Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The effects of YB1 knockdown on global gene expression in tumour cell lines.

ABSTRACT: Y-box binding factor 1 (YB1) has been associated with prognosis in many tumor types. Reduction of YB-1 inhibits tumor cell growth in vitro and in vivo Total RNA was isolated from A549, MCF7 and HCT116 tumor cell lines following 48hr treatment with 5nM Yb1 siRNA

ORGANISM(S): Homo sapiens

SUBMITTER: Hamish Campbell

PROVIDER: E-GEOD-28433 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Effects of YB-1 protein reduction on microRNA abundance in breast cancer cell-lines

Project description:To assess the association of the nucleic acid binding protein yb-1 with mature microRNAs levels in breast cancer. To do this we performed YB-1 siRNA treatement in triplicates alongside an siRNA control Two breast cancer cell-lines, representative of Luminal A and Basal molecular subtypes were used, MCF7 and MDA-MB-435S. Two cell-lines, treated with either siYB-1 or si-Ctrl in triplicate samples.

2014-01-23 | E-GEOD-50087 | biostudies-arrayexpress

Human KASUMI-1 cells: Control vs Radotinib (RD) 5uM

Project description:Transcriptional profiling of KASUMI-1 cells comparing between control (DMSO-treated) and radotinib treated Kasumi-1 cells at 48hr one-condition experiment, Control vs RD 5 uM. Biological replicates: 1.

2015-09-11 | E-GEOD-72926 | biostudies-arrayexpress

Gene expression profiling of FOXP1-silenced diffuse large B-cell lymphoma (DLBCL) cell lines

Project description:To identify differentially expressed genes regulated by FOXP1 in DLBCL cells via gene expression profiling of GCB-DLBCL (DB, K422) and ABC-DLBCL (OCI-Ly3, HBL-1) cell lines treated with siRNA targeting FOXP1 or non-silencing siRNA control. Two GCB-DLBCL (DB, K422) and two ABC-DLBCL (OCI-Ly3, HBL-1) cell lines were each treated separately with two independent siRNA oligonucleotides targeting FOXP1 (siFOXP1_308, siFOXP1_309) or non-silencing siRNA (siCtrl). Biological replicates derived from three independent experiments were obtained, RNA-extracted and subsequently hybridized into a human microarray platform for gene expression profiling.

2015-10-27 | E-GEOD-71526 | biostudies-arrayexpress

IMPDH1/YB-1 Positive Feedback Loop Assembles Cytoophidia and Represents a Therapeutic Target in Metastatic Tumors

Project description:Recently, cytoophidium, a non-membrane-bound intracellular polymeric structure, has been shown to exist in various organisms, including tumor tissues, but its function and mechanism have not yet been examined. Examination of cytoophidia-assembled gene IMPDH and CTPS mRNA levels showed that only IMPDH1 levels were significantly higher in the clear cell renal cell carcinoma (ccRCC). IMPDH1 was positively correlated with the metastasis-related gene YB-1, and served as an independent prognostic factor in ccRCC. Kaplan–Meier analysis indicated that patients with tumors that expressed high IMPDH1 levels had a shorter overall survival (OS) and disease-free survival (DFS). Furthermore, detection of cytoophidia by immunofluorescence staining in ccRCC tissues showed that IMPDH1-assembled cytoophidia are positively associated with tumor metastasis. Mechanistically, IMPDH1 and YB-1 formed an autoregulatory positive feedback loop: IMPDH1 maintained YB-1 protein stabilization; YB-1 induced IMPDH1 expression by binding to the IMPDH1 promoter motif. Functionally, IMPDH1-assembled cytoophidia physically interacted with YB-1 and translocated YB-1 into the cell nucleus, thus correlating with ccRCC metastasis. Our findings provide the first solid theoretical rationale for targeting the IMPDH1/YB-1 axis to improve metastatic renal cancer treatment.

