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| Status |
Public on Oct 24, 2016 |
| Title |
A549_ChIP_SMC1_A300-055A_NA_EtOH_60min_Rep1 |
| Sample type |
SRA |
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| Source name |
A549-CHIP-SMC1A
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| Organism |
Homo sapiens |
| Characteristics |
cell line: A549 (ATCC, CCL-185)
cell type: Lung adenocarcinoma-derived cells
passages: 9
treated with: 0.01% EtOH, 60min
chip antibody: SMC1 (Bethyl, A300-055A, lot:3)
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| Treatment protocol |
For EtOH treatment, 250 ul of 1% EtOH were added directly to cell medium (25 ml) and incubated for 1 hour at 37C. For estradiol treatment, 100nM of Beta-Estradiol (SIGMA, E8875) was added directly to cell medium and incubated for two hours at 37C.
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| Growth protocol |
HEPG2 were grown in DMEM (Gibco, 11965-092) and A549 were grown in F12K medium (Gibco, 21127022) as recommended by the supplier. All cell mediums were supplemented with 10% fetal bovine serum (Invitrogen, qualified 12483020), 100 μM MEM nonessential amino acids (Cellgro, 25-0250), 2 mM L-glutamine (Gibco, 25030-081), 100 U/ml penicillin, 100 μg/ml streptomycin (Gibco, 15170-063). MCF7 were kept in DMEM w/o phenol-red (Gibco, 31053-028) supplemented with 5% of Charcoal/Dextran treated FBS (Hyclone, AVH78911), 100 μM MEM nonessential amino acids (Cellgro, 25-0250) and 2 mM L-glutamine (Gibco, 25030-081) for 3 days prior to 100nM of Beta-Estradiol (SIGMA, E8875) for two hours.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde in culture medium for 10 minutes at room temperature. Cells were then lysed in 10 ml lysis buffer (0.1%SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl ph 8.0 and 150 mM NaCl) and chromatin was sheared to 200-600 bp fragments using a Bioruptor Sonicator (Diagenode). Chromatin extract from 5x10^7 cells was incubated overnight at 4oC with 100 ul of Dynabeads Protein G magnetic beads (Life Technologies, 10004D) previously incubated with 10 ug of selected antibodies. After ChIP, samples were washed and bound complex were reversed cross-linked and eluted in 10mM Tris-HCl pH 8
The TruSeq DNA sample prep kit with indexing adapters was used according to the manufacturer's recommendations (Illumina)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
A549-CHIP-SMC1A-rep1
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| Data processing |
All datasets were analyzed with the ChIP-Seq pipeline developed at the McGill University and Génome Québec Innovation Centre (https://bitbucket.org/mugqic/mugqic_pipelinest) (version 2.1.0)
All samples were processed using Trimmomatic 0.33 with the following parameters: LEADING=30, TRAILING=30, SLIDINGWINDOW=4:30, MINLEN=30. Reads were mapped against the hg19 build of the human reference genome using BWA 0.7.12 with default parameters and MACS2 2.1.0 with default parameters was used for peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak files were generated with MACS2 2.1.0 with default parameters. The enrichment ratio of each replicate were calculated with the 2 control files available for each cell line.
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| Submission date |
Jan 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Steve Bilodeau |
| E-mail(s) |
Steve.Bilodeau@crchudequebec.ulaval.ca
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| Phone |
418 525-4444 15550
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| Organization name |
Centre de recherche du CHU de Québec
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| Street address |
9 McMahon
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| City |
Quebec |
| State/province |
Quebec |
| ZIP/Postal code |
G1R 3S3 |
| Country |
Canada |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE76893 |
FOXA and master transcription factors recruit Mediator and Cohesin to the core transcriptional regulatory circuitry of cancer cells |
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| Relations |
| BioSample |
SAMN04415511 |
| SRA |
SRX1531782 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2040034_A549_CHIP_ctrl_SMC1A_2WCE_rep1_peaks.narrowPeak.gz |
1.4 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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