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Sample GSM1034506 Query DataSets for GSM1034506
Status Public on Nov 10, 2012
Title R53-L8-Wdr5-Sequences
Sample type SRA
 
Source name Human neonatal epidermis_Wdr5_ChIP
Organism Homo sapiens
Characteristics cell type: human differentited primary keratinocytes (NHEK)
chip antibody: Anti-WDR5 antibody
chip antibody vendor: AbCam
chip antibody cat. #: ab56919
Treatment protocol Medium containing high calcium levels (1.8mM) was used to induce differentiation in NHEK cells. Cells were collected 24 hours after the switch to high calcium medium
Growth protocol NHEK cells were grown in DermaLife medium (LifeLine Cell Technologies) at 37C, 5%CO2
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. 24 ug of sonicated chromatin was used for each IP. The following antibodies were used : Grhl3 (Andersen Lab), WDR5 (AbCam cat#ab56919)
Sequencing libraries were generated for the GRHL3, WDR5, and Input samples using the NEB Next reagents and Illumina adaptors and oligos, according to the Illumina protocol for ChIP-Seq library preparation, with some modification. After adaptor ligation, PCR amplification was performed prior to size selection of the library [PMID 19275939]. Clustering and 50-cycle single end sequencing were performed on the Illumina Hi-Seq 2000 Genome Analyzer.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Base-calls were made using RTA version 1.12.4.2.
Reads were aligned to human genome hg19 using Bowtie version 0.12.7, only uniquely aligning reads were retained (-m 1)
Bam file were converted to BED using Bedtools (bamToBed v2.11.2)
Peaks were called using macs14, with input aligned sequences as the control file, m fold of 8,30, and p-value 1e-7
Galaxy was used for further data analysis (performing intersection/subtraction analysis, extracting features)
Genome_build: Human hg19
Supplementary_files_format_and_content: interval files from galaxy, containing chromosome and coordinates of peak locations
 
Submission date Nov 09, 2012
Last update date May 15, 2019
Contact name Amelia Soto Hopkin
E-mail(s) sotoa@uci.edu
Phone 9498249372
Organization name University of California Irvine
Department Biological Chemistry & Medicine
Lab Bogi Andersen
Street address 250 Sprague Hall
City Irvine
State/province CA
ZIP/Postal code 92617
Country USA
 
Platform ID GPL11154
Series (1)
GSE42180 Genome-wide binding of WDR5 and GRHL3
Relations
SRA SRX204109
BioSample SAMN01805315

Supplementary file Size Download File type/resource
GSM1034506_Wdr5MACSpeaks.interval.txt.gz 698.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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