79511f39-052c-47dc-9c90-6a0906a36915 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001006040 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:This data set contains for 10 Egyptian individuals the WGS reads mapping to chrM. These were subsequently used for haplogroup assignment.
| EGAD00001006038 | EGA
Project description:Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS. Raw sequencing data of 16S rRNA amplicon sequencing, shotgun metagenomics (short reads: Illumina; long reads: Oxford Nanopore Technologies), metagenome assembly, raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates) can be found at SRA in https://www.ncbi.nlm.nih.gov/bioproject/PRJNA682552. This dataset contains proteomics data for 2 conditions (heterotrophic and autotrophic growth conditions) in triplicates.
2021-05-17 | PXD023186 | Pride
Project description:Trisomy mapping has long been a powerful means for assigning genes to chicken microchromosome 16 (GGA16). The major histocompatibility complex (MHC-Y, MHC-B) and CD1 genes were previously assigned to GGA16 by trisomy mapping. Here we combined array comparative genomic hybridization (aCGH) with trisomy mapping to investigate unassigned genomic contigs (temporarily assigned to chrUn_random) by the chicken genome sequencing projects for sequences originating from GGA16. We used the Cornell Trisomy chicken line in our study, as this line contains an extra copy of GGA16 and crosses between these individuals generate disomic, trisomic, and tetrasomic GGA16 offspring. Through the analysis of these individuals with aCGH, we compare signal intensities from unknowns to those expected based on copy number, and putatively assign or reject assignment to GGA16 accordingly.
2013-11-22 | GSE47690 | GEO
Project description:RNA-seq and Iso-seq reads used used for gene charaterization. Pacbio amplicon sequencing reads used for mutant characterization
2022-03-31 | GSE197479 | GEO
Project description:RNA-seq and Iso-seq reads used used for gene charaterization. Pacbio amplicon sequencing reads used for mutant characterization
2022-03-31 | GSE197480 | GEO
Project description:Panicum virgatum AP13xWBC3xDAC6xVS16 - 217 - Mapping Population genome sequencing
| PRJNA363278 | ENA
Project description:We have performed a Proteogenomics meta-analysis of data sets deposited in ProteomeXchange: PXD000265, PXD000313, PXD000923, PXD001030, PXD001058, PXD002291, PXD002739, PXD002740 and PXD003156 and using 29 RNA-Seq data sets on rice (Oryza sativa). We created a search database comprising translated reads that had been mapped onto the rice genome, as well as officially annotated rice proteins sequences. The RNA Seq database was pre-processed to identify “novel transcripts” for those not mapping fully to an existing exon, and “novel junctions” for those reads mapped with a gap, implying a potential novel splice site that was not annotated in the official gene set. Confidentially identified “novel peptides” i.e. those mapping to a novel junction or novel transcript were post-processed to ensure that there were no other better explanations for the corresponding spectra e.g. peptide from a canonical gene with a modification or amino acid substitution. Data were exported from the pipeline in PSI mzIdentML 1.2 format, containing chromosomal coordinates, and further converted to PSI proBed format for genome visualisation. Novel peptides were searched against other plant databases using BLAST to see if they had predicted in genes from other species. A total of 1584 novel peptides were identified, mapping to ~700 genomic loci in which either new genes have been predicted (~100) or updates to existing gene models have been predicted (~600).
2018-10-30 | PXD008960 | Pride
Project description:This data set contains 1376 mass spectrometry reads from root, rhizosphere and leaf sample of Populus Trichocarpa, as well as associated controls. This metabolomics data set was collected as part of a larger campaign which complements the metabolomics data with metagenome sequencing, transcriptomics, and soil measurement data.
2022-12-12 | MSV000090886 | MassIVE
Project description:The phytochromes (PHYs) are a family of photoreceptors which absorb light of red and far-red wavelengths to modulate developmental responses in photosynthetic organisms. We developed knockout mutants of PHYB and PHYC in wheat and performed replicated RNA-seq studies to analyze and compare the regulons of each phytochrome under long day photoperiods. Illumina Truseq v2 RNA-seq libraries were constructed from four biological replicates of phyBnull mutants and their wild-type sister lines and of phyCnull mutants and their wild-type sister lines. Subsequently, the entire experiment was replicated. Reads were mapped to the draft assembly (v2.2) of the wheat genome provided by the International Wheat Genome Sequencing Consortium (IWGSC) and transcribed regions were identifed by mapping a non-redundant set of transcripts to this genomic assembly. Sequencing reads mapping uniquely within these identified transcribed regions were used to determine relative expression profiles. Loci which were differentially expressed in both experimental replicates were designated high-confidence PHYB-regulated and PHYC-regulated genes, respectively. A GTF file is provided detailing the location of the 150,754 loci within the IWGSC pseduomolecules and contig scaffold followed by the longest transcribed sequence mapping to this region. Most, but not all, transcribed sequences are annotated through Ensembl.
2016-06-29 | E-GEOD-79049 | biostudies-arrayexpress
Project description:OBJECTIVES: Amplification of the 11q13 locus is commonly observed in a number of human cancers including both breast and ovarian cancer. Cyclin D1 and EMS1 have been implicated as candidate oncogenes involved in the emergence of amplification at this locus. Detailed analysis of the 11q13 amplicon in breast cancer led to the discovery of four regions of amplification suggesting the involvement of other genes. Here, we investigate the role of EMSY, a recently described BRCA2 interacting protein, as a key element of the 11q13 amplicon in ovarian cancer. EMSY maps to 11q13.5 and is amplified in 13% of breast and 17% of ovarian carcinomas. METHODS: EMSY amplification was assessed by fluorescent in-situ hybridization (FISH) in 674 ovarian cancers in a tissue microarray and correlated with histopathological subtype and tumor grade. A detailed map of the 11q13 amplicon in 51 cases of ovarian cancer was obtained using cDNA-array-based comparative genomic hybridization (aCGH). To further characterize the role of EMSY within this amplicon, we evaluated both the amplification profiles and RNA expression levels of EMSY and two other genes from the 11q13 amplicon in an additional series of 22 ovarian carcinomas. : EMSY amplification was seen in 52/285 (18%) high grade papillary serous carcinomas, 4/27 (15%) high grade endometrioid carcinomas, 3/38 (8%) clear cell carcinomas, and 3/10 (30%) undifferentiated carcinomas. aCGH mapping of 11q13 in ovarian cancer showed that EMSY localized to the region with the highest frequency of copy number gain. Cyclin D1 and EMS1 showed a lower frequency of copy number gain. A highly significant correlation between EMSY gene amplification and RNA expression was also observed (P = 0.0001). This was a stronger correlation than for other genes at 11q13 including Cyclin D1 and PAK1. CONCLUSIONS: These findings support the role of EMSY as a key oncogene within the 11q13 amplicon in ovarian cancer. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2009-06-04 | GSE16408 | GEO