For example, we have applied light-activatable cMOs to interrogate transcription factor function during zebrafish notochord, pancreas, and vascular patterning.
NanoCAGE dramatically reduces the amount of input RNA needed to interrogate transcription start sites genome wide, although this comes at the expense of low sequencing depth and genome coverage [ 8, 9].
A new technology, the maskless oligonucleotide tiling array, has recently emerged as a powerful tool to interrogate transcription activities on the whole genomic scale and at unprecedented high resolution [ 1, 2].
Of the 19,000 control probes included in the re-array, 7669 have a GC content higher than 15, which is the case for all probes interrogating transcription units.
Specifically, the following terms were interrogated: transcription, blood vessel development, angiogenesis, cell growth, cell morphogenesis, cell motion, cell migration, cell signaling, mammary gland development, cell differentiation, cell proliferation, cell division and cytoskeletal organization.
Expression arrays enable us to interrogate the transcription level of all known genes in a single hybridization experiment.
This therefore suggests that high-resolution X-ChIP-seq can achieve single nucleotide resolution, and by using immunoprecipitation, has the advantage that it can be used to interrogate individual transcription factors.
Putative GRE were identified with the GenespringGX mouse genome9999 application which allows sequences up to 9999 bp upstream of the transcriptional start sites of all annotated MOE4302.0 transcripts to be interrogated for transcription factor binding sites.
It is difficult to interrogate the underlying transcription landscape of individual neurons.
In order to assess the relevance of the PDGF/Abl pathway we interrogated global gene transcription data from two publically available global gene transcription data sets from ER+ breast cancer cell lines (ZR-75.1, MDA MB 361 and HCC-1428) thad had been adapted to LTED [ 11, 15].
Specifically, we used micro cDNA amplification methods and custom gene microarrays [15] [16] to interrogate nearly all identified transcription factor (TF) genes in the SE of the chick cochlea and utricle during the early phases of regeneration.
