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Series GSE150732 Query DataSets for GSE150732
Status Public on Dec 07, 2020
Title Transcriptiome dynamics of cyanopodovirus S-SBP1 and its host Synechococcus sp. WH7803
Organisms Synechococcus sp. WH 7803; Synechococcus phage S-SBP1
Experiment type Expression profiling by high throughput sequencing
Summary Whole-genome expression dynamics of cyanopodovirus P-SSP7 and its host Prochlorococcus strain MED4 have been reported. To investigate whether cyanopodoviruses infecting Prochlorococcus and Synechococcus have similar transcription strategy and host response to phage infection, genomic and transcriptomic analyses were conducted on cyanopodovirus S-SBP1 that infects Synechococcus strain WH7803. S-SBP1 has a latent period of 8 h and a burst size of 30 progeny phages per cell. S-SBP1 was most similar to cyanopodovirus S-RIP2 that also infects Synechococcus WH7803, in terms of whole genome phylogenetic relationship and average nucleotide identity (ANI). Three hypervariable genomic islands were found when comparing the genomes of S-SBP1 and S-RIP2, and single nucleotide variants (SNV) were observed on three genes of S-SBP1, which are located within the island regions. Based on RNA-seq analysis, genes of S-SBP1 were clustered into three temporal express classes, with gene content within each class similar to that of P-SSP7. Thirty-two host genes were upregulated during phage infection, including those involved in carbon metabolism, ribosome component and stress response. These upregulated genes were also similar to those of Prochlorococcus MED4 in response to infection by P-SSP7. Our study demonstrates a programmed temporal expression pattern of cyanopodoviruses and hosts during infection.
 
Overall design Exponentially growing Synechococcus WH7803 culture was inoculated with phage S-SBP1 at a multiplicity of infection (MOI) of two. At the time points 15 min, 1 h, 3 h, 5 h and 7 h after phage lysate additon, cells from single treatment were collected for transcriptomic analysis. A parallel of control group without phage addition was also sampled at the time point of 30 min and 8 h. Seven RNA-seq libraries, which are five time points of phage addition treatment and two time points of control, were sequenced using the Illumina HiSeq platform.
 
Contributor(s) Huang S, Sun Y, Zhang S, Long L
Citation(s) 33377630
Submission date May 18, 2020
Last update date Mar 02, 2021
Contact name Sijun Huang
E-mail(s) huangsijun@scsio.ac.cn
Organization name Chinese Academy of Sciences
Street address 164 Xingangxi St
City Guangzhou
State/province Guangdong
ZIP/Postal code 510301
Country China
 
Platforms (2)
GPL28546 Illumina HiSeq 4000 (Synechococcus sp. WH 7803)
GPL28547 Illumina HiSeq 4000 (Synechococcus phage S-SBP1; Synechococcus sp. WH 7803)
Samples (7)
GSM4557357 Whole transcriptome at 15 min after S-SBP1 infection of WH7803
GSM4557358 Whole transcriptome at 1 h after S-SBP1 infection of WH7803
GSM4557359 Whole transcriptome at 3 h after S-SBP1 infection of WH7803
Relations
BioProject PRJNA633474
SRA SRP262107

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Supplementary file Size Download File type/resource
GSE150732_S-SBP1.rpkm.xls.gz 6.9 Kb (ftp)(http) XLS
GSE150732_WH7803.Differential_Expression.xls.gz 347.8 Kb (ftp)(http) XLS
GSE150732_WH7803.rpkm.xls.gz 191.1 Kb (ftp)(http) XLS
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Processed data are available on Series record

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