Project description:Mate pair sequencing for the detection of chromosomal aberrations in patients with intellectual disability and congenital malformations

| PRJEB4453 | ENA

Extra-long mate-pair sequenicng of genome of BN Rats

Project description:Extra-long mate-pair sequenicng of genome of BN Rats to improve scaffolding of reference rat genome

2012-05-15 | E-MTAB-1082 | biostudies-arrayexpress

Osteosarcoma mate-pair and RNA-sequencing

Project description:DNA mate pair and RNA sequencing data of conventional osteosarcomas. Mate pair libraries, with average insert sizes of 2-4 kb, were prepared for sequencing using the Nextera Mate Pair Library Preparation Kit. Paired-end 76 base pair reads were generated using an Illumina NextSeq 500 sequencing instrument. Total RNA was enriched for polyadenylated RNA using magnetic oligo(dT) beads. Enriched RNA was prepared for sequencing using the TruSeq RNA Sample Preparation Kit v2 and paired-end 151 base pair reads were generated from the cDNA libraries using an Illumina NextSeq 500 instrument.

| EGAS00001003842 | EGA

Extra-long mate-pair sequenicng of genome of BN Rats

Project description:Extra-long mate-pair sequenicng of genome of BN Rats

| PRJEB3119 | ENA

Wheat chromosome 7A mate-pair data from flow-sorted chromosomes.

Project description:Wheat chromosome 7A mate-pair data from flow-sorted chromosomes.

| PRJEB26335 | ENA

Comparison of constitutional and replication stress-induced genome structural variation by SNP array and mate-pair sequencing

Project description:Copy number variants (CNVs) are a major source of genetic variation in human health and disease. Previous studies have suggested replication stress, such as that caused by the polymerase inhibitor aphidicolin, as a causative factor in CNV formation, but existing data are technically limited in the quality of the comparisons which can be made to experimentally induced variants. Here we used 1M feature single-nucleotide polymorphism (SNP) arrays and mate-pair sequencing as high resolution methods for characterizing CNVs in a common set of samples, to compare both the properties of constitutional and induced CNVs as well as the utility of the two methods in an experimental setting. Although the optimized methods provided complementary information, sequencing was more sensitive to small variants and provided superior structural descriptions that allowed some CNVs to be associated with inversions, ectopic duplications or LINE insertions. The majority of constitutional and all aphidicolin-induced CNVs appear to be formed via homology-independent mechanisms, while aphidicolin-induced CNVs were of a larger median size than constitutional events even when mate-pair data were considered. Aphidicolin thus appears to stimulate formation of CNVs that closely resemble human pathogenic CNVs and the subset of larger nonhomologous constitutional CNVs. One untreated and one aphidicolin-treated subclone of human fibroblast cell line HGMDFN090 were analyzed by Illumina HumanOmni1-Quad SNP array and low-density mate-pair sequencing.

2010-12-18 | E-GEOD-26121 | biostudies-arrayexpress

Auanema

Project description:Auanema sp. overview

| PRJNA1156888 | ENA