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Gene expression profiles upon knocking down Cops2 or Cops5 in mouse embryonic stem cells

ABSTRACT: To understand the role of Cops2 in mouse embryonic stem cells, we applied expression microarray analysis with GFP knockdown, Cops2 knockdown (2 different hairpins), and Cops5 knockdown mouse ESCs.

ORGANISM(S): Mus musculus

PROVIDER: GSE72436 | GEO | 2016/05/17

SECONDARY ACCESSION(S): PRJNA294058

REPOSITORIES: GEO

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Gene expression profiles upon knocking down Cops2 or Cops5 in mouse embryonic stem cells

Project description:To understand the role of Cops2 in mouse embryonic stem cells, we applied expression microarray analysis with GFP knockdown, Cops2 knockdown (2 different hairpins), and Cops5 knockdown mouse ESCs. Mouse ESCs were transfected with shGFP, shCops2(two different shRNAs), or shCops5 plasmids. 72 hours after transfection, cells were harvested for RNA prep and microarray analysis.

2016-05-17 | E-GEOD-72436 | biostudies-arrayexpress

Nascent transript profiling upon in mouse embryonic stem cells under control conditions or Phf5a knockdown

Project description:Phf5a regulates transcription elongation in mouse embryonic stem cells (ESCs), through regulation of the Paf1 complex. In this study we assayed nascent RNA profiling using global run-on sequncing in mouse ESCs under conditions of self-renewal, differentiation and Phf5a knockdown. These results revealed that genes positively regulated by Paf1 in ESCs exibit RNA elongation pausing on their promoters. We used conditions of self-renewal, differentiation, Phf5a knockdown and Paf1 knockdown to monitor nascent transcript expression changes during Phf5a depletion using global run-on RNA sequencing (GRO-seq). These results revealed that Phf5a through the control of Paf1 complex regulates pause release and elongation of pluripoency-associated genes in embryonic stem cells.

2016-08-31 | GSE73441 | GEO

Max is a repressor of germ-cell-related gene expression in mouse embryonic stem cells

Project description:Embryonic stem cells (ESCs) and primordial germ cells (PGCs) express many pluripotency-associated genes, but ESCs do not normally undergo conversion into PGCs. Thus, we predicted that there is a mechanism that represses PGC-related gene expression in ESCs. Here we identify genes involved in this putative mechanism, by using an ESC line with a Vasa reporter for an RNAi screen of transcription factor genes expressed in ESCs. We identify 5 genes that result in the expression of Vasa when silenced. Of these, Max is the most striking. Transcriptome analysis reveals that Max knockdown (KD) in ESCs results in selective, global derepression of germ-cell-specific genes. Max interacts with histone H3K9 methyltransferases and associates with the germ-cell-specific genes in ESCs. In addition, Max-KD results in a decrease in histone H3K9 dimethylation at their promoter regions. We propose that Max is part of a protein complex that acts as a repressor of germ-cell-related genes in ESCs. Gene expression profile of Vasa-positive cells isolated from Max knockdown ESCs was compared to that of normal ESCs and in vivo PGCs. As an ESCs sample, a mouse embryonic stem cell line that carries a Venus reporter driven by the Vasa gene promoter (VV3) was used for this study. VV3 ESCs were transfected with non-silencing negative control siRNA (AllStars) or siRNA against the Max gene. Vasa-positive cells were purified using fluorescence-activated cell sorting (FACS). As a PGCs sample, a mouse strain that carries a germ-cell-specific GFP reporter (Oct4M-NM-^TPE-GFP) was used. PGCs were also purified using FACS. RNA samples were isolated from each sample and labeled and hybridized to Agilent microarrays. Three biological replicates were performed for each group of samples.

2013-05-01 | E-GEOD-45181 | biostudies-arrayexpress

WTX interacts with the transcriptional regulator TRIM28 to mediate cellular differentiation

Project description:WTX encodes a tumor suppressor implicated in Wilms tumor and in mesenchymal differentiation, with distinct functions in the cytoplasm, at the plasma membrane and in the nucleus. Here we report that the transcriptional corepressor TRIM28 is the major binding partner for nuclear WTX. The WTX-TRIM28 interaction supports chromatin binding by TRIM28, enhancing transcriptional silencing of some TRIM28 target sequences. In mouse ES cells, where TRIM28-mediated silencing of repetitive sequences is best characterized, Wtx knockdown similarly derepresses endogenous retroviruses and LINE elements. We performed digital gene expression (DGE) profiling using Helicos RNA sequencing. Helicos sequencing does not involve an amplification step, hence it has less bias, especially in sequencing of repetitive elements. We sequenced RNA extracted from mouse ESCs harboring GFP, Wtx or Trim28 hairpins. The resulting sequence reads were aligned with the RefSeq database as well as Repbase, which is a database for the repetitive sequences.

