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| Status |
Public on Dec 01, 2019 |
| Title |
MCF7 Input |
| Sample type |
SRA |
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| Source name |
MCF7
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
treatment: Ethanol as vehicle control
antibody: None
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| Treatment protocol |
For hormone (Estrogen) depletion, cells were changed to charcoal-stripped hormone-free medium (Gibco, Grand Island, NY) supplemented with 10% charcoal dextran-treated fetal bovine serum (Thermal Scientific Hyclone, Logan, UT) for 72 hours. Estrogen induction was performed using 10 nM of 17β-estradiol (Sigma, St. Louis, MO) for 3 hours (E2pos), and Ethanol was used as a vehicle control (E2neg), as previously described (Tsai et al, Nature, 2010. PMID:21164480)
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| Growth protocol |
MCF7 cells were obtained from the American Type Culture Collection and cultured in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum, as previously described (Tsai et al, Nature, 2010. PMID:21164480)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immuoprecipitation (ChIP) experiments with MCF7 cells were performed as previously described (Tsai et al, Nature, 2010. PMID:21164480). Briefly, the fragmented chromatin lysate was immunoprecipitated overnight using TRIM24 antibody. The protein-DNA complexes were washed several times and the phenol-chloroform-extracted DNA was used for library construction and sequencing.
For ChIP-seq, sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using single-end sequencing technology on Illumina HiSeq 3000 platform.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie v1.1.0
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.4.2; Scores represent the ChIP-seq tag numbers.
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| Submission date |
Apr 25, 2018 |
| Last update date |
Dec 01, 2019 |
| Contact name |
Jiejun Shi |
| E-mail(s) |
jiejuns@uci.edu
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| Organization name |
University of California Irvine
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| Department |
School of Medicine
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| Lab |
Li lab
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| Street address |
5270 California Ave
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| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92617 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE113654 |
Cyclic LSD1 recruitment and dynamic H3K4 methylation establish TRIM24-activated estrogen response |
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| Relations |
| BioSample |
SAMN08981313 |
| SRA |
SRX3993993 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3110729_MCF7_Input.bw |
145.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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