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pmid:26697359

Transcriptome analysis of Streptococcus pneumoniae D39 in the presence of cobalt.

Irfan Manzoor · Sulman Shafeeq · Oscar P Kuipers

Genomics data · 2015 doi:10.1016/j.gdata.2015.08.033

Paper

complete

Experiment

complete

Data

partial

Analysis

partial

Execution

absent

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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pmid:26697359
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title
Transcriptome analysis of Streptococcus pneumoniae D39 in the presence of cobalt.
doi
10.1016/j.gdata.2015.08.033
pmid
26697359
authors array · 3 items
[0]
Irfan Manzoor
[1]
Sulman Shafeeq
[2]
Oscar P Kuipers
journal
Genomics data
year
2015
abstract
Cobalt (Co(2 +)) is an important transition metal ion that plays a vital role in cellular physiology of bacteria. The role of Co(2 +) in the regulation of several genes/operons in Streptococcus pneumoniae has recently been reported [1]. The data described in this article relate to the genome-wide transcriptional profiling of Streptococcus pneumoniae D39, either in the presence or absence of 0.5 mM Co(2 +) in chemically defined medium (CDM) using DNA microarray analysis. Genes belonging to a broad range of cellular processes such as virulence, transport and efflux systems, stress response and surface attachment were differentially expressed in the presence of Co(2 +). We used transcriptional lacZ assays and electrophoretic mobility shift assays (EMSAs) to confirm our results [1]. The dataset is publicly available at the Gene Expression Omnibus (GEO) repository (http://www.ncbi.nlm.nih.gov/geo/) with accession number GSE57696.
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sections[8] "Microarray data analysis" paragraph 2
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Finally, Cyber-T was used to analyze the data generated using Microprep for the identification of statistically significant differentially expressed genes.
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The raw and processed DNA microarray dataset has been deposited in the Gene Expression Omnibus (GEO) database and can be accessed under following link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57696.
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The raw and processed DNA microarray dataset has been deposited in the Gene Expression Omnibus (GEO) database and can be accessed under following link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57696.
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Low Co vs high Co in CDM
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Microarray data analysis
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[0]
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[1]
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http://www.molgenrug.nl/index.php/molgensoftware
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[0]
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[1]
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[2]
http://genome2d.molgenrug.nl/
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[0]
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[1]
Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes
[2]
http://bioinformatics.biol.rug.nl/standalone/fiva/
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Summary of downregulated genes in transcriptome comparison of S. pneumoniae D39 wild-type grown in CDM plus 0 mM Co2 + and CDM plus 0.5 mM Co2 +.
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Discussion
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Summary of downregulated genes in transcriptome comparison of S. pneumoniae D39 wild-type grown in CDM plus 0 mM Co2 + and CDM plus 0.5 mM Co2 +.
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[3]
2.09E-06
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[3]
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[3]
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[3]
6.93E-05
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[3]
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[3]
2.47E-10
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[0]
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[3]
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[3]
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[3]
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Heat-inducible transcription repressor, HrcA
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[3]
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Heat shock protein, GrpE
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[3]
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Cell wall-associated serine protease, PrtA
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[3]
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Mn2 + ABC transporter, ATP binding protein, PsaB
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2.18E-14
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Manganese ABC transporter, permease protein, PsaC
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[3]
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XRE family Transcriptional regulator
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[3]
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Zn2 +-containing alcohol dehydrogenase
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[3]
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MerR family transcriptional regulator
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[3]
1.41E-10
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Cation efflux system, CzcD
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[3]
0
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Choline binding protein, PcpA
[2]
− 5.0
[3]
5.48E-06
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[1]
Rod shape-determining protein, MreD
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[3]
8.75E-11
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Co2 + ABC transporter, permease protein, CbiQ
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[3]
1.22E-09
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CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase PgsA
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[3]
1.13E-06
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[3]
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Summary of upregulated genes in transcriptome comparison of S. pneumoniae D39 wild-type grown in CDM plus 0 mM Co2 + and CDM plus 0.5 mM Co2 +.
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Summary of upregulated genes in transcriptome comparison of S. pneumoniae D39 wild-type grown in CDM plus 0 mM Co2 + and CDM plus 0.5 mM Co2 +.
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ABC transporter, ATP-binding protein
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Tryptophan synthase, alpha subunit
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Finally, Cyber-T was used to analyze the data generated using Microprep for the identification of statistically significant differentially expressed genes.
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data:geo:GSE57696
type
dataset
label
GEO GSE57696
agent
agent:corpus-assay-engine
[1] object · 4 fields
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activity-read-26697359
type
extraction
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source:pmid:26697359
agent
agent:minimax-reader
[2] object · 4 fields
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activity-resolve-GSE57696
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used array · 1 item
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data:geo:GSE57696
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agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
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agent:corpus-assay-engine
type
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[1] object · 3 fields
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agent:minimax-reader
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dsl_catalogue_fingerprint
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lineage object · 4 fields
parent_id
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fork_of
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gaps array · 7 items
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asset:data:geo:GSE57696 licence not read
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asset:data:geo:GSE57696 not downloaded
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execution.not_run
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method.reader_named_unmapped
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assays array · 1 item
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definition_version
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required_operations array · 0 items
support_state
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source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.93
evidence array · 1 item
[0]
in chemically defined medium (CDM) using DNA microarray analysis. Genes belonging to a broad range o
order_basis
paper_text_order:491
id
assay:1
Complete file
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The data described in this article relate to the genome-wide transcriptional profiling of Streptococcus pneumoniae D39, either in the presence or absence of 0.5 mM Co(2 +) in chemically defined medium (CDM) using DNA microarray analysis. Genes belonging to a broad range of cellular processes such as virulence, transport and efflux systems, stress response and surface attachment were differentially expressed in the presence of Co(2 +). We used transcriptional lacZ assays and electrophoretic mobility shift assays (EMSAs) to confirm our results [1]. 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