Ena-DATASET-SCI-19-05-2017-14:11:25:029-170 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001003342 | EGA |
REPOSITORIES: EGA
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Project description:Fusion transcripts and their exact breakpoints were identified in RNA-seq data (30X) of an ER-,HER2+ breast cancer. DNA-level breakpoints associated with the fusion events were determined by analyzing whole genome sequencing (WGS) data (30X) from the same donor. The RNA-seq and WGS data for this case were generated on the Illumina platform using standard protocols. The patient (MB-0152) derives from the METABRIC cohort for which array based copy number and gene expression data were previously described (EGAS00000000083).
| EGAS00001002475 | EGA
Project description:Identification of novel fusion transcripts in neuroblastoma
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Project description:12plex_wheat_2012-05 - 12plex-wheat_2012-05 - The objective is to better understand the adaptive response of the wheat plant to an elevated mean temperature. Besides the morphological and ecophysiological responses, the changes in the expression of genes are investigated. Two genotypes (SxB49 and SxB139) are subjected to two different temperature regimes during the lag-phase of the developing grains. The profiling of the accumulation of gene transcripts throughout 12 developmental stages is carried out using a custom-designed 12x135K Roche NimbleGen gene expression microarray comprising the most recent NCBI wheat contig assembly and annotation (about 45 000 unigenes). This should permit both the identification of differentially expressed genes after heat treatment and the comparison of the behaviours of two wheat genotypes (SxB139 and SxB49). - The effect of the temperature on the expression of genes along with the effect of genotype
2017-07-04 | GSE100642 | GEO
Project description:Rat liver microsomes were analysed using offline strong cation exchange fractionation followed by reverse-phase chromatography coupled to quadrupole-time-of-flight high-resolution mass spectrometry using trypsin and pepsin parallel digestions. MS/MS files were searched against the UniProt protein database (release date 12-07-2011, 241 MB) by ProteinPilot software (version 4.1) using Paragon algorithm with the following parameters: Protein identification with thorough ID search effort, iodoacetamide for cysteine alkylation and no specified proteolytic enzyme, species set for rattus norvegicus with ID focus on biological modifications. Detection protein threshold of unused ProtScore > 0.05 (confidence > 10.0%) with false discovery rate (FDR) analysis. MS tolerance 0.05 Da on precursor ions and 0.1 Da on fragments. Search was performed for +2 to +4 charge states.
2013-02-19 | PXD000128 | Pride
Project description:Staphylococcus aureus strain:05-25 Genome sequencing and assembly
| PRJNA248197 | ENA
Project description:Enterococcus casseliflavus 14-MB-W-14 Genome sequencing and assembly
| PRJNA179543 | ENA
Project description:Idiopathic achalasia is a relatively infrequent esophageal motor disorder for which major histocompatibility complex (MHC) genes are well-identified risk factors. However, no information about HLA-achalasia susceptibility in Mexicans has previously been reported. We studied a group of 91 patients diagnosed with achalasia and 234 healthy controls with Mexican admixed ancestry. HLA alleles and conserved extended haplotypes were analyzed using high-resolution HLA typing based on Sanger and next-generation sequencing technologies. Admixture estimates were determined using HLA-B and short tandem repeats. Results were analyzed by non-parametric statistical analysis and Bonferroni correction. P-values < 0.05 were considered significant. Patients with achalasia had 56.7% Native American genes, 24.7% European genes, 16.5% African genes and 2.0% Asian genes, which was comparable with the estimates in the controls. Significant increases in the frequencies of alleles DRB1*14:54 and DQB1*05:03 and the extended haplotypes DRB1*14:54-DQB1*05:03 and DRB1*11:01-DQB1*03:01, even after Bonferroni correction (pC<0.05), were found in the achalasia group compared to those in the controls. Concluding, the HLA class II alleles HLA-DRB1*14:54:01 and DQB1*05:03:01 and the extended haplotype are risk factors for achalasia in mixed-ancestry Mexican individuals. These results also suggest that the HLA-DRB1*14:54-DQB1*05:03 haplotype was introduced by admixture with European and/or Asian populations.
| S-EPMC6084941 | biostudies-literature
Project description:PurposePalbociclib is a cyclin-dependent kinase 4 and 6 inhibitor approved for advanced breast cancer. In the adjuvant setting, the potential value of adding palbociclib to endocrine therapy for hormone receptor-positive breast cancer has not been confirmed.Patients and methodsIn the prospective, randomized, phase III PALLAS trial, patients with hormone receptor-positive, human epidermal growth factor receptor 2-negative early breast cancer were randomly assigned to receive 2 years of palbociclib (125 mg orally once daily, days 1-21 of a 28-day cycle) with adjuvant endocrine therapy or adjuvant endocrine therapy alone (for at least 5 years). The primary end point of the study was invasive disease-free survival (iDFS); secondary end points were invasive breast cancer-free survival, distant recurrence-free survival, locoregional cancer-free survival, and overall survival.ResultsAmong 5,796 patients enrolled at 406 centers in 21 countries worldwide over 3 years, 5,761 were included in the intention-to-treat population. At the final protocol-defined analysis, at a median follow-up of 31 months, iDFS events occurred in 253 of 2,884 (8.8%) patients who received palbociclib plus endocrine therapy and in 263 of 2,877 (9.1%) patients who received endocrine therapy alone, with similar results between the two treatment groups (iDFS at 4 years: 84.2% v 84.5%; hazard ratio, 0.96; CI, 0.81 to 1.14; P = .65). No significant differences were observed for secondary time-to-event end points, and subgroup analyses did not show any differences by subgroup. There were no new safety signals for palbociclib in this trial.ConclusionAt this final analysis of the PALLAS trial, the addition of adjuvant palbociclib to standard endocrine therapy did not improve outcomes over endocrine therapy alone in patients with early hormone receptor-positive breast cancer.
| S-EPMC10476784 | biostudies-literature
Project description: Not available
| S-IHECRE00000022.1 | biostudies-other