Literature DB >> 23494306

Transcriptional profiling of Dictyostelium with RNA sequencing.

Edward Roshan Miranda1, Gregor Rot, Marko Toplak, Balaji Santhanam, Tomaz Curk, Gad Shaulsky, Blaz Zupan.   

Abstract

Transcriptional profiling methods have been utilized in the analysis of various biological processes in Dictyostelium. Recent advances in high-throughput sequencing have increased the resolution and the dynamic range of transcriptional profiling. Here we describe the utility of RNA sequencing with the Illumina technology for production of transcriptional profiles. We also describe methods for data mapping and storage as well as common and specialized tools for data analysis, both online and offline.

Entities:  

Mesh：

Substances：

Year:  2013        PMID： 23494306      PMCID： PMC3892559          DOI： 10.1007/978-1-62703-302-2_8

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  16 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

2.  A novel developmental mechanism in Dictyostelium revealed in a screen for communication mutants.

Authors:  Kirsten Kibler; Tu-Lan Nguyen; Jessica Svetz; Nancy Van Driessche; Miroslava Ibarra; Christopher Thompson; Chad Shaw; Gad Shaulsky
Journal:  Dev Biol       Date:  2003-07-15       Impact factor: 3.582

3.  Microarray data mining with visual programming.

Authors:  Tomaz Curk; Janez Demsar; Qikai Xu; Gregor Leban; Uros Petrovic; Ivan Bratko; Gad Shaulsky; Blaz Zupan
Journal:  Bioinformatics       Date:  2004-08-12       Impact factor: 6.937

4.  The Dictyostelium developmental cDNA project: generation and analysis of expressed sequence tags from the first-finger stage of development.

Authors:  T Morio; H Urushihara; T Saito; Y Ugawa; H Mizuno; M Yoshida; R Yoshino; B N Mitra; M Pi; T Sato; K Takemoto; H Yasukawa; J Williams; M Maeda; I Takeuchi; H Ochiai; Y Tanaka
Journal:  DNA Res       Date:  1998-12-31       Impact factor: 4.458

5.  Epistasis analysis with global transcriptional phenotypes.

Authors:  Nancy Van Driessche; Janez Demsar; Ezgi O Booth; Paul Hill; Peter Juvan; Blaz Zupan; Adam Kuspa; Gad Shaulsky
Journal:  Nat Genet       Date:  2005-04-10       Impact factor: 38.330

6.  Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis genes.

Authors:  Ezgi O Booth; Nancy Van Driessche; Olga Zhuchenko; Adam Kuspa; Gad Shaulsky
Journal:  Bioinformatics       Date:  2005-10-18       Impact factor: 6.937

7.  The transcriptional landscape of the yeast genome defined by RNA sequencing.

Authors:  Ugrappa Nagalakshmi; Zhong Wang; Karl Waern; Chong Shou; Debasish Raha; Mark Gerstein; Michael Snyder
Journal:  Science       Date:  2008-05-01       Impact factor: 47.728

8.  Stem cell transcriptome profiling via massive-scale mRNA sequencing.

Authors:  Nicole Cloonan; Alistair R R Forrest; Gabriel Kolle; Brooke B A Gardiner; Geoffrey J Faulkner; Mellissa K Brown; Darrin F Taylor; Anita L Steptoe; Shivangi Wani; Graeme Bethel; Alan J Robertson; Andrew C Perkins; Stephen J Bruce; Clarence C Lee; Swati S Ranade; Heather E Peckham; Jonathan M Manning; Kevin J McKernan; Sean M Grimmond
Journal:  Nat Methods       Date:  2008-05-30       Impact factor: 28.547

9.  Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples.

Authors:  Andrew M Smith; Lawrence E Heisler; Robert P St Onge; Eveline Farias-Hesson; Iain M Wallace; John Bodeau; Adam N Harris; Kathleen M Perry; Guri Giaever; Nader Pourmand; Corey Nislow
Journal:  Nucleic Acids Res       Date:  2010-05-11       Impact factor: 16.971

10.  Protocols for growth and development of Dictyostelium discoideum.

Authors:  Petra Fey; Anthony S Kowal; Pascale Gaudet; Karen E Pilcher; Rex L Chisholm
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491
View more
  10 in total

1.  Terpene synthase genes in eukaryotes beyond plants and fungi: Occurrence in social amoebae.

Authors:  Xinlu Chen; Tobias G Köllner; Qidong Jia; Ayla Norris; Balaji Santhanam; Patrick Rabe; Jeroen S Dickschat; Gad Shaulsky; Jonathan Gershenzon; Feng Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2016-10-07       Impact factor: 11.205

2.  The GATA transcription factor gene gtaG is required for terminal differentiation in Dictyostelium.

Authors:  Mariko Katoh-Kurasawa; Balaji Santhanam; Gad Shaulsky
Journal:  J Cell Sci       Date:  2016-04-15       Impact factor: 5.285

3.  ABC transporters in Dictyostelium discoideum development.

Authors:  Edward Roshan Miranda; Olga Zhuchenko; Marko Toplak; Balaji Santhanam; Blaz Zupan; Adam Kuspa; Gad Shaulsky
Journal:  PLoS One       Date:  2013-08-14       Impact factor: 3.240

4.  The GATA transcription factor GtaC regulates early developmental gene expression dynamics in Dictyostelium.

Authors:  Balaji Santhanam; Huaqing Cai; Peter N Devreotes; Gad Shaulsky; Mariko Katoh-Kurasawa
Journal:  Nat Commun       Date:  2015-07-06       Impact factor: 14.919

5.  Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum.

Authors:  Rafael David Rosengarten; Balaji Santhanam; Danny Fuller; Mariko Katoh-Kurasawa; William F Loomis; Blaz Zupan; Gad Shaulsky
Journal:  BMC Genomics       Date:  2015-04-13       Impact factor: 3.969

6.  Gene discovery by chemical mutagenesis and whole-genome sequencing in Dictyostelium.

Authors:  Cheng-Lin Frank Li; Balaji Santhanam; Amanda Nicole Webb; Blaž Zupan; Gad Shaulsky
Journal:  Genome Res       Date:  2016-06-15       Impact factor: 9.043

7.  The Long Noncoding RNA Transcriptome of Dictyostelium discoideum Development.

Authors:  Rafael D Rosengarten; Balaji Santhanam; Janez Kokosar; Gad Shaulsky
Journal:  G3 (Bethesda)       Date:  2017-02-09       Impact factor: 3.154

8.  Curcumin affects gene expression and reactive oxygen species via a PKA dependent mechanism in Dictyostelium discoideum.

Authors:  William S Swatson; Mariko Katoh-Kurasawa; Gad Shaulsky; Stephen Alexander
Journal:  PLoS One       Date:  2017-11-14       Impact factor: 3.240

Review 9.  When Dicty Met Myco, a (Not So) Romantic Story about One Amoeba and Its Intracellular Pathogen.

Authors:  Elena Cardenal-Muñoz; Caroline Barisch; Louise H Lefrançois; Ana T López-Jiménez; Thierry Soldati
Journal:  Front Cell Infect Microbiol       Date:  2018-01-09       Impact factor: 5.293

10.  Transcriptional milestones in Dictyostelium development.

Authors:  Mariko Katoh-Kurasawa; Karin Hrovatin; Shigenori Hirose; Amanda Webb; Hsing-I Ho; Blaž Zupan; Gad Shaulsky
Journal:  Genome Res       Date:  2021-06-28       Impact factor: 9.043
  10 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.