisgau, Germany Person Affiliation: Max-Planck-Institute for Immunobiology and Epigenetics Publication Title: Heterochromatin boundaries are hotspots for de novo kinetochore formation. Publication Author List: Agata Olszak, Dominic van Essen, Antonio J. Pereira, Sarah Diehl, Thomas Manke, Helder Maiato, Simona Saccani and Patrick Heun
2012-01-20 | GSE30997 | GEO
Project description:Whole genome trancription study of Citrobacter rodentium grown in rich media. Publication Title: Citrobacter rodentium is an Unstable Pathogen Showing Evidence of Significant Genomic Flux Publication Author List: Nicola K. Petty, Theresa Feltwell, Derek Pickard, Simon Clare, Ana L. Toribio, Maria Fookes, Kevin Roberts, Rita Monson, Satheesh Nair, Robert A. Kingsley, Richard Bulgin, Siouxsie Wiles, David Goulding, Craig Corton, Nicola Lennard, David Harris, David Willey, Richard Rance, Lu Yu, Jyoti S. Choudhary, Carol Churcher, Michael A. Quail, Julian Parkhill, Gad Frankel, Gordon Dougan, George P.C. Salmond, Nicholas R. Thomson ArrayExpress Release Date: 2011-02-12 Person Roles: investigator Person Last Name: Thomson Person First Name: Nicholas Person Mid Initials: Person Email: nrt@sanger.ac.uk Person Phone: Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: submitter Person Last Name: Service Person First Name: Submission Person Mid Initials: Person Email: datahose@sanger.ac.uk Person Phone: Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom Person Affiliation: Wellcome Trust Sanger Institute
2011-07-14 | GSE30610 | GEO