|Title||FAANG Reference Data Datasets for the Pig Ipec-J2 and Chicken SL-29 Epithelial Cell Lines|
|Event||The Plant and Animal Genome XXIIV Conference (PAG), San Diego, 2017-1-16/2017-1-16|
Animal Breeding and Genetics
|Publication type||Unpublished lecture|
|Abstract||We have developed a FAANG data set for a pig and chicken epithelial cell line respectively, that we propose to be used a reference for laboratories aiming to implement ChIP-seq procedures. For pig we have chosen the small intestinal epithelial cell line IPEC-J2 which was established from normal intestinal epithelium cells isolated from the jejunum of a neonatal, unsuckled pig. For chicken we have chosen the SL-29 epithelial cell line, derived from a 11 day old chicken embryo. The chicken SL-29 and pig Ipec-J2 cell lines are available from the ATCC (www.lgcstandards-atcc.org ) and DSMZ (www.dsmz.de) repositories respectively. For both cell lines we have obtained the following data: (1) ChIP-seq for 4 histone marks (H3K27ac, H3K4me3, H3K27m33, H3K4me1) (2) ChIP-seq for the highly conserved insulator-binding protein CCCTC-binding factor (CTCF) (3) DNA methylation (50x whole genome bisulphite sequences) (4) Whole genome sequences (30x) (5) Stranded RNA-seq. We also have developed a set of different PCR primers that can be used for quality control of the above mentioned ChIP experiments. This allows evaluation of the ChIP experiments prior to sequencing the DNA.