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| Status |
Public on Apr 01, 2020 |
| Title |
Genome-wide Identification of genes that transcriptionally respond to altered states of Hedgehog signaling in embryos of the spider Parasteatoda tepidariorum |
| Organism |
Parasteatoda tepidariorum |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Hedgehog signaling plays pivotal roles in formation of the embryonic anterior-posterior axis in the spider Parasteatoda tepidariorum. In this work, using the combination of RNA-sequencing and parental RNA interference (pRNAi), we genome-widely identified genes that transcriptionally responded to altered states of Hedgehog signaling in spider embryos, which were caused by Pt-hedgehog (Pt-hh) pRNAi and Pt-patched (Pt-ptc) pRNAi. The identified genes were classified into four classes (Classes I to IV) based on the positive/negative responses to the Pt-hh pRNAi and Pt-ptc pRNAi states. The Class II genes were negatively regulated by Hh signaling (positive response to Pt-hh pRNAi and negative response to Pt-ptc pRNAi). Among the Class II genes, we identified Pt-msx1 as a key segmentation gene in the spider embryo. Moreover, we conducted a transcriptomic analysis of Pt-msx1 pRNAi embryos and identified additional genes whose expression showed patterns associated with segmentation.
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| Overall design |
We used RNA-sequencing to obtain transcriptomic data for comparison between untreated (normal) and Pt-hh pRNAi-treated embryos, between untreated (normal) and Pt-ptc pRNAi-treated embryos, and between untreated (normal) and gfp pRNAi-treated embryos. We obtained at least two replicates from independent parents for each comparison. Poly(A) RNA was extracted from early stage 3 and late stage 5 embryos derived from mated females before (normal) and after (pRNAi-treated) injection of dsRNA targeted for each of Pt-hh and Pt-ptc. The RNAs were sequenced using the Illumina Miseq, and differentially expressed genes (DEGs) were evaluated in each comparison using EdgeR. The comparisons between the untreated and the gfp pRNAi-treated embryos served as negative controls. Based on the analyses of the expression and function of the identified DEGs, our study was focused on the Pt-msx1 gene. An additional transcriptomic analysis of Pt-msx1 pRNAi embryos was carried out.
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| Web link |
https://www.brh2.jp/
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| Contributor(s) |
Akiyama-Oda Y, Oda H |
| Citation(s) |
32917677 |
| |
| Submission date |
Aug 26, 2019 |
| Last update date |
Jul 28, 2021 |
| Contact name |
Hiroki Oda |
| E-mail(s) |
hoda@brh.co.jp
|
| Organization name |
JT Biohistory Research Hall
|
| Lab |
Laboratory of Evolutionary Cell and Developmental Biology
|
| Street address |
1-1 Murasaki-cho
|
| City |
Takatsuki |
| State/province |
Osaka |
| ZIP/Postal code |
569-1125 |
| Country |
Japan |
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| Platforms (1) |
| GPL24841 |
Illumina MiSeq (Parasteatoda tepidariorum) |
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| Samples (75)
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| Relations |
| BioProject |
PRJNA562306 |
| SRA |
SRP219680 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE136357_DEG_hh_st3.txt.gz |
31.8 Kb |
(ftp)(http) |
TXT |
| GSE136357_DEG_hh_st5.txt.gz |
92.7 Kb |
(ftp)(http) |
TXT |
| GSE136357_DEG_msx_st5.txt.gz |
4.5 Kb |
(ftp)(http) |
TXT |
| GSE136357_DEG_msx_st6.txt.gz |
15.6 Kb |
(ftp)(http) |
TXT |
| GSE136357_DEG_ptc_st3.txt.gz |
22.3 Kb |
(ftp)(http) |
TXT |
| GSE136357_DEG_ptc_st5.txt.gz |
36.9 Kb |
(ftp)(http) |
TXT |
| GSE136357_HTseq_count_per_gene_aug3.txt.gz |
2.4 Mb |
(ftp)(http) |
TXT |
| GSE136357_HTseq_count_per_gene_aug3_RPKM.txt.gz |
3.7 Mb |
(ftp)(http) |
TXT |
| GSE136357_RAW.tar |
24.5 Gb |
(http)(custom) |
TAR (of BW, WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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