NPAS3-HEK293-standardcond-Illumina
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Li Sha
PROVIDER: E-TABM-1078 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The fragments of FLNPAS3 and DeltaNPAS3 were transferred into a similar TET-inducible expression plasmid and transfected into HEK293 [T-REx-293] cells (Invitrogen). At the zero hour time-point, cells were shifted into a serum-rich medium plus tetracycline in order to induce circadian cycling and NPAS3 overexpression. Parental HEK293 [T-REx-293] cells after circadian rhythmcity induction for +12hr/+24hrs were used as negative controls because stably integrated FLNPAS3/DeltaNPAS3 cell lines showed a low level of leaky transcription in the absence of tetracycline. At +2 hours, cells were washed with DMEM and then incubated with the same plus tetracycline for the remaining period of the experiment. Cell samples were collected at +12hrs and +24hrs respectively. For all circadian cell culture experiments with FLNPAS3/DeltaNPAS3/parental negative control cell lines, duplicate biological samples were assessed. Microarray probes synthesised from RNA extraction products was quantified using an Agilent Bioanalyzer to ensure high quality probes of equal quantity between experiments. Sentrix® HumanRef-8 v2 chips were used to detect gene expression profiles.
2011-10-03 | E-TABM-1079 | biostudies-arrayexpress
Project description:The HEK293 cells were transiently transfected by pDEST40-SOX11 or control plasmid (pDEST40).Cells were collected at 24 hours post-transfection.Total RNA from alll samples was extracted.Biotinylated cRNA was prepared using the Illumina total Prep RNA application Kits.Hybridization, washing and scanning were performed according to the Illumina BeadStation 500* manual (revision C)
2011-10-18 | E-TABM-1082 | biostudies-arrayexpress
Project description:We have carried out a cell line-based overexpression study coupled with microarray analysis to characterise the set of genes regulated by SOX11 and therefore critical for neurodevelopmental processes important in health and disease. The HEK293 cells were transiently transfected by pDEST40-SOX11 or control plasmid (pDEST40).Cells were collected at 24 hours post-transfection.Total RNA from alll samples was extracted.Biotinylated cRNA was prepared using the Illumina total Prep RNA application Kits.Hybridization, washing and scanning were performed according to the Illumina BeadStation 500* manual (revision C)
2011-06-21 | E-TABM-1025 | biostudies-arrayexpress
Project description:The aim of the study was to determine the effect of the tumour suppressor RASSF1A in a stably induced YAP system, as both are members of the growth regulatory HIPPO pathway. YAP1 expression was induced by Doxycycline in stably transfected HEK293 cells. In addition the cells were transfected with RASSF1A/GFP or GFP. Transfected cells were FACS-sorted by the GFP-signal and lysed for transcriptome analysis.
2017-05-15 | E-MTAB-4781 | biostudies-arrayexpress
Project description:Even though ubiquitination controls a plethora of cellular processes, modifications by linear polyubiquitin have so far only been linked with acquired and innate immunity, lymphocyte development and genotoxic stress response. Until now, a single E3 ligase complex (LUBAC), one specific deubiquitinase (Otulin) and a very few substrates have been identified. The existing methods for the study of lysine-based polyubiquitination are not suitable for the detection of linear polyubiquitin-modified proteins. Here, we present a novel approach to discovering linear polyubiquitin-modified substrates by combining lysine-less internally tagged ubiquitin (INT-Ub.7KR) with SILAC-based mass spectrometry. We applied our approach in TNFα-stimulated T-Rex HEK293T cells and afterwards validated newly identified linear polyubiquitin targets. Moreover, we demonstrated that linear polyubiquitination of the novel LUBAC substrate TRAF6 is essential for the NFkappaB signalling. Overall, we have established a powerful method for the detection of linear polyubiquitin substrates.
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2017-05-04 | PXD005120 | Pride
Project description:Human LIN28A and B are RNA-binding proteins (RBPs) conserved in animals with important roles during development and stem cell reprogramming. We used Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in HEK293 cells and identified a largely overlapping set of ~3,000 mRNAs at ~9,500 sites located in the 3M-bM-^@M-^YUTR and CDS. In vitro and in vivo, LIN28 preferentially bound single-stranded RNA containing a uridine-rich element and one or more flanking guanosines, and appeared to be able to disrupt base-pairing to access these elements when embedded in predicted secondary structure. In HEK293 cells, LIN28 protein binding mildly stabilized target mRNAs and increased protein abundance. The top targets were its own mRNAs and those of other RBPs and cell-cycle regulators. Alteration of LIN28 protein levels also negatively regulated the abundance of some, but not all let-7 miRNA family members, indicating sequence-specific binding of let-7 precursors to LIN28 proteins and competition with cytoplasmic miRNA biogenesis factors. To assess whether the transcripts identified by PAR-CLIP are regulated by LIN28B we analyzed the mRNA levels of LIN28B overexpressing and LIN28B-depleted cells using microarrays. Transcripts crosslinked to LIN28B were slightly downregulated upon LIN28B knockdown compared to LIN28B overexpression indicating that LIN28B stabilizes transcripts. The RBP LIN28B was depleted by siRNAs and the expression levels was compared to mock-transfected HEK293 cells The RBP LIN28B was depleted by siRNAs and the expression levels was compared to mock-transfected HEK293 cells
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Project description:Human LIN28A and B are RNA-binding proteins (RBPs) conserved in animals with important roles during development and stem cell reprogramming. We used Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in HEK293 cells and identified a largely overlapping set of ~3,000 mRNAs at ~9,500 sites located in the 3M-bM-^@M-^YUTR and CDS. In vitro and in vivo, LIN28 preferentially bound single-stranded RNA containing a uridine-rich element and one or more flanking guanosines, and appeared to be able to disrupt base-pairing to access these elements when embedded in predicted secondary structure. In HEK293 cells, LIN28 protein binding mildly stabilized target mRNAs and increased protein abundance. The top targets were its own mRNAs and those of other RBPs and cell-cycle regulators. Alteration of LIN28 protein levels also negatively regulated the abundance of some, but not all let-7 miRNA family members, indicating sequence-specific binding of let-7 precursors to LIN28 proteins and competition with cytoplasmic miRNA biogenesis factors. To assess whether miRNAs are regulated by LIN28B we analyzed the miRNA levels of LIN28B overexpressing and LIN28B-depleted cells using small RNA cDNA library sequencing. The RBP LIN28B was depleted by siRNAs and the expression levels was compared to mock-transfected HEK293 cells.
2013-02-26 | E-GEOD-44568 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-02-26 | E-GEOD-44616 | biostudies-arrayexpress
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