Long Fragment enrichment
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ABSTRACT:
PROVIDER: PRJEB12651 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Microarray-based enrichment of selected genomic loci is a powerful method for genome complexity reduction. Since the vast majority of exons in vertebrate genomes are smaller than 150 nt, we have explored the use of short fragment libraries (85-110bp) to achieve higher enrichment specificity by reducing carryover and adverse effects of flanking intronic sequences. These short fragment libraries were enriched for 1.69 Mb of exonic sequences, using custom 244K microarrays, and sequenced using AB/SOLiD. High enrichment specificity (60 M-bM-^@M-^S 75%) was obtained at 67-213x average coverage, with 77-92% and 90-98% of targeted regions covered with more than 25% and 10% of the average coverage, respectively. As a more appropriate measure of the evenness of coverage, which is relatively independent of sequencing depth, we introduce the evenness of coverage parameter E. E values up to 75% were achieved. To verify the accuracy of SNP/mutation detection we evaluated 384 known non-reference SNPs in the targeted regions. At ~ 200x average sequence coverage, we were able to survey 96.4% of 1.69 Mb of genomic sequence with only 4.2% false negative calls while 3.6% of targeted regions were marked as unsurveyed. A total of 1197 new variants were detected. Verification revealed only 8 false positive calls, resulting in an overall false positive rate of less than 1 per ~200,000 bp (0.0005%, equivalent to an overall phred score of 55). 4 samples + capture design file
2010-02-01 | E-GEOD-18542 | biostudies-arrayexpress
Project description:Microarray-based enrichment of selected genomic loci is a powerful method for genome complexity reduction. Since the vast majority of exons in vertebrate genomes are smaller than 150 nt, we have explored the use of short fragment libraries (85-110bp) to achieve higher enrichment specificity by reducing carryover and adverse effects of flanking intronic sequences. These short fragment libraries were enriched for 1.69 Mb of exonic sequences, using custom 244K microarrays, and sequenced using AB/SOLiD. High enrichment specificity (60 – 75%) was obtained at 67-213x average coverage, with 77-92% and 90-98% of targeted regions covered with more than 25% and 10% of the average coverage, respectively. As a more appropriate measure of the evenness of coverage, which is relatively independent of sequencing depth, we introduce the evenness of coverage parameter E. E values up to 75% were achieved. To verify the accuracy of SNP/mutation detection we evaluated 384 known non-reference SNPs in the targeted regions. At ~ 200x average sequence coverage, we were able to survey 96.4% of 1.69 Mb of genomic sequence with only 4.2% false negative calls while 3.6% of targeted regions were marked as unsurveyed. A total of 1197 new variants were detected. Verification revealed only 8 false positive calls, resulting in an overall false positive rate of less than 1 per ~200,000 bp (0.0005%, equivalent to an overall phred score of 55).
2010-02-01 | GSE18542 | GEO
Project description:mRNA profiling of epididymal tissue of mice treated with obestatin, its N-terminal fragment residues 1-13 and a N-terminal fragment analog Nt8U
2012-02-08 | GSE35588 | GEO
Project description:mRNA profiling of epididymal tissue of mice treated with obestatin, its N-terminal fragment residues 1-13 and a N-terminal fragment analog Nt8U Four groups of six mice each were placed in individual metabolic cages and acclamatised to fasting from 6AM to 6PM and ad libitum water. The mice were administered 80ng/kg of the respective peptides intraperitoneally for 8 days and the epididymal tissue was subjected to mRNA extraction and microarray analysis.
2012-02-08 | E-GEOD-35588 | biostudies-arrayexpress
Project description:On mouse tiled microarrays (GPL17802), we profile 5hmC in WT mouse livers and brains following fragment enrichment by one of three affinity based techniques: i- antibody (HmeDIP), ii- Chemical capture (hMeSeal) and iii-JBP-1 protein affinity (JBP). HmeDIP and hMeSeal both return similar patterns of 5hmC whilst JBP enriched patterns (carriedo out on brain only) resemble background noise. 5hmC is largely found to reside in the bodies of active genes as well as being enriched over enhancer and promoter proximal regions. WT C57BL/6 mice aged 30-32 days old at time of organ removal. Tissues taken and frozen in liquid nitrogen prior to DNA extraction. Genomic DNA was sonicated (Bioruptor, Diagenode) to produce DNA fragments ranging in size from 200 to 1,000 bp, with a mean fragment size of around 300 bp. i- HmeDIP: antibody enrichment carried out as previously reported by Thomson et al 2013 (doi:10.1093/nar/gkt232). ii- HmeSeal: Enrichment based on the hMe-Seal based techniques described by Song et al 2010 (doi: 10.1038/nbt.1732) and marketed by Active motif under the name hydroxymethyl-collector kit. iii- JBP-1 affinity purification: Enrichment carried out using the Quest 5hmC DNA enrichment kit marketed by Zymo research.
2013-12-01 | E-GEOD-51577 | biostudies-arrayexpress
Project description:Whole genome sequence analysis of BT-474 using Complete Genomics’ standard and Long Read Fragment technologies
| PRJEB10587 | ENA
Project description:Synovial fluid was obtained weekly from nine horses throughout a 70-day study period and subjected to small RNA sequencing. Nine skeletally mature Standardbred trotters (seven mares and two geldings, 2.5-7 years old, weighing 397-528 kg) were included in this study. OA was surgically induced in the left middle carpal joint and the right middle carpal joint underwent sham surgery. Under arthroscopic guidance, an osteochondral fragment was created in the left middle carpal joint by chiselling off a fragment on the dorsodistal surface of the radial carpal bone using an 8 mm curved osteotome. The fragment was left adherent to the joint capsule proximally, and an incongruent defect bed of approximately 15 mm in width was created in the exposed subchondral bone between the fragment and radial carpal bone by drilling with an arthroscopic burr. Debris from the procedure was left inside the joint. Sham surgery (arthroscopy alone) was performed in the right middle carpal joint. All portals were sutured using 2-0 propylene (Surgipro, Medtronic Danmark A/S, Copenhagen, Denmark). Both carpi were bandaged with sterile dressings. Bandages were changed at day 2 and removed at day 5. Sutures were removed 10 days after surgery. From 2 weeks following OA induction and onwards, horses were exercised in 2 min of trot (4.4-5.3 m/sec) , 2 min of fast trot/gallop (9 m/sec) and 2 min of trot (4.4-5.3 m/sec) 5 days a week on a treadmill. The horses were euthanized on day 71 or 72 with an overdose of pentobarbital sodium (140 mg/kg, Euthasol Vet, Dechra Veterinary Products, Uldum, Denmark). One horse, Horse 5, was euthanized according to predefined humane endpoints at day 49, as it became lame at the walk.
2023-03-01 | E-MTAB-11840 | biostudies-arrayexpress
Project description:BCDIN3D regulates tRNAHis 3’ fragment processing
| PRJNA542102 | ENA
Project description:The spatial organization of cells within tissues is tightly linked to their biological function. Yet, methods to probe the entire transcriptome of multiple native tissue microenvironments at single cell resolution are lacking. Here, we introduce fragment-sequencing, a method that enables the transcriptomic characterization of single cells within spatially distinct tissue niches. Fragment-sequencing of the mouse metastatic liver revealed previously uncharacterized zonated genes and ligand-receptor interactions enriched in the different hepatic microenvironments and the metastatic niche.
2022-10-27 | GSE216189 | GEO
Project description:Cellular active small molecule inhibitors of Mycobacterium tuberculosis by NMR fragment screen.
2015-01-01 | GSE17424 | GEO