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ABSTRACT:
PROVIDER: PRJNA516389 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The 112kb congenic was identified via routine monitoring of the proximal and distal SNP sites of the heterozygous Line 4a C57Bl/6J (B6J)-DBA/2J (D2J) congenic offspring (PMID: 26658939). The 112kb congenic was identified via routine monitoring of the proximal and distal SNP sites of the heterozygous Line 4a C57Bl/6J (B6)-DBA/2J (D2) congenic offspring (Yazdani et al. 2015). Like the Line4a congenic, the original mouse of interest possessed a D2J SNP site at the proximal end of the D2J interval (rs29383600; mm9 - chr11:50,186,508, mm10 - chr11:50,373,006). To identify the distal D2J boundary of this new congenic, we generated a list of known SNPs within a roughly 55kb interval spanning downstream from the distal end of the originally characterized 206kb “critical interval” harboring Hnrnph1 and Rufy1 (mm9 - chr11:50,295,887-50,352,284, mm10 - chr11:50,482,385-50,538,782). Starting from the upstream portion of the interval, PCR primers were designed to every five SNPs, and 200bp region around each SNP was amplified, run on a 1.5% agarose gel, visualized for band specificity. Single appropriately-sized bands were then excised and gel purified (Promega Wizard SV Gel and PCR Clean-Up System, Cat A9281), and prepared for sanger sequencing (Genewiz). Using the SNP data from the Mouse Genome Project (Sanger Institute) for reference, the sequenced SNPs were deemed as either heterozygous for B6J and D2J SNPs or homozygous/wildtype B6J. The final SNP we identified as D2 was rs29459915 (mm9 - chr11:50,297,762, mm10 - chr11:50,484,260), and the first SNP we identified as B6 was rs254771403 (mm9 - chr11:50,300,250, mm10 - chr11: 50,486,748).
2019-11-30 | GSE141195 | GEO
Project description:TERT promoter muatations occur frequently in tumors of various origin. We here accessed the frequency of TERT pomoter mutations in 131 human primary neuroblastomas and 20 human neuroblastoma cell lines. No TERT promoter mutations were found in the 131 primary neuroblastomas. However, in the three cell lines SH-SY5Y, SH-EP and SK-N-SH a TERT promoter mutation was detected. Sanger sequencing indicated a homozygous mutation. To confirm loss of heterozygosity (LOH) we performed Affymetrix CytoScanHD SNP arrays. Indeed LOH could be confirmed.
2015-03-03 | GSE66422 | GEO
Project description:Clinical findings of this case has been reported previously by Sergio de Sousa (American Journal of Medical Genetics Part A 146A:2799–2803 (2008)). RSPO2 gene has been identified by our group (İstanbul, Turkey, 2014) as responsible gene for Tetra-Amelia with lung aplasia phenotype. To find causative pathogenic variations, sanger sequencing of fetal DNA was performed and did not reveal any variations. 300K SNP array was performed to analyse possible CNVs. A homozygous 154kb deletion on chr8 (deletion break points:108,809,266-108,963,256) covering intron 5 (partial), exon 6 and 3'UTR (partial) of RSPO2 gene was identified as the causative deletion.
2018-04-04 | GSE111781 | GEO
Project description:we combined their genome-wide profiles of tumors and normal adjacent tissues in 10 ccRCC patients. The results showed that 283 miRNAs were down-regulated and 187 up-regulated, meanwhile 7473 mRNAs were up-regulated and 3439 down-regulated in ccRCC. Expressions of 12 miRNAs and genes were validated in 10 patients we studied by RT-qPCR (validation rate from 60% to 100%). Differentially expressed gene analysis showed the collective change of miR-200 and SLC22A gene family, and pathway analysis revealed down-regulation of multiple metabolic pathways and up-regulation of focal adhesion, ECM-receptor interaction, etc. Moreover, A miRNA cluster located in chromosome Xq27.3 were significantly down-regulated in ccRCC, which were verified in 53 ccRCC patients by RT-qPCR (validation rate from 63.8% to 88.6%).56 and 586 potentially novel miRNAs and mRNA we detected according to statistical analyses. In addition, 14 miRNA candidates were randomly selected to validate using qRT-PCR and Sanger sequcencing technology, 10 of out 14 could be successfully amplified,.Plus, the sequences of all 5 randomly selected amplified products were confirmed by cloned Sanger sequencing.Our data demonstrated a combined profiling of miRNAs and mRNAs in ccRCC, which showed the decreased metabolism and the perturbation of renal cell function. Moreover, this study identified the expression alteration of a miRNA cluster on Xq27.3, which suggested its potential function in carcinogenesis of ccRCC
2013-09-29 | GSE24457 | GEO
Project description:This is the validation data for candidate de novo CNV calls made in the asthma trios by Itsara et al., Genome Research 2010. In this study, de novo CNV calls in the asthma data set were initially made with Illumina 550K SNP arrays. Validation was performed with custom Nimblegen array CGH for which DNA was available. de novo CNVs would be expected to validate in the child of each trio tested, and not be detected in either parent.
2010-09-01 | GSE23572 | GEO
Project description:With the whole genome SNP array information obtained from tumor and matched normal control, we could evaluate the acquired copy number alterations (CNAs) and uniparental disomies (UPDs) . Here we identified somatic mutations by whole-exome sequencing in 25 NKTCL patients and extended validation through targeted sequencing in an additional 80 cases.
2015-05-29 | GSE69382 | GEO
Project description:Trypanosoma vivax is a vector-borne blood parasite of cattle throughout sub-saharan Africa. For some years the genome sequence of this organism has been in development at the Wellcome Trust Sanger Institute and is shortly to be completed. Analysis of the genome has revealed various putative genes encoding unknown proteins. In an effort to validate these features we will sequence mRNA transcripts from the bloodstream stage of the genome strain Y486. Most of the novel gene families identified from the genome sequence are too diverse to be validated individually, i.e. through RT-PCR, so it is necessary to sequence all cellular transcripts. We hope to confirm the transcription of one or all members of the novel gene families from the resulting transcriptome. While essential for the scientific rigour of the present genome project, this transcriptome will also provide an additional resource for the longer-term benefit of the research community. ArrayExpress Release Date: 2011-02-16 Person Roles: submitter Person Last Name: Quan Person First Name: Lin Person Mid Initials: Person Email: ql3@sanger.ac.uk Person Phone: 01223 834244 Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: Investigator Person Last Name: Jackson Person First Name: Andrew Person Mid Initials: P Person Email: aj4@sanger.ac.uk Person Phone: 01223 834244 Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK Person Affiliation: Wellcome Trust Sanger Institute Person Roles: Project Coordinator Person Last Name: Sanders Person First Name: Mandy Person Mid Initials: J Person Email: mjs@sanger.ac.uk Person Phone: 01223 834244 Person Address: Wellcome Trust Genome Campus,Hinxton,Cambridge. CB10 1SA UK Person Affiliation: Wellcome Trust Sanger Institute
2011-07-14 | GSE30609 | GEO