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Sample GSM4443819 Query DataSets for GSM4443819
Status Public on Dec 06, 2023
Title Pooled Input
Sample type SRA
Source name mouse primary keratinocytes
Organism Mus musculus
Characteristics strain: C57BL/6
age: E18.5
cell type: primary keratinocytes
chip antibody: none
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
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
BioSample SAMN14485363
SRA SRX8026199

Supplementary file Size Download File type/resource
GSM4443819_7_02JP_00A7Moffitt_Pooled_Input_mm_i96.tdf 69.9 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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