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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of human SH-EP neuroblastoma cell line with SOX11 overexpression as compared to control at 9h timepoint

ABSTRACT: RNA-seq to define downstream targets of adrenergic SOX11 upon 1ug/ml doxycyline inducible SOX11 overexpression in a SOX11 non-expressing mesenchymal cell line SH-EP. Analysis was performed 48h upon treatment with doxycycline, control samples are the untreated cells. 2 biological replicates were used.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Sarah-Lee Bekaert

PROVIDER: E-MTAB-11892 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNA-seq of human SH-EP neuroblastoma cell line with SOX11 overexpression as compared to control

Project description:RNA-seq to define downstream targets of adrenergic SOX11 upon 1ug/ml doxycyline inducible SOX11 overexpression in a SOX11 non-expressing mesenchymal cell line SH-EP. Analysis was performed 48h upon treatment with doxycycline, control samples are the untreated cells. 3 biological replicates from different monoclonal expansions (F2, C11, G2) of SH-EP cells were used.

2022-12-13 | E-MTAB-9338 | biostudies-arrayexpress

ATAC-seq of human SH-EP neuroblastoma cell line with SOX11 overexpression as compared to control

Project description:ATAC-seq to define open and closed chromatin in the human SH-EP neuroblastoma cell upon 1ug/ml doxycyline inducible SOX11 overexpression. Analysis was performed 48h upon treatment with doxycycline, control samples are the untreated cells. 3 biological replicates from different monoclonal expansions of SH-EP cells were used.

2023-12-30 | E-MTAB-11898 | biostudies-arrayexpress

Methylation profiling by array shows that mIDH-associated DNA hypermethylation in acute myeloid leukemia reflects differentiation blockage rather than inhibition of TET-mediated demethylation

Project description:Isocitrate dehydrogenases 1 and 2 (IDH1/2) are recurrently mutated in acute myeloid leukemia (AML), but their mechanistic role in leukemogenesis is poorly understood. The inhibition of TET enzymes by D-2-hydroxyglutarate (D-2-HG), which is produced by mutant IDH1/2 (mIDH1/2), has been suggested to promote epigenetic deregulation during tumorigenesis. In addition, mIDH also induces a differentiation block in various cell culture and mouse models. Here we analyze the genomic methylation patterns of AML patients with mIDH using Infinium 450K data from a large AML cohort and found that mIDH is associated with pronounced DNA hypermethylation at tens of thousands of CpGs. Interestingly, however, myeloid leukemia cells overexpressing mIDH, cells that were cultured in the presence of D-2-HG or TET2 mutant AML patients did not show similar methylation changes. In further analyses, we also characterized the methylation landscapes of myeloid progenitor cells and analyzed their relationship to mIDH-associated hypermethylation. Our findings identify the differentiation state of myeloid cells, rather than inhibition of TET-mediated DNA demethylation, as a major factor of mIDH-associated hypermethylation in AML. Furthermore, our results are also important for understanding the mode of action of currently developed mIDH inhibitors.

2017-09-15 | E-MTAB-6059 | biostudies-arrayexpress

SILAC quantification of proteins in the control and UFBP1-expressing MGC803 cells

Project description:In this project, we used SILAC quantitative proteomics to identify proteins that are differentially regulated by UFM1-binding and PCI domain-containing protein 1 (UFBP1, also called DDRGK domain-containing protein 1 or DDRGK1) in a gastric cancer cell line. The aim of this study is to discover the proteins that are responsible for the biological function of UFBP1.

2021-02-15 | PXD013590 | Pride

Profiling of ADAM12S regulated proteins in H1688 cells

Project description:In this project, we used SILAC quantitative proteomics to identify proteins that are differentially regulated by the short secreted form of A Disintegrin And Metalloproteinase 12, ADAM12S, in a small cell lung cancer cell line H1688. The aim of this study is to discover the proteins that are responsible for the cell proliferation, migration, and invasion and then to elucidate the molecular mechanism by which ADAM12S promotes these processes in small cell lung cancer cells.

