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

Metagenomic regulatory sequence library characterized in RpoD ortholog strains

ABSTRACT: Characterization of a metagenomic regulatory sequence library derived from M. xanthus, E. coli, and O. urethralis genomes in strains expressing different RpoD ortholog variants. Targeted DNA and RNA seq used to profile relative DNA and RNA abundances, respectively of each regulatory sequence construct in the library.

INSTRUMENT(S): NextSeq 550

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

SUBMITTER: Jimin Park

PROVIDER: E-MTAB-9111 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Biosynthetic Gene Cluster regulatory sequence library profiled in S. albidoflavus

Project description:Here, we profiled the transcriptional capacity of a library of regulatory sequences mined from diverse Biosynthetic Gene Clusters in S. albidoflavus (S. albus J1074) to investigate BGC gene regulation.

2022-06-07 | E-MTAB-9223 | biostudies-arrayexpress

Interleukin-23-induced transcription factor Blimp1 promotes pathogenicity of T helper 17 cells

Project description:Interleukin-23 (IL-23) is a pro-inflammatory cytokine required for the pathogenicity of T helper 17 (Th17) cells but the molecular mechanisms governing this process remain unclear. We identified the transcription factor Blimp-1 (Prdm1) as a key IL-23-induced factor that drove the inflammatory function of Th17 cells. In contrast to thymic deletion of Blimp-1, which causes T cell development defects and spontaneous autoimmunity, peripheral deletion of this transcription factor resulted in reduced Th17 activation and reduced severity of autoimmune encephalomyelitis. Furthermore, genome wide occupancy and overexpression studies in Th17 cells revealed that Blimp-1 co-localized with transcription factors RORÎ³t, STAT-3 and p300 at the Il23r, Il17a/f and Csf2 cytokine loci to enhance their expression. Blimp-1 also directly bound to and repressed cytokine loci Il2 and Bcl6. Taken together, our results demonstrate that Blimp-1 is an essential transcription factor downstream of IL-23 that acts in concert with RORÎ³t to activate the Th17 inflammatory program. Genome-wide binding analysis of Blimp1 from in vitro generated T effector and regulatory cells

2016-06-15 | E-GEOD-75724 | biostudies-arrayexpress

Chromatin position effects assayed by thousands of reporters integrated in parallel (mPGK TRIP pools)

Project description:Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here we describe a multiplexing approach for the parallel monitoring of transcriptional activity of thousands of randomly integrated reporters. More than 27,000 distinct reporter integrations in mouse embryonic stem cells, obtained with two different promoters, show ~1,000-fold variation in expression levels. Data analysis indicates that lamina-associated domains act as attenuators of transcription, likely by reducing access of transcription factors to binding sites. Furthermore, chromatin compaction is predictive of reporter activity. We also found evidence for cross-talk between neighboring genes, and estimate that enhancers can influence gene expression on average over ~20 kb. The multiplexed reporter assay is highly flexible in design and can be modified to query a wide range of aspects of gene regulation. TRIP assay of mPGK promoter; 6 experiments, each with 2 technical replicates.

2013-08-16 | E-GEOD-48608 | biostudies-arrayexpress

Direct GR binding sites potentiate clusters of TF binding across the human genome [1]

Project description:The glucocorticoid receptor (GR) binds the human genome at >10,000 sites, but only regulates the expression of hundreds of genes. To determine the functional effect of each site, we measured the glucocorticoid (GC) responsive activity of nearly all GR binding sites (GBSs) captured using chromatin immunoprecipitation (ChIP) in A549 cells. 13% of GBSs assayed had GC-induced activity. The responsive sites were defined by direct GR binding via a GC response element (GRE) and exclusively increased reporter- gene expression. Meanwhile, most GBSs lacked GC-induced reporter activity. The non-responsive sites had epigenetic features of steady state enhancers and clustered around direct GBSs. Together, our data support a model in which clusters of GBSs observed with ChIP-seq reflect interactions between direct and tethered GBSs over tens of kilobases. We further show that those interactions can synergistically modulate the activity of direct GBSs, and may therefore play a major role in driving gene activation in response to GCs. Glucoroticoid receptor binding site chip-seq libraries were cloned into STARR-seq for massively parallel functional analysis. The results were confirmed by ChIP-Exo performed on the GR in A549 cells treated with 100 nM dexamethasone for one hour. This dataset [1] contains rna seq from BAC DNA tagments (nucleic acids that have been treated with Nextera transposase to fragment the nucleic acids and add sequencing adapters) cloned into the STARR-seq plasmid backbone, transfected into A549 cells and treated with DEX or ETOH.

