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

Effect of OVO-like 1 knockdown on global transcript expression in differentiated BeWo trophoblast cells

ABSTRACT: We had previously discovered that the transcription factor OVO-like 1 (OVOL1) was highly induced during trophoblast differentiation. In this study, we used an lentiviral shRNA strategy to decrease OVOL1 expression in BeWo trophoblast cells. Control cells were transduced with shRNAs targeting no known mammalian transcript (shCont). Following stimulation of differentiation (48h exposure to 8-bromo-cyclic adenosine monophosphate), a RNA-seq approach was used to determine global transcript differences in OVOL1-knockdown cells compared to control cells. Trophoblast cells transduced with control shRNAs were used as controls. Cells transduced with shRNAs targeting OVOL1 were used as treatment. All cells received 250 uM 8-bromo-cyclic adenosine monophosphate to stimulate differentiation. Three independent replicates of control and treatment groups were analyzed.

ORGANISM(S): Homo sapiens

SUBMITTER: Stephen Renaud

PROVIDER: E-GEOD-66962 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Effect of OVO-like 1 knockdown on global transcript expression in differentiated BeWo trophoblast cells

Project description:We had previously discovered that the transcription factor OVO-like 1 (OVOL1) was highly induced during trophoblast differentiation. In this study, we used an lentiviral shRNA strategy to decrease OVOL1 expression in BeWo trophoblast cells. Control cells were transduced with shRNAs targeting no known mammalian transcript (shCont). Following stimulation of differentiation (48h exposure to 8-bromo-cyclic adenosine monophosphate), a RNA-seq approach was used to determine global transcript differences in OVOL1-knockdown cells compared to control cells.

2015-08-01 | GSE66962 | GEO

Gene expression in undifferentiated or cyclic adenosine monophosphate-exposed BeWo trophoblast cells

Project description:BeWo trophoblast cells differentiate in response to expsure to cyclic adenosine monophosphate (cAMP) analogs. Differentiation includes syncytialization (fusion) and hormonogenesis. The goal of this study was to globally determine transcripts differentially expressed in BeWo trophoblast cells following a 24-h exposure to 250 uM 8-bromo-cAMP. 3 replicates undifferentiated BeWo trophoblast cells; and 3 replicates BeWo trophoblast cells treated with 250 uM 8-Br-cAMP for 24 h.

2015-08-01 | E-GEOD-66840 | biostudies-arrayexpress

Gene expression in undifferentiated or cyclic adenosine monophosphate-exposed BeWo trophoblast cells

2015-08-01 | GSE66840 | GEO

Homo sapiens

Project description:Gene expression in undifferentiated or cyclic adenosine monophosphate-exposed BeWo trophoblast cells

| PRJNA278069 | ENA

Lentiviral shRNA library screen to identify growth-related genes in malignant melanoma

Project description:Little is known about genes that promote melanoma cell growth and proliferation. siRNAs may be used to address the role of individual genesin these processes. RNAi library screens were used in the past to gain a comprehensive overview of all genes involved in cell growth, proliferation, migration and other cellular processes. A large-scale loss-of-function screen for eight different melanoma cell lines was performed using a pooled lentiviral shRNA library (GeneNet Human 50K lentiviral shRNA Library,cat#SI206B-1, System Biosciences) to identify genes relevant for melanoma cell growth and proliferation. shRNAs that lead to cell death or reduced growth of transduced melanoma cells are negatively selected and thereby underrepresented in the final cellular shRNA pool and vice versa. The shRNAs of the shRNA library (3-5 per gene) have complementary sequences to probes on the custom Affymetrix microarray HG-U133Plus2 and were analysed using this array. Well-known melanoma cell lines SK-Mel-103, A375, SK-Mel-147, SK-Mel-19, SK-Mel-28, SK-Mel-29, SK-Mel-5, WM3523cln6 were transduced with the lentiviral shRNA library and grown for 10 days under puromycin selection (day 10), control cells of respective cell lines were transduced and frozen immediately after transduction and genomic integration of shRNAs (day 0). Totel DNA was extracted and genomically integrated shRNAs were hybridized to Affymetrix microarrays (HG-U133Plus2.0 array).

