title: NextSeq 500 paired end sequencing; DNA- and RNA-seq to study the impact of 5-formylcytosine on nucleosome organization and gene expression in embryonic mouse tissues and stem cells
design: DNA- and RNA-seq to study the impact of 5-formylcytosine on nucleosome organization and gene expression in embryonic mouse tissues and stem cells
library_name: gDNA_hmC_p
library_construction_protocol: Tissues were collected from timed matings with the day of the copulation plug as E0.5. Embryos were dissected into hindbrain and heart. Genomic DNA was extracted from mouse embryonic tissues at 11.5 days using the DNeasy Blood & Tissue kit (Qiagen) Indexed DNA libraries were obtained by end repair, A-tailing and adapter ligation (NEBNext Ultra II DNA library Prep kit) following the manufacturer's guideline. Per indexed library, cytosine or fully modified 5mC, 5hmC or 5fC DNA was subsequently generated by PCR (25 cycles) using the Taq polymerase and dCtp, dmCtp, dhmCtp and dfCtp and purified by GeneJET PCR Purification Kit and eluted with ultra pure water to generate gDNA_C, gDNA_mC, gDNA_hmC and gDNA_fC input samples.
attributes.tag: Experimental Factor: protocol
attributes.value: DNA-seq
attributes.tag: Experimental Factor: organism
attributes.value: Mus musculus
attributes.tag: Experimental Factor: genotype
attributes.value: wild type genotype
attributes.tag: Experimental Factor: organism part
attributes.value: hindbrain
attributes.tag: Experimental Factor: compound
attributes.value: 5-hydroxymethylcytosine
attributes.tag: Experimental Factor: immunoprecipitate
attributes.value: none