Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-seq assay for RocS binding to the Streptococcus pneumoniae genome

ABSTRACT: We performed ChIP-seq, comparing immunoprecipitation of FLAG-labelled RocS with whole-cell extract. We did not detect any significant peaks in any of the samples. This might be due to data quality, but, additionally, other data showed that RocS binds DNA aspecifically and therefore no specific peaks are expected.

ORGANISM(S): Streptococcus pneumoniae

PROVIDER: GSE129717 | GEO | 2019/04/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Chromosome segregation in Streptococcus pneumoniae

Project description:Segregation of replicated chromosomes during cell division is an essential process in all organisms. Chromosome segregation is promoted by the action of the DNA-binding ParB protein in the rod-shaped model bacterium Bacillus subtilis. How oval shaped bacteria, such as the human pathogen Streptococcus pneumoniae, efficiently segregate their chromosomes is poorly understood. Here, we show that the pneumococcal homolog of ParB is enriched at four centromere-like DNA sequences (parS sites) that are present near the origin of replication. Amplified ChIP DNA was fluorescently labelled using the BioPrime Total Genomic Labeling kit from Invitrogen. Eluate DNA was labelled with AlexA Fluor 3 and input DNA with Alexa Fluor 5. Labelled DNA was hybridized to a DNA-microarray containing amplicons of all open reading frames of S. pneumoniae (Kloosterman et al., 2006).

2011-06-11 | E-GEOD-26839 | biostudies-arrayexpress

Development of an automated and multiplexed serotyping assay for Streptococcus pneumoniae.

Project description: Not available

| S-EPMC3209018 | biostudies-literature

Streptococcus pneumoniae R6 genomic DNA

Project description:The most basic level of transcription regulation in Streptococcus pneumoniae is the organization of its chromosome in topological domains. In response to drugs that caused DNA-relaxation, a global transcriptional response was observed. Separate domains were identified depending of the transcription of their genes: up-regulated (U), down-regulated (D), non-regulated (N), and flanking (F). We show here that these distinct domains have different expression and conservation tendencies. Microarray fluorescence units under non-relaxation conditions, taken as a measure of gene transcription level, were significantly lower in F genes than in the other domains in the same range of AT content. Transcription level categorization of the domains was D>U>F. In addition, a comparison of 12 S. pneumoniae genome sequences evidenced conservation of gene composition in the U and D domains and extensive gene interchange in F domains. We tested domain organization by measuring the relaxation-mediated transcription of eight insertions of a heterologous Ptccat cassette, two in each type of domain, showing that transcription depended on their chromosomal location. Moreover, transcription from the four promoters directing the five genes involved in supercoiling homeostasis, located either in U (gyrB), D (topA), or N (gyrA and parEC) domains was analyzed both in their chromosomal locations and in a replicating plasmid. Although expression from the chromosomal PgyrB and PtopA showed the expected domain regulation, their expression was down-regulated in the plasmid, which behaved as a D domain. However, both PparE and PgyrA carried their own regulatory signals, their topology-dependent expression being equivalent in the plasmid or in the chromosome. In PgyrA a DNA bend acted as a DNA supercoiling sensor. These results revealed that DNA topology works as a general transcriptional regulator, superimposed to other kind of more specific regulatory mechanisms.

2014-12-29 | GSE58186 | GEO

Use of genomics to design a diagnostic assay to discriminate between Streptococcus pneumoniae and Streptococcus pseudopneumoniae.

Project description: Not available

| S-EPMC6113875 | biostudies-literature

Development of PCRSeqTyping-a novel molecular assay for typing of Streptococcus pneumoniae.

Project description: Not available

| S-EPMC5471960 | biostudies-literature

Identification of Streptococcus pneumoniae by a real-time PCR assay targeting SP2020.

Project description: Not available

| S-EPMC6397248 | biostudies-literature

ChIP-seq analysis of the C. elegans CEBP-1 protein

Project description:Purpose: The goal of this study is to identify genes selectively associated with C. elegans CEBP-1. Methods: We generated transgenic animals expressing FLAG-tagged CEBP-1 in a cebp-1(tm2807) mutant background (cebp-1(0); juIs418 [Pcebp-1::FLAG::CEBP-1::cebp-1 3’UTR]) and then immunoprecipitated FLAG-CEBP-1-associated DNA fragments using anti-FLAG antibodies (M2 anti-FLAG magnetic beads; Sigma). We collected mixed stage worms grown at 20˚C on NGM plates followed by 2% formaldehyde and sonicated the samples as described (Mukhopadhyay et al., 2008). We next generated ChIP-seq DNA libraries. Briefly, both ChIPed DNA and input genomic DNA were ligated to specific adaptors and amplified by barcode primers followed by sequencing on the Illumina HiSeq-2000 platform. We performed two independent ChIP-seq experiments, with parallel genomic DNA controls prepared from the same strain. We conducted peak-calling using CLC genomics workbench 6.0 (CLCbio). To define genes associated with the peaks, we used the annotation of transcription start site (TSS) and transcription end site (TES) from WS220 and annotated the peak if it overlapped the gene or the 3 kb upstream of the TSS. We then manually confirmed the peaks and associated genes using UCSC browser and update to WS252. Results: We found 209 CEBP-1 ChIP-seq peaks in the genome that were associated with 212 coding genes. Through motif discovery tools, we also found that CEBP-1 binds conserved DNA motifs. Conclusions: The conservation of C.elegans CEBP-1 binding motif supports functional parallels between C. elegans CEBP-1 and vertebrate C/EBPs.

2016-09-13 | GSE83330 | GEO

Chip-chip from C-33 cells expressing FLAG-HPV1 E2 with FLAG-HPV1 E2

Project description:HPV1 E2 binds with Brd4 to host mitotic chromosomes. To identify the targets, chromatin was prepared from mitotic C-33 cells expressing HPV1 E2, and analyzed by ChIP-chip analysis for binding to a portion of the human genome. E2 and Brd4 bind to active promoters in interphase C-33 cells (Jang et al., 2009), however, in mitosis E2 was observed instead to bind to a few extremely broad peaks on several chromosomes. These peaks ranged in size from several hundred Kb to >1 Mb and, for the most part, overlapped coding regions. Signals of anti-FLAG E2 ChIP DNA from mitotic HPV1 E2 expressing C-33 cells

2014-04-14 | E-GEOD-52312 | biostudies-arrayexpress

recA-based PCR assay for accurate differentiation of Streptococcus pneumoniae from other viridans streptococci.

Project description: Not available

| S-EPMC3043496 | biostudies-literature

Evaluation of semiautomated multiplex PCR assay for determination of Streptococcus pneumoniae serotypes and serogroups.

Project description: Not available

| S-EPMC149661 | biostudies-literature