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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 18, 2021 |
| Title |
MDAMB2: JUNB_MBMDA231_2 |
| Sample type |
SRA |
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| Source name |
Breast cancer cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell type: MDA-MB-231 cells
transformation status: --
chip antibody: STAT3 (Cell Signaling Technology, 9139s)
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| Treatment protocol |
1-0.4 μM Tamoxifen (Sigma, H7904) + 2-4 μM AZD0530 (Selleck Chemicals, S1006) were used to induce the transformation.
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| Growth protocol |
MCF-10A-ER-Src cells (Iliopoulos et al., 2009; Iliopoulos et al., 2010) were grown in DMEM/F12 without phenol red (Thermo Fisher Scientific, 11039-047) + 5% charcoal stripped FBS (Sigma, F6765) + 1% pen/strep (Thermo Fisher Scientific, 15140122)+20 ng/ml EGF (Peprotech, AF-100-15) + 0.5 μg/ml Hydrocortisone (Sigma, H-0888) + 0.1 μg/ml cholera toxin (Sigma, C-8052) + 10 μg/ml insulin (Sigma, 10516).
MDA-MB-231 cells were grown in DMEM (Thermo Fisher Scientific, 11995-073) + 10% FBS (Sigma, TMS-013-B) + 1% pen/strep.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were dual cross-linking with a mixture of 2 mM each of ethylene glycol bis (succinimidyl succinate) (EGS) and disuccinimidyl glutarate (DSG) and 1% formaldehyde. Chromatin was digested with 60 units MNase (New England Biolabs, M0247S) at 37 0C for 10 minutes and then sonicated using Branson Microtip Sonifier 450 (4X15 second at output 4.5 and duty cycle 60%) to the sizes mostly between 150-500 bp.
50 μg chromatin, antibodies for transcription factors (listed in Table S6), and 15 μl Dynabead protein G (Thermo Fisher Scientific, 10004D) was used for the chromatin immunoprecipitation (ChIP)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
base-calling performed by Illumina Hiseq 2000
process the fastq file follwing ENCODE ChIP-seq pipeline to obtain IDR peaks
remove IDR peaks that overlap manually picked blacklisted regions and centromere regions
Genome_build: hg38
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| Submission date |
Feb 17, 2021 |
| Last update date |
Feb 18, 2021 |
| Contact name |
Kevin Struhl |
| E-mail(s) |
[email protected]
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| Phone |
617-432-2104
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| Fax |
617-432-2529
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| Organization name |
Harvard Medical School
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| Department |
Biological Chemistry and Molecular Pharamcology
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| Lab |
Kevin Struhl
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| Street address |
240 Longwood Ave.
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE166941 |
YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation (ChIP-seq) |
| GSE166943 |
YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation |
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| Relations |
| BioSample |
SAMN17950976 |
| SRA |
SRX10119394 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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