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Analysis of ARID3A regulated genes in K562 cells

ABSTRACT: To test the function and regulated genes of ARID3A gene, we conducted lentivirus-mediated short hairpin RNA (shRNA) against ARID3A in K562 cell line.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Xiong Ma

PROVIDER: E-MTAB-12603 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Arid3a is required for mammalian placenta development

Project description:Previous studies in the mouse indicated that Arid3a plays a critical role in the first cell fate decision required for generation of trophectoderm (TE). Here, we demonstrate that Arid3a is widely expressed during mouse and human placentation and essential for early embryonic viability. Arid3a is located within trophoblast giant cells and other trophoblast-derived cell subtypes in the junctional and labyrinth zones of the placenta. Conventional Arid3a knockout embryos suffer restricted intrauterine growth with sever defects in placental structural organization. Arid3a null placentas show aberrant expression of subtype-specific markers as well as significant alteration in inflammatory response-related genes, cytokines and chemokines. We provide evidence that BMP4-mediated induction of trophoblast stem (TS)-like cells from human induced pluripotent (iPS) stem cells results in ARID3A upregulation and cytoplasmic to nuclear translocation. Overexpression of ARID3A in human iPS and BMP4-mediated TS-like cells up-regulated TE markers, whereas pluripotent markers were down-regulated. Our results indicate that the roles of Arid3a are conserved and essential for mammalian placental development through regulation of both intrinsic and extrinsic developmental programs. Placentas of E10.5 and E11.5 wild type (WT) and Arid3a-/- mice were generated by deep sequencing, using Illumina

2016-07-01 | E-GEOD-79638 | biostudies-arrayexpress

CMK LC-MS/MS after CoIP of ARID3A

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Comparative transcriptome analysis in monocyte-derived macrophages of asymptomatic GBA mutation carriers and patients with GBA-associated Parkinson’s disease

Project description:We compared transcriptome of monocyte-derived macrophages of 5 patients with GBA-PD (4 L444P/N, 1 N370S/N) and 4 asymptomatic GBA mutation carriers (GBA-carriers) (3 L444P/N, 1 N370S/N) and 4 controls. We also conducted comparative transcriptome analysis for L444P/N only GBA-PD patients and GBA-carriers. Revealed deregulated genes in GBA-PD independently of GBA mutations (L444P or N370S) were involved in immune response, neuronal function. We found upregulated pathway associated with zinc metabolism in L444P/N GBA-PD patients. The potential important role of DUSP1 in the pathogenesis of GBA-PD was suggested.

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RNA sequencing of winner and loser hPSCs grown in either separate culture or upon co-culture.

Project description:The observation that human Pluripotent Stem Cells (hPSCs) may acquire non-random genetic changes during prolonged culture is a major concern for their use in regenerative medicine and disease modelling. The mechanisms through which genetically variant cells are selected for in culture remain poorly characterized. We have shown that the dominance of variant hPSCs with enhanced growth rates is enhanced through competitive interactions resulting in the elimination of the slower growing loser population. This experiment compares the gene expression of winner (H7v1,12,17q,20q-GFP) and loser (H7v1q) grown either in separate culture or competitively in co-culture together.

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RNA-Seq analysis of Arabidopsis heterozygous mutant of gene (AT1G31870), which encodes a pre-mRNA-splicing factor of RES complex protein against the wild type (Col)

Project description:The homozygous of mutants of Arabidopsis gene (AT1G31870) are lethal. The gene encodes a homolog of yeast BUD13 of RES complex, AtBUD13, which is involved in pre-mRNA splicing of target genes. To assay the introns characters of target genes of AtBUD13 in Arabidopsis thaliana, the siliques at 0, 1 and 2 days after pollination of wild type and heterozygous mutants were used for RNA-Seq.

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Arid3a modulates the first cell fate decision by direct regulation of both embryonic and extraembryonic gene expression (ChIP-Seq)

Project description:Arid3a, a transcription factor known for its requirement in B-lymphocyte development, has been recently identified as a member of ES cell pluripotency network. Arid3a is moderately expressed in ES cells, and its expression is gradually increased during differentiation. Since Arid3a shows the highest expression in placenta, we hypothesized that Arid3a may play important roles in TE development. We report that Arid3a is a central regulator of both TE-specific and pluripotency-associated gene expression during ES cell differentiation. While dispensable for self-renewal, we observed that knockdown of Arid3a delays differentiation of ES cells. Induction of Arid3a leads ES cells to promote differentiation, specifically towards TE lineage. Moreover, these Arid3a-overexpressing cells maintained in TE culture media are sufficient to generate functional trophoblast stem-like cells, suggesting roles of Arid3a in TE differentiation. By integrative analyses using the chromosomal targets of Arid3a with expression profiling, we revealed the dual roles of Arid3a, as a direct activator of TE-specific genes and a repressor of pluripotency-associated genes. We further revealed the repressive roles of Arid3a are mediated by histone deacetylases (HDACs). Taken together, our results demonstrate that Arid3a is a critical novel regulator in TE lineage specification. Arid3a ChIP was performed using bioChIP-sequencing. Control ChIP-sequencing was performed using BirA cells. HDAC1 ChIP was performed as native antibody ChIP-sequencing.

2014-10-16 | E-GEOD-56876 | biostudies-arrayexpress

Analysis of ARID3A regulated genes in K562 cells

Project description:Analysis of ARID3A regulated genes in K562 cells

| PRJEB59894 | ENA

Arid3a is required for mammalian placenta development

2016-07-01 | GSE79638 | GEO

Transcriptome Analysis of Avicel Utilization by Thermomyces lanuginosus

Project description:Thermomyces lanuginosus is a thermophilic fungus whose genome encodes many carbohydrate-active enzymes involved in Avicel degradation. This study examined and compared the transcriptomes of T. lanuginosus during cultivation on Avicesl or glucose. We identified approximately 4485 genes that showed expression differences when T. lanuginosus was cultured on Avicel compared to glucose. Functional annotation of up-regulated genes showed enrichment for proteins predicted to be involved in Avicel degradation, but also many genes encoding proteins of unknown function. Our study represents the first analysis of transcriptomes, with biologic replicates, generated by RNA-seq technology. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. mRNA profiles of 2-day old Thermomyces lanuginosus were generated by deep sequencing,in duplicate, using Illumina GAIIx.

2015-06-17 | E-GEOD-69763 | biostudies-arrayexpress

ARID3a is Required for Erythrocyte Lineage Differentiation of Hemin Stimulated Human K562 Cells

Project description:Inhibition of ARID3a by shRNA in hemin-induced K562 cells results in significant decrease of erythroid specific lineage factors and alpha-globin genes.

2021-09-25 | GSE131649 | GEO

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