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To confirm this increase in intestinal Wnt signaling, we surveyed for expression of a number of Wnt pathway genes in isolated epithelial crypt cells using qRT-PCR.
When we surveyed for expression of Nlrp1b SVs in fourteen other tissues (Additional file 1: Table S1), we found that in contrast to Nlrp1a, Nlrp1b was expressed in all tissues of BALB/cJ animals, except the stomach.
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In summary, using a distant reference transcriptome resulted in a) fewer tags mapping, b) some genes not being surveyed for differential expression and c) lower than expected levels of expression for genes whose most abundant mapping position was not conserved.
Fifteen EST libraries from the DFCI Rice Gene Index (http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl gudb=Rice) were surveyed for the expression of each OXO gene by BLAST.edu/tgi/cgi-bin/tgi/gimain.pl gudb=Rice
A total of 24 normal tissues and 24 tumors were surveyed for CLDN expression.
To more completely understand the role(s) of Nlrp1 paralogs in mice, we surveyed for their expression in a large set of LT-resistant and sensitive mouse macrophages.
Y was the number of genes surveyed for differential expression by both platforms (the exact value of Y differed in separate analyses dependent on which reference transcriptome and mapping strategy was used for tag profiling).
When using the small A. thaliana dataset, the number of genes surveyed for gene expression increased with the number of allowed mismatches during mapping (from 3,884 genes in A0 to 5,233 genes in A1 to 5,490 genes in A2, Figure 2a) but did not reach the number of genes analyzed when using the small P. fastigiatum dataset.
To survey for the expression of different Nlrp1b (splice) variants in LT-resistant and sensitive macrophages, we designed two exon 2 specific primer sets that allowed us to distinguish the unique C57-SV1 and C57-SV2 transcripts from C57-SV3 all all other Nlrp1b variants.
To do so, we grouped patients based on established outcomes and surveyed for differences in BCAR3 expression between groups.
All cells in three randomly selected view fields (×10 magnification) were surveyed for CD44 and PLK1 expression, and the percentage of CD44high cells that were also PLK1high was calculated.
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