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Expression analysis of 3T3 cells that express Arabidopsis-derived Diaminopimelate Decarboxylase (DDC) in response to growth on meso-2,6-diaminopimelic acid (DAP) versus L-Lysine

ABSTRACT: This experiment aimed to investigate whether cells that express the L-Lysine-producing enzyme DDC exhibit any mRNA changes when grown on precursor DAP relative to L-Lysine. Total RNA obtained from DDC-expressing 3T3 cells after 3 days in culture with amino acid precursor DAP, L-Lysine, or starved of both.

ORGANISM(S): Mus musculus

SUBMITTER: Nicholas Gauthier

PROVIDER: E-GEOD-43894 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression analysis of 3T3 cells that express Arabidopsis-derived Diaminopimelate Decarboxylase (DDC) in response to growth on meso-2,6-diaminopimelic acid (DAP) versus L-Lysine

Project description:This experiment aimed to investigate whether cells that express the L-Lysine-producing enzyme DDC exhibit any mRNA changes when grown on precursor DAP relative to L-Lysine.

2013-06-30 | GSE43894 | GEO

Expression analysis of MDA-MD-231 cells that express lysine racemase (lyr) when grown on D-Lysine versus L-Lysine

Project description:This experiment aimed to investigate whether cells that express the L-Lysine-producing enzyme lyr exhibit any mRNA changes when grown on precursor D-Lysine relative to L-Lysine. Total RNA obtained from lyr-expressing MDA-MB-231 cells after 3 days in culture with amino acid precursor D-Lysine, L-Lysine, or starved of both.

2013-06-30 | E-GEOD-43895 | biostudies-arrayexpress

SWIZ DAP-Seq

Project description:SWIZ DAP-Seq

| PRJEB42851 | ENA

Expression analysis of Mll3 knockdown p53-/- HSPC vs. control p53-/- HSPC

Project description:Recurring deletions of chromosome 7 and 7q [-7/del(7q)] occur in myelodysplastic syndromes and acute myeloid leukemia (AML) and are associated with poor prognosis. However, the identity of specific tumor suppressors on 7q remains elusive. Using RNAi and CRISPR/Cas9 approaches, we show that a ~50% reduction in gene dosage of the mixed lineage leukemia 3 (MLL3) gene, located on 7q36.1, cooperates with other events occurring in -7/del(7q) AMLs to promote leukemogenesis. Mll3 suppression impairs the differentiation of HSPC. Interestingly, Mll3 suppressed leukemias, like human -7/del(7q) AMLs, are refractory to conventional chemotherapy but sensitive to the BET inhibitor JQ1. Thus, our mouse model functionally validates MLL3 as a haploinsufficient 7q tumor suppressor, and suggests a therapeutic option for this aggressive disease. Total RNA obtained from sorted lin-ckit+ hematopoietic stem and progenitor cells of recipient mice transplanted with shRen;p53-/- or shMll3;p53-/- cells at 6 weeks after transplant

2014-03-19 | E-GEOD-54313 | biostudies-arrayexpress

The DNA affinity purification DAP-Seq assay [ChIP-seq]

Project description:As 5-15% of higher eukaryotes genes are transcription factors (TFs), the lack of transcription factor binding site (TFBS) information for most factors in most organisms limits the study of gene regulation. Here we describe a next-generation sequencing method, DNA affinity purification (DAP-Seq), an in vitro gDNA/TF interaction assay that produces whole-genome TFBS annotation for any factor from any organism. Like ChIP-Seq, DAP-Seq resolves TFBS as discrete peaks at genomic locations which allows for accurate motif prediction direct assignment of functionally relevant target genes, and shows better overlap with ChIP-Seq peaks than indirect motif assignment approaches. We applied DAP-Seq to a set of 50 transcription factors in eight Arabidopsis thaliana and one Zea Mays families to gain novel biological insight into TFBS architectures, functions, evolution and methylation-sensitivity. Overall, DAP-Seq offers a low-cost high-throughput approach to identify TFBS in native sequence context for any organism complete with all DNA chemical modifications.

2016-05-25 | GSE60142 | GEO

Expression analysis of MDA-MD-231 cells that express lysine racemase (lyr) when grown on D-Lysine versus L-Lysine

2013-06-30 | GSE43895 | GEO

DAP-seq reveals FvSEP3 directly targets downstream genes relevant to strawberry fruit ripening

Project description:To better understand FvSEP3-mediated transcriptional regulation of fruit ripening, we performed DNA affinity purification sequencing (DAP-seq) to uncover FvSEP3 directly binding sites at the genome level. For DAP-seq analysis, the recombinant FvSEP3 fusion protein was used to purify the sheared genomic DNA of strawberry fruits. Two independent biological replicates of DAP-seq and DNA 'input' negative control libraries were prepared and submitted for deep sequencing.

2024-11-05 | GSE260824 | GEO

eQTL analysis of 5 DAP maize kernel

Project description:Kernel development is accompanied by complex gene networks. Expression quantitative trait loci (eQTL) analysis is an efficient way to detect the regulatory elements of genes, especially the trans-eQTLs help to construct the regulatory networks of genes and contribute to a better understanding of the intrinsic mechanisms of biological processes. Till now, the 15 DAP (day after pollination) eQTL has been elucidated in maize kernel, but little is known about the early stage. Here, we conduct eQTL analysis for 5 DAP maize kernel using 318 maize inbred lines. The results will provide insights into the genetic basis of early kernel development.

2019-10-01 | GSE110315 | GEO

Transcriptional profiling of turkey muscle satellite cells transfected with DAP-siRNA during proliferation and differentiation

Project description:In this study, we directly compared turkey muscle satellite cell gene expression between satellite cells with the gene Death-Associated Protein (DAP) knocked down by siRNA transfection and those transfected with a lipofectamine control using our 6K Turkey Skeletal Muscle Long Oligo (TSKMLO) microarray (GPL9788). The DAP gene was previously identified as differentially expressed by genetic line and during development of turkey skeletal muscle (Sporer et al., 2011). Gene expression changes were investigated in satellite cells after 72 h of proliferation and after 48 h of differentiation. We identified novel candidate genes and pathways as playing potentially crucial roles in the DAP-mediated attenuation of the normal processes of proliferation and differentiation in turkey satellite cells previously identified by Velleman et al. (submitted). This experiment was designed to investigate the role of DAP expression in turkey satellite cells during two crucial processes in muscle development: proliferation and differentiation. Satellite cells were isolated from 7-week-old turkeys from the RBC2 line. Cells were transfected with either DAP siRNA or a lipofectamine control; DAP expression was knocked down by over 50% with siRNA transfection (Velleman et al., submitted). Satellite cells were then induced to proliferate for 72h or differentiate for 48h; culture plates from each stage (n=4) were frozen until RNA extraction. Microarrays directly compared the DAP-knockdown to control from each of 4 culture plates and utilized a dye swap to equal 8 arrays for each of the cell developmental stages, proliferation and differentiation, and 16 arrays for the overall experiment investigating the role of DAP expression in satellite cell development and function. Hybridizations were performed in random order.

2012-05-31 | E-GEOD-35660 | biostudies-arrayexpress

Identification of NAC094-targeted genes using DNA affinity purification sequencing (DAP-seq)

Project description:To identify binding sites and nodule SAGs that are directly targeted by NAC094, we used DAP-seq, which allows the capture of the NAC094 regulatory targets at the whole-genome scale. A total of 2,819 binding peaks corresponding to 2,721 genes were identified from two repeats of the DAP-seq experiment.

2023-03-23 | GSE197359 | GEO

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