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| Status |
Public on Aug 04, 2022 |
| Title |
Ku70_Veh_exp3 |
| Sample type |
SRA |
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| Source name |
MCF7 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
cell type: human breast cancer cells
treatment: Veh
antibody: Bethyl A302-624A (Lot#A302-624A-1)
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| Treatment protocol |
For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM. TNFalpha(R&D systems) was added to a final concentration of 20 ng/ml. 5α-dihydrotestosterone (DHT, Sigma) was added to a final concentration of 100 nM. The ethanol (EtOH) vehicle control was 0.05% in all samples.
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| Growth protocol |
MCF7 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM, GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen). LNCAP cells were maintained at 37°C and 5% CO2 in Advanced RPMI 1640 medium (GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked with 1% formaldehyde at room temperature for 10 min. And then the cross-linking was quenched with 0.125M glycine for 5 min. Chromatin was fragmented using a Bioruptor® Pico (Diagenode) for 10 min at high power, with an interval of 30 s between pulses to get around 200bp fragments and precleared using 20 μl Protein G Dynabeads (Life Technologies, Cat# 10009D). Subsequently, the soluble chromatin was incubated with 2-5 μg antibodies at 4°C overnight. Immunoprecipitated complexes were collected using 30 μl Protein G Dynabeads, which have been saturated with PBS/1% BSA over night at 4°C, per reaction. For all ChIPs, after de-crosslinking overnight at 65°C, final ChIP DNA was extracted and purified using QIAquick spin columns (QIAGEN).
The libraries were constructed following Illumina’s Chip-Seq Sample prep kit.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Basecalls performed using CASAVA version 1.4
Reads were aligned to the hg38 genome assembly using Bowtie2.
Genome_build: hg38
Supplementary_files_format_and_content: bed and bedgraph
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| Submission date |
Dec 06, 2021 |
| Last update date |
Aug 04, 2022 |
| Contact name |
Yuliang Tan |
| E-mail(s) |
yut020@ucsd.edu
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| Organization name |
University of California, San Diego
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| Department |
School of Medicine
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| Street address |
Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648
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| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92037-0648 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE135807 |
ChIP-seq assay in human cancer cells |
| GSE135808 |
Topoisomerase 1 Nicking-dependent HP1gamma Engagement Mediates Acute Activation of Phase-separated Enhancers |
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| Relations |
| BioSample |
SAMN23705391 |
| SRA |
SRX13327981 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5719148_Ku70_Veh_exp3.bed.gz |
382.0 Kb |
(ftp)(http) |
BED |
| GSM5719148_Ku70_Veh_exp3.ucsc.bedGraph.gz |
212.4 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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