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| Status |
Public on Jan 04, 2011 |
| Title |
Locusta_nerve |
| Sample type |
SRA |
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| Source name |
Central nervous system cell
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| Organism |
Locusta migratoria manilensis |
| Characteristics |
tissue: Brain, thoracic ganglion chain and the ventral nerve cord
cell type: Central nervous system cell
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| 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 HiSeq™ 2000.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| 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.
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| Submission date |
Oct 04, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhengyi Zhang |
| E-mail(s) |
zhy_zhang@yahoo.cn
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| Organization name |
Chongqing University
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| Street address |
Shapinba
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| City |
Chongqing |
| ZIP/Postal code |
400044 |
| Country |
China |
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| Platform ID |
GPL11245 |
| Series (1) |
| GSE24498 |
Deep sequencing of the locust Locusta migratoria manilensis central nervous system transcriptome |
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| 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 Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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