Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-sequencing of Streptomyces albus S4 WT and fscRI

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Streptomyces albus

SUBMITTER: Ryan Seipke

PROVIDER: E-MTAB-5122 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

Project description: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).

2019-02-28 | E-MTAB-7700 | biostudies-arrayexpress

Gene expression in human monocyte differentiation (3D-MO)

Project description:This dataset consists of RNA-seq data data from human monocytes, monocyte-derived dendritic cells or monocyte-derived macrophages as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, it includes 63 samples.

2022-06-20 | E-MTAB-10844 | biostudies-arrayexpress

Gene expression in LPS-stimulated human monocyte-derived macrophages (3D-MO)

Project description:This dataset consists of RNA-seq data from human monocyte-derived macrophages that were subjected to siRNA treatment targeting RAD21 and either left untreated, or stimulated with LPS. In total, it includes 24 samples.

2022-06-20 | E-MTAB-10845 | biostudies-arrayexpress

RNA-seq of ventricle and fat tissues of male and female cardiac myocyte-specific estrogen receptor KO mice

Project description:Cardiac myocyte-specific ERalpha KO mice were generated to assess the role of ERα in the heart. Female ERαHKO mice displayed a modest cardiac phenotype, but unexpectedly, an the most striking obesity phenotype developed was obesity in female ERαHKO but not male ERαHKO mice. In female ERαHKO mice we identified cardiac dysfunction, mild glucose and insulin intolerance, and reduced ERα gene expression in skeletal muscle and white adipose tissue (WAT). RNA-seq analysis was conducted on the ventricles and WAT of male and female ERαHKO mice to further elucidate the transcriptomic alterations associated with the shift in metabolic profiles in the tissues of interest.

2023-01-24 | E-MTAB-12564 | biostudies-arrayexpress

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

Project description:RNA-seq was performed to determine gene expression changes in monocytes during in vitro differentiation. In addition to control cells, we also studied the impact of siRNA mediated knock-down of key transcription factors on gene expression in monocyte-derived dendritic cells.

2021-02-03 | E-MTAB-9929 | biostudies-arrayexpress

DNA methylation (MCIP-seq) of human acute leukemias and healthy donors

Project description:To measure methylation, we employed Methyl-CpG-immunoprecipitation (MCIP) a technique which relies on a fusion protein consisting of the methyl-binding domain (MBD) of MBD2 and the Fc portion of IgG1 to detect methylated regions, exploiting the natural preference of MBD for 5-methylcytosine (5-mC). MCIP-seq was performed using the EpiMark® Methylated DNA Enrichment Kit. MCIP-seq of 77 primary samples obtained from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). Moreover, MCIP-seq of CD34+ HSPCs from 3 healthy donors is included. Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011052 (dataset).

2023-08-31 | E-MTAB-13120 | biostudies-arrayexpress

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

5hmC capture-seq of human monocytes and human monocyte-derived cells

Project description:We performed 5'-hydroxymethylcytosine (5hmC) capture sequencing to study the dynamics of 5hmC deposition during monocyte differentiation

2021-02-03 | E-MTAB-9928 | biostudies-arrayexpress

Molecular reprogramming of primary human resting memory CD4+ T cells by HIV-1 Vpr

Project description:Resting CD4+ T cells are infected by HIV-1 in vivo, however are refractory to cell-free HIV-1 infection in vitro. We show that they are efficiently infected by cell-to-cell spread. To allow resting T cell infection, uninfected resting target cells were co-cultured with infected donor T cells. Cells were infected with HIV-1 WT, dVpr or left mock treated and cultures with or without IL7. After 72h of co-culture, resting target cells were recovered by flow cytometry sorting and total RNA was extracted. RNASequencing revealed global transcriptomic reprogramming of resting memory T cells by HIV-1 Vpr.

2022-03-31 | E-MTAB-11454 | biostudies-arrayexpress

CTCF ChIP-seq of human acute leukemias

Project description:CTCF ChIP-seq of 39 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011059 (dataset).

2023-08-31 | E-MTAB-13117 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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