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| Status |
Public on Aug 25, 2024 |
| Title |
48-doxrep3 |
| Sample type |
SRA |
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| Source name |
Breast cancer
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast cancer
cell line: MCF7 RTA16 tet-ind. GRHL2-GFP cl. 62 (OE)
chip antibody: GRHL2 (Millipore, #HPA004820)
treatment: vehicle
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| Treatment protocol |
Cells were treated with 1 μg/mL doxycycline hyclate and 10 nM 17β-estradiol for 24, 48, or 72 hours, changing the media every 24 hours.
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| Growth protocol |
Cells were maintained in Dulbecco’s Modified Eagle Medium, supplemented with 10% VWR fetal bovine serum, 1% sodium pyruvate, and 1% penicillin streptomycin in 10% CO₂ at 37°C. Prior to treatment, cells were synchronized and stripped of any contaminates after being cultured for 3 days in phenol-red free DMEM, supplemented with 10% 6x charcoal stripped FBS, 1% sodium pyruvate, 1% Pen/Strep, and 2% L-glutamine.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes prior to quenching and cell lysis. Genomic material was sonicated using a 550 sonic dismembrator (Fisher Scientific)
Libraries were prepared using the NEBNext Ultra II DNA Library. Prep Kit for Illumina. 500 pg DNA was used as starting material for IP samples and inputs. Libraries were amplified using 14 cycles on the Thermocycler. Amplified libraries were size selected for 370 bp using AMPure XP beads from Beckman Coulter. Final libraries were validated using the Agilent High Sensitivity DNA kit.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq X Plus |
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| Data processing |
Data was processed from NovaSeq 6000 with bcl2fastq
ChIP-seq raw files were mapped using bowtie2 with standard parameters ( -x input file) with sam file output.
Sam files were converted with samtools into sorted and indexed bam files
HOMER was used to process the bam files, find peaks, and create the bigWig files.
Assembly: hg38
Supplementary files format and content: bigWig
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| Submission date |
Jul 11, 2024 |
| Last update date |
Aug 26, 2024 |
| Contact name |
Elaine Alarid |
| E-mail(s) |
etalarid@wisc.edu
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| Organization name |
University of Wisconsin Madison
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| Street address |
111 Highland Avenue
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53792 |
| Country |
USA |
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| Platform ID |
GPL34284 |
| Series (1) |
| GSE272059 |
Elevated GRHL2 imparts plasticity in estrogen receptor positive breast cancer cells [ChIP-Seq] |
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| Relations |
| BioSample |
SAMN42437680 |
| SRA |
SRX25289344 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8392233_MCF7GRHL2tet_GRHL2_nodox48h_rep3.tagdirnew.ucsc-0.bigWig |
182.7 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
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