Lacy Chick in town from Tennessee after IBS conference.
Meeting to discuss Aphaenogaster project:
Yesterday, test extraction to see if I can resolve last week’s failure to get DNA from Aphaenogaster. Set up two extractions
Followed tissue homogenization protocol without RNAse A incubation and shorten air-dry time after centrifugation.
Genomic-tip DNA extraction. Saw DNA nice and clear at isopropanol precipitation step in both tubes, qualitatively more in the Aphaenogaster tube!
Eluted in 500ul Buffer AE
Initially concerning, but I eluted with 500ul so 3.3 ng/ul * 500 ul = 1650 ng DNA! This would be quite good extraction if correct. The Pogo extraction less encouraging. Method seems to be quite finicky!
Message from Mahesh that he updated VGN website with results of BLAST of the transcriptome set against itself:
Precipitated Ap DNA with 70% ethanol, rehydrated in 100ul Buffer AE. Nothing. argh.
In process of modifying scripts to generate transcriptome using all reads from both colonies as done by Mahesh, but using diginorm. Then map each sample individually to combined transcriptome.
Interview questions to Richard Lenski
Roux, J., Privman, E., Moretti, S., Daub, J.T., Robinson-Rechavi, M. & Keller, L. (2013). Patterns of positive selection in seven ant genomes. arXiv:1311.4706 [q-bio]. Retrieved November 21, 2013, from http://arxiv.org/abs/1311.4706
Araújo, M.B., Ferri-Yáñez, F., Bozinovic, F., Marquet, P.A., Valladares, F. & Chown, S.L. (2013). Heat freezes niche evolution. Ecology Letters, 16, 1206–1219.
Signorotti, L., Jaisson, P. & d’ Ettorre, P. (2014). Larval memory affects adult nest-mate recognition in the ant Aphaenogaster senilis. Proceedings of the Royal Society B: Biological Sciences, 281, 20132579.
Brown, S., Savage, P.E., Ko, A.M.-S., Stoneking, M., Ko, Y.-C., Loo, J.-H. & Trejaut, J.A. (2014). Correlations in the population structure of music, genes and language. Proceedings of the Royal Society B: Biological Sciences, 281, 20132072.
Pickrell, J. (2013). Joint analysis of functional genomic data and genome-wide association studies of 18 human traits. bioRxiv. Retrieved November 19, 2013, from http://biorxiv.org/content/early/2013/11/19/000752
Johnson, V.E. (2013). Revised standards for statistical evidence. Proceedings of the National Academy of Sciences, 201313476.
In group meeting, discussed R markdown, data formatting and worked on analyzing a qPCR dataset of Andrew’s. Used
ddply to efficiently calculate slope for 8 targets!
ddply(datasub, .(target), summarize, slope = lm(Ct ~ log(dilution))$coef)
Gradually have realized that having all analyses for ‘climate cascade’ project in a single git repository is neither achievable or practical. Makes much more sense to have a github organization or lab (e.g GotelliLab) that has a fork of each individual’s github repository for a specific project or analysis. In this vein, transferring
ApTranscriptome project from within climate-cascade repository to a stand-alone project and repository. At same time, redoing analysis with the following changes:
--min_kmer_cov 2parameter which uses only those kmers occurring at least twice. this will control for Illumina sequencing error-rate
Then, as before, use UCLUST and CAP3 to remove redundant transcripts and merge overlapping transcripts, respectively. Map reads from each sample to assembly individually.
Phone call with Sonia Dobias, Qiagen Technical Service Project Leader
Guide to using ggplot2
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