Uninfected Trichoplusia ni midgut at 72 hour post mock-inoculation, ... - SRA

SRX4515360: Uninfected Trichoplusia ni midgut at 72 hour post mock-inoculation, replicate 3
1 ILLUMINA (Illumina HiSeq 4000) run: 28.3M spots, 1.4G bases, 490.1Mb downloads

Design: Total RNA was extracted from 5th instar larvae midguts that were dissected at 72 h post mock-inoculation (oral) with 5ul of a 10% sucrose solution containing no virus. Following total RNA extraction using TRIzol reagent (Ambion), strand-specific RNA-Seq libraries were constructed. Briefly, poly(A) mRNA isolated from 3 g of total RNA using oligo(dT)25 Dynabeads (Invitrogen) were fragmented at 94C for 5 min in buffer containing ProtoScript II reaction buffer (NEB), hexamer (Qiagen), and oligo (dT)23 VN (NEB). Subsequently, first-strand cDNA was synthesized using ProtoScript II and second strand synthesis was carried out with a reaction mix consisting of RNase H (NEB), the Klenow fragment of DNA polymerase I (NEB), and dNTP mix with dUTP (dATP, dCTP, dGTP, and dUTP) (Promega Corporation). Further, TruSeq universal adapters were ligated to end-repaired and dA-tailed cDNA fragments. Subsequently, dUTP containing strands were removed and PCR amplification was performed with library-specific TruSeq PCR primers. Following purification and quantification of the libraries, libraries were sequenced on the Illumina HiSeq4000 platform at the CLC Genomics and Epigenomics Core Facility at the Weill Cornell Medical College.

Submitted by: Cornell University

Study: Global analysis of baculovirus Autographa californica Multiple Nucleopolyhedrovirus (AcMNPV) gene expression in the midgut of the Trichoplusia ni larvae

PRJNA484772 • SRP156551 • All experiments • All runs

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The baculovirus AcMNPV is a large dsDNA virus that encodes approximately 156 genes and is highly pathogenic to a variety of larval lepidopteran insects in nature. Oral infection of larval midgut cells is initiated by the occlusion derived virus (ODV), while secondary infection of other tissues is mediated by the budded virus (BV). Global viral gene expression has been studied in detail in BV-infected cell cultures, but studies of ODV-infection in the larval midgut are limited. In this study, we examined expression of the ~156 AcMNPV genes in Trichoplusia ni midgut tissue using a transcriptomic approach. We analyzed expression profiles of viral genes in the midgut, and compared them with profiles from a T. ni cell line (Tnms42). Several viral genes (p6.9, orf76, orf75, pp31, Ac-bro, odv-e25, and odv-ec27) had high expression levels in the midgut throughout the infection. Also, the expression of genes associated with occlusion bodies (polh and p10) appeared to be delayed in the midgut in comparison with the cell line. Comparisons of overall viral gene expression profiles revealed remarkable similarities between the midgut and cell line for most genes, although substantial differences were also observed for some viral genes. These included genes associated with high level BV production (fp-25k), acceleration of systemic infection (v-fgf), and enhancement of viral movement (arif-1/orf20). These differential expression patterns appear to represent specific adaptations for virus infection and movement through the polarized cells of the lepidopteran midgut.

Sample: Trichoplusia ni midgut uninfected at 72 hour post mock-infection

SAMN09769650 • SRS3633927 • All experiments • All runs

Organism: Trichoplusia ni

Library:

Name: H_72h_MG_8_rep3

Instrument: Illumina HiSeq 4000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: PolyA

Layout: SINGLE

Runs: 1 run, 28.3M spots, 1.4G bases, 490.1Mb

Run	# of Spots	# of Bases	Size	Published
SRR7652935	28,282,848	1.4G	490.1Mb	2018-08-18

ID:: 6113791

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