Short answer:  Yes, but not in the way we expected.First, here's a diagram showing the toxTA operon and the mutants we're examining:The grey bars show the extents of the deletions.  The ∆toxT and ∆toxTA mutants have a SpcR/strR cassette inserted at the deletion point, but the ∆toxA mutant has only a short 'scar' sequence at the deletion point.A few months ago I wrote a post about evidence that ToxA prevents transcription of the toxTA operon…

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Short answer:  Yes, but not in the way we expected.First, here's a diagram showing the toxTA operon and the mutants we're examining:The grey bars show the extents of the deletions.  The ∆toxT and ∆toxTA mutants have a SpcR/strR cassette inserted at the deletion point, but the ∆toxA mutant has only a short 'scar' sequence at the deletion point.A few months ago I wrote a post about evidence that ToxA prevents transcription of the toxTA operon…

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As part of our workup for the toxin/antitoxin manuscript, I want to find expression data for the homologs of the Haemophilus influenzae toxin and antitoxin genes.  The former post-doc recommends that I use NCBI's Gene Expression Omnibus ('GEO') for this.I'll need to learn how to search the GEO for specific accession data and data from specific taxa.I'll also need to find out the specific identifiers for the genes I'm interested in, in the species I'm…

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As part of our workup for the toxin/antitoxin manuscript, I want to find expression data for the homologs of the Haemophilus influenzae toxin and antitoxin genes.  The former post-doc recommends that I use NCBI's Gene Expression Omnibus ('GEO') for this.I'll need to learn how to search the GEO for specific accession data and data from specific taxa.I'll also need to find out the specific identifiers for the genes I'm interested in, in the species I'm…

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For the RNAseq part of the toxin-antitoxin paper, we should describe what we learn about how transfer to the competence-inducing starvation medium MIV affects genes not known to be involved in competence.The former undergrad left us with a set of Edge and DEseq2 analyses of changes in gene expression.  I discussed them here last summer (http://rrresearch.fieldofscience.com/2016/08/making-sense-of-rna-seq-comparisons.html).  Unfortunately I don't know how to properly interpret them.  The former post-doc suggested some analyses, but I'm reluctant to…

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For the RNAseq part of the toxin-antitoxin paper, we should describe what we learn about how transfer to the competence-inducing starvation medium MIV affects genes not known to be involved in competence.The former undergrad left us with a set of Edge and DEseq2 analyses of changes in gene expression.  I discussed them here last summer (http://rrresearch.fieldofscience.com/2016/08/making-sense-of-rna-seq-comparisons.html).  Unfortunately I don't know how to properly interpret them.  The former post-doc suggested some analyses, but I'm reluctant to…

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So, we did a massive RNAseq study of competence, with 124 samples of H. influenzae cultures at different growth stages, in the rich medium sBHI and the competence-inducing medium MIV, and with wildtype or mutant genes affecting competence.  (You can use the Search box to find all the previous posts about this work...)  Here I specifically want to think about what we learned about competence from the competence-induced cultures (cells transferred from sBHI to MIV).…

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Based on the analysis in the previous post, we can calculate lower-bound and upper-bound estimates for the Rd contamination levels  for each of our 12 'uptake' DNA samples (3 replicates each of 4 treatments).  And we can correct the lower-bound estimate (and maybe the upper-bound one too) to get an estimate of the true contamination level for each sample. But what do we do with this information?To think about this, first consider how we expect…

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OK, here's another try at understanding the interactions of repeated sequences, reads with no SNPs, and RD contamination in our DNA uptake sequencing data.A reminder of what the problem is that I'm trying to solve:  We have three 'uptake' samples for each treatment in our big analysis of DNA uptake specificity, but they can't be directly compared because, in the different samples, the recovered 'donor' DNA (from strain NP) probably has different levels of contamination by…

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I'm working on getting a clear plan for how we will infer uptake bias for each genome position (genome-wide uptake ratios) from our DNA uptake sequencing data.In principle, at each position in the genome, we just divide the sequencing coverage for the recovered DNA samples (taken up by cells) by the coverage for the input DNA.(We are using DNAs from two donor strains 'NP' and 'GG').  Below I'll just describe things for NP, but exactly…

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