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| Status |
Public on May 23, 2023 |
| Title |
MDA-MB-453_UNT |
| Sample type |
SRA |
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| Source name |
MDA-MB-453
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-453
cell type: Human breast cancer
chip antibody: pY88-H4
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| Treatment protocol |
5x10^7 MDA-MB-453 cells were treated with R-9b (dz67) inhibitor overnight (5 uM) and lysates were prepared by sonication in RLB bufffer.
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| Growth protocol |
MDA-MB-453 cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 degreeC
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The lysates were immunoprecipitation with pY88-H4 antibodies (2 ug) for overnight.
Ten nanograms of immunoprecipitated DNA was fragmented to 300 base pairs using a Covaris M220 Focused-ultrasonicator (Covaris, Inc., Woburn, MA) and then used to generate sequencing libraries using the Kapa Hyper Prep Kit (Roche Sequencing Solutions Inc., Pleasanton, CA). The size and quality of the library was evaluated using the Agilent BioAnalyzer (Agilent Technologies, Inc., Santa Clara, CA), and the library was quantitated with the Kapa Library Quantification Kit. Each enriched DNA library was then sequenced on an Illumina NextSeq 500 sequencer to generate 40-50 million 75-base paired-end reads (Illumina, Inc., San Diego, CA). The raw sequence data were aligned using BowTie 2 [1], and the binding sites were identified using the MACS peak-finding software
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw fastq files were aligned against human genome hg38 assembly using Burrows-Wheeler Alignment tool and then processed using methylQA to generate bed and bigwig files.
The MACS2 peak caller was used to compare the ChIP-Seq signal to a corresponding input control to identify narrow regions of enrichment (peaks) using default parameters.
ChIP-Seq signals and peak locations were further visualized using UCSC Genome Browser.
The top 500-1000 ChIP-Seq peaks were assigned to the nearest genes using the annotatePeaks function from HOMER2, motif binding sites were determined using HOMer2, and GO and pathway enrichment analyses were performed by EnrichR.
Assembly: hg38
Supplementary files format and content: narrowPeak
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| Submission date |
May 17, 2022 |
| Last update date |
May 23, 2023 |
| Contact name |
Tiandao Li |
| Organization name |
Washington University
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| Street address |
4444 Forest Park Ave
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| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63108 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE203230 |
ACK1/TNK2 Epigenetically Regulates Cell Cycle Program to Promote Breast Cancer Resistance to CDK4/6 inhibitor (ChIP-Seq) |
| GSE203232 |
ACK1/TNK2 Epigenetically Regulates Cell Cycle Program to Promote Breast Cancer Resistance to CDK4/6 inhibitor |
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| Relations |
| BioSample |
SAMN28500274 |
| SRA |
SRX15317096 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6165053_453_UNT_DZ_peaks.narrowPeak.gz |
17.9 Kb |
(ftp)(http) |
NARROWPEAK |
| GSM6165053_453_UNT_peaks.narrowPeak.gz |
18.5 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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