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qGPL-1, qSPL-1-2, qSPL-8 and qYLD-4, which were introgressed from the donor parent revealed by background marker analysis using BC2F7 generation.
To further validate the sorted populations, we performed marker analysis using RT-qPCR for GATA4, SOX17 and CXCR4.
First-generation RAD marker analysis using microarrays has proven to be an effective method for mapping genomic alterations in various species.
Table 3 shows the statistical assessments and ancestry predictions for each case sample reported to the investigation based primarily on AIM-SNP likelihoods although an assessment was also made of the uni-parental marker analysis, using published data of Y-chromosome [4] [16] and mtDNA [17] [21] variability in each region.
ADSC surface marker analysis using flow cytometry was performed on a FACS Calibur unit (Becton Dickinson Biosciences, San Jose, CA, USA).
Additional experiments for intracellular cytokine staining (ICS) combined with surface marker analysis, using an 8-colour panel were performed on a BD Biosciences LSRII flow cytometer.
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The genetic marker analysis used for the discovery cohort was a custom Illumina array that composed of 1337 SNPS to tag common SNP variation across the 3.44 Mb of the MHC.
[14] The genetic marker analysis used for the replication cohort was a custom Illumina array that included the 1337 SNPS used to tag common SNP variation across the 3.44 MB of the MHC, 29 to 44 Mb as well as other SNPs in genes of interest that are neither described nor analyzed in the present manuscript.
Inheritance tests of these SNPs were examined in the linkage population by performing a χ test at 0.01 probability, and SNPs following Mendelian expectations were used in single-marker analysis using PLINK version 1.07.
We have shown that the RT-qPCR-based multi-marker analysis using the six genes: CCNE2, DKFZp762E1312, EMP2, MAL2, PPIC, or SLC6A8 more than doubled the number of positive patients with recurrent breast cancer compared to the analysis of hMAM or EpCAM gene expression alone.
Because chromosome 8 inversions have been reported in some populations [51], we verified our chromosome 8 marker order by conducting two-point marker-to-marker linkage analysis using LODLINK (S.A.G.E. v5.3); this analysis demonstrated that the published marker order was correct (data not shown).
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