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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Array comparative hybridization (array-CGH) for detection of gene dose alterations in VACTERL association [4x180k Array v.025990]

ABSTRACT: The aim of the study was to screen for pathogenic gene dose alterations in patients and fetal cases with VACTERL association using a 180K oligonucleotide microarray. The experiment was performed by hybridization of genomic DNA from patients, labelled with Cy3 fluorophore, with a mix of DNA from healthy sex-matched controls labelled with Cy5 fluorophore (fetal case FC17 was analysed with sex-mismatch for the control DNA). 36 patients/fetal cases were analyzed using a Oxford Gene Technology (OGT) 180K oligonucleotide platform with whole genome coverage (27 patients were analyzed on version 025990 and 9 patients on version 031035). The raw microarray image files were initially analyzed using the Feature Extraction software from Agilent Technologies. Further data analysis was performed using the CytoSure Interpret software from OGT.

ORGANISM(S): Homo sapiens

SUBMITTER: Johanna Winberg

PROVIDER: E-GEOD-51957 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Array comparative hybridization (array-CGH) for detection of gene dose alterations in VACTERL association [4x180k Array v.031035]

Project description:The aim of the study was to screen for pathogenic gene dose alterations in patients and fetal cases with VACTERL association using a 180K oligonucleotide microarray. The experiment was performed by hybridization of genomic DNA from patients, labelled with Cy3 fluorophore, with a mix of DNA from healthy sex-matched controls labelled with Cy5 fluorophore (fetal case FC17 was analysed with sex-mismatch for the control DNA). 36 patients/fetal cases were analyzed using a Oxford Gene Technology (OGT) 180K oligonucleotide platform with whole genome coverage (27 patients were analyzed on version 025990 and 9 patients on version 031035). The raw microarray image files were initially analyzed using the Feature Extraction software from Agilent Technologies. Further data analysis was performed using the CytoSure Interpret software from OGT.

2014-06-01 | E-GEOD-51956 | biostudies-arrayexpress

Array comparative hybridization (array-CGH) for detection of gene dose alterations in VACTERL association

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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A central role for TFIID in the pluripotent transcription circuitry [PP003]

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A central role for TFIID in the pluripotent transcription circuitry

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2013-03-21 | E-GEOD-33646 | biostudies-arrayexpress

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2014-03-20 | E-GEOD-51345 | biostudies-arrayexpress

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Project description:Pluripotent stem cells can be isolated from early embryos or induced by cell fusion, somatic nuclear transfer, or expression of a selected set of transcription factors. Embryonic stem (ES) cells are characterized by an open chromatin configuration and high transcription levels achieved via autoregulatory and feed-forward transcription factor loops. How the general transcription machinery is involved in pluripotency is unclear. Here, we show that TFIID knockdown affected the pluripotent circuitry in ES cells and inhibited reprogramming of fibroblasts. TFIID and pluripotency factors form a feed-forward loop to induce and maintain a stable transcription state. Strikingly, transient expression of TFIID subunits greatly enhanced reprogramming by Oct4, Sox2, Klf4 and c-Myc reaching efficiencies upto 50%. These results show that TFIID is a critical and selective component for transcription factor-mediated reprogramming. We anticipate that by creating plasticity in gene expression programs, basal transcription complexes such as TFIID assist reprogramming into different cellular states. Two Taf5 knockdown cell lines and two control knockdown lines were each grown in duplicate and analysed on microarray against a pool of RNA from the parental ES-cells

2013-03-21 | E-GEOD-33644 | biostudies-arrayexpress

Molecular characterization of tumor cells from the cerebrospinal fluid and matched primary tumors from metastatic breast cancer patients with leptomeningeal disease

Project description:We purified tumor cells in the CSF (M-bM-^@M-^\CSFTCM-bM-^@M-^]) from 15 metastatic breast cancer patients diagnosed with leptomeningeal disease using a two-step method involving immunomagnetic enrichment and fluorescence-activated cell sorting (IE/FACS). Magnetic beads coated with mAb to the epithelial cell adhesion marker (EPCAM) were used to enrich for tumor cells and were further purified by FACS analysis. For DNA profiling, isolated CSFTC were subjected to molecular characterization through genome-wide copy number analyses. Genomic analyses were then compared with those performed on the corresponding archival primary tumors. For RNA profiling, isolated CSFTC were then subjected to molecular characterization through gene expression profiling via QPCR analysis of 64 cancer-related genes CGH: 17 CSFTC samples from 13 patients were successfully profiled ,1 patient had 5 timepoints, 6 of 13 patients had matched to copy number data archival tumors RNA: 18 samples from 5 patients had successful gene expression data of the 64 genes measured in triplicates. For non-tumor controls, 9 of the samples had matching gene expression data from sorted leuckocytes (+CD45 cells) obtained from the same draw.

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TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS

Project description:TET proteins convert 5-methylcytosine to 5-hydroxymethylcytosine, an emerging dynamic epigenetic state of DNA that can influence transcription. Evidence has linked TET1 function to epigenetic repression complexes, yet mechanistic information, especially for the TET2 and TET3 proteins, remains limited. Here, we show a direct interaction of TET2 and TET3 with O-GlcNAc transferase (OGT). OGT does not appear to influence hmC activity, rather TET2 and TET3 promote OGT activity. TET2/3-OGT co-localize on chromatin at active promoters enriched for H3K4me3 and reduction of either TET2/3 or OGT activity results in a direct decrease in H3K4me3 and concomitant decreased transcription. Further, we show that Host Cell Factor 1 (HCF1), a component of the H3K4 methyltransferase SET1/COMPASS complex, is a specific GlcNAcylation target of TET2/3-OGT, and modification of HCF1 is important for the integrity of SET1/COMPASS. Additionally, we find both TET proteins and OGT activity promote binding of the SET1/COMPASS H3K4 methyltransferase, SETD1A, to chromatin. Finally, studies in Tet2 knockout mouse bone marrow tissue extend and support the data as decreases are observed of global GlcNAcylation and also of H3K4me3, notably at several key regulators of haematopoiesis. Together, our results unveil a step-wise model, involving TET-OGT interactions, promotion of GlcNAcylation, and influence on H3K4me3 via SET1/COMPASS, highlighting a novel means by which TETs may induce transcriptional activation. ChIP-Seq experiments were performed on Illumina HiScanSQ sequencer in wild-type HEK293T cells for H3K4me3 histone marks, O-GlcNAc and HCF1, for HT-TET2, HT-TET3 and HT-OGT in HEK293T cells overexpressing those three fusion proteins and in TET2 Kd HEK293T cells for H3K4me3 histone marks. ChIP-Seqs were also performed in mouse bone marrow tissues for H3K4me3 histone marks, O-GlcNAc, endogenous Tet2 and in Tet2 Ko bone marrow tissues for H3K4me3 histone marks.

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