Ena-DATASET-MUG-25-01-2020-09:49:23:596-166 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001005812 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Paired end shallow whole genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fractions in plasma DNA of renal cell carcinoma (RCC) patients (MonRec Cohort)
| EGAD00001005804 | EGA
Project description:Paired end shallow whole genome sequencing (sWGS) data of tumor tissue from RCC patients (DAIMOND cohort)
| EGAD00001005815 | EGA
Project description:Paired end shallow whole genome sequencing (sWGS) data of cell-free DNA from plasma and urine from RCC patients (DAIMOND cohort)
| EGAD00001005814 | EGA
Project description:Mutation analysis of 10 frequently mutated genes in renal cell carcinoma (BAP1, KDM5C, MET, MTOR, PBRM1, PIK3CA, PTEN, SETD2, TP53, VHL) in plasma DNA of RCC patients using a custom QIASeq panel (MonRec Cohort)
| EGAD00001005806 | EGA
Project description:A 2.077Mb (57306 probes) personalised capture panel [Tailored Panel Sequencing (TAPAS)] was designed based upon the somatic SNVs identified by WES of RCC patient FF and FFPE tissue samples and applied to cfDNA in plasma and urine.
| EGAD00001005813 | EGA
Project description:(23S)-23,25-Dihydroxycholecalciferol was converted into at least five metabolites in kidney homogenates prepared from 1,25-dihydroxycholecalciferol-treated chickens. One of these has been positively identified as 23,25,26-trihydroxycholecalciferol by u.v.-absorbance analysis, mass spectrometry and chemical formation of derivatives. 23,25,26-Trihydroxycholecaciferol produces 25-hydroxycholecalciferol-26,23-lactone when incubated in chick kidney homogenates.
| S-EPMC1158566 | biostudies-other
Project description:Gene conversion (GCV), a mechanism mediated by activation-induced cytidine deaminase (AID) is well established as a mechanism of immunoglobulin diversification in a few species. However, definitive evidence of GCV-like events in human immunoglobulin genes is scarce. The lack of evidence of GCV in human rearranged immunoglobulin gene sequences is puzzling given the presence of highly similar germline donors and the presence of all the enzymatic machinery required for GCV. In this study, we undertook a computational analysis of rearranged IGHV3-23(*)01 gene sequences from common variable immunodeficiency (CVID) patients, AID-deficient patients, and healthy individuals to survey "GCV-like" activities. We analyzed rearranged IGHV3-23(*)01 gene sequences obtained from total PBMC RNA and single-cell polymerase chain reaction of individual B cell lysates. Our search identified strong evidence of GCV-like activity. We observed that GCV-like tracts are flanked by AID hotspot motifs. Structural modeling of IGHV3-23(*)01 gene sequence revealed that hypermutable bases flanking GCV-like tracts are in the single stranded DNA (ssDNA) of stable stem-loop structures (SLSs). ssDNA is inherently fragile and also an optimal target for AID. We speculate that GCV could have been initiated by the targeting of hypermutable bases in ssDNA state in stable SLSs, plausibly by AID. We have observed that the frequency of GCV-like events is significantly higher in rearranged IGHV3-23-(*)01 sequences from healthy individuals compared to that of CVID patients. We did not observe GCV-like events in rearranged IGHV3-23-(*)01 sequences from AID-deficient patients. GCV, unlike somatic hypermutation (SHM), can result in multiple base substitutions that can alter many amino acids. The extensive changes in antibody affinity by GCV-like events would be instrumental in protecting humans against pathogens that diversify their genome by antigenic shift.
| S-EPMC3375636 | biostudies-literature
Project description:The conservation of virulence factors across the genus Acinetobacter based on a large-scale comparative genomics analysis
| PRJNA172672 | ENA
Project description:modENCODE_submission_59 This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis
2009-06-02 | GSE16281 | GEO
Project description:modENCODE_submission_59 This submission comes from a modENCODE project of Susan Celniker. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will generate over 600 RNA samples in biological triplicate and use them to generate expression profile maps detailing the sites of transcription across the fly genome using whole genome tiling arrays at 38 bp resolution as a broad survey of the transcriptome and 7 bp arrays resolution to identify at high resolution transcripts ends, splice sites, and small RNAs. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: Transcript tiling array analysis EXPERIMENT TYPE: Transcript tiling array analysis BIOLOGICAL SOURCE: Cell Line: ML-DmD32 TISSUE: dorsal mesothoracic disc GENOTYPE: y v f mal SEX: Unknown NUMBER OF REPLICATES: 3; Replicate 1 applied to 1 array(s), Replicate 2 applied to 1 array(s), Replicate 3 applied to 1 array(s), No dye swap. EXPERIMENTAL FACTORS: Cell Line ML-DmD32
2010-04-09 | E-GEOD-16281 | biostudies-arrayexpress