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| Status |
Public on Nov 18, 2010 |
| Title |
Kc H2Av Knockdown 600 mM Salt Extracted Chromatin Pellet |
| Project |
modENCODE
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| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
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| Summary |
modENCODE_submission_2760
This submission comes from a modENCODE project of Steven Henikoff. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80 mM or 150 mM NaCl after digestion contain predominantly mononucleosomes and represent classical "active" chromatin. Profiles of these low-salt soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of histone H2Av (H2A.Z) and RNA polymerase II. This correspondence suggests that transcription can result in loss of H3.3+H2Av nucleosomes and generate low-salt soluble nucleosomes. Nearly quantitative recovery of chromatin is obtained with 600 mM NaCl; however, the remaining insoluble chromatin is enriched in actively transcribed regions. Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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| Overall design |
EXPERIMENT TYPE: tiling array analysis. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS: Cell Line Kc167; biochemical fraction (extract) precipitate; sodium chloride concentration (Compound) 600 mM; extraction time (sampling_time_point) 1 to 2 hours
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| Web link |
http://www.ncbi.nlm.nih.gov/projects/geo/info/ENCODE.html
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| Contributor(s) |
Henikoff S, Henikoff J, Ahmad K |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA63467 |
| |
| Submission date |
Nov 15, 2010 |
| Last update date |
May 29, 2013 |
| Contact name |
DCC modENCODE |
| E-mail(s) |
[email protected]
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| Phone |
416-673-8579
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| Organization name |
Ontario Institute for Cancer Research
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| Lab |
modENCODE DCC
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| Street address |
MaRS Centre, South Tower, 101 College Street, Suite 800
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| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A3 |
| Country |
Canada |
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| Platforms (1) |
| GPL6888 |
Henikoff_Dmel_r52_ChIP tiling design |
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| Samples (2) |
| GSM624889 |
Kc_H2Av_Knockdown_600_mM_Salt_Extracted_Chromatin_Pellet extraction1_array1 |
| GSM624890 |
Kc_H2Av_Knockdown_600_mM_Salt_Extracted_Chromatin_Pellet extraction2_array1 |
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