Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-sequencing of 3xFLAG-AntA from Streptomyces albus S4

ABSTRACT: To evaluate the DNA binding of AntA in Streptomyces albus S4, in vivo ChIP-Seq experiments were performed 3xFLAG-AntA and anti-FLAG antibodies using two biological replicates. The wild type strain was used as a control in experiments using the anti-FLAG antibodies as well as a DNA only control (which were published previously, E-MTAB-5122).

INSTRUMENT(S): Illumina HiSeq 3000

ORGANISM(S): Streptomyces albus

SUBMITTER: Ryan Seipke

PROVIDER: E-MTAB-7700 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ChIP-sequencing of Streptomyces albus S4 WT and fscRI

Project description:To evaluate the DNA binding of FscRI in Streptomyces albus S4 in vivo ChIP-Seq experiments were carried out on dusing anti-FLAG antibodies against 3xFLAG-FscRI protein using two biological replicates. The wild type strain was used as a control in experiments using the anti-FLAG antibodies as well as a DNA only control.

2016-11-14 | E-MTAB-5122 | biostudies-arrayexpress

SvenBldMWhiIChIPSeq

Project description:To determine the influence of BldM and WhiI on the binding of each other to their respective binding sites in the genome of Streptomyces venezuelae, ChIP-Seq experiments were carried out using polyclonal antibodies against the wild type proteins as well as anti-FLAG antibodies against FLAG-tagged proteins. Null mutants of Streptomyces venezuelae lacking WhiI or BldM were used as controls. The wild tpe strain was used as control in experiments using the anti-FLAG antibodies.

2015-05-19 | E-MTAB-2698 | biostudies-arrayexpress

Comparative proteomic and RNA-seq analyses identify glypican-3 as a hepatocyte host cell receptor for Plasmodium falciparum sporozoite invasion

Project description:Understanding the liver stage invasion and development of Plasmodium falciparum parasites is difficult due to limitations in current methodologies, namely, a hepatocyte cell line that supports the invasion of sporozoites. In this work we seek to develop and characterize a subclone of the HC-04 cell line that supports higher invasion rates than the parental line. We make use of both RNA-seq and LC-MS/MS proteomics to characterize cells grown in two different mediums. Finally, we identify and validate a surface protein, glypican-3, which is deferentially expressed between parental and subclone cell lines, when compared to HepG2 cells, and demonstrate that antibodies against glypican-3 decrease parasite invasion.

2019-03-02 | E-MTAB-6919 | biostudies-arrayexpress

Identification by ChIP-Seq of the binding sites of the developmental protein WhiH in the genome of Streptomyces venezuelae

Project description:The whiH gene is required for the differentiation of aerial hyphae into spores in Streptomyces species. It is a predicted member of the GntR family of transcription factors and has been shown to bind specifically to a sequence in its own promoter. This ChIP-Seq experiment was carried out to determine all the binding sites whiH binds to in the genome of Streptomyces venezuelae. A whiH deletion strain was made and a FLAG tagged whiH protein was expressed in it from a genome-integrated plasmid. Then anti-FLAG antibodies were used for chromatin immunoprecipitation followed by high throughput sequencing. The wild type Streptomyces venezuelae strain (ATCC 10712) was used as a negative control. For both the FLAG-WhiH strain and the WT strain, non-immunoprecipitated (total) DNA was also sequenced to arrive at a background enrichment which could be subtracted from the enrichment in the immunoprecipated sample.

2018-12-31 | E-MTAB-6702 | biostudies-arrayexpress

Mutation of the cysteine residues that coordinate the WhiB [4Fe-4S] cluster prevents in vivo DNA binding by both WhiB and WhiA

Project description:The purpose of this experiment was to show that the iron-sulphur cluster ([4Fe-4S]) of whiB is essential for the DNA binding by WhiB and WhiA. The \\"serine version of whiB\\" mentioned below is a whiB in which the 4 cysteine residues which coordinate the [4Fe-4S] cluster were mutated to serines. ChIP-Seq using anti-FLAG anitbodies was performed in the following: 1. A whiB deletion strain expressing the FLAG-tagged serine version of WhiB (WhiBFLAG-Ser). 2. A whiB and whiA deletion strain expressing the FLAG-tagged serine version of WhiB (delAB_WhiBFLAG-Ser). 3. A whiB and whiA deletion strain expressing the serine version of WhiB and FLAG-tagged whiA (delAB_WhiAFLAG_WhiBcomp-Ser).

