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Sample GSM742026 Query DataSets for GSM742026
Status Public on Jul 10, 2012
Title PolyA RNA_A. queenslandica precompetent larvae_library2_a
Sample type SRA
 
Source name Precompetent larvae
Organism Amphimedon queenslandica
Characteristics developmental stage: Precompetent larvae
tissue: Amphimedon tissues
Growth protocol Amphimedon tissues were collected at different developmental stages: precompetent (<3 hours after emergence from brood chambers); competent (>6 hours after emergence); postlarva (>4 hours after settlement); adult (no brood chambers)
Extracted molecule polyA RNA
Extraction protocol RNA from larvae and postlarvae was extracted directly with Trizol [Invitrogen]. Adult tissues without brood chambers were cleaned of macroscopic debris then ground in liquid nitrogen before RNA extraction with Trizol. Contaminating DNA was removed using the DNAfree kit [Ambion]. The poly(A) RNA fraction was enriched using the MicroPoly(A)Purist kit [Ambion] and ribosomal RNA was depleted using the RiboMinus Eukaryote kit [Invitrogen]. RNA quality was monitored using the Agilent Bioanalyzer RNA 6000 Pico Assay. Fragment libraries were prepared as described in Cloonan et al. (2008) Nat. Methods 5(7). Briefly, approximately 250ng of purified poly(A) RNA was subjected to 95°C until most of the RNA formed 50-200nt fragments. First-strand cDNA synthesis was primed with a 3’ adapter-tagged random hexamer primer using SuperScript II reverse transcriptase. Second strand cDNA was synthesized using a 5’ template switching adapter-tagged oligonucleotide. cDNA libraries were amplified using limited PCR cycles and fragments averaging 150bp in length were purified. Libraries were quantified by PCR and fragment size was verified using the Agilent Bioanalyzer DNA 1000 Assay. Fragment libraries were sequenced at 50 base pair reads using the Applied Biosystems SOLiD sequencer (version 3.0).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB SOLiD System 3.0
 
Description PRE2
Precompetent larvae (<3 hours after emergence from brood chambers)
Data processing 50nt reads obtained from sequencing runs were analyzed in color space using the SOLiD RNA Analysis Pipeline Tool (http://solidsoftwaretools.com/gf/project/transcriptome). Reads were aligned to sponge contigs using the ‘anchor-extend’ method as previously described (Tang, Barbacioru et al. (2010) Nature Protocols 5(3)). Assembled sponge contigs and gene models (processed data file build: Aqu1) are publicly available at http://spongezome.metazome.net/ (Srivastava, Simakov et al. (2010) Nature 466(7307)). Peak files were generated by plotting read coverage across all contigs for each run.
 
Submission date Jun 15, 2011
Last update date May 15, 2019
Contact name Cecilia Conaco
E-mail(s) conaco@lifesci.ucsb.edu
Phone (805)8934586
Organization name University of California at Santa Barbara
Department Neuroscience Research Institute
Street address BioII
City Santa Barbara
State/province California
ZIP/Postal code 93106
Country USA
 
Platform ID GPL13724
Series (1)
GSE29978 Transcriptome of the demosponge Amphimedon queenslandica at life cycle transitions
Relations
SRA SRX079849
BioSample SAMN00630449

Supplementary file Size Download File type/resource
GSM742026_PRE2_a.wig.gz 24.5 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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