2020-03-03 | GSE146231 | GEO

An NSD3-targeting PROTAC suppresses the NSD3 and cMyc oncogenic nodes in cancer cells

Project description:Nuclear receptor binding SET domain protein 3 (NSD3), a gene located within the 8p11-p12 amplicon frequently detected in cancers, encodes a chromatin modulator and an attractive onco-target. However, agent that can effectively suppress the NSD3-mediated oncogenic actions is currently lacking. We report an NSD3-targeting proteolysis targeting chimera (PROTAC), termed MS9715, which achieves effective and specific depletion of NSD3 and interacting partners (including cMyc) in tumor cells. MS9715-induced NSD3 degradation relies on BI-9321, an antagonist module binding the PWWP1 domain of NSD3, and VHL, which is chemically conjugated to BI-9321 via a linker and VHL ligand module. Importantly, compared to BI-9321, a recently disclosed NSD3 antagonist, MS9715 is more potent in suppressing growth of the NSD3-dependent hematological cancer including models of MLL-rearranged acute myeloid leukemia (AML) and B-cell acute lymphoblastic leukemia (B-ALL) and multiple myeloma (MM), and uniquely mediate simultaneous depletion of cellular NSD3 and cMyc. Transcriptome profiling further demonstrates effective actions of MS9715 but not BI-9321 in suppressing both NSD3- and cMyc-associated gene-expression programs, a phenomenon reminiscent of the CRISPR/cas9-mediated knockout (KO) of NSD3. Together, this study reports a first-in-class NSD3 PROTAC/degrader suitable for co-suppressing NSD3- and cMyc-related oncogenic nodes in cancer cells, suggesting a novel therapeutic strategy.

2021-08-27 | PXD021901 | Pride

Mechanism and transcriptional program of YB-1 in breast cancer cell lines.

Project description:YB-1 controls epithelial-mesenchymal transitions by restricting translation of growth-related mRNAs and enabling expression of EMT-inducing transcription factors. We used microarrays to characterize the direct transcriptional and indirect translational regulation of mRNAs by exogenous YB-1 in breast cancer cell lines. Keywords: gene expression profiling To evaluate this in a genome-wide manner we compared microarray expression profiles of total mRNA and mRNAs isolated from Ps (translationally active) or post-Ps (translationally inactive) fractions of MCF10AT-MSCV vs. MCF10AT-YB-1 cells

2008-10-30 | E-GEOD-13410 | biostudies-arrayexpress

Transcriptome (RNA-Seq), translatome (Ribo-Seq), and YB-1/YB-3-bound mRNAs (RIP-Seq) of HEK293T, HEK293TdeltaYB-1, and HEK293T+HA-YB-1 cells

Project description:We present results of RNA-Seq, Ribo-Seq, and RIP-Seq (YB-1, YB-3) experiments performed in HEK293T cells, as well as in HEK293T cells with YB-1 knockout and overexpression. The data shows YB-1 function as a global translation inhibitor and YB-3 ability to substitute YB-1 in its function in YB-1 knockout mutant.

2020-01-08 | GSE130781 | GEO

The effects of YB1 knockdown on global gene expression in tumour cell lines.

Project description:Y-box binding factor 1 (YB1) has been associated with prognosis in many tumor types. Reduction of YB-1 inhibits tumor cell growth in vitro and in vivo

2011-11-30 | GSE28433 | GEO

Investigating the changes in gene expression of liver tissue exposed to phenanthrene over 72hr

Project description:FHM were exposed to 29ng/L phenanthrene. Fish were euthanized and samples taken after 24, 48 and 72hr. There were 28 samples analyzed; control liver tissues at 24hr (n=4) 5) phen treated liver tissues at 24hr 5) control liver tissues at 48hr 5) phen treated liver tissues at 48hr 5)control liver tissues at 72hr 4)phen treated liver tissues at 72hrs. There was a total of 28 microarrays processed.

2013-08-27 | E-GEOD-44840 | biostudies-arrayexpress

Requirements for multivalent Yb body assembly in transposon silencing in Drosophila

Project description:Female sterile (1) Yb (Yb) is a primary component of Yb bodies, perinuclear foci known as the site of PIWI-interacting RNA (piRNA) biogenesis in Drosophila ovarian somatic cells. Yb consists of Helicase C-terminal (Hel-C), RNA helicase and extended Tudor (eTud) domains. We previously showed that the RNA helicase domain is necessary for Yb−RNA interaction, Yb body formation and piRNA biogenesis. Here, we investigated the functions of the two other domains and found that Hel-C and eTud are necessary for Yb to self-associate and to interact with RNAs and other Yb body components, respectively. Both domains were essential for Yb body formation and transposon silencing. Without eTud, piRNA production was completely impaired. Loss of Hel-C severely reduced the levels of transposon-targeting piRNAs, although genic piRNAs unrelated to transposon silencing were still produced. Similar phenotypes were observed when mutations in flamenco, the primary source of transposon-targeting piRNAs, led to the expression of attenuated RNAs. Yb bodies are liquid-like multivalent condensates whose assembly depends on Yb self-association and widespread Yb−flamenco RNA binding.

2019-04-29 | GSE121605 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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