Filter Results
438 results
The increasing resolution of techniques improves the description of the Drosophila MSL binding activity. The nature of Drosophila MSL binding sites is illustrated according to the method used to describe them. (a) Immunofluorescent staining of polytene chromosomes shows chromatin binding, with an enrichment on the male X chromosome. Less intense autosomal binding of MOF is also apparent. (b) Schematic representation of available genome-wide ChIP-chip and ChIP-seq profiles. The increased resolution of these techniques confirms the polytene observations, and allows precise description of the binding sites. (c) Examination of profiles over gene units reveals differential binding of MSL proteins. MSL1, MSL3 and MOF colocalize across the transcribed portion of genes, especially toward the 3′ end. MOF also binds the 5′ regions of genes, peaking at the transcription start site. ... Strategies to achieve dosage compensation. Dosage compensation is the mechanism by which species featuring an unequal number of X chromosomes (pictured) between the two sexes balance the expression of X-linked genes. In a noncompensated system, cells belonging to opposite sexes would generate different amount of X-linked gene products. Different organisms compensate for dose following a variety of strategies: mammalian females transcriptionally inactivate one out of the two X chromosomes, Drosophila males hyperactivate the single X chromosome, and Caenorhabditis elegans hermaphrodites partially repress both of the X chromosomes.
Data Types:
  • Image
Transcription Analysis (A) Summary of genome-wide methods for studying transcription is shown. Each method can provide information about specific stages of transcription (horizontal arrows). In some stages, and especially in the initial phases (on the left), the available methods do not allow discrimination between different steps of transcription. These resolution limitations are depicted as arrows spanning boundaries between multiple stages. The dashed arrow in “GRO-seq No Sarkosyl” indicates the lack of data for paused Pol II. ChIP Pol II, chromatin immunoprecipitation targeting Pol II followed by either sequencing (ChIP-seq) or microarray hybridizations (ChIP-chip); Ser2P, serine 2 phosphorylation marking elongating Pol II; GRO-seq, global run-on sequencing with sarkosyl treatment to detect paused and active Pol II or without sarkosyl to detect active Pol II only; 5′ RNAs, sequencing of short 5′ capped nuclear transcripts to measure 5′ pausing; Nascent-seq, sequencing of nascent transcripts. (B) A schematic representation of the cDNA-based and direct nascent RNA sequencing (DnRS) protocols is shown. Nascent transcripts were isolated using the same protocol, followed by two different sequencing approaches. In cDNA sequencing, strand-specific cDNA is synthesized by random priming of the entire nascent transcript, with a resulting decrease in read density from the 5′ end to 3′ end (red). In contrast, the 3′ end of the nascent transcript is sequenced directly in DnRS, thus providing a precise map of Pol II position (green). See also Figure S1.
Data Types:
  • Image
  • Document
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor CNC from WPP generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Most factors binding profiles are generated by using specific antibodies for the protein of interest. However, some factors have been tagged by GFP in a transgenic line. In that case, ChIP is generated using an anti-GFP antibody. This submission represents the ChIP-seq component of the study.
Data Types:
  • Text
  • File Set
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor GFP from R13-E1-6h-Set2 generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Most factors binding profiles are generated by using specific antibodies for the protein of interest. However, some factors have been tagged by GFP in a transgenic line. In that case, ChIP is generated using an anti-GFP antibody. This submission represents the ChIP-seq component of the study
Data Types:
  • Text
  • File Set
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Kr-D2 from E16-24h generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Most factors binding profiles are generated by using specific antibodies for the protein of interest. However, some factors have been tagged by GFP in a transgenic line. In that case, ChIP is generated using an anti-GFP antibody. This submission represents the ChIP-seq component of the study
Data Types:
  • Text
  • File Set
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor HP1-Covance from E16-24h generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Most factors binding profiles are generated by using specific antibodies for the protein of interest. However, some factors have been tagged by GFP in a transgenic line. In that case, ChIP is generated using an anti-GFP antibody. This submission represents the ChIP-seq component of the study
Data Types:
  • Text
  • File Set
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor GFP from 15T_8-16_NW generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Most factors binding profiles are generated by using specific antibodies for the protein of interest. However, some factors have been tagged by GFP in a transgenic line. In that case, ChIP is generated using an anti-GFP antibody. This submission represents the ChIP-seq component of the study
Data Types:
  • Text
  • File Set
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW4-Hr39-D1 from E16-24h generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Most factors binding profiles are generated by using specific antibodies for the protein of interest. However, some factors have been tagged by GFP in a transgenic line. In that case, ChIP is generated using an anti-GFP antibody. This submission represents the ChIP-seq component of the study
Data Types:
  • Text
  • File Set
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor GFP from E16-24h generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Most factors binding profiles are generated by using specific antibodies for the protein of interest. However, some factors have been tagged by GFP in a transgenic line. In that case, ChIP is generated using an anti-GFP antibody. This submission represents the ChIP-seq component of the study.
Data Types:
  • Text
  • File Set
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor GFP from 5T-0-6 generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Most factors binding profiles are generated by using specific antibodies for the protein of interest. However, some factors have been tagged by GFP in a transgenic line. In that case, ChIP is generated using an anti-GFP antibody. This submission represents the ChIP-seq component of the study.
Data Types:
  • Text
  • File Set
8