2021-08-16 | E-MTAB-10818 | biostudies-arrayexpress

Analysis of RNA coimmunoprecipitated with 3xFLAG-tagged peptide peTrpL from Sinorhizobium meliloti

Project description:We show that specific RNAs are coimmunoprecipitated in a tetracycline-dependent manner with the Flag-tagged peptide peTrpL of S. meliloti

2020-05-18 | GSE118688 | GEO

Genome-wide maps of JMJ28pro::JMJ28:3xFLAG in 14 days old arabidopsis

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of JMJ28 in 14 days old arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we generated genome-wide JMJ28-binding maps of 14 days old arabidopsis. To reveal bound genes by JMJ28, chimeric protein JMJ28-3xFLAG was expressed under JMJ28 promoter in jmj28 (JMJ28pro:JMJ28:3xFLAG/ jmj28). ChIP was performed using anti-FLAG antibody (FLAG-M2, F1804; SIGMA), and ChIP DNA were analyzed by Illumina Novaseq 6000.

2021-03-30 | GSE155623 | GEO

ChIP-seq of human monocytes and human monocyte-derived cells.

Project description:ChIP-seq was performed to map transcription factor (TF) binding in monocytes during in vitro differentiation. To map binding sites for TF lacking suitable antibodies we also performed mRNA transfections using synthetic mRNAs translating into 3xFLAG TF versions that were ChIPed using Anti-Flag antibody.

2021-02-03 | E-MTAB-9927 | biostudies-arrayexpress

Immunoprecipitation was performed with HCT116 cells overexpressing 3xFLAG-SET/TAF-Ib with anti-FLAG antibodies

Project description:Immunoprecipitation was performed with HCT116 cells overexpressing 3xFLAG-SET/TAF-Ib with anti-FLAG antibodies. The immunoprecitates were separated by SDS-PAGE and putative interaction partners of SET/TAF-Ib were identified with mass spectrometry.

2022-12-13 | MSV000090898 | MassIVE

Genes required for aerial growth, cell division, and chromosome segregation are targets of WhiA before sporulation in Streptomyces venezuelae.

Project description:WhiA is a highly unusual transcriptional regulator related to a family of eukaryotic homing endonucleases. WhiA is required for sporulation in the filamentous bacterium Streptomyces, but WhiA homologues of unknown function are also found throughout the Gram-positive bacteria. To better understand the role of WhiA in Streptomyces development and its function as a transcription factor, we identified the WhiA regulon through a combination of chromatin immunoprecipitation-sequencing (ChIP-seq) and microarray transcriptional profiling, exploiting a new model organism for the genus, Streptomyces venezuelae, which sporulates in liquid culture. The regulon encompasses ~240 transcription units, and WhiA appears to function almost equally as an activator and as a repressor. Bioinformatic analysis of the upstream regions of the complete regulon, combined with DNase I footprinting, identified a short but highly conserved asymmetric sequence, GACAC, associated with the majority of WhiA targets. Construction of a null mutant showed that whiA is required for the initiation of sporulation septation and chromosome segregation in S. venezuelae, and several genes encoding key proteins of the Streptomyces cell division machinery, such as ftsZ, ftsW, and ftsK, were found to be directly activated by WhiA during development. Several other genes encoding proteins with important roles in development were also identified as WhiA targets, including the sporulation-specific sigma factor (WhiG) and the diguanylate cyclase CdgB. Cell division is tightly coordinated with the orderly arrest of apical growth in the sporogenic cell, and filP, encoding a key component of the polarisome that directs apical growth, is a direct target for WhiA-mediated repression during sporulation.

2016-05-20 | E-MTAB-4673 | 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