Wednesday 31 August 2016
Tuesday 23 August 2016
Co-localization of Interval Sets in ChIP-seq
ColoWeb: a resource for analysis of colocalization of genomic features
LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor
Cited from COPS: Detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets
"In order to compare the in vivo overlap with the expected (background) overlap, an overlap analysis was performed for the frequent motif patterns for which genome-wide data was available. The expected overlap was measured by randomly permuting (1000 times) the same number of regions bound by one TF through the genome and the mean overlap was subsequently calculated. The significance of the observed compared to the expected overlap was calculated by assuming that the overlap follows a Poisson distribution."
CGATOxford Tools
LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor
Cited from COPS: Detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets
"In order to compare the in vivo overlap with the expected (background) overlap, an overlap analysis was performed for the frequent motif patterns for which genome-wide data was available. The expected overlap was measured by randomly permuting (1000 times) the same number of regions bound by one TF through the genome and the mean overlap was subsequently calculated. The significance of the observed compared to the expected overlap was calculated by assuming that the overlap follows a Poisson distribution."
CGATOxford Tools
Thursday 18 August 2016
Tuesday 2 August 2016
Monday 1 August 2016
HaloTagging Protein for Purifcation,Interactions and Imaging
Cited from HaloTag Technology for Protein Purification, Protein Interactions and Imaging
- The HaloTag protein can be fused with protein of interest.
- A family of HaloTag ligands come with different functionalities.
- Ligands consist of two parts: a reactive linker and a functional group, such as fluorescent dye or biotin.
- Binding of the ligand to the HaloTag protein is rapid and irreversible.
- The HaloTag protein is genetically modified hydrolase that covalently binds hydrolase substrate like the HaloTag ligands.
Chromatin Digestion by Micrococcal Nuclease
Cited from the paper "Assays of nucleosome assembly and the inhibition of histone acetyltransferase activity. (11) Digestion of chromatin; and (12) Purification and characterization of DNA after digestion of chromatin"
"Digestion of chromatin by micrococcal nuclease (MNase) provides a relatively simple method for obtaining information about the locations of nucleosomes along DNAstrands. When nuclei in permeabilized cells are exposed to MNase in the presence of a divalent cation, the enzyme makes double-stranded cuts between nucleosomes. Treatment of chromatin substrates with very high concentrations of MNase yields mononucleosome-length DNA prodominantly, while lower concentrations of the enzyme generate one double-stranded cut at intervals of 10 to 50 nucleosomes, depending on the concentration of the enzyme and the substrate. MNase can also make single-stranded DNA cuts at the sites of histone octamers, and, thus, attempts to map the positions of nucleosomes are usually performed with native double-stranded DNA."
"Digestion of chromatin by micrococcal nuclease (MNase) provides a relatively simple method for obtaining information about the locations of nucleosomes along DNAstrands. When nuclei in permeabilized cells are exposed to MNase in the presence of a divalent cation, the enzyme makes double-stranded cuts between nucleosomes. Treatment of chromatin substrates with very high concentrations of MNase yields mononucleosome-length DNA prodominantly, while lower concentrations of the enzyme generate one double-stranded cut at intervals of 10 to 50 nucleosomes, depending on the concentration of the enzyme and the substrate. MNase can also make single-stranded DNA cuts at the sites of histone octamers, and, thus, attempts to map the positions of nucleosomes are usually performed with native double-stranded DNA."
Cell Line: G1E ER4
Cited from the Paper "Tissue-Specific Mitotic Bookmarking
by Hematopoietic Transcription Factor GATA1"
"To monitor GATA1 localization on a global scale in living, unsynchronized erythroid cells, GATA1-YFP fusion constructs were stably introduced into G1E cells."
"G1E cells are erythroid precursors that lack GATA1 and consequently fail to mature (Weiss et al., 1997). Introduction of
a conditional form of GATA1 (GATA1 fused to the ligand binding
domain of the estrogen receptor [ER]) conveys estradiol (E2)-
dependent erythroid maturation in a manner faithfully reproducing that of normal erythroid cells."
"GATA1-ER target gene occupancy and expression closely match that of endogenous GATA1 in primary erythroblasts, providing a physiological assay for GATA1 function. Both N-terminal and C-terminal YFP fusions of GATA1-ER were
generated to account for potential effects of YFP on GATA1-ER
function. YFP-GATA1-ER and GATA1-ER-YFP were expressed
at levels similar to endogenous GATA1 and were equally capable of inducing erythroid differentiation when compared to wild-type GATA1."
by Hematopoietic Transcription Factor GATA1"
"To monitor GATA1 localization on a global scale in living, unsynchronized erythroid cells, GATA1-YFP fusion constructs were stably introduced into G1E cells."
"G1E cells are erythroid precursors that lack GATA1 and consequently fail to mature (Weiss et al., 1997). Introduction of
a conditional form of GATA1 (GATA1 fused to the ligand binding
domain of the estrogen receptor [ER]) conveys estradiol (E2)-
dependent erythroid maturation in a manner faithfully reproducing that of normal erythroid cells."
"GATA1-ER target gene occupancy and expression closely match that of endogenous GATA1 in primary erythroblasts, providing a physiological assay for GATA1 function. Both N-terminal and C-terminal YFP fusions of GATA1-ER were
generated to account for potential effects of YFP on GATA1-ER
function. YFP-GATA1-ER and GATA1-ER-YFP were expressed
at levels similar to endogenous GATA1 and were equally capable of inducing erythroid differentiation when compared to wild-type GATA1."
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