Microarray data on the comparison of transcript expression between normal and Pt-Delta RNAi embryos in the common house spider Parasteatoda tepidariorum

We conducted a custom microarray experiment to detect the differences in the transcript expression levels between untreated (normal) and Pt-Delta-RNAi embryos at late stage 6 in the common house spider Parasteatoda tepidariorum. The array probes were designed based on accumulated EST and cDNA sequences. The microarray dataset has been deposited in the Gene Expression Omnibus (GEO) Database at the National Center for Biotechnology Information (NCBI) under the accession GSE113064. The expression of the transcripts selected based on the detected differences was examined in embryos by whole-mount in situ hybridization.


a b s t r a c t
We conducted a custom microarray experiment to detect the differences in the transcript expression levels between untreated (normal) and Pt-Delta-RNAi embryos at late stage 6 in the common house spider Parasteatoda tepidariorum. The array probes were designed based on accumulated EST and cDNA sequences. The microarray dataset has been deposited in the Gene Expression Omnibus (GEO) Database at the National Center for Biotechnology Information (NCBI) under the accession GSE113064. The expression of the transcripts selected based on the detected differences was examined in embryos by whole-mount in situ hybridization.

Data
Transcript expression was compared between untreated (normal) and Pt-Delta RNAi-treated (Pt-Delta RNAi) embryos at late stage 6 using a Combimatrix custom microarray in 12K format (Fig. 1), which was designed based on the accumulated Parasteatoda tepidariorum EST and cDNA sequences. The microarray dataset deposited in the GEO Database at NCBI (GSE113064) consists of a data table showing the details of probe sequences for array spots (Platform: GPL24882) and that showing the Specifications Table   Subject area  Biology  More specific subject area  Developmental Biology  Type of data  Tab-delimited text, table,

Value of the data
The dataset is useful for identifying the candidate genes whose expression is regulated by Delta-Notch signaling in P. tepidariorum embryos. The dataset is useful for identifying the genes whose expression marks specific cell types or regions of P. tepidariorum embryos.
The dataset is useful for investigating the gene regulatory networks in the embryonic development of spider.   Table 2. Whole-mount in situ hybridizations (WISHs) of stage 5e8 embryos showing expression of the transcripts related to these EST clones are displayed in Fig. 2. The original images, including highmagnification images showing the transcript expression patterns and nuclear stains, are available in a data repository [1].

Experimental design, materials and methods
The primary objective of this experiment was to identify the genes whose expression might be affected by parental RNA interference (pRNAi) against Pt-Delta in P. tepidariorum embryos [2]. Flow of the microarray experiment is schematically shown in Fig. 1.

Custom microarray design
40-mer oligonucleotide probes were designed based on the accumulated P. tepidariorum EST and cDNA sequences [2,3] using OligoArray 2.1 [4] and embedded in a custom microarray (CombiMatrix CustomArray 12K, CustomArray, Inc.). There were single or multiple probes designed from each EST or cDNA sequence. Four or three spot replicates of control probes (Table 1) were included to validate the experiment. The details of the microarray design, including the probe sequences, are available from the GEO database (GPL24882).

Microarray analysis
A mated female was injected with approximately 1.5 ml of Pt-Delta dsRNA solution (2 mg/ml) 4 times at 2e3 days intervals. Embryos derived from an egg sac produced by the female one day before (normal) and 25 days after (Pt-Delta RNAi) the first injection of Pt-Delta dsRNA were used for RNA extraction. The total RNA was extracted from approximately 250 embryos at late stage 6 using MagExtractor (Toyobo). The RNA integrity was examined with an Agilent Bioanalyzer 2100. cRNA labeled with Cy3 or Cy5 was prepared from 2 mg of total RNA using RNA Transcript SureLABEL Core Kit (Takara). The cRNA probes were hybridized to microarray using Hybridization buffer (5X SSC, 0.1% SDS, 10% formamide) at 42 C for 16e20 h. The microarray slide was scanned using a GenePix 4000B Scanner (Molecular Devices). There were no biological replicates. The obtained image was analyzed using an Array-Pro Analyzer ver. 4.5 (Media Cybernetics, Inc.). The quantitative data were subjected to Loess normalization. The ratio of the normalized intensity values ([Pt-Delta RNAi]/[normal]) for each probe was calculated. The probes for alpha-catenin (GB_ACC: AB433907; GI: LOC107439705), elongation factor 1-alpha (GB_ACC: AB433908; GI: LOC107441347), and histone H3 (GB_ACC: AB433909; GI, LOC107447866) served as negative controls, and the probes for a homolog of Drosophila caudal, Ptcad (GB_ACC: AB096075; GI: LOC107437910) [2], served as positive controls to validate the experiment (Table 1).

Embryo staining
EST clones that were selected based on the [Pt-Delta RNAi]/[normal] ratio (<0.6) were used for the synthesis of Digoxigenin-labeled RNA probes for WISH. Normal embryos at stages 5e8 were stained by WISH as described [5]. They were counter-stained with 4',6-diamidino-2-phenylindole for visualization of the nuclei. The stained embryos were photographed using a stereomicroscope (SZX12, Olympus) equipped with a color CCD camera (C7780-10, Hamamatsu Photonics) and examined using a fluorescence microscope (Axiophot 2, Zeiss).