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TranscriptomicsAgo-APP: a GW peptide-based Argonaute affinity capture strategy
During microRNA (miRNA)-guided gene silencing, Argonaute (Ago) proteins interact with a member of the TNRC6/GW protein family. Here we used a short GW protein-derived peptide fused to GST and demonstrate that it binds to Ago proteins with high affinity. This allows for the simultaneous isolation of ...
ORGANISM(S): Arabidopsis thaliana 
2015-09-08 | E-GEOD-70553 | biostudies-arrayexpress
TranscriptomicsHigh-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection
Small RNA deep sequencing analysis was conducted on primary human fibroblasts infected with human cytomegalovirus (HCMV). HCMV-encoded miRNAs accumulated to ~20% of the total smRNA population at late stages of infection, and our analysis led to improvements in viral miRNA annotations and identificat...
ORGANISM(S): Homo sapiens 
2011-11-10 | E-GEOD-33584 | biostudies-arrayexpress
GenomicsSystematic identification of G-quadruplex sensitive lethality by genome-wide genetic screening
A375 and HT1080 cells are treated with G-quadruplex ligands PDS or PhenDC3 following genome-wide shRNA knockdown. This enables the identification of genes that when silenced, specifically compromises cell growth in the presence of the ligand. First, a pilot screen was performed to determine a ligand...
ORGANISM(S): Homo sapiens 
2019-06-22 | E-MTAB-6367 | biostudies-arrayexpress
TranscriptomicsExpression data from SHP specific siRNA or nonspecefic siRNA transfected rat astrocytes
To clarify the effect of SHP in LXRs-mediated signaling pathway, we performed global gene expression analysis of SHP siRNA transfected- or control siRNA transfected- astrocytes after IFN-γ and LXRs agonist. Microarray analysis revealed that expression of several genes encoding inflammatory mediator...
ORGANISM(S): Rattus norvegicus 
2016-01-21 | E-GEOD-76704 | biostudies-arrayexpress
TranscriptomicsSmall molecule inhibitors suppress expression of both type III secretion and amylovoran biosynthesis genes in Erwinia amylovora
Microarray analysis of E. amylovora treated with compounds no. 3 and no. 9 identified a total of 588 significantly differentially expressed genes. Among them, 95 and 78 genes were, respectively, induced and suppressed by both compounds as compared to DMSO control. Majority of T3SS genes in E. amylov...
ORGANISM(S): Erwinia amylovora 
2013-12-24 | E-GEOD-45602 | biostudies-arrayexpress
GenomicsChIP-seq of Tcfap2c in Neu mammary cancer cells
Tumors were harvested from mice carrying the rat activated Neu-oncogene and made into a single cell suspension. ChIP-SEQ was carried out as previously described in Kulak MV, Cyr AR, Woodfield GW, Bogachek M, Spanheimer PM, Li T et al. Transcriptional regulation of the GPX1 gene by TFAP2C and aberran...
ORGANISM(S): Mus musculus 
2015-04-01 | E-GEOD-61394 | biostudies-arrayexpress
Transcriptomicsm6A-dependent regulation of messenger RNA stability
N6-methyladenosine (m6A) is the most prevalent internal modification present in the mRNA of all higher eukaryotes. Here we present that m6A is selectively recognized by human YTH domain family (YTHDF2) protein to regulate mRNA degradation. By using crosslinking and immunoprecipitation, we have ident...
ORGANISM(S): Homo sapiens 
2013-11-29 | E-GEOD-49339 | biostudies-arrayexpress
TranscriptomicsMicroRNA expression data from differentiation of human Cyt49 ESCs into definitive endoderm in feeder-free conditions
Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm is the first step into the pathway to endoderm dreived tissues (pancreas, liver, gut, lung). We used microarrays to detail the changes ...
ORGANISM(S): Homo sapiens 
2010-07-29 | E-GEOD-16678 | biostudies-arrayexpress
TranscriptomicsHER2-positive breast cancer cells resistant to trastuzumab and lapatinib lose reliance upon HER2 and are sensitive to the multitargeted kinase inhibitor sorafenib
HER2 targeting with trastuzumab has changed the prognosis of breast cancer patients carrying amplification and/or overexpression of this oncogene. Despite this progress, however, resistance to trastuzumab occurs in the vast majority of patients. Newer anti-HER2 therapies, like the dual tyrosine-kina...
ORGANISM(S): Homo sapiens 
2010-12-15 | E-GEOD-17630 | biostudies-arrayexpress
TranscriptomicsMicroRNA expression data from differentiation of human Cyt49 ESCs into definitive endoderm on MEF feeder layers
Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm is the first step into the pathway to endoderm dreived tissues (pancreas, liver, gut, lung) We used microarrays to detail the changes i...
ORGANISM(S): Homo sapiens 
2010-07-30 | E-GEOD-16687 | biostudies-arrayexpress
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