Journal: Nucleic Acids Research

Article Title: Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape

doi: 10.1093/nar/gkn899

Figure Lengend Snippet: Schematic of the CLADE approach. CLADE as utilized in this study starts at the top of the schematic with an initial choice of DNA sequences. These sequences may be generated entirely in silico , or optionally, as with some of the sequences here, utilizing prior knowledge generated in vitro . These sequences are synthesized on a custom microarray and bound with the chosen ligand, here the APC protein. Analysis of binding intensities gives a distribution of fitnesses; the frequency distribution of Generation 1 binding to APC protein is shown by way of example. Some of these sequences are selected in silico , based on the in vitro score distribution, here using tournament selection (see Materials and methods section). These sequences are then mutated in silico to generate a new sequence set which can then be synthesised in vitro , and so on round the cycle as often as is required. The final aptamer set offers a greatly increased binding affinity to the ligand.

Article Snippet: Image analysis used Combimatrix Microarray Imager ( https://webapps.combimatrix.com/customarray/customarrayHome.jsp ).

Techniques: Generated, In Silico, In Vitro, Synthesized, Microarray, Protein Binding, Binding Assay, Selection, Sequencing

Journal: BMC Genomics

Article Title: Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements

doi: 10.1186/1471-2164-11-151

Figure Lengend Snippet: Custom microarrays analysis . A) Bar plot of UCEs expressed across 4 mouse developmental stages tested (ES, E12.5, E14.5 and E16.5) based on the analysis of our UCE custom microarray. Blue bars indicate UCEs which show expression on a single strand, green columns indicate UCEs which show expression on both strands B) Venn diagram of UCE transcription results showing the overlap across the 4 stages analyzed. More than half (n = 140, 56%) of the transcribed UCEs are expressed in all the stages analyzed.

Article Snippet: We therefore designed a custom microarray (CustomarrayTM 12K arrays from Combimatrix, Mukilteo, WA) encompassing 3 different probes on each DNA strand of UCEs (of the currently annotated 481 UCEs, probes could be designed for 475), as well as a large number of negative controls (exogenous sequences from bacteria and plants, negative controls used in the Affymetrix platform, rRNAs sequences), which were used to assess the levels of background signal.

Techniques: Microarray, Expressing

Journal: BMC Genomics

Article Title: Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements

doi: 10.1186/1471-2164-11-151

Figure Lengend Snippet: UCEs transcription and enhancer function overlap . Overlap between the enhancer dataset (Pennacchio et al, 2006) and the mouse microarray dataset in all samples analyzed, divided by stage. The yellow portion of each bar indicates UCEs that are only transcribed, the green portion UCEs that are transcribed and act as enhancers, the blue portion UCEs that are only transcribed.

Article Snippet: We therefore designed a custom microarray (CustomarrayTM 12K arrays from Combimatrix, Mukilteo, WA) encompassing 3 different probes on each DNA strand of UCEs (of the currently annotated 481 UCEs, probes could be designed for 475), as well as a large number of negative controls (exogenous sequences from bacteria and plants, negative controls used in the Affymetrix platform, rRNAs sequences), which were used to assess the levels of background signal.

Techniques: Microarray

Journal: BMC Genomics

Article Title: Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements

doi: 10.1186/1471-2164-11-151

Figure Lengend Snippet: UCE classification using External datasets . A) Comparison between the mouse enhancer dataset (Pennacchio et al. 2006) (green oval), our mouse development microarray dataset, (red oval), the human UCE expression dataset (Calin et al. 2007) (blue oval) and the mouse ES cell SOLiD expression dataset (Cloonan et al. 2008) (orange oval). B) Comparison of the SOLiD ES cell RNAseq dataset (Cloonan et al. 2008) for UCEs vs. randomly chosen non-transcribed genomic regions (outliers not shown).

Article Snippet: We therefore designed a custom microarray (CustomarrayTM 12K arrays from Combimatrix, Mukilteo, WA) encompassing 3 different probes on each DNA strand of UCEs (of the currently annotated 481 UCEs, probes could be designed for 475), as well as a large number of negative controls (exogenous sequences from bacteria and plants, negative controls used in the Affymetrix platform, rRNAs sequences), which were used to assess the levels of background signal.

Techniques: Comparison, Microarray, Expressing