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Sample GSM1645716 Query DataSets for GSM1645716
Status Public on Nov 12, 2015
Title pol2_ChIP_BAFi
Sample type SRA
 
Source name human keratinoctyes with Brg1/Brm si
Organism Homo sapiens
Characteristics cell type: primary human neonatal keratinocytes
knockdown: Brg1/Brm
chip antibody: Pol II (millipore, cat#05-623, lot#1776417) (millipore)
Treatment protocol 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)
Growth protocol neonatal keratinocyte were isolated from discarded foreskin, cultured in KSF and 154 keratinocyte medium
Extracted molecule genomic DNA
Extraction protocol 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
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description ChIP-seq in differentiated keratinocytes with Brg1/Brm knockdown
Data processing 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
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are in standard bed/whole bed format
 
Submission date Mar 27, 2015
Last update date Oct 11, 2022
Contact name Douglas Porter
Organization name Stanford
Department Dermatology
Lab Khavari
Street address 269 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL16791
Series (1)
GSE67382 BAF controls genome accessibility
Relations
BioSample SAMN03450213
SRA SRX971587

Supplementary file Size Download File type/resource
GSM1645716_pol2_BB_peaks.bed.gz 98.6 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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