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[E-MTAB-444] Transcription profiling by high throughput sequencing of Cleome gynandra developing and mature leaves

ABSTRACT: Cleome gynandra leaf development RNA-seq RNA-seq have been performed on developing (2mm length) and mature (10mm length) leaves of the C4 photosynthesis plant Cleome gynandra. 6 runs of Illumina 36-42 bp single end have been performed ArrayExpress Release Date: 2010-12-01 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: Aubry Person First Name: Sylvain Person Mid Initials: Person Email: sa530@cam.ac.uk Person Phone: +441223 330 220 Person Address: Department of Plant Sciences. University of Cambridge. Downing Street. CB2 3EA Cambridge Person Affiliation: University of Cambridge

ORGANISM(S): Gynandropsis gynandra

PROVIDER: GSE30605 | GEO | 2011/07/14

SECONDARY ACCESSION(S): PRJNA144505

REPOSITORIES: GEO

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[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-706] Quantitative RNA-seq analysis of the transcriptome of Campylobacter jejuni

Project description:RNA-seq analysis of the transcriptome of wild type C.jejuni NCTC11168, and of an rpoN mutant of the same strain, both grown in vitro. ArrayExpress Release Date: 2011-06-14 Publication Title: Quantitative RNA-seq analysis of the transcriptome of Campylobacter jejuni Publication Author List: Roy R. Chaudhuri, Lu Yu, Alpa Kanji, Timothy T. Perkins, Paul P. Gardner, Jyoti Choudhary, Duncan J. Maskell, Andrew J. Grant Person Roles: submitter Person Last Name: Chaudhuri Person First Name: Roy Person Mid Initials: R Person Email: roy.chaudhuri@gmail.com Person Phone: 441000000000 Person Address: Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, United Kingdom Person Affiliation: University of Cambridge

2011-07-14 | GSE30621 | GEO

[E-MTAB-502] Citrobacter rodentium transcriptomics (Regulation)

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

[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-TABM-722] Transcription factor binding evolution in five vertebrates

Project description:Five-vertebrate ChIP-seq reveals the evolutionary dynamics of trancription factor binding. The SRF files for this experiment can be found in the European Read Archive with study accession number ERP000054. ArrayExpress Submission Date: Apr 07 2010 ArrayExpress Release Date: Apr 08 2010 Publication Author List: Dominic Schmidt; Michael D Wilson; Benoit Ballester; Petra C Schwalie; Gordon D Brown; Aileen Marshall; Claudia Kutter; Stephen Watt; Celia P Martinez-Jimenz; Sarah MacKay; Iannis Talianidis; Paul Flicek; Duncan T Odom Publication Title: Transcription factor binding evolution in five vertebrates Person Roles: submitter Person Last Name: Flicek Person First Name: Paul Person Email: flicek@ebi.ac.uk Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Person Affiliation: EBI

2010-06-02 | GSE22078 | 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-341] Individual-nucleotide resolution CLIP using high throughput sequencing of human HeLa cells to enable precise mapping of protein-RNA interactions in intact cells

Project description:UV-crosslinking and immunoprecipitation (CLIP) combined with high-throughput sequencing was previously used to generate transcriptome-wide binding maps of several RNA-binding proteins. However, since identification of binding sites relied on the analysis of overlapping sequence clusters, distances of less than 30 nucleotides were not resolved. An additional disadvantage of CLIP is the requirement of reverse transcription to pass over residual amino acids that remain covalently attached to the RNA at the crosslink site. Primer extension assays have shown that the vast majority of cDNAs prematurely truncate immediately before the 'crosslink nucleotide'. Here, we exploited this apparent limitation to achieve single nucleotide resolution by capturing these truncated cDNAs through the introduction of a second adapter after reverse transcription via self-circularization. In order to quantify cDNA molecules that truncate at the same nucleotide, we added a random barcode to the DNA adapter. This allowed us to discriminate between unique cDNA products and PCR duplicates . Taken together, individual-nucleotide resolution CLIP (iCLIP) enables precise mapping of protein-RNA interactions in intact cells. ArrayExpress Release Date: 2010-09-03 Publication Title: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution Publication Author List: Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J. Person Roles: submitter Person Last Name: Konig Person First Name: Julian Person Email: jkonig@mrc-lmb.cam.ac.uk Person Phone: 0044 7531 502686 Person Address: Hills Road, CB2 0QH Cambridge, UK Person Affiliation: MRC LMB

2010-12-04 | GSE25681 | GEO

[E-MTAB-599] Mouse Transcriptome

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

[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-935] GENCODE PCR-Seq Batch VII

Project description:As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. Selected transcript models are verified experimentally by RT-PCR amplification followed by sequencing. This is batch VII, which targets annotations from Gencode 8 (March 2011). ArrayExpress Release Date: 2012-02-01 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: Gonzalez Person First Name: Jose Person Mid Initials: M Person Email: jmg@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

2012-04-25 | GSE37592 | GEO

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