Schema for BDTNP DNase Accs - Berkeley Drosophila Transcription Network Project Chromatin Accessibility (DNase)
  Database: dm3    Primary Table: bdtnpDnaseAccS10    Row Count: 23,766   Data last updated: 2010-08-27
Format description: Browser extensible data
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr2Lvarchar(255) values Reference sequence chromosome or scaffold
chromStart 5291int(10) unsigned range Start position in chromosome
chromEnd 6345int(10) unsigned range End position in chromosome

Sample Rows
 
binchromchromStartchromEnd
585chr2L52916345
585chr2L73307618
585chr2L88299038
585chr2L1016810358
585chr2L1246612882
585chr2L1521615300
585chr2L1630616540
585chr2L1717619294
585chr2L1969519913
585chr2L2148722051

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

BDTNP DNase Accs (bdtnpDnase) Track Description
 

Description

This track shows the accessibility of genomic DNA to DNase I digestion in the D. melanogaster embryo for five stages of development: 5, 9, 10, 11 and 14 (Thomas et al.). These data have been used to show the dynamics of chromatin accessibility during embryogenesis (Thomas et al) and that chromatin accessibility plays a dominant role in determining the widespread, overlapping patterns of binding by functionally distinct transcription factors in Drosophila embryos (Li et al.; Kaplan et al.).

Display Conventions and Configuration

Subtracks are provided showing either the density of DNA sequence tags in 75 bp windows across the genome or the locations of 5% FDR accessible regions. DNA sequence tag density data for independent replica for each stage are provided, though by default only one replica is shown. The DNA tag density subtracks are by default shown in "full" and the locations of 5% FDR regions that are concordant in both replicas are shown in "squish". Data for each stage is shown in a different color: green for stage 5, orange for stage 9, red for stage 10, light blue for stage 11 and purple for stage 14.

The graphical configuration options for the subtracks are shown at the top of the track controls page, followed by a list of subtracks. To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide. For more information about the graphical configuration options, click the Graph configuration help link.

Methods

One hour collections of wild type embryos were aged to the appropriate developmental stage and then nuclei were isolated and briefly digested with DNase I. The DNA released by digestion was size fractionated through a sucrose gradient to capture 100 - 400 bp fragments, which were then used to generate an average of ~14 million sequence tags per sample to the Drosophila genome with an Illumina GA2. The data were analyzed to determine short genomic regions that are accessible to digestion at a 5% false discovery rate; see Thomas et al. for further details.

References

Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet. 2011 Feb 3;7(2):e1001290. PMID: 21304941; PMC: PMC3033374

Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol. 2011;12(4):R34. PMID: 21473766; PMC: PMC3218860

Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE et al. Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol. 2011;12(5):R43. PMID: 21569360; PMC: PMC3219966