Assay summary for ChIP-seq_Zon_Lab_nanog-like_0001AS
Zon Lab, Boston Children's Hospital
Samples were prepared with the Illumina/Solexa Genomic DNA kit (Illumina- IP-102-1001) according to the manufacturer’s instructions. Briefly 200ng of Input DNA and various amounts of ChIP DNA were used. DNA overhangs were turned into phosphorylated blunt ends and the samples were purified with the PCR purification kit (Qiagen 28104). Sample preparation continued by the addition of a single A in the 3’ end to allow for directional ligation. Samples were purified with the MinElute PCR purification kit (Qiagen 28004). Illumina adapter oligos (1/100 dilution) were added to the sample followed by purification of the samples with the PCR purification kit. The samples were amplified by PCR (limited amplification to 18 cycles) that added additional linker sequence to the fragments to prepare them for annealing to the Genome Analyzer flow-cell. The amplified samples were separated on a 2% agarose gel (products between 150-350 base pairs were selected that include fragments of 50-250bp with approximately 100bp of primer sequence) and gel extraction was performed with the Gel Extraction Kit (Qiagen 28704).