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Peak analysis of small cell-free RNA in oral cancer plasma finds recurrently protected narrow regions with clinical potential

ABSTRACT: Peak analysis of small cell-free RNA in oral cancer plasma finds recurrently protected narrow regions with clinical potential

PROVIDER: PRJNA998367 | ENA |

REPOSITORIES: ENA

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Peak analysis of small cell-free RNA in oral cancer plasma finds recurrently protected narrow regions with clinical potential

Project description:Oral cancer is characterized by poor prognosis and low survival rate despite sophisticated surgical and radiotherapeutic modalities. Lymphatic metastasis of oral cancer is a complex process involving multiple post-transcriptional biological processes. Thus, feasible detection of cancer metastasis in plasma could be challenging and beneficial. We recruited patients with oral squamous cell carcinoma (OSCC), one of the common oral cancer types, and checked the lymphatic metastatic status and profiled small RNA in plasma samples.

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Project description:We sought to define the cutaneous response at 24 hours following erythemogenic doses of narrow-band UVB (NB-UVB, 312 nm peak) exposure and determine the differences between irradiated and non-irradiated skin.

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Expression data from mouse embryo (E5) cultured in the narrow and wide cavity

Project description:The mouse anterior-posterior (A-P) axis polarization is preceded by formation of the distal visceral endoderm (DVE). However, the mechanism of the emergence of DVE cells is not well understood. Here, we show by in vitro culturing of embryos immediately after implantation in micro-fabricated cavities (narrow; 90 micro-meter, wide; 180 miro-meter in diameter) that the external mechanical cues exerted on the embryo, i.e. cultured in the narrow cavity, are crucial for DVE formation as well as elongated egg cylinder shape. This implies that these developmental events immediately after implantation are not simply embryo-autonomous processes but require extrinsic mechanical factors. Further whole genome-wide gene expression profiles with DNA microarray revealed that no significant difference of transcripts were evident with or without mechanical cues except DVE-related markers. Thus, we propose that external mechanical cues rather than not specific molecular pathways can trigger the establishment of the A-P axis polarization, which is one of the fundamental proccesses of mammalian embryogenesis. To identify the differences between the embryos cultured with or without external mechanical cues, we collected mouse embryos at E5.0 and cultured in the narrow (90 micro-meter in diameter) or the wide (180 micro-meter in diameter) cavities for 8 hours for RNA extraction and hybridization on Affymetrix microarrays. Arrays were performed using Affymetrix mouse Gene 1.0 ST arrays. Analysis was performed on three biological replicates of the mouse embryos cultured in the narrow and wide cavities for 8 hours.

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Early Origins Meta-peak generation

Project description:modENCODE_submission_3441 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes. These experiments will be conducted in multiple cell types and developmental tissues. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Output file represents the union of the coordinates of peak data from various experiments peak calls. These unioned areas, referred to as meta-peaks, cover any genomic coordinate that has been experimentally shown to be capable of sustaining a peak.

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