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A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation [RBP screening K562 cells]

ABSTRACT: We process mass spectrome datasets of RNA binding proteins(RBPs) in soluble nuclear extract (SNE) and chromatin-pellet extract (CPE) from K562 cells.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Yue Huo

LAB HEAD: Jia Yu

PROVIDER: PXD028668 | Pride | 2021-09-27

REPOSITORIES: Pride

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A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation [RBP screening 293T cells]

Project description:We process mass spectrome datasets of RNA binding proteins(RBPs) in soluble nuclear extract (SNE) and chromatin-pellet extract (CPE) from 293T cells.

2021-09-27 | PXD028660 | Pride

A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation [RBP screening THP-1 cells]

Project description:We process mass spectrome datasets of RNA binding proteins(RBPs) in soluble nuclear extract (SNE) and chromatin-pellet extract (CPE) from THP-1 cells.

2021-09-27 | PXD028787 | Pride

Carboxypeptidase E transmits its anti-migratory function in glioma cells via transcriptional regulation of cell architecture and motility regulating factors.

Project description:They aim of the study is to identify targets of Carboxypeptidase E (CPE) as well as signaling cascades that are affected by CPE which are specific for transmitting its anti-migratory effects in glioma cells by overexpressing CPE and using transcriptomics profiling of mRNAs and microRNAs.

2017-11-29 | E-MTAB-5297 | biostudies-arrayexpress

Carboxypeptidase E transmits its anti-migratory function in glioma cells via transcriptional regulation of cell architecture and motility regulating factors.

2017-11-29 | E-MTAB-5299 | biostudies-arrayexpress

Gene expression of the mouse choroid plexus epithelium (CPE)

Project description:We investigated the gene expression of the mouse CPE. We isolated CPE cells from three mouse brains with laser dissection microscopy. Next, we performed RNA isolation, amplification, labeling and hybridization against 44k Agilent microarrays. We performed the microarrays against a common reference sample, which was mouse RPE/choroid RNA. We performed 3 mouse CPE replicates from 3 different mouse from the same strain, namely C57BL/6 .

2013-09-27 | E-GEOD-49973 | biostudies-arrayexpress

Comparisons of the global gene profile between C-CPE treated- and untreated- SKOV-3 ovarian cancer cells.

Project description:A microarray analysis was performed to compare the global gene expression profile between C-CPE treated- and untreated- SKOV-3 ovarian cancer cells. SKOV-3 cells were treated with or without C-CPE for 72 hours, and total RNA was extracted and microarray was perfomed to compare the gene profiling changes between C-CPE treated- and untreated- cells. The experiment was performed in triplicate.

2010-06-23 | E-GEOD-22421 | biostudies-arrayexpress

RNA-Seq of native and FusionRed-transfected canine tumor cell lines after 3 hours C-CPE treatment

Project description:Claudin (CLDN) proteins are commonly expressed in cancers and accordingly targeted in novel therapeutic approaches. C-terminus of Clostridium perfringens enterotoxin (C-CPE) binds efficiently several claudins and can be used to specifically target cancer cells. This experiment used RNA-seq to profile gene expression changes of native and FusionRed transfected canine tumor cell lines;TihoDTCC0840 (0840) and TihoDProAdCarc0846 (0846) after a 3 hours of C-CPE treatment (20µg/ml).

2021-11-30 | E-MTAB-10839 | biostudies-arrayexpress

Gene expression of the human choroid plexus epithelium (CPE)

Project description:We investigated the gene expression of the human CPE.We isolated CPE cells from healthy human donor choroid plexus tissues with laser dissection microscopy. Next, we performed RNA isolation, amplification, labeling and hybridization against 44k Agilent microarrays. We performed the microarrays against a common reference sample, namely human RPE/choroid RNA. We performed 7 replicates of human CPE samples from 7 different donors.

2013-09-27 | E-GEOD-49969 | biostudies-arrayexpress

Mass spectrometry (MS) datasets of QKI5 co-immunoprecipitation samples in THP-1 cells

Project description:We performed QKI5 co-immunoprecipitation followed by MS analysis to identify QKI5-interacting proteins in THP-1 cells.

2021-09-27 | PXD028743 | Pride

Microarray analysis profiling of the effect of cowpea phenolic extract on gene expression in bovine peripheral blood in vitro

Project description:Plant-derived secondary metabolites found in animal feed sources are beneficial for nutrition and health. Cowpea is a protein and phenolic-rich forage used as feed resource in animal system. The objective of this study was to understand the effect of cowpea secondary metabolites on gene expression in cows blood in vitro. Whole blood collected from Holstein Friesian cows (n=5) were treated with 10 ug/ml of cowpea leaf phenolic extract and untreated samples served as control. Total RNA was isolated and pooled together for microarray analysis. The Agilent one color bovine (v2) 4x44KÂ array was used and preliminary gene expression profiles generated using Cy3 labeled cDNA from CPE-stimulated and untreated samples. Gene expression analysis revealed a total of 3170 differentially expressed genes- 1716 up regulated and 1454 down regulated genes respectively. Pathway analysis identified CPE treatment association with innate immune response pathways including Toll-like receptor (TLR) signaling pathway, the Wnt signaling pathway, inflammation response pathway, and increased expression of the transcription factor NFKB1 were observed. Treatment with CPE decreased the expression of proinflammatory cytokines IL1A, IL1B and IL21. Quantitative real time PCR was performed to validate some gene members of the Toll-like receptor, inflammation response and Wnt signaling pathways. In vitro treatment with CPE impacted global gene expression profile in cow blood and results obtained in this study shows the potential immuno-modulatory properties of cowpea feed phenolic in cows. The global gene expression of the effect of cowpea phenolic extract (CPE) was measured in bovine peripheral blood.The experiment involved two groups; cowpea phenolic extract (CPE) treated samples vs untreated control group. Pooled RNA samples from each group was hybridized on Agilent one color bovine (v2) 4x44KÂ microarray slides. Two slides were prepared each with 4 array compartment.

2015-11-21 | E-GEOD-75239 | biostudies-arrayexpress

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