Functional Annotation of Cotesia congregata Bracovirus: Identificatio... - SRA

SRX424346: Functional Annotation of Cotesia congregata Bracovirus: Identification of Viral Genes Expressed in Parasitized Host Immune Tissues
8 LS454 (454 GS FLX Titanium) runs: 735,037 spots, 418.6M bases, 278.2Mb downloads

Design: The cDNA libraries were prepared by using SMARTer™ PCR cDNA Synthesis Kit (Clontech). First-strand cDNA synthesis was performed with 3’ SMART CDS Primer II A as described in the supplier protocol and using 995 and 70 ng of total RNA from fat body and hemocytes respectively. Double-strand cDNAs were prepared by long-distance PCR (LD-PCR) from 1 and 10 µl of first-strand cDNA from fat body and hemocytes respectively. A pool of three independent LD-PCRs was used for deep sequencing of each cDNA library. Reads generated by 454 sequencing were trimmed for poly(A), 454 adaptors (A and B) and PCR primers. The origin of reads was established by mapping on two reference genomes, M. sexta (Manduca Base: www.agripestbase.org) and CcBV (chromosomal form) (Bézier et al. 2013). Mapping was performed using GS Reference Mapper from Newbler software package (version 2.5.6, Roche) with the following parameters: -cdna -ss 1 –sl 16 –ml 80% -mi 95 –d 10. To distinguish and annotate genes belonging to gene families and sharing high sequence similarity, CcBV reads were aligned to CcBV genome using Exonerate with the following parameters: -m cdna2genome –geneseed 100 –codonwordlimit 1 –refin region. For each cluster of reads aligned with a given genomic region, a consensus sequence was generated by de novo assembling reads using GS De Novo Assembler from Newbler software package with the following parameters: -cdna -it 1 –ig 1 –icc 1 –ss 1 –sl 16 –ml 90% -mi 80.

Submitted by: UMR 7261

Study: Cotesia congregata bracovirus strain:CcBV Transcriptome or Gene expression

PRJNA232126 • SRP035265 • All experiments • All runs

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CcBV cDNA sequenced by 454 technology from 2 tissues (hemocytes and fat body) from Manduca sexta parasitized by Cotesia congregata

Sample: General Sample for Cotesia congregata bracovirus

SAMN02469122 • SRS528019 • All experiments • All runs

Organism: Bracoviriform congregatae

Library:

Name: CcBV reads from parasitized Manduca sexta hemocytes and fat body

Instrument: 454 GS FLX Titanium

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: PolyA

Layout: SINGLE

Spot descriptor:

5 forward

Runs: 8 runs, 735,037 spots, 418.6M bases, 278.2Mb

Run	# of Spots	# of Bases	Size	Published
SRR1105561	60,667	33M	22Mb	2014-01-20
SRR1282021	225	121,155	118,514b	2014-05-09
SRR1587997	18,739	10.3M	6.9Mb	2014-09-29
SRR1587999	49,656	26.3M	17.1Mb	2014-09-29
SRR1588003	44,508	23.7M	15.6Mb	2014-09-29
SRR1588008	75,838	39.6M	25.4Mb	2014-09-29
SRR1588012	93,792	50.7M	33.3Mb	2014-09-29
SRR1588015	391,612	234.9M	157.6Mb	2014-09-29

ID:: 599934

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