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| Status |
Public on Nov 12, 2014 |
| Title |
ATAC-seq (DMSO) |
| Sample type |
SRA |
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| Source name |
IMR90 fetal lung fibroblasts
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| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
treatment: DMSO (6hrs)
passages: 30-35
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| Treatment protocol |
Proliferating IMR90 fibroblasts were treated with either DMSO or nutlin3a (5uM final) for 6hrs before harvesting.
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| Growth protocol |
IMR90 fibroblasts were grown in DMEM with 10% FBS at 3% oxygen.
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| 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
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
library stategy: ATAC-seq
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| 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.
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| Submission date |
Jun 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Morgan Sammons |
| Organization name |
University of Pennsylvania
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| Street address |
3400 Civic Center Blvd
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19129 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE58740 |
Chromatin dynamics of p53 binding sites in IMR90 |
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| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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