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Sample GSM1526935 Query DataSets for GSM1526935
Status Public on Nov 12, 2014
Title H3K4me2 ChIP (Nutlin-3a)
Sample type SRA
Source name IMR90 fetal lung fibroblasts
Organism Homo sapiens
Characteristics cell line: IMR90
treatment: Nutlin-3a (5uM final, 6hrs)
passages: 30-35
antibody: H3K4me2 (Millipore)
Treatment protocol Proliferating IMR90 fibroblasts were treated with either DMSO or nutlin3a (5uM final) for 6hrs before harvesting.
Growth protocol IMR90 fibroblasts 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 Diagenode Bioruptor.
For RNA-seq, cells were harvested and PolyA+ RNA was isolated using the NEBNext Ultra RNA-seq Isolation Module.
Sequencing libraries for ChIP-seq were constructed using the NEBNext Ultra kit as per manufacturer's recommended instructions.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description ChIP of H3K4me2 from Nutlin-treated IMR90.
Data processing Raw fastq files were aligned to hg19/ncbi37 using Bowtie2, allowing for only uniquely aligned reads to be reported.
bowtie2 -k1 -N1
Significant Peaks were called using macs (v1.4) with input controls and default mfold
macs -t <> -n <> -s 50 -f SAM -g 3107677273
Only peaks with an F.D.R < 1% were used in the analysis.
HOMER was used to generate BedGraph files for visualization. First, HOMER-specifc TagDirectories were generated from bowtie output files ( using the command 'makeTagDirectory <ChIP_TagDirectory> <> '
BedGraphs were then generated using the command 'makeUCSCfile <ChIP_TagDirectory> -o auto', and bigWigs were generated using
TSS, Enhancers, and Protoenhancer BED files were processed using H3K4me1 and H3K4me3 overlap with p53_Nutlin_Peaks_hg19_FDR1.txt.
Genome_build: ncbi37/hg19
Supplementary_files_format_and_content: Peak BED files (3 column, from MACS)
Supplementary_files_format_and_content: BigWig files (from HOMER, for visualization in UCSC)
Supplementary_files_format_and_content: FPKM values of gene expression from RNA-seq data in tab-delimited text format.
Submission date Oct 16, 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 GPL18573
Series (1)
GSE58740 Chromatin dynamics of p53 binding sites in IMR90
BioSample SAMN03113076
SRA SRX952177

Supplementary file Size Download File type/resource
GSM1526935_H3K4me2_Nutlin.hg19.bam_TagDir.ucsc.bigWig 416.4 Mb (ftp)(http) BIGWIG
GSM1526935_H3K4me2_Nutlin_Peaks_hg19_FDR1.bed.gz 595.3 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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