NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM603235 Query DataSets for GSM603235
Status Public on Jan 04, 2011
Title Locusta_nerve
Sample type SRA
 
Source name Central nervous system cell
Organism Locusta migratoria manilensis
Characteristics tissue: Brain, thoracic ganglion chain and the ventral nerve cord
cell type: Central nervous system cell
Extracted molecule total RNA
Extraction protocol Beads with Oligo(dT) are used to isolate poly(A) mRNA after total RNA is collected from the tissue. Fragmentation buffer is added for interrupting mRNA to short fragments. Taking these short fragments as templates, random hexamer-primer is used to synthesize the first strand cDNA. The second-strand cDNA is synthesized using buffer, dNTPs, RNaseH and DNA polymerase I, respectively. Short fragments are purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments are connected with sequencing adapters. And, after the agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. At last, the library could be sequenced using Illumina HiSeqâ„¢ 2000.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Transcriptome de novo assembly is carried out with short reads assembling program SOAPdenovo (Li, Zhu et al . 2009). SOAPdenovo firstly combines reads with certain length of overlap to form longer fragments without N, which are called contigs. Then the reads are mapped back to contigs; with paired-end reads it is able to detect contigs from the same transcript as well as the distances between these contigs. Next, SOAPdenovo connects the contigs using N to represent unknown sequences between each two contigs, and then Scaffolds are made. Paired-end reads are used again for gap filling of scaffolds to get sequences with least Ns and cannot be extended on either end. Such sequences are defined as Unigenes.
 
Submission date Oct 04, 2010
Last update date May 15, 2019
Contact name Zhengyi Zhang
E-mail(s) zhy_zhang@yahoo.cn
Organization name Chongqing University
Street address Shapinba
City Chongqing
ZIP/Postal code 400044
Country China
 
Platform ID GPL11245
Series (1)
GSE24498 Deep sequencing of the locust Locusta migratoria manilensis central nervous system transcriptome
Relations
SRA SRX054622
BioSample SAMN00254206

Supplementary file Size Download File type/resource
GSM603235_Locusta_nerve-Unigene.fa.gz 7.0 Mb (ftp)(http) FA
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap