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Sample GSM1418975 Query DataSets for GSM1418975
Status Public on Nov 12, 2014
Title ATAC-seq (DMSO)
Sample type SRA
 
Source name IMR90 fetal lung fibroblasts
Organism Homo sapiens
Characteristics cell line: IMR90
treatment: DMSO (6hrs)
passages: 30-35
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.
For ATAC-seq, cells were harvested, nuclei were prepped,and transposase was added for 30 minutes at 30C.
Sequencing libraries for ChIP-seq were constructed using the NEBNext Ultra kit as per manufacturer's recommended instructions.
Sequencing libraries for ATAC-seq were constructed using custom Nextera-compatible primers, from Nextera-adapted DNA fragments
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description library stategy: ATAC-seq
Data processing Processed data files were generated for both genome builds hg18 and hg19.

hg18 (file names do not include "hg18"):
Raw fastq files were aligned to hg18/ncbi36 using Bowtie, allowing for only uniquely aligned reads to be reported.
bowtie --chunkmbs 512 -m 1 --best <hg18_index> -q <file.fastq> <file.map>
Significant Peaks were called using macs (v1.4) with input controls and default mfold
macs -t <ChIP_Bowtie_output.map> -n <Condition_Input.map> -s 50 -f BOWTIE -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 (file.map) using the command 'makeTagDirectory <ChIP_TagDirectory> <ChIP_Bowtie_output.map> '
Bedgraphs were then generated using the command 'makeUCSCfile <ChIP_TagDirectory> -o auto'
Genome_build: ncbi36/hg18
Supplementary_files_format_and_content: Peak BED files (3 column, from MACS)
Supplementary_files_format_and_content: BedGraph files (from HOMER, for visualization in UCSC)
Supplementary_files_format_and_content: FPKM values of gene expression from RNAseq data in tab-delimited text format

hg19 (file names include "hg19"):
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 <ChIP_Bowtie_output.map> -n <Condition_Input.map> -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 (file.map) using the command 'makeTagDirectory <ChIP_TagDirectory> <ChIP_Bowtie_output.map> '
BedGraphs were then generated using the command 'makeUCSCfile <ChIP_TagDirectory> -o auto', and bigWigs were generated using bedGraph2bigWig.pl
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 Jun 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 GPL18573
Series (1)
GSE58740 Chromatin dynamics of p53 binding sites in IMR90
Relations
BioSample SAMN02870097
SRA SRX620752

Supplementary file Size Download File type/resource
GSM1418975_ATAC_DMSO.hg19.bam_MACS_peaks.bed.gz 817.3 Kb (ftp)(http) BED
GSM1418975_ATAC_DMSO.hg19.bam_TagDir.ucsc.bigWig 355.0 Mb (ftp)(http) BIGWIG
GSM1418975_ATAC_DMSO.ucsc.bedGraph.gz 91.4 Mb (ftp)(http) BEDGRAPH
GSM1418975_ATAC_DMSO_Peaks.bed.txt.gz 455.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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