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Sample GSM1572249 Query DataSets for GSM1572249
Status Public on Jul 31, 2015
Title Trp53 R172H/R172H mouse H3K4me3
Sample type SRA
Source name Trp53 R172H/R172H mouse
Organism Mus musculus
Characteristics p53 mutation status: Trp53 R172H/R172H
treatment: Untreated
antibody: H3K4me3 Abcam (ab8580)
Treatment protocol As indicated in the SAMPLES section
Growth protocol All cells were grown in DMEM with 10% FBS, at 3% oxygen.
Extracted molecule genomic DNA
Extraction protocol For ChIP-seq, cells were crosslinked with formaldehyde (1% final) for 10min at room temperature, and harvested for sonication. Nuclei were extracted and chromatin was sheared to an average size of 200bp using a Covaris S220 sonicator
For RNA-seq, polyA+ RNA was isolated by two rounds of polyA selection using the Life Technologies mRNADirect kit per manufacturer's recommendations.
Sequencing libraries for ChIP-seq were constructed using the NEBNext Ultra kit as per manufacturer's recommended instructions. Sequencing libraries for polyA+, stranded-RNA-seq were constructed using the NEBnext Ultra Directional RNAseq kit as per manufacturer's recommended instructions.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description ChIPseq for H3K4me3 in primary p53 R172H Knock-in MEFs
Data processing Raw fastq files were aligned to mm9 using Bowtie2, allowing for only uniquely aligned reads to be reported.
bowtie2 -N1 -k1 mm9
Uniquely mapped reads were processed into HOMER TagDirectories (makeTagDirectory <file> <TagDir_file>)
Bedgraphs were then generated using the command 'makeUCSCfile <ChIP_TagDirectory> -o auto'
Expression values (FPKM) for RNAseq experiments were derived using HOMER ( mm9 -condenseGene)
genome build:mm9
processed data files format and content: Text file (of FPKM expression values from RNAseq)
processed data files format and content: BedGraph files (from HOMER, for visualization in UCSC)
Submission date Dec 23, 2014
Last update date May 15, 2019
Contact name Morgan Sammons
Organization name University of Pennsylvania
Street address 3400 Civic Center Blvd
City Philadelphia
State/province PA
ZIP/Postal code 19129
Country USA
Platform ID GPL19057
Series (1)
GSE59176 Prevalent p53 gain-of-function mutants co-opt epigenetic pathways to drive cancer growth
BioSample SAMN03273079
SRA SRX835934

Supplementary file Size Download File type/resource
GSM1572249_R172H_H3K4me3_ACAGTG.sam_TagDir.ucsc.bedGraph.gz 29.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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