Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

32 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequence Requirements for Cascade Function in a Type I-E CRISPR System: ChIP Library-seq

ABSTRACT: We generated a collection of 13 plasmids, with each plasmid containing a variant of a CRISPR protospacer targeted by spacer 8 of the E. coli CRISPR-I array. We transformed the plasmids as a pool into delta cas3 E. coli cells expressing all other cas genes constitutively, with FLAG-tagged casA. We then used ChIP to enrich for CasA-bound protospacers. DNA surrounding the protospacers was PCR-amplified from input (pre-immunocrecipitation) and ChIP (post-immunoprecipitation) samples and sequenced.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Anne Stringer

PROVIDER: E-MTAB-5972 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-Seq of wild type E. coli MG1655 versus those with a deletion in the hns gene (Histone-like protein H-NS)

Project description:The aim of the experiment was to determine differences in RNA levels between wild-type E. coli and E. coli with an hns deletion. We used RNA-seq, but to control for variation in sample preparation and sequencing, we combined each E. coli RNA sample with a spike-in Salmonella RNA sample of known concentration. Libraries constructed in duplicate from strains grown with and without Salmonella spike-in to assess absolute genome-wide changes in transcription.This allowed us to normalise RNA levels between samples during data analysis.

2016-06-14 | E-MTAB-4751 | biostudies-arrayexpress

The evolutionary impact of Intragenic FliA Promoters

Project description:We compared RNA levels in wild-type Salmonella enterica serovar Typhimurium with RNA levels in a mutant strain in which the fliA gene was deleted.

2017-09-18 | E-MTAB-6048 | biostudies-arrayexpress

RNA-seq of MG1655 wt and MG1655 delta-phoB strains grown in MOPS media with low phosphate (0.2 mM)

Project description:We used RNA-seq to determine differences in RNA levels between wild-type E. coli K-12 and a ΔphoB mutant, each grown in MOPS media with low phosphate (0.2 mM).

2020-07-12 | E-MTAB-9292 | biostudies-arrayexpress

RNA-seq of MG1655 wt and MG1655 delta-phoB strains grown in MOPS media with low phosphate (0.2 mM)

Project description:We used RNA-seq to determine differences in RNA levels between wild-type E. coli K-12 and a ΔphoB mutant, each grown in MOPS media with low phosphate (0.2 mM).

2020-10-03 | E-MTAB-9591 | biostudies-arrayexpress

SuhB associates with Nus factors to facilitate 30S ribosome biogenesis in Escherichia coli

Project description:This experiment consists of two studies. The first where two independent biological replicates of MG1655, MG1655 thyA suhB::thyA and MG1655 thyA nusB::thyA were each grown in LB to mid-exponential phase. RNA-seq and associated data analysis were performed as described previously (Stringer et al., 2014. PMID 24272778). The second where five cultures of MG1655 thyA suhB::thyA were grown overnight from single colonies at 37 C in LB. 5 L of each overnight culture was spread on LB agar and incubated at 30 C, the non-permissive temperature for suhB mutants. One suppressor mutant colony was selected from each plate. rnc was PCR amplified from colonies using oligonucleotides JW836-JW837, and the PCR products were sequenced to identify the presence, if any, of suppressor mutations. Genomic DNA from a strain with wild-type rnc was prepared using a DNeasy Blood and Tissue Kit (Qiagen). A DNA library was prepared using a Nextera kit (Illumina). The library was sequenced (paired-end reads) using an Illumina MiSeq instrument.

2016-01-20 | E-MTAB-4240 | biostudies-arrayexpress

Sequence Requirements for Cascade Function in a Type I-E CRISPR System: Plasmid Loss

Project description:We generated a collection of 13 plasmids, with each plasmid containing a variant of a CRISPR protospacer targeted by spacer 8 of the E. coli CRISPR-I array. We transformed the plasmids as a pool into delta cas3 E. coli cells expressing all other cas genes constitutively. We then transformed these cells with either an empty vector or a plasmid expressing the Cas3 nuclease. DNA surrounding the protospacers was PCR-amplified and sequenced.

2017-08-24 | E-MTAB-5969 | biostudies-arrayexpress

Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding

Project description:We investigated the effect that intragenic s54 binding sites have on transcripton elongation. In an rpoN deletion we have over-expressed rpoN from a plasmid (with vector only contol) and then looked at changes in transcription elongation around intragenic s54 binding sites by RNA-seq. We are also looking at changes in transcription initiation/elongation at sites of sigma factor overlap.

2015-08-06 | E-MTAB-3699 | biostudies-arrayexpress

Mapping the Regulatory Network for Salmonella Typhimurium Invasion

Project description:Using RNAseq, the goal of the study is to investigate transcription factor regulation of virulence genes in 14028s Salmonella Typhimurium grown in SPI-1-inducing conditions. Transcription factors were cloned into pBAD24. RNA levels were compared in 14028s Salmonella Typhimurium with the transcription factor-encoding gene deleted, carrying either empty pBAD24, or pBAD24 expressing the transcription factor corresponding to the deletion. The Transcription factors analyzed are HilA, HilC, HilD, SprB, InvF, RtsA and RtsB.

2015-08-17 | E-MTAB-3765 | biostudies-arrayexpress

Sequence Requirements for Cascade Function in a Type I-E CRISPR System: RNA-Seq

Project description:We measured global RNA levels using RNA-seq in cas3 E. coli cells with intact CRISPR arrays or cells with the CRISPR-I array deleted to determine if off-target events driven by endogenous spacers affect local gene expression.

2017-08-24 | E-MTAB-5971 | biostudies-arrayexpress

Sequence Requirements for Cascade Function in a Type I-E CRISPR System: RNA-Seq

Project description:We measured global RNA levels using RNA-seq in cas3+ E. coli cells with intact CRISPR arrays or cells with the CRISPR-I array deleted to determine if off-target events driven by endogenous spacers affect RNA levels.

2018-02-10 | E-MTAB-6446 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data