E-MTAB-6271:rnaseq_brain_KO_3_p
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
DNA- and RNA-seq to study the impact of 5-formylcytosine on nucleosome organization and gene expression in embryonic mouse tissues and stem cells
rnaseq_brain_KO_3_p
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.
Senior research associate
E-MTAB-6271:rnaseq_brain_KO_3_p
Experimental Factor: protocol
RNA-seq
Experimental Factor: organism
Mus musculus
Experimental Factor: genotype
Tdg knockout
Experimental Factor: organism part
hindbrain
Experimental Factor: compound
none
Experimental Factor: immunoprecipitate
none