2021-02-15 | PXD013242 | Pride

RNA-seq of human IMR-32 neuroblastoma cell line with SOX11 knockdown as compared to control

Project description:RNA-seq to define downstream targets of adrenergic SOX11 upon knockdown using 4 siRNAs against SOX11 in the SOX11 expressing adrenergic cell line IMR-32. Analysis was performed 48h upon after nucleofections, control samples are treated with siNTC (non-targeted control). 4 biological replicates were used.

2022-12-13 | E-MTAB-9340 | biostudies-arrayexpress

ATAC-seq of human CLB-GA neuroblastoma cell line with SOX11 knockdown as compared to control

Project description:ATAC-seq to define open and closed chromatin in the human CLG-GA neuroblastoma cell line upon SOX11 knockdown using siRNAs. Analysis was performed 48h upon after nucleofection, control samples are treated with siNTC (non-targeting control). 2 biological replicates were used.

2023-12-30 | E-MTAB-9463 | biostudies-arrayexpress

High resolution ChIP sequencing reveals novel bindings targets and prognostic role for SOX11 in Mantle cell lymphoma (RNA-Seq)

Project description:SOX11 (Sex determining region Y-box 11) expression is specific for MCL as compared to other Non-HodgkinM-bM-^@M-^Ys lymphomas. However, the function and direct binding targets of SOX11 in MCL are largely unknown. We used high-resolution ChIP-Seq to identify the direct target genes of SOX11 in a genome-wide, unbiased manner and elucidate its functional significance. Pathway analysis identified WNT, PKA and TGF-beta signaling pathways as significantly enriched by SOX11 target genes. qCHIP confirmed that SOX11 directly binds to individual genes in these pathways in both MCL cell lines and patients. Interrogation of an eighty-two patientM-BM- gene-expression dataset demonstrated that SOX11 mRNA expression was inversely proportional to Ki-67, a marker of cell proliferation. Functional studies using RNA interference demonstrate that SOX11 directly regulates WNT signaling and modulates chemotherapy sensitivity to cytarabine in MCL. We analyzed SOX11 expression in three independent well-annotated tissue microarrays from the University of Wisconsin (UW), Karolina Institute and British Columbia Cancer Agency (BCCA). Our findings suggest that high SOX11 expression is associated with improved survival in a subset of MCL patients, particularly those treated with intensive chemotherapy incorporating cytarabine. Transcriptional regulation of WNT and other biological pathways affects by SOX11 target genes may help explain the impact of SOX11 expression on patient outcomes. RNA-seq experiments studying SOX11-mediated regulation of gene transcription by examining genes differentially expressed following SOX11 depletion in 3 MCL cell lines, Granta-519, Z138 and JEKO-1

2014-08-07 | E-GEOD-52148 | biostudies-arrayexpress

Sox11 loss-of-function mutant cortex at E17.5

Project description:Expression profiling of cortex from embryonic day (E) 17.5 telencephalon of Sox11(+/+) and Sox11(-/-) mouse embryos. Sox11 is implicated in regulating proliferation, neuronal migration and differentiation. We used microarray to identify genes that were differentially expressed in the cortex in the wild type and Sox11 knockout embryos at E17.5. To uncover the molecular mechanisms undelying the function of Sox11 in cortical development, we conducted microarray analysis of E17.5 cortices from wild type and Sox11(-/-) mice. Total RNA was isolated from the cortex of one wild type embryo and one Sox11(-/-) littermate at E17.5. cRNA probe synthesis, hybridization, scanning, and data collection were performed following the manufacturer's instruction.

2013-07-11 | E-GEOD-44308 | biostudies-arrayexpress

RNA-seq of human CLB-GA and NGP neuroblastoma cell lines with SOX11 knockdown as compared to control

Project description:RNA-seq upon SOX11 knockdown in the neuroblastoma cell lines CLB-GA and NGP. Cells were nucleofected with a pool of four different siRNAs targeting SOX11 and a non-targeting control (NTC). Analysis was performed 2 days upon SOX11 knockdown, including four biological replicates per condition.

2022-12-13 | E-MTAB-11883 | biostudies-arrayexpress

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