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Sample GSM4443816 Query DataSets for GSM4443816
Status Public on Dec 06, 2023
Title Wild-type ChIP-Seq mouse keratinocytes
Sample type SRA
 
Source name mouse primary keratinocytes
Organism Mus musculus
Characteristics strain: C57BL/6
age: E18.5
cell type: primary keratinocytes
genotype: Wild-type
chip antibody: p63 (Santa Cruz, sc-8344, lot # F2008)
Growth protocol WT, TAp63-/-, and ΔNp63-/- primary keratinocytes were grown to near confluence on J2- 3T3m feeder cells in F media. Feeder cells were removed with 0.02% EDTA 24 hours prior to collecting keratinocytes for chromatin extraction.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. An automated system (Apollo 342, Wafergen Biosystems/Takara) was used. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing The data quality was assessed using FastQC
ChIP-Seq reads were mapped to the mouse genome build UCSC mm10 using bowtie2 and duplicate reads were removed.
ChIP-Seq tracks were prepared using bedtools, normalized to reads per million reads mapped (rpm).
Binding sites (peaks) were determined using MACS2, with and FDR<0.05
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-Seq tracks represented signal normalized to reads per million mapped in TDF format
 
Submission date Mar 30, 2020
Last update date Dec 06, 2023
Contact name Elsa Renee Flores
E-mail(s) Elsa.Flores@moffitt.org
Organization name Moffit Cancer Center
Department Department of Molecular Oncology
Lab The Flores Lab
Street address 12902 USF Magnolia Drive
City Tampa
State/province FL
ZIP/Postal code 33612
Country USA
 
Platform ID GPL19057
Series (1)
GSE147723 ChIP-seq analysis comparing WT, TAp63-/-, and ΔNp63-/- primary murine keratinocytes
Relations
BioSample SAMN14485366
SRA SRX8026196

Supplementary file Size Download File type/resource
GSM4443816_4_02JC_00A7Moffitt_wild-type_p63_mm-dm_i93.tdf 59.5 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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