2016-08-25 | E-GEOD-79424 | biostudies-arrayexpress

Direct GR binding sites potentiate clusters of TF binding across the human genome [5]

Project description:The glucocorticoid receptor (GR) binds the human genome at >10,000 sites, but only regulates the expression of hundreds of genes. To determine the functional effect of each site, we measured the glucocorticoid (GC) responsive activity of nearly all GR binding sites (GBSs) captured using chromatin immunoprecipitation (ChIP) in A549 cells. 13% of GBSs assayed had GC-induced activity. The responsive sites were defined by direct GR binding via a GC response element (GRE) and exclusively increased reporter- gene expression. Meanwhile, most GBSs lacked GC-induced reporter activity. The non-responsive sites had epigenetic features of steady state enhancers and clustered around direct GBSs. Together, our data support a model in which clusters of GBSs observed with ChIP-seq reflect interactions between direct and tethered GBSs over tens of kilobases. We further show that those interactions can synergistically modulate the activity of direct GBSs, and may therefore play a major role in driving gene activation in response to GCs. Glucoroticoid receptor binding site chip-seq libraries were cloned into STARR-seq for massively parallel functional analysis. The results were confirmed by ChIP-Exo performed on the GR in A549 cells treated with 100 nM dexamethasone for one hour. In dataset [5], the files contain RNA-seq from GR-ChIP-reporters that were transfected into A549 cells and treated with DEX or EtOH. [5] contains the reporter assay specific RNA-seq from plasmids described in [4].

2016-08-25 | E-GEOD-79428 | biostudies-arrayexpress

Chromatin position effects assayed by thousands of reporters integrated in parallel

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-08-16 | E-GEOD-48606 | biostudies-arrayexpress

Predictive design of sigma factor-specific promoters

Project description:To engineer synthetic gene circuits, molecular building blocks are developed which can modulate gene expression without interference, mutually or with the host’s cell machinery. Promoter libraries of E. coli sigma factor 70 and B. subtilis B-, F- and W-dependent promoters are exploited to construct prediction models, capable of both predicting promoter TIF and orthogonality of the specific promoters. This is achieved by the creation of high-throughput DNA sequencing data from fluorescence-activated cell sorted promoter libraries.

2020-08-01 | E-MTAB-8734 | biostudies-arrayexpress

Global analyses of how 3' UTR-isoform choice influences mRNA stability and translational efficiency

Project description:We obtained global measurements of decay and translation rates for mammalian mRNAs with alternative 3' untranslated regions (3' UTRs). 1 3P-Seq sample from 3T3 cells and 1 3P-Seq sample from mouse ES cells; 2 2P-Seq steady state and 4 2P-Seq with actinomycin D; 6 polysome fraction 2P-Seq

2013-02-28 | E-GEOD-44698 | biostudies-arrayexpress

Flag-RBM47 HITS-CLIP in brain metastatic derivatives of MDA-MB-231

Project description:Brain metastatic breast cancer cells were subjected to HITS-CLIP to identify the targets of the RNA binding protein RBM47 MDA231-BrM2a is characterized in PMID: 19421193; Related data published together with these data are found in GSE53779 Non-clonal brain metastatic breast cancer cells stably expressing Flag-tagged, wild-type RBM47 under a doxycline-inducible promoter were treated for three days with doxycycline then UV-irradiated and subjected to Flag HITS-CLIP

2014-06-11 | E-GEOD-58380 | biostudies-arrayexpress

Chromatin position effects assayed by thousands of reporters integrated in parallel (tet-Off TRIP pools)

Project description:Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here we describe a multiplexing approach for the parallel monitoring of transcriptional activity of thousands of randomly integrated reporters. More than 27,000 distinct reporter integrations in mouse embryonic stem cells, obtained with two different promoters, show ~1,000-fold variation in expression levels. Data analysis indicates that lamina-associated domains act as attenuators of transcription, likely by reducing access of transcription factors to binding sites. Furthermore, chromatin compaction is predictive of reporter activity. We also found evidence for cross-talk between neighboring genes, and estimate that enhancers can influence gene expression on average over ~20 kb. The multiplexed reporter assay is highly flexible in design and can be modified to query a wide range of aspects of gene regulation. TRIP assay of tet-Off promotor; 4 experiments, each with 2 technical replicates. Each experiment was induced at 4 different concentrations of doxycycline.

2013-08-16 | E-GEOD-49806 | 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