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| Status |
Public on Feb 23, 2021 |
| Title |
H3K4me3_1 |
| Sample type |
SRA |
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| Source name |
MDA-MB-231 cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell type: breast cancer cell line
tumor type: triple negative - basal b
chip antibody: H3K4me3 Ab8580 from Abcam
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| Treatment protocol |
experiments were carried out in 2 independent replicates except for p300/CBP
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| Growth protocol |
MDA-MB-231 cells (ATCC, Rockville, MD, USA) were cultured cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal calf serum and penicillin/streptomycin (100µg/ml each) in a humidified 5% CO2 atmosphere at 37°C. Cells freshly amplified and frozen after obtention from the ATCC were used every 3months and were routinely tested for the absence of mycoplasma contamination
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the appropriate antibodies.
ChIP-seq libraries were prepared using the TruSeq ChIP sample reparation kit from Illumina by the MGX sequencing Platform (Montpellier, France)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
CT_3
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| Data processing |
Reads were aligned to hg19 genome using Bowtie2 allowing no more than 2 mismatches and no multiple alignment sites.
Aligned reads were processed with R package PASHA (Fenouil et al., 2013; doi: 10.1093/bioinformatics/btw206) to eliminate PCR artefacts, extend reads to an estimated fragment length and generate WIG files.
R Package PASHA was used to normalize the WIG files to calculate the scores per million reads sequenced and Input DNA signal was subtracted from normalized WIG files.
Wig files from biological replicates were merged.
Peaks were called using Thresholding function of Integrated Genome Browser (https://bioviz.org/) with the following settings : H3K4me1 threshold=30, Max gap=1000, Min run=250; H3K4me3 threshold=30, Max gap=500, Min run=150; H3K27ac threshold=50, Max gap=500, Min run=150; p300/CBP threshold=60, Max gap=50, Min run=50 ; PolII threshold=50, Max gap=800, Min run=100; CTCF threshold=50, Max gap=50, Min run=50
Genome_build: Hg19
Supplementary_files_format_and_content: wig files
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| Submission date |
Mar 11, 2020 |
| Last update date |
Feb 23, 2021 |
| Contact name |
Isabelle Jariel-Encontre |
| E-mail(s) |
isabelle.jariel@inserm.fr
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| Phone |
00 33 (0)4 11 28 31 53
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| Organization name |
IRCM-U1194- INSERM
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| Street address |
208 Avenue des Apothicaires
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| City |
Montpellier |
| State/province |
Montpellier Cedex5 |
| ZIP/Postal code |
34298 |
| Country |
France |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE146822 |
Mapping of epigenetic marks (H3K4me1, H3K4me3, H3K27ac), p300/CBP, PolII and CTCF on MDA-MB-231 genome |
| GSE146825 |
Transcriptional regulation by Fra-1 in triple negative breast cancers |
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| Relations |
| BioSample |
SAMN14360520 |
| SRA |
SRX7897890 |
| 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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