General Information
Name
Chromatin_types_mE2.BG3
Species
D. melanogaster
Result type
FlyBase ID
FBlc0000200
Title
9-state chromatin model derived from analysis of histone modification ChIP, ML-DmBG3-c2 cells.
Status
Current
Accessions
Biosample Source
Overview
Strain
Stage
Sex
Tissue isolated
Other tissues studied
Cell component
Key genes
Methods
Sample preparation
Biosamples analyzed by this result (17)
Biosample
Type
Title
D. melanogaster, ML-DmBG3-c2 cell line, source for ChIP.
D. melanogaster, ML-DmBG3-c2 cell line, source for ChIP.
D. melanogaster, ML-DmBG3-c2 cell line, source for ChIP.
D. melanogaster, ML-DmBG3-c2 cell line, source for ChIP.
D. melanogaster, ML-DmBG3-c2 cell line, source for ChIP.
D. melanogaster, ML-DmBG3-c2 cell line, source for ChIP.
D. melanogaster, ML-DmBG3-c2 cell line, source for ChIP.
D. melanogaster, ML-DmBG3-c2 cell line, source for ChIP.
D. melanogaster, ML-DmBG3-c2 cell line, source for ChIP.
D. melanogaster, ML-DmBG3-c2 cell line, source for ChIP.
Showing 10 / 17 records. Use Export to HitList above to see all
Data Analyzed
Assay methods
Key genes
(bait_protein)
Protocol
A rabbit polyclonal anti-His3K18ac (Abcam ab1191) antibody was used for ChIP.
Mode of Assay
Raw Data Analyzed (17)
Assay / Reagent collection
Type
Title
ChIP-chip of H3K18ac in D. melanogaster, ML-DmBG3-c2 cell line.
ChIP-chip of H3K23ac in D. melanogaster, ML-DmBG3-c2 cell line.
ChIP-chip of H3K27ac in D. melanogaster, ML-DmBG3-c2 cell line.
ChIP-chip of H3K27me3 in D. melanogaster, ML-DmBG3-c2 cell line.
ChIP-chip of H3K36me1 in D. melanogaster, ML-DmBG3-c2 cell line.
ChIP-chip of H3K36me3 in D. melanogaster, ML-DmBG3-c2 cell line.
ChIP-chip of H3K4me3 in D. melanogaster, ML-DmBG3-c2 cell line.
ChIP-chip of H3K4me1 in D. melanogaster, ML-DmBG3-c2 cell line.
ChIP-chip of H3K4me2 in D. melanogaster, ML-DmBG3-c2 cell line.
ChIP-chip of H3K79me1 in D. melanogaster, ML-DmBG3-c2 cell line.
Showing 10 / 17 records. Use Export to HitList above to see all
Processed Data Analyzed (0)
Result
Type
Title
Analysis
Methods
Reference Genome
Reference Annotation
Data analysis
Genome-wide histone modification distributions in S2-DRSC and ML-DmBG3-c2 cells, as determined by ChIP-chip, were used in this analysis. Only ChIP data using antibodies that showed less than 50% of total signal associated with non-histone proteins, and more than fivefold higher affinity for the corresponding histone peptide, were considered. To derive the chromatin state model, the genome was divided into 200 bp bins, and average enrichment was calculated per bin based on unsmoothed log2 intensity ratio values. For H1, H4 and H3K23ac, regions of significant depletion rather than enrichment were called. Polycomb (Pc) distribution was used to discount the genome-wide difference in S2 H3K27me3 profiles. Bin-average values of each modification were shifted by the genome-wide mean, scaled by the genome-wide variance, and quantile-normalized between the two cells. The hidden Markov model (HMM) with multivariate normal emission distributions was then determined from the Baum–Welch algorithm using data from both cell types, and 30 seeding configurations determined with K-means clustering. States with minor intensity variations (Euclidian distance of mean emission values ,0.15) were merged.
Comments
State c1: Active promoter/transcription start site region.
State c2: Actively transcribed exon.
State c3: Actively transcribed intron (enhancer).
State c4: Other open chromatin.
State c5: Actively transcribed exon on the male X chromosome (dosage compensation).
State c6: Region of Polycomb-mediated repression.
State c7: Heterochromatin.
State c8: Heterochromatin-like region embedded in euchromatin.
State c9: Transcriptionally silent intergenic euchromatin.
Associated Data
Size
20734 chromatin domains (nine types)
Files
Additional Information
Synonyms and Secondary IDs (3)
Reported As
Symbol Synonym
9-state chromatin model in BG3 cells
Chromatin_types_mE2.BG3
Name Synonyms
9-state chromatin model derived from analysis of histone modification ChIP, ML-DmBG3-c2 cells.
Secondary FlyBase IDs
    References (4)