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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions

ABSTRACT: The Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV) can be propagated using H. zea insect cell cultures, for use as a biopesticide against Heliothine agricultural pests.This study sequenced, assembled and functionally annotated 29,586 transcript sequences from cultured H. zea cells using Illumina 100 bps and paired-end transcriptome sequencing (RNA-seq). From these sequences, a genome-scale microarray platform was constructed and validated for effective expression analysis of H. zea genes. This array also included probes for all HaSNPV genes, thereby allowing virus and host gene changes to be monitored simultaneously. A 4x180,000 SurePrint Agilent expression array (Agilent, Santa Clara, CA) was employed so that a high number of probes can be included to test all 29,586 assembled H. zea sequences and to eventually select a best probe for each transcript. Two biological replicates for uninfected H. zea cells and two other biological replicates for infected samples at 18 hours post infection were analyzed. Six Agilent 60-mer oligonucleotide probes were designed by eArray (Agilent) for each transcript, in which each orientation had three probes randomly distributed across the sequences. Probes that had potential cross-hybridization (Xhyb) were removed. The final probe set for H. zea sequences included 153,583 probes. In addition, probes for all 135 H.armigera single-capsid nucleopolyhedrovirus (HaSNPV) genes were added to investigate host-virus interaction in culture.

ORGANISM(S): Helicoverpa zea

SUBMITTER: Quan Nguyen

PROVIDER: E-GEOD-34418 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions

Project description:The Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV) can be propagated using H. zea insect cell cultures, for use as a biopesticide against Heliothine agricultural pests.This study sequenced, assembled and functionally annotated 29,586 transcript sequences from cultured H. zea cells using Illumina 100 bps and paired-end transcriptome sequencing (RNA-seq). From these sequences, a genome-scale microarray platform was constructed and validated for effective expression analysis of H. zea genes. This array also included probes for all HaSNPV genes, thereby allowing virus and host gene changes to be monitored simultaneously.

2012-03-01 | GSE34418 | GEO

Genome scale analysis of host-virus mRNA differential expression in Helicoverpa zea insect cells infected by H. armigera baculovirus from early till late infection

Project description:A custom microarray, based on deep transcriptome sequencing ((GEO accession number: GSE34418), was used to simultaneously investigate expression of over 24,000 Helicoverpa zea insect transcripts and 134 H. armigera nucleopolyhedrovirus (HearNPV) genes throughout the infection process at 0, 12, 24 and 48 hours post infection A cutom 8x60,000 SurePrint Agilent expression slide (Agilent, Santa Clara, CA) was used to analyzed eight samples, including biological replicates of HaSNPV-infected cultures at 0, 12, 24 and 48 hpi.The microarray probes included probes for 27,400 H. zea sequences that were validated previously (Nguyen et al., 2012. PLOS ONE, 7(5), e36324) and all 134 H. armigera single-capsid nucleopolyhedrovirus (HearNPV) genes (Accession: NC_002654).

2013-03-01 | E-GEOD-44184 | biostudies-arrayexpress

Comparison of gene expression in three strains of Spodoptera Frugiperda (Insecta: Lepidoptera: Noctuidae)

Project description:The aim of this experiment was to compare the transciptome of the fall armyworm (Spodoptera frugiperda) strain SUS (a laboratory insecticide-susceptible standard) with organophosphate (OP) and pyrethroid (PYR) resistant strains were collected in cornfields located in Minas Gerais and Mato Grosso States, Brazil, in 2008 and maintained in the laboratory under selection with chlorpyrifos (at increasing discriminating doses from 100 up to 400 µg of insecticide/g of insect in a topical bioassay) or lambda-cyhalothrin (from 8.4 up to 27 µg of insecticide/g of insect) respectively The custom microarray used in this study was designed using the Agilent eArray platform (Agilent Technologies). A SurePrint HD (8×15k) expression array was designed using the base composition and the best probe methodologies to design sense orientation 60-mer probes with a 3′ bias. The FAW EST database (SPODOBASE) was used as the reference transcriptome (Negre, Hotelier et al. 2006). These sequences are derived from 8 cDNA libraries as follows: Sf1F: Fat body, Sf1H: Hemocyte, Sf1M: Midgut, Sf1P: Pool of various tissues, Sf2H: Immune Challenged hemocytes, Sf2L: Sf21 Cell lines sequences, Sf2M: Xenobiotic Induced Midgut and Sf9L: Sf9 cell lines sequences. All assembled contigs and singlets were kindly sent by the website maintainers. The BLAST2GO software v.2.3.1 (http://www.blast2go.org) was used to annotate the EST database. 60-mer probes were designed for all 7,552 assembled contigs and 5,519 annotated singlets (BlastX), totaling 13,071 sequences. For contigs encoding detoxification enzymes (P450s, GSTs and CEs) three probes were designed. Additional probe groups for 15 control genes were also included. For reference all sequences are included in the zip file with array data. References: Negre, V., T. Hotelier, et al. (2006). "SPODOBASE : an EST database for the lepidopteran crop pest Spodoptera." BMC Bioinformatics 7: 322.

