Ena-DATASET-MCGILL-13-10-2014-13:37:46:242-181 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001001033 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:We performed whole exome sequencing (WES) on genomic DNA derived from two patients with Sotos Syndrome Features. Sequencing (100 base pair paired-end) was performed on an Illumina Hiseq 2000 sequencer after enrichment of 62Mb of exonic and adjacent intronic sequences with TruSeq Exome Enrichment Kit (Illumina, San Diego, CA, USA).
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Project description:Differential marking of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, histone density and H3K36me3 patterns in fission yeast
2011-03-16 | E-TABM-946 | biostudies-arrayexpress
Project description:Methods: The DNT cells incubation with anti-CD3/CD28 antibodies were stimulated with UDCA (60uM) for 48 hours, then transcriptome sequencing studies were performed on DNT cells RNA.Transcriptome sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and sequenced on an Illumina Hiseq platform (Illumina, San Diego, CA). Sequences were aligned to the reference genome with TopHat and processed with Cufflinks, which quantifies each transcript in each sample using reference annotations produced by the University of California Santa Cruz UCSC. Differentially expressed genes with a fold change of >=1.41 and pvalue <= 0.05 between UDCA treated and control DNT cells were submitted to GO and KEGG enrichment analysis, which uses unbiased methods to assess pathway enrichment.
2022-02-28 | GSE167116 | GEO
Project description:High-grade serous ovarian cancer (HGSC), the principal cause of death from gynecological malignancies in the world, has not significantly benefited from recent progress in cancer immunotherapy. While HGSC infiltration by lymphocytes correlates with superior survival, the nature of antigens that can elicit anti-HGSC immune responses is unknown. The goal of this study was to establish the global landscape of HGSC tumor-specific antigens (TSAs) using a mass spectrometry pipeline that interrogates all reading frames of all genomic regions. In 23 HGSC tumors, we identified 113 TSAs. Classic TSA discovery approaches focusing only on mutated exonic sequences would have uncovered only seven of these TSAs. Other mutated TSAs resulted from out-of-frame exonic translation or from non-exonic sequences. The most interesting group of TSAs (n = 94) derived from aberrantly expressed unmutated genomic sequences which are not expressed in normal tissues. These aberrantly expressed TSAs (aeTSAs) derived primarily from non-exonic sequences, in particular intronic (31%) and intergenic (22%). Their expression was regulated at the transcriptional level by variations in gene copy number and DNA methylation. While mutated TSAs were unique to individual tumors, aeTSAs were shared by a large proportion of HGSCs. We conclude that, in view of their number and the fact that they are shared by many tumors, aeTSAs may be the most attractive targets for HGSC immunotherapy.
2020-02-18 | PXD014062 | Pride
Project description:Gene expression profiling of 17 fresh frozen chondrosarcoma biopsies using the Human-6 v2 Expression BeadChip (Illumina Inc., San Diego, CA, USA). DNA copy number analyses was also performed in these tumors. Keywords: chondrosarcoma, gene expression profiling, Illumina
2009-04-01 | GSE12475 | GEO
Project description:To address co-transcriptional pre-mRNA processing events, Saccharomyces nascent RNA was isolated by chromatin fractionation and analyzed on a genome-wide high density tiling microarray. Co-transcriptional splicing efficiencies were derived by determination of intronic relative to exonic sequence concentrations.
2010-11-26 | GSE24040 | GEO
Project description:Intragenic microRNAs (miRNAs), including both intronic and exonic miRNAs, accounting approximately 50% of total mammalian miRNAs. Previous studies showed that intragenic miRNAs are often co-expressed with their host genes, and thus it was believed that intragenic miRNAs and their host genes are derived from the same primary transcripts. However, we provide evidence to show here that the observations from previous studies might be biased due to the small number and the predominance of "broadly conserved" intronic miRNAs they studied. We analyzed expression correlation of hundreds intragenic miRNAs with their host genes in two human and one mouse sample sets resulting from genome-wide miRNA arrays and exon arrays. We found that on average over 60% of intragenic miRNAs might not be co-expressed with their host genes. We show that evolution conservation is the most important factor related to the probability of co-expression of intragenic miRNAs with host genes, and the greater conservation degree of intragenic miRNAs is associated with the higher co-expression rate. Surprisingly, exonic miRNAs have a much lower rate of coexpression with host genes than intronic miRNAs, and 80% of them likely do not share primary transcripts with overlapping exons in biogenesis. Although "broadly conserved" intronic miRNAs have much shorter introns and a higher co-expression rate than (less broadly) "conserved" or "poorly conserved" ones, there is no consistently significant link between host intron size and co-expression probability of intronic miRNAs. In sum, our data suggest that the majority of intragenic miRNAs might be transcribed independently from their host genes. We used microRNA array and exon array to get the correlation between miRNA and mRNA in different datasets: 81 human leukemia samples and 14 mouse es-eb samples. In this study, we analyzed 26 mouse samples using the Affymetrix Mouse Exon 1.0 ST platform. Array data was processed by Affymetrix Expression Console. No techinical replicates were performed.
2011-03-02 | E-GEOD-27397 | biostudies-arrayexpress
Project description:Intragenic microRNAs (miRNAs), including both intronic and exonic miRNAs, accounting approximately 50% of total mammalian miRNAs. Previous studies showed that intragenic miRNAs are often co-expressed with their host genes, and thus it was believed that intragenic miRNAs and their host genes are derived from the same primary transcripts. However, we provide evidence to show here that the observations from previous studies might be biased due to the small number and the predominance of "broadly conserved" intronic miRNAs they studied. We analyzed expression correlation of hundreds intragenic miRNAs with their host genes in two human and one mouse sample sets resulting from genome-wide miRNA arrays and exon arrays. We found that on average over 60% of intragenic miRNAs might not be co-expressed with their host genes. We show that evolution conservation is the most important factor related to the probability of co-expression of intragenic miRNAs with host genes, and the greater conservation degree of intragenic miRNAs is associated with the higher co-expression rate. Surprisingly, exonic miRNAs have a much lower rate of coexpression with host genes than intronic miRNAs, and 80% of them likely do not share primary transcripts with overlapping exons in biogenesis. Although "broadly conserved" intronic miRNAs have much shorter introns and a higher co-expression rate than (less broadly) "conserved" or "poorly conserved" ones, there is no consistently significant link between host intron size and co-expression probability of intronic miRNAs. In sum, our data suggest that the majority of intragenic miRNAs might be transcribed independently from their host genes. We used microRNA array and exon array to get the correlation between miRNA and mRNA in different datasets: 81 human leukemia samples and 14 mouse es-eb samples. In this Series, we analyzed 81 human leukemia samples using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Expression Console. No techinical replicates were performed.
2011-03-02 | E-GEOD-27370 | biostudies-arrayexpress
Project description:Cytosine methylation analysis of genomic DNA from 31 MPAL patients bone marrow samples was performed using Illumina’s Infinium MethylationEPIC Kit (EPIC) that covers approximately 850,000 CpG probes (Illumina, San Diego, CA).
2018-04-24 | GSE113545 | GEO
Project description:Targeted capture of exonic and intronic regions of interest for the study of genomic alterations in multiple myeloma.
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