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Sample GSM2247255 Query DataSets for GSM2247255
Status Public on Jun 25, 2017
Title Smc1a ChIP-seq Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 6
Sample type SRA
 
Source name Primary Epidermal Keratinocyte - Differentiation Day 6
Organism Homo sapiens
Characteristics cell type: primary epidermal keratinocyte
differentiation state: Late differentiation (Day 6)
individual: Donor2
Sex: male
chip antibody: Smc1a (Bethyl, catalog# A300-055A, lot# A300-055-5)
Treatment protocol In the case of siRNA knockdown, progenitor keratinocytes were nucleofected with scrambled control, KLF4, ZNF750, or EHF targeting siRNAs
Growth protocol Human primary keratinocytes were cultured in 50/50 growth media and induced to differentiated for three or six days as previously described (Zarnegar et al., 2012)
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked with 1% formaldehyde for 10 minutes, then quenched with 0.125M glycine for 5 minutes. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with an antibody.
NEB Next ChIP-seq library prep kit was used.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description Sample 15
Data processing Reads were aligned with bowtie2 using default parameters.
Aligned reads were filtered for MAPQ > 30 and deduplicated with samtools.
Signal tracks were generated by first using the bedtools genomeCoverageBed to produce bedGraph files.
The UCSC utility bedGraphToBigWig was used with default parameters to generate bigwig files.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for each ChIP experiment are in UCSC format.
 
Submission date Jul 21, 2016
Last update date May 15, 2019
Contact name Paul Khavari
Organization name Stanford University
Street address 269 Campus Drive, CCSR 2150
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL18573
Series (2)
GSE84657 Dynamic and stable enhancer-promoter contacts regulate terminal differentiation [ChIP-Seq]
GSE84662 Dynamic and stable enhancer-promoter contacts regulate terminal differentiation
Relations
BioSample SAMN05425738
SRA SRX1967784

Supplementary file Size Download File type/resource
GSM2247255_SMC1A_ChIPseq_Donor2_Day6.bigWig 159.0 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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