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| Status |
Public on Jul 07, 2010 |
| Title |
Desai PolII-4H8 |
| Project |
modENCODE
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| Organism |
Caenorhabditis elegans |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
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| Summary |
modENCODE_submission_174
This submission comes from a modENCODE project of Jason Lieb. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-chip analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
Keywords: CHIP-chip
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| Overall design |
EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: N2; Developmental Stage: Mixed Embryo; Genotype: wild type; Sex: mixed Male and Hermaphrodite population; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS: Strain N2; temperature 20; Antibody ab5408 (target is RNA polymerase II CTD repeat YSPTSPS); Developmental Stage Mixed Embryo
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| Web link |
http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
http://www.modencode.org
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| Contributor(s) |
Gassmann R, Desai A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA63461 |
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| Submission date |
Jul 01, 2010 |
| Last update date |
Jun 28, 2012 |
| Contact name |
DCC modENCODE |
| E-mail(s) |
help@modencode.org
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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 (3) |
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| Samples (6)
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| GSM562194 |
ABAB5408_4H8_N2_MXEMB_1 extraction1_array1 |
| GSM562195 |
ABAB5408_4H8_N2_MXEMB_1 extraction1_array2 |
| GSM562196 |
ABAB5408_4H8_N2_MXEMB_1 extraction1_array3 |
| GSM562197 |
ABAB5408_4H8_N2_MXEMB_2 extraction2_array1 |
| GSM562198 |
ABAB5408_4H8_N2_MXEMB_2 extraction2_array2 |
| GSM562199 |
ABAB5408_4H8_N2_MXEMB_2 extraction2_array3 |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE22669_ABAB5408_4H8_N2_MXEMB_1.wig.gz |
5.5 Mb |
(ftp)(http) |
WIG |
| GSE22669_ABAB5408_4H8_N2_MXEMB_2.wig.gz |
5.5 Mb |
(ftp)(http) |
WIG |
| GSE22669_ABAB5408_4H8_N2_MXEMB_peaks.gff.gz |
337.2 Kb |
(ftp)(http) |
GFF |
| GSE22669_RAW.tar |
131.4 Mb |
(http)(custom) |
TAR (of PAIR) |
| Processed data are available on Series record |
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