GEO help: Mouse over screen elements for information.
|Public on Nov 12, 2015
|cell type: primary human neonatal keratinocytes
chip antibody: none (input)
|To induce differentiaiton, keratinocytes were seeded in confluence and cultured with the addition of 1.2mM of calcium to growth medium. 1nM of siRNA for each target were nucleofected (Lonza to keratinocytes)
|neonatal keratinocyte were isolated from discarded foreskin, cultured in KSF and 154 keratinocyte medium
|For ATAC-seq, around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition. For ChIP-seq, a mininum of 2 million cells were crosslinked with 1% formaldehyde, sonicated, and immunoprecipiated with antibodies recognizing Brg1/Brm (J1), H3K27Ac, H3K27me3, H3K4me1, p300, pol II, and p63.
For ATAC-seq, sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit. For ChIP-seq, NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina were use for library construction
|Illumina HiSeq 2500
|input for ChIP-seq in differentiated keratinocytes
|Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard.ATACseq peaks were called using the MACS2 algorithm,ChIPseq peaks were called using MACS14.
Number of Raw reads in each peak was calculated using in house generated script, and data matrix was normalized using R
Supplementary_files_format_and_content: Peak files are in standard bed/whole bed format
|Mar 27, 2015
|Last update date
|Oct 11, 2022
|269 Campus Drive
|BAF controls genome accessibility