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| Status |
Public on Feb 18, 2011 |
| Title |
Identification of Transcription Factor CEH-30::GFP Binding Regions in Late Embyros |
| Project |
modENCODE
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| Organism |
Caenorhabditis elegans |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
modENCODE_submission_2620
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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| Overall design |
EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP120(made_by : R Waterston 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 CEH-30::EGFP fusion protein is expressed in the correct ceh-30 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-30 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs120(ceh-30::TY1 EGFP FLAG;unc119) official name : OP120 ); Developmental Stage: late embryo; Genotype: unc119(ed3);wgIs120(ceh-30::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage late embryo; Target gene ceh-30; Strain OP120(made_by : R Waterston 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 CEH-30::EGFP fusion protein is expressed in the correct ceh-30 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the CEH-30 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs120(ceh-30::TY1 EGFP FLAG;unc119) official name : OP120 ); temp (temperature) 20 degree celsius
Series_type: CHIP-seq
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| Web link |
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(s) |
21177976, 21177963 |
| BioProject |
PRJNA63461 |
| |
| Submission date |
Dec 02, 2010 |
| Last update date |
May 15, 2019 |
| 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
|
| 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) |
| GPL9309 |
Illumina Genome Analyzer (Caenorhabditis elegans) |
|
| Samples (4)
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| GSM677683 |
Snyder_CEH-30_GFP_lemb_rep1 extraction1_seq1 aliquote 1 |
| GSM677684 |
Snyder_CEH-30_GFP_lemb_rep1 extraction1_seq1 aliquote 2 |
| GSM677685 |
Snyder_CEH-30_GFP_lemb_rep2 extraction2_seq1 aliquote 1 |
| GSM677686 |
Snyder_CEH-30_GFP_lemb_rep2 extraction2_seq1 aliquote 2 |
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| Relations |
| SRA |
SRP005886 |
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