2014-01-24 | E-GEOD-46675 | biostudies-arrayexpress

RNA-seq of human cancer cell line OVCA420* following TIGAR knockdown with shRNA

Project description:To identify differentially expressed genes following TIGAR knockdown, OVCA420* was transduced with TIGAR-targeting or non-targeting (control) shRNAs. 54 hours after the transduction, RNA was extracted and Illumina TruSeq RNA Sample Preparation Kit v2 was used to prepare the libraries. Each group contains 3 replicates. NextSeq 500 was used for sequencing.

2018-10-24 | E-MTAB-7284 | biostudies-arrayexpress

Genome-wide gene expression analysis of MDA-MB-468 human breast cancer cells treated with PLA2G7 shRNA

Project description:The aim was to investigate the functional role of PLA2G7 in breast cancer using PLA2G7 silencing in cultured breast cancer cells. For stable knockdown of PLA2G7, shRNAs were transduced to MDA-MB-468 cells before genome-wide gene expression analysis. Gene expression profiles of the PLA2G7 silenced samples were compared with the scrambled control treated samples and two replicate samples were studied for each treatment.

2017-06-02 | E-MTAB-5398 | biostudies-arrayexpress

shRNA cassette sequencing from disomic and trisomic fibroblasts cultured in the presence of shRNA kinome library for 14 days

Project description:Kinome-wide shRNA screen to identify kinases differentially required for survival of cells disomic and trisomic for chromosome 21 Cells were transduced in triplicate and propagated for 14 days to allow for enrichement or depletion of shRNAs from the population

2016-07-29 | E-GEOD-79840 | biostudies-arrayexpress

Genome-wide mapping of Eset-binding sites and H3K9me3 state in mouse embryonic stem cells

Project description:The histone H3 lysine 9 (H3K9) methyltransferase Eset is an epigenetic regulator critical for the development of the inner cell mass (ICM). Although ICM-derived embryonic stem (ES) cells are normally unable to contribute to the trophectoderm (TE) in blastocysts, we find that depletion of Eset by shRNAs leads to differentiation with the formation of trophoblast-like cells and induction of trophoblast-associated gene expression. Using ChIP-seq analyses, we identified Eset target genes with Eset-dependent H3K9 trimethylation. We confirmed that genes that are preferentially expressed in the TE (Tcfap2a and Cdx2) are bound and repressed by Eset. Single cell PCR analysis shows that the expression of Cdx2 and Tcfap2a is also induced in Eset-depleted morula cells. Importantly, Eset-depleted cells can incorporate into the TE of a blastocyst and subsequently placental tissues. Co-immunoprecipitation and ChIP assays further demonstrates that Eset interacts with Oct4, which in turn recruits Eset to silence these trophoblast-associated genes. Our result suggests that Eset restricts the extraembryonic trophoblast lineage potential of pluripotent cells and links an epigenetic regulator to key cell fate decision through a pluripotency factor. Keywords: Epigenetics Examine Eset-binding sites and compare the H3K9me3 state between Eset knockdown mouse ES cells and control knockdown mouse ES cells.

2009-11-04 | E-GEOD-17642 | biostudies-arrayexpress

Identification of Zdhhc20 knock-down cell palmitome

Project description:An shRNA screen to search for the mediators of pancreatic cancer metastasis identified palmitoyl transferase ZDHHC20 as a protein that mediates this process by promoting the outgrowth of metastatic cells in vivo. We sought to identify the changes in the palmitome of the cells expessing scrambled shRNA or shRNAs targeting Zdhhc20.

2023-02-09 | PXD038048 | Pride

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