2013-08-01 | GSE43295 | GEO

Sparus aurata transcriptomic data comparing long-term starvation and feeding with three diets differing in the macronutrient composition

Project description:Agilent custom-made 8x60k 60-mer oligonucleotide microarray slides were used, covering unique sequences (21,093 annotated sequences and 4,299 unannotated sequences) of Sparus aurata transcriptomic data obtained from assembling of reads deposited in the NCBI SRA database corresponding to BioProject ID PRJNA391557, together with controls (8 transcripts of Sparus aurata plus Agilent controls). Two probes per sequence were used (in sense orientation for annotated sequences).

2017-10-31 | GSE100744 | GEO

Using pooled earthworm RNA to test 244K probes on TA-2 test array design 2520023 antisense 1

Project description:To validate the 244K 60-mer probes using a custom-designed Agilent oligo array and assuming antisense orientation of all target sequences.

2009-06-12 | GSE16548 | GEO

Using pooled earthworm RNA to test 244K probes on TA-1 test array design 2520022 sense 1

Project description:To validate the 244K 60-mer probes using a custom-designed Agilent oligo array and assuming sense orientation of all target sequences.

2009-06-12 | GSE16536 | GEO

Identification of responsive probes for mRNA transcripts of the pig (S. scrofa) genome

Project description:Pig mRNAs Ensembl transcripts (Ver. 56) and UniGene (Ver. 38) sequences were used to produce a dedicated microarray platform to analyze mRNAs gene expression. Based on sequence similarity we rejected UniGene features that overlapped more than 40% with an Ensembl transcript. After this filter we obtained 40,267 UniGene clusters and 19,603 Ensembl transcripts (protein coding + pseudogenes + retrotransposed elements). Starting from these sequences, the microarray probes were computed using 6 different algorithms (YODA, Picky, ArrayOligoSelector, OligoPicker, OligoFaktory, CommOligo). Two probes in the most 3M-bM-^@M-^Y end was tested for their specificity and performance. For any transcript with a replicated tested probe, we used the most responsive and specific in an hybridization trial with a pool of mRNAs from 20 tissues to construct the definitive gene expression microarray for the pig. Definitive 90K Combimatrix gene expression microarrays were composed by 17,048 replicated probes and 963 not replicated specific for the Ensembl transcripts, 11,363 replicated probes specific for the UniGene clusters of length comprised between 778 nt and 1,348 nt, and 28,790 single probes specific for the remaining UniGene clusters (GEO: GPL13259). Microarray was probed with a pool of RNAs from 20 different tissues (superior vena cava, adipose tissue, lung, spleen, stomach, liver, intestine, kidney, descending aorta, left atrium, left ventricle, skeletal muscle, pulmonary aorta, skin, tongue, ascending aorta, arterial white cells blood, venal white cells blood, coronary valve, lymph node). Moreover each tissue sample was performed by a pool of 3 different adult pigs because they was not inbred.

2014-03-31 | E-GEOD-28636 | biostudies-arrayexpress

Using pooled earthworm RNA to test 244K probes on TA-4 test array design 2520025 antisense 2

Project description:To validate the 244K 60-mer or 40-mer probes using a custom-designed Agilent oligo array and assuming antisense orientation of all target sequences.

2009-06-12 | GSE16550 | GEO

Using pooled earthworm RNA to test 244K probes on TA-3 test array design 2520024 sense 2

Project description:To validate the 244K 60-mer or 40-mer probes using a custom-designed Agilent oligo array and assuming sense orientation of all target sequences.

2009-06-12 | GSE16549 | GEO

Expression analysis of leafy spurge crown buds during seasonal dormancy transitions.

Project description:This submission contains the RNAseq data from a study of leafy spurge crown buds transitioning through a seasonal dormancy time course where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy. The sequences in this study were mapped to an assembled transcriptome built from sequences from this study along with sequences from : 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (Series GSE71317). 2) A study identical to this study but where leafy spurge plants were first treated with glyphosate (Series GSE71406). 3) A previously submitted study of leafy spurge shoots following treatment with glyphosate was also used to assemble the transcriptome (Series GSE56509). This crown buds transitioning through a seasonal dormancy time course study has 4 biological replicates collected at each of the three dormancy states (paradormant, endodormant, and ecodormant).

2015-08-05 | E-GEOD-71321 | biostudies-arrayexpress

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