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| Status |
Public on Dec 18, 2008 |
| Title |
Mapping Novel Chromatin Regions Using Sono-Seq |
| Project |
ENCODE
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| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We found that sonication of crosslinked chromatin produces breaks at non-random sites in DNA and can be used to map sites of high chromatin accessibility when combined with high-throughput tag sequencing using the GA II platform from Illumina. This technique, which we named Sono-Seq, can be a simple and broadly applicable method for mapping many open chromatin sites. Furthermore, these results give insights into reference sample types, such as Input DNA, normal IgG ChIP DNA, MNase-digested DNA, and naked DNA, that have been used in ChIP-chip and ChIP-Seq experiments.
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 |
For this analysis, seven samples from HeLa S3 cells were included: RNA Polymerase II (GEO accession GSM320734), Sono-Seq/Input DNA (small fragments) that was size selected at 100-350 bp (GEO accession GSM320735), Sono-Seq/Input DNA (large fragments) size selected between 350-800 bp, naked DNA, normal mouse IgG, Sono-Seq/Input DNA stimulated with interferon-gamma (GEO accession GSM320737), and MNase-digested DNA. Two replicates were used for MNase-digested DNA and Sono-Seq/Input DNA (large fragments) whereas three replicates were used for all other samples. Naked DNA was used as a reference for scoring peaks.
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| Web link |
http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/projects/geo/info/ENCODE.html
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| Contributor(s) |
Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Struhl K, Gerstein M, Snyder M |
| Citation(s) |
19706456 |
| BioProject |
PRJNA63443 |
| Submission date |
Dec 17, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
Raymond K Auerbach |
| Organization name |
Yale University
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| Street address |
266 Whitney Ave
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
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| Platforms (1) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
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| Samples (4)
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| GSM352183 |
Naked DNA from HeLa S3 cells |
| GSM352184 |
MNase-digested DNA from HeLa S3 cells |
| GSM352185 |
Large fragment Sono-Seq DNA (350-800 bp) |
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| Relations |
| SRA |
SRP001365 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE14022_INFG_InputDNA_vs_NakedDNA_Peaks.txt.gz |
898.4 Kb |
(ftp)(http) |
TXT |
| GSE14022_INFG_InputDNA_vs_NakedDNA_Peaks_stringent.txt.gz |
436.4 Kb |
(ftp)(http) |
TXT |
| GSE14022_IgG_mouse_vs_NakedDNA_Peaks.txt.gz |
605.3 Kb |
(ftp)(http) |
TXT |
| GSE14022_IgG_mouse_vs_NakedDNA_Peaks_stringent.txt.gz |
98.6 Kb |
(ftp)(http) |
TXT |
| GSE14022_PEAKS_README.txt.gz |
1.0 Kb |
(ftp)(http) |
TXT |
| GSE14022_PolII_vs_NakedDNA_Peaks.txt.gz |
869.7 Kb |
(ftp)(http) |
TXT |
| GSE14022_PolII_vs_NakedDNA_Peaks_stringent.txt.gz |
552.1 Kb |
(ftp)(http) |
TXT |
| GSE14022_RAW.tar |
3.9 Gb |
(http)(custom) |
TAR (of TXT) |
| GSE14022_Sono-Seq_LargeFragments_vs_NakedDNA_Peaks.txt.gz |
119.4 Kb |
(ftp)(http) |
TXT |
| GSE14022_Sono-Seq_LargeFragments_vs_NakedDNA_Peaks_stringent.txt.gz |
41.8 Kb |
(ftp)(http) |
TXT |
| GSE14022_Sono-Seq_SmallFragments_vs_NakedDNA_Peaks.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
| GSE14022_Sono-Seq_SmallFragments_vs_NakedDNA_Peaks_stringent.txt.gz |
361.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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