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| Status |
Public on Apr 23, 2012 |
| Title |
Lieb SDQ4129_Y39G10AR18_N2_MXEMB |
| 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_2970
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
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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: Developmental Stage Mixed Embryo; temp (temperature) 20 degree celsius; Antibody SDQ4129 Y39G10AR18 (target is Y39G10AR.18); Strain N2
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| Web link |
http://www.modencode.org
http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
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| Contributor(s) |
Jensen M, Lieb J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA63461 |
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| Submission date |
Apr 23, 2012 |
| Last update date |
Feb 02, 2015 |
| 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 (1) |
| GPL8647 |
080922_modEncode_Caenorhabditis elegans_2M tiling chip_HX1 |
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| Samples (2) |
| GSM811253 |
SDQ4129_Y39G10AR18_N2_MXEMB extraction1_array1 channel_1 |
| GSM811254 |
SDQ4129_Y39G10AR18_N2_MXEMB extraction2_array1 channel_1 |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE37488_RAW.tar |
279.4 Mb |
(http)(custom) |
TAR (of GFF3, PAIR, WIG) |
| GSE37488_SDQ4129_Y39G10AR18_N2_MXEMB_1_A+2_A_DS_peaks.gff3.gz |
99.8 Kb |
(ftp)(http) |
GFF3 |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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