title: Illumina HiSeq 2000 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: rnaseq_brain_WT_2_p
library_construction_protocol: TDG KO mice contain a deletion of the coding sequence for the catalytic domain of TDG, which is replaced by a neomycin-resistant cassette. Genotyping was carried out using DNA isolated from the yolk sac as template with the following primers:TDG KO/WT forward: 5′-GGGCAGCAAGGATCTGTCTA-3′TDG KO/WT reverse: 5′-GCCAGTTCCTCTGACACTTAGC-3′Mice were maintained as heterozygotes and intercrossed to generate homozygous knockout embryos for analysis. Tissues were collected from timed matings with the day of the copulation plug as E0.5. Embryos were dissected into hindbrain and heart. Tissues were collected from timed matings with the day of the copulation plug as E0.5. Embryos were dissected into hindbrain and heart. Total RNA for each sample was extracted using RNeasy mini kit (QIAGEN) and following the manufacturer's instructions.  For RNA-seq, total RNA for each sample was extracted using RNeasy mini kit (QIAGEN) and following the manufacturer's instructions. Extracted RNA was polyA-enriched. Then, RNA was used for library preparation using the TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer's instructions.
attributes.tag: Experimental Factor: protocol
attributes.value: RNA-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: none
attributes.tag: Experimental Factor: immunoprecipitate
attributes.value: none