customarraytm 12k arrays  (CombiMatrix)

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