Magnoliopsida
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB16071 | ENA |
REPOSITORIES: ENA
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Project description:Degenerate oligonucleotide primer MIG-seq: an effective PCR-based Method for High through-put Genotyping.
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Project description:Evaluation of the applicability of dpMIG-seq in multiple crop species.
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Project description:High-throughput sequencing (HTS) of antibody amplicon libraries has become a powerful method in the emerging field of systems immunology. However, numerous sources of bias in HTS workflows may affect antibody repertoire data. A crucial step in antibody amplicon library preparation is the addition of adapter sequences, which are platform-specific short nucleotide sequences. In addition to conventional ligation-based adapter addition, it is also possible to use PCR-based methods such as Direct Addition (one-step adapter addition, DA) and Primer Extension (two-step adapter addition, PE), which have led to the lack of a consensus method and uncertainty regarding the impact of adapter addition on repertoire HTS data. Therefore, we compared all three methods by performing HTS with the Illumina MiSeq platform using total RNA originating from mouse antibody-secreting cells. We used technical replicate-based validation and clonal overlap and rank statistics to demonstrate that the two PCR-based methods produced HTS repertoires equivalent to ligation. Specifically: Nine BALB/c mice (8-10 weeks old, Charles River, specific-pathogen free) were immunized with 50 ug alum-precipitated chicken gamma globulin (CGG) conjugated to 4-hydroxy-3-nitrophenylacetyl (NP, NP-CGG, BioCat). Mice were sacrificed 14 days post-immunization (dpi) and their spleens and bone marrow (from femurs and tibia) were harvested. Antibody-secreting CD138-positive cells were enriched from spleen and bone marrow 14 dpi as previously described (Reddy, 2010, Nat Biotech).
2014-02-20 | E-MTAB-2226 | biostudies-arrayexpress
Project description:We have designed a method for direct measurement of in vitro noise. Using a synthetic STR sequencing library, we have measured the stutter patterns at various levels of PCR amplification during targeted amplification and library preparation processes
2019-01-26 | E-MTAB-7602 | biostudies-arrayexpress
Project description:Comparison between 3'-DGE and Conventional mRNA-Sequencing Methods
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Project description:A method for PCR-free library preparation for sequencing palaeogenomes
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Project description:Clinical biomarker discovery is often based on the analysis of human plasma samples. However, the high dynamic range and complexity of plasma pose significant challenges to mass spectrometry-based proteomics. Current methods for improving protein identifications require laborious pre-analytical sample preparation. In this study, we developed and evaluated a TMTpro-specific spectral library for improved protein identification in human plasma proteomics. The library was constructed by LC-MS/MS analysis of highly fractionated TMTpro-tagged human plasma, human cell lysates, and relevant arterial tissues. The library was curated using several quality filters to ensure reliable peptide identifications. Our results show that spectral library searching using the TMTpro spectral library improves the identification of proteins in plasma samples compared to conventional sequence database searching.
2023-10-24 | PXD042546 | Pride