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ABSTRACT:
PROVIDER: PRJEB90666 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Optimizing high molecular weight extractions
| PRJNA1114081 | ENA
Project description:Polyacrylamide gel electrophoresis (PAGE) is a powerful technique for separating proteins extracted from complex biological samples. Unfortunately, the difficulty of recovering intact proteins in high yield from polyacrylamide matrices often limits further analyses. We discovered that staining proteins with Coomassie brilliant blue (CBB) immediately after electrophoresis improves extraction efficiency. Post-staining, proteins widely varying in molecular weight were recovered at high efficiency with a 10 minute procedure that did not employ a surfactant. High recoveries were also obtained from dried, archived gels. Native-PAGE separated protein complexes larger than 400 kDa were recovered in an alternative procedure that substituted the mild detergent octyl-β-D glucopyranoside for CBB. Recovered proteins retained their native structure and were amenable to structural analysis by native mass spectrometry. The established workflows facilitate in-depth proteomic and protein structure analyses as well as the purification, storage, and transport of protein samples.
2020-07-13 | PXD010592 | Pride
Project description:To understand the molecular basis for differences of common bean wild-type and mutant in sulphur amino acid content, transcripts were profiled at four developmental stages of seeds from wild-type SARC1 and major seed storage protein-deficient line SMARC1N-PN1 using a CustomArray 90K array. Microarray data confirmed that transcripts of storage and sulphur-rich proteins and sulphur-metabolism related genes were differentially expressed between the lines. The common bean (Phaseolus vulgaris) mutant line, SMARC1N-PN1 and its wild type, SARC1 used in the microarray experiment were grown in the field in London, ON, in 2009. Four developmental stages of seeds, based on fresh seed weight, were harvested. The stages of seeds used are Stage IV M-bM-^@M-^S cotyledon, 25 mg seed weight; Stage V M-bM-^@M-^S cotyledon, 50 mg seed weight; Stage VI M-bM-^@M-^S maturation, 150 mg seed weight, corresponding to the most active phase of reserve accumulation; and Stage VIII M-bM-^@M-^S maturation, 380 mg seed weight, corresponding to the onset of desiccation, were harvested for total RNA extraction. Four biological replicates for Stage IV and V and 3 biological replicates for Stage VI and VIII.
2012-11-06 | E-GEOD-34233 | biostudies-arrayexpress
Project description:Extraction of high-molecular-weight DNA from Streptococcus spp. for long-read sequencing in resource-limited settings
| PRJNA1082471 | ENA
Project description:<h4><strong>BACKGROUND: </strong>We describe a new approach to the recovery of information from faecal samples, based on the analysis of the molecular signature generated by rapid evaporative ionisation mass spectrometry (REIMS).</h4><h4><strong>RESULTS: </strong>Faecal pellets from five different rodent species were analysed by REIMS, and complex mass spectra were acquired rapidly (typically a few seconds per sample). The uninterpreted mass spectra (signatures) were then used to seed linear discriminant analysis and classification models based on random forests. It was possible to classify each species of origin with a high rate of accuracy, whether faeces were from animals maintained under standard laboratory conditions or wild-caught. REIMS signatures were stable to prior storage of the faecal material under a range of different conditions and were not altered rapidly or radically by changes in diet. Further, within species, REIMS signatures could be used to discriminate faeces from adult versus juvenile mice, male versus female mice and those from three different laboratory strains.</h4><h4><strong>CONCLUSIONS: </strong>REIMS offers a completely novel method for the rapid analysis of faecal samples, extending faecal analysis (previously focused on DNA) to an assessment of phenotype, and has considerable potential as a new tool in the armamentarium of the field biologist.</h4>
2022-02-03 | MTBLS1095 | MetaboLights
Project description:Optimizing DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae direct from urine samples
| PRJEB35173 | ENA
Project description:The Guthrie 903 card archived dried blood spots (DBS) are a unique but terminal resource amenable for individual and population wide genomic profiling. The limited amounts of DBS-derived genomic DNA (gDNA) can be whole-genome amplified (WGA) producing sufficient gDNA for genomic applications, albeit with variable success, and optimizing the isolation of high-quality DNA from these finite, low-yield specimens is essential. Visual automated fluorescence electrophoresis (VAFE) is a novel QC technology affording precise quality, quantity and molecular weight of double-stranded DNA from a single microliter of sample. The VAFE QC data were correlated with subsequent sample performance in PCR, sequencing, and high-density comparative genome hybridization array. The Swedish Repository of DBS samples collected on Guthrie 903 cards for neonatal screening of inborn diseases provided deidentified 3mm blood spot punches. There were total of eight (8) samples representing two (2) decades; 1970s: 1975, 1976, 1977, 1978; 1980s: 1980, 1982, 1984, 1986. gDNA was extracted and whole genome amplified prior to aCGH experiments using control female reference genomic DNA. The objective was to show that large rearrangements (e.g. loss of chrX in male samples) can be detected in WGA gDNA from blood spots >30 years old.
2013-07-01 | E-GEOD-44249 | biostudies-arrayexpress