Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Bdellovibrio bacteriovorus infection of E. coli

ABSTRACT: The transcriptional response of E. coli being predated by Bdellovibrio bacteriovorus Keywords: Transcriptional analysis 5 biological replicates with 2 technical replicates each of E. coli cells only and E. coli cells 15 minutes post-infection arrays 4 arrays, with samples swapped for each biological replicate. Gel image files generated by the ImageQuant scanning software. Each raw data txt file has the "control" samples which are the E. coli samples reading on the entire array and thus with the 2 technical replicates, and the "data" samples to which it is compared by Arrayvision. the "data" samples of ec1 to ec5 are Bdellovibrio only controls 2 technical replicates). The "data" samples of t1 to t5 are the test samples. Hence t1 to t5 are the raw data files for samples test1 to test10 and ec1 to ec5 are the raw data files for all of samples ec-1 to ec-10 and bd-1 to bd-10.

ORGANISM(S): Escherichia coli

SUBMITTER: Carey Lambert

PROVIDER: E-GEOD-9495 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A transcriptional "Scream" early response of E. coli prey to predatory invasion by Bdellovibrio.

Lambert Carey C Ivanov Pavel P Sockett Renee Elizabeth RE

Current microbiology 20091220 6

We have transcriptionally profiled the genes differentially expressed in E. coli prey cells when predatorily attacked by Bdellovibrio bacteriovorus just prior to prey cell killing. This is a brief, approximately 20-25 min period when the prey cell is still alive but contains a Bdellovibrio cell in its periplasm or attached to and penetrating its outer membrane. Total RNA was harvested and labelled 15 min after initiating a semi-synchronous infection with an excess of Bdellovibrio preying upon E. ...[more]

PMID: 20024656

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Project description:The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here, we describe a novel strategy termed Parallel Analysis of RNA Structure (PARS), which is based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in-vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. We apply PARS to profile the secondary structure of the mRNAs of the budding yeast S. cerevisiae and obtain structural profiles for over 3000 distinct transcripts. Analysis of these profiles reveals several RNA structural properties of yeast transcripts, including the existence of more secondary structure over coding regions compared to untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions, and a relationship between the efficiency with which an mRNA is translated and the lack of structure over its translation start site. PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale. RNA sample was treated with one of two structure-specific enzymes (RNase V1 or RNase S1). Four independent V1 experiments and three independent S1 experiments were carried out. Processed data file linked below. Data processing involves merging (or rather log-ratio-ing) the 7 lanes of SOLiD sequencing data against each other. Also linked below are the genome and transcriptome FASTA files used for mapping, and the annotation file having the format: gene_ID, chromosome, start, end, feature. Start and end are 1-based; feature is "Transcript" for the entire transcript (including introns), "Intron", "Exon", "5UTR" or "3UTR". Genome-wide measurement of RNA secondary structure in yeast, Kertesz et al., Nature Volume:467, Pages:103-107, Date published:(02 September 2010) http://www.nature.com/nature/journal/v467/n7311/abs/nature09322.html

Dataset Information

Bdellovibrio bacteriovorus infection of E. coli

Publications

A transcriptional "Scream" early response of E. coli prey to predatory invasion by Bdellovibrio.

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