3 protocols
AccessionType
feature_extraction
ChIP-seq reads were aligned to the genome (mouse mm9, chicken gg3) using Bowtie version 0.12.7 (Langmead et al., 2009). Reads were mapped uniquely using the '-M 1 --best --strata' switches and one mismatch was allowed (-v 1). ChIP peaks were identified using MACS version 1.4.1 (Zhang et al., 2008) using default arguments, input as control, and a cutoff p-value = 10-25 was used. Peaks of all p-values are supplied here. Genome_build: MGSCv37 Supplementary_files_format_and_content: BED files containing called peaks (all p-values).
feature_extraction
ChIP-seq reads were aligned to the genome (mouse mm9, chicken gg3) using Bowtie version 0.12.7 (Langmead et al., 2009). Reads were mapped uniquely using the '-M 1 --best --strata' switches and one mismatch was allowed (-v 1). ChIP peaks were identified using MACS version 1.4.1 (Zhang et al., 2008) using default arguments, input as control, and a cutoff p-value = 10-25 was used. Peaks of all p-values are supplied here. Genome_build: Gallus_gallus-2.1 Supplementary_files_format_and_content: BED files containing called peaks (all p-values).
nucleic acid library construction protocol
ChIP was performed as described (Chen et al., 2008) except that testes were macerated on ice and then fixed with 1.5% (w/v) formaldehyde for 20 min. Samples were then further crushed using 20 strokes with a 'B' pestle in a Dounce homogenizer (Kimble-Chase, Vineland, NJ, USA). Chromatin was sheared by sonication and immunoprecipitated using anti-A-MYB (HPA008791; Sigma, St. Louis, MO, USA), anti-H3K4me3 (ab8580; Abcam, Cambridge, MA, USA), or anti-RNA polymerase II antibody (N20, sc899, Santa Cruz Biotechnology, Santa Cruz, CA, USA); immunoglobulin G (IgG; Sigma, item 2729) served as a control. ChIP-seq libraries were prepared following the Illumina ChIP-seq protocol and sequenced on a HiSeq 2000 (50 nt reads).