2015-04-16 | E-GEOD-60418 | biostudies-arrayexpress

Gene expression profiling using RNA-sequencing in mouse embryonic stem cells under control conditions or Phf5a knockdown

Project description:Phf5a regulates transcription elongation in mouse embryonic stem cells (ESCs), through regulation of the Paf1 complex. In this study we assayed gene expression profiling using RNA-sequncing in mouse ESCs under conditions of self-renewal, Phf5a knockdown and Paf1 knockdown. These results revealed that Phf5a and Paf1 regulate similar gene expression signatures in mouse ESCs.

2016-08-31 | GSE86248 | GEO

RNA-sequencing analysis of VEGFR2 knocking down in retinal pigment epithelial (RPE) cells upon glucose depletion.

Project description:RNA-sequencing analysis was utilized to investigate the impact of VEGFR2 knockdown via siRNA on transcriptome profiling in primary human RPE cells under the glucose depletion condition compared to the control siRNA.

2021-06-16 | GSE164167 | GEO

Expression profiling from mouse embryonic stem cells (ESCs)

Project description:Sin3a, a known master scaffold, provides unique contact surfaces for interaction with particular accessory proteins to repress the transcription of specific genes. Surprisingly, our results also suggest that Sin3a has a role in transcriptional activation. We compared gene expression differences between Sin3a knockdown and control ESCs with mouse gene expression microarrays and identified an approximately equal distribution of up- and down-regulated genes following Sin3a knockdown in mouse ESCs. We propose that Sin3a collaborates with Tet1 to demethylate adjacent genomic regions and, ultimately, facilitates actively transcribed gene expression in mouse ESCs.

2018-05-01 | GSE104192 | GEO

Transcriptome of U251 cells knocking down RPL13

Project description:RPL13 was identified to be downregulated in brain of Alzheimer's disease (AD). To explore the involved pathways in response to RPL13 reduction, we knockdownRPL13 using siRNA in U251 cell line with a stably expressed mutant APP (K670N/M671L, U251-APP cells). RNA-seq (by IlluminaHiseq 4000) and following analyses were then performed to detect genes whose expression were influenced by RPL13 knockdown.

2023-12-31 | GSE101564 | GEO

ASXL1 Knock Down in Normal CD34+ Cord Blood and UKE1 Cell Lines

Project description:Gene expression analysis of Normal CD34+ Cord Blood and UKE1 cell lines treated with hairpins targeting ASXL1. Two independent studies where 1) CD34+ cord blood from normal donors were treated with either A) GFP Vector or B) ASXL1 specific short hairpin and 2) UKE1 cell lines treated with either A) GFP Vector or B) ASXL1 specific short hairpin.

2012-08-21 | E-GEOD-38692 | biostudies-arrayexpress

Identification of differentially expressed genes upon shRNA knockdown of TAL1 and its regulatory partners in T-ALL cells (Jurkat)

Project description:The oncogenic transcription factor TAL1/SCL is aberrantly overexpressed in over 40% of cases of T-cell acute lymphoblastic leukemia (T-ALL), emphasizing the importance of the TAL1-regulated transcriptional program in the molecular pathogenesis of T-ALL. Here we identify the core transcriptional regulatory circuit controlled by TAL1 and its regulatory partners HEB, E2A, GATA3, ETS1 and RUNX1 in T-ALL cells. We find that TAL1 forms an interconnected auto-regulatory loop with its partners, which contributes to the sustained upregulation of its direct target genes. Importantly, we also find the MYB oncogenic transcription factor is directly activated by the TAL1 complex and positively regulates many of the same target genes, thus forming a feed-forward positive regulatory loop that further promotes the TAL1-regulated oncogenic program. Two experiments were performed: 1. Duplicate hairpins for each transcription factor (TAL1, TCF12/HEB, TCF3/E2A, GATA3, MYB) and control hairpins (GFP and Luciferase) were used to idenfity the expression change in the T-ALL cell line (Jurkat) 2. Duplicate hairpins for RUNX1 and control hairpins (GFP and Luciferase) were used to idenfity the expression change in the T-ALL cell line (Jurkat)

2012-08-16 | E-GEOD-29179 | biostudies-arrayexpress

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