Journal: Nucleic Acids Research

Article Title: Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities

doi: 10.1093/nar/gkp1122

Figure Lengend Snippet: Hybridization isotherms obtained on two different microarray platforms for rRNA target and Probe 596. Left and middle panels represent replicated Erie microarrays while the right panels represent VWR microarrays. Different rows represent distinct spotted probe concentrations. Each data point is the mean of at least six replicated spots. Error is measured as standard deviation. Isotherms from Erie microarrays are linear (but plotted on a log scale) while VWR microarrays followed the Langmuir model.

Article Snippet: The neutral charge surface explains the reason why hybridization isotherms on CombiMatrix microarrays are so different in shape compared to those produced on other platforms.

Techniques: Hybridization, Microarray, Standard Deviation

Journal: Nucleic Acids Research

Article Title: Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities

doi: 10.1093/nar/gkp1122

Figure Lengend Snippet: K versus spotted probe concentration for Probe 596. Open circles, August experiment, Erie microarrays; Closed circles, April experiment, Erie microarrays; Open squares, VWR microarrays.

Article Snippet: The neutral charge surface explains the reason why hybridization isotherms on CombiMatrix microarrays are so different in shape compared to those produced on other platforms.

Techniques: Concentration Assay

Journal: Nucleic Acids Research

Article Title: Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities

doi: 10.1093/nar/gkp1122

Figure Lengend Snippet: K versus spotted probe concentration for the pure rRNA target and the same probes ( n = 95) but different microarray platforms. Top and middle panels, replicated Erie microarrays; Bottom panel, VWR microarray. Red line shows the general trend based on the mean.

Article Snippet: The neutral charge surface explains the reason why hybridization isotherms on CombiMatrix microarrays are so different in shape compared to those produced on other platforms.

Techniques: Concentration Assay, Microarray

Journal: Nucleic Acids Research

Article Title: Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities

doi: 10.1093/nar/gkp1122

Figure Lengend Snippet: Distribution of fluorescence density ( F d , fluorophores/µm 2 ) at equilibrium by probe concentration on Erie microarrays hybridized for 4 h. Same probes and target were used for each probe concentration

Article Snippet: The neutral charge surface explains the reason why hybridization isotherms on CombiMatrix microarrays are so different in shape compared to those produced on other platforms.

Techniques: Fluorescence, Concentration Assay

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