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| Status |
Public on Jan 31, 2012 |
| Title |
Identification of Transcription Factor GEI-11::GFP Binding Regions in L3 |
| Project |
modENCODE
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| Organism |
Caenorhabditis elegans |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
modENCODE_submission_3066
This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
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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| |
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| Overall design |
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ); Developmental Stage: L3; Genotype: unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene gei-11; Strain OP179(official name : OP179 genotype : unc-119(ed3) III; wgIs179 [unc-119(+) gei-11::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The GEI-11::EGFP fusion protein is expressed in the correct gei-11 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the GEI-11 transcription factor. made_by : R. Waterston ); temp (temperature) 20 degree celsius
|
| Web link |
http://www.modencode.org
http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
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| |
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| Contributor(s) |
Zhong M, Snyder M, Slightam C, Kim S, Murray J, Waterston R, Gerstein M, Niu W, Janette J, Raha D, Agarwal A, Reinke V, Sarov M, Hyman A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA63461 |
| |
| Submission date |
Jan 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
DCC modENCODE |
| E-mail(s) |
help@modencode.org
|
| Phone |
416-673-8579
|
| Organization name |
Ontario Institute for Cancer Research
|
| Lab |
modENCODE DCC
|
| Street address |
MaRS Centre, South Tower, 101 College Street, Suite 800
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A3 |
| Country |
Canada |
| |
|
| Platforms (1) |
| GPL9309 |
Illumina Genome Analyzer (Caenorhabditis elegans) |
|
| Samples (4)
|
| GSM864851 |
Snyder_GEI-11_Input_L3_rep1 extraction1_seq1 aliquote 1 |
| GSM864852 |
Snyder_GEI-11_Input_L3_rep2 extraction1_seq1 aliquote 1 |
| GSM864853 |
Snyder_GEI-11_GFP_L3_rep1 extraction1_seq1 aliquote 1 |
| GSM864854 |
Snyder_GEI-11_GFP_L3_rep2 extraction1_seq1 aliquote 1 |
|
| Relations |
| SRA |
SRP010664 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE35276_Snyder_GEI-11_GFP_L3.sdrf.txt.gz |
704 b |
(ftp)(http) |
TXT |
| GSE35276_Snyder_GEI-11_GFP_L3_combined.bedgraph.gz |
32.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE35276_Snyder_GEI-11_GFP_L3_combined_peaks.GFF3.gz |
134.1 Kb |
(ftp)(http) |
GFF3 |
| GSE35276_Snyder_GEI-11_GFP_L3_rep1.GFF3.gz |
94.9 Kb |
(ftp)(http) |
GFF3 |
| GSE35276_Snyder_GEI-11_GFP_L3_rep1.bedgraph.gz |
18.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE35276_Snyder_GEI-11_GFP_L3_rep2.GFF3.gz |
57.7 Kb |
(ftp)(http) |
GFF3 |
| GSE35276_Snyder_GEI-11_GFP_L3_rep2.bedgraph.gz |
13.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE35276_Snyder_GEI-11_Input_L3.bedgraph.gz |
119.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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