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Series GSE193511 Query DataSets for GSE193511
Status Public on Jun 10, 2022
Title Genome-wide identification of candidate genes whose transcripts are locally expressed in early embryos of the spider Parasteatoda tepidariorum
Organism Parasteatoda tepidariorum
Experiment type Expression profiling by high throughput sequencing
Summary The early embryo of the spider Parasteatoda tepidariorum initially shows spherical symmetry in morphology. Following a symmetry breaking event, it forms a radially symmetric germ disc in the hemisphere of the egg. In this work, we conducted RNA-sequencing of cells isolated from small different regions of radially symmetric forming/formed germ discs, aming to identify candidate genes whose transcripts are locally expressed in early spider embryos.
 
Overall design We isolated cells from small regions (central [c], peripheral [p], and intermediate [i]) of radially symmetric forming/formed germ discs at stage 3 (approximately 20 h after egg laying [AEL]), stage 4 (approximately 28-29 h AEL) and early stage 5 (approximately 31-32 h AEL) using glass capillary. We then conducted RNA-sequencing of the isolated cells to obtain transcriptomic data for comparison between different regions of the germ discs. Two or three biological replicates were obtained for each region for each stage. The RNAs were sequenced using the Illumina Miseq platform, and differentially expressed genes (DEGs) were evaluated in each comparison using EdgeR. The comparisons based on the early stage 5 samples allowed us to detect expected differences in gene expression between the central and peripheral regions of the germ disc (e.g., Pt-hh [aug3.g4322], Pt-lab [aug3.g7954], and Pt-opa [aug3.g12202]), which provided technical validation.
Web link https://www.brh2.jp/
 
Contributor(s) Iwasaki-Yokozawa S, Akiyama-Oda Y, Oda H
Citation(s) 36203191
Submission date Jan 12, 2022
Last update date Oct 24, 2022
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
 
Platforms (1)
GPL24841 Illumina MiSeq (Parasteatoda tepidariorum)
Samples (16)
GSM5811734 st3_i1
GSM5811735 st3_i2
GSM5811736 st3_i3
Relations
BioProject PRJNA796503

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE193511_HTseq_count_per_gene_aug3.txt.gz 1010.0 Kb (ftp)(http) TXT
GSE193511_HTseq_count_per_gene_aug3_RPKM.txt.gz 1.5 Mb (ftp)(http) TXT
GSE193511_RAW.tar 302.2 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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