Expression data of human melanoma cells plus/minus Androgen Receptor (AR) silencing by two independent shRNAs
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ABSTRACT: Cancer susceptibility of male versus female individuals is significantly different in melanoma, with females showing greater survival than males. Accrued information on the role fo sex hormones in melanoma is mostly limited to estrogen signaling, with only circumstantial evidence related to androgen receptor. We used Clariom™ D GeneChip Assay to study the global gene expression changes upon silencing of AR by two independent shRNAs in three human melanoma cell lines.
Project description:This study was undertaken in order to characterize the functions of Rex-1 and identify potential Rex-1 target genes.Both alleles of the Rex-1 gene were disrupted in J1 mouse embryonic stem cells. Gene expression levels in one of the resulting Rex-1 knockout cell lines was compared to that of J1 wild type cells. Keywords: cell type comparison
Project description:Purpose: Generate a large, high quality database of paired shRNA efficacy/sequence datapoints. Methods:Twelve shRNAs for each Refseq annotated human gene were selected based on the DSIR algorithm. Twelve batches of ~22K shRNAs (corresponding to 12 agilent chips) were then assessed for efficacy via the sensor method outlined in Fellmann et al, Mol Cell, 2011. Conclusions: Neighboring nucleotide combinations are best at predicting shRNA efficacy.
Project description:Whole transcriptome of IRF3-depleted myeloma cells was analysed using a high-throughput RNA-seq approach. IRF3 was depleted by 2 different shRNAs in MM1.S cells, and total RNA was isolated on day 4 post-lentiviral transduction. Poly A-tail enriched RNA was sequenced and the analysis of commonly regulated genes by both shRNAs from 2 independent experiments revealed that IRF3 regulates genes that are involved in cell cycle regulation.
Project description:Comparison of gene expression in C. elegans with biofilm compared to C. elegans without biofilm. Background: Yersinia pseudotuberculosis YpIII strain forms a biofilm on C. elegans. The biofilm develops over a period of hours. Thus, at 1 hour the worm has little actual biofilm but exhibits abnormal movement; at 24 hours the worm has a large mass of biofilm, mostly over anterior end. Yersinia pseudotuberculosis 3384 does not form a biofilm on C. elegans. Yersinia pseudotuberculosis mutant in the ypsR/ytbR locus does not form a biofilm by virtue of having a non-functional quorum sensing system.
Project description:shRNAs selected with the shERWOOD algorithm were converted to have a U at the 5' end of their guide. When endogenous 1U shRNAs were compared to artificial shRNA via the sensor algorithm, the endogenous shRNAs were found to be more efficacious.
Project description:Gene expression profiling of prostate adenocarcinoma LNCaP cells stably transfected with shRNAs targeting ADRB2 (shADRB2-2 and shADRB2-3) or control shRNA (shCtrl) incubated in 10% FCS.
Project description:Although the dynamic instability of microtubules (MTs) is fundamental to many cellular functions, quiescent MTs with unattached free distal ends are commonly present and play important roles in various events to power cellular dynamics. However, how these free MT tips are stabilized remains poorly understood. Here, we report that centrosome and spindle pole protein 1 (CSPP1) caps and stabilizes both plus and minus ends of static MTs. Real-time imaging of laser-ablated MTs in live cells showed deposition of CSPP1 at the newly generated MT ends, whose dynamic instability was concomitantly suppressed. Consistently, MT ends in CSPP1-overexpressing cells were hyper-stabilized, while those in CSPP1-depleted cells were much more dynamic. This CSPP1-elicited stabilization of MTs was demonstrated to be achieved by suppressing intrinsic MT catastrophe and restricting polymerization. Importantly, CSPP1-bound MTs were resistant to mitotic centromere-associated kinesin-mediated depolymerization. These findings delineate a previously uncharacterized CSPP1 activity that integrates MT end capping to orchestrate quiescent MTs.