Experiment Detail
| Title | Illumina HiSeq 2000 sequencing; ChIPSeq profiling of LIR3 binding sites in C.elegans |
| Design Description | ChIPSeq profiling of LIR3 binding sites in C.elegans |
| Organism | Caenorhabditis elegans |
Library Description
| Name | Input |
| Strategy | ChIP-Seq |
| Source | GENOMIC |
| Selection | ChIP |
| Layout | SINGLE |
| Construction Protocol | Worm staging was achieved by bleaching and L1 starvation. Arrested L1 animals were plated on peptone-enriched NGM plates seeded with OP50 bacteria and grown for 48 hours for L4 collection at 20C. Samples were crosslinked with 2% formaldehyde for 30 minutes at room temperature and then quenched with 1 M Tris pH 7.5. The pelleted worms were subsequently flash frozen in liquid nitrogen and stored at -80C. Samples were sonicated using a microtip to obtain mostly 200 to 800 bp DNA fragments. For each sample, 2.2 or 4.4 mg of cell extract was immunoprecipitated using a goat anti-GFP, GoatV (gift from Kevin White). The enriched DNA fragments and input control (genomic DNA from the same sample) for two biological replicates were used for library preparation and sequencing as previously described (Kasper et al., 2014). Briefly, samples were libraried and multiplexed using the Ovation Ultralow DR Multiplex Systems 1-8 and 9-16 (NuGEN Technologies Inc., San Carlos, CA) following the manufacturers protocol except Qiagen MinElute PCR purification kits were used to isolate the DNA. Library size selection in the 200-800 bp range was achieved using the SPRIselect reagent kit (Beckman Coulter, Inc., Brea, CA |
Platform
| Platform | ILLUMINA |
| Instrument Model | Illumina HiSeq 2000 |
Processing
| Base Calls | |
|---|---|
| Sequence Space | |
| Base Caller | |
Spot Information
| Number of Reads per Spots | 0 |
| Spot Length | 0 |
Read Spec
Navigation
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Submission | ERA549954 |
 FTP
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Study | ERP013715 | ||
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Sample | ERS1026566 | ||
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Run | ERR1198083 |
FASTQ
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SRA
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