|
| Status |
Public on Sep 07, 2023 |
| Title |
H3K9me3, PML knockdown, MDA231, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell type: Human breast cancer
chip antibody: anti-H3K9me3 Abcam 8898
|
| Treatment protocol |
Silencing of PML was performed via lentiviral shRNA
|
| Growth protocol |
DMEM, 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 2 mM Di(N-succinimidyl) glutarate for 45 min at RT and with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using the Diagenode Bioruptor 300.
ChIP-seq libraries were prepared using ChIPSeq Illumina protocol. Libraries were validated using the High Sensitivity D5000 ScreenTape (Agilent Technologies).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base-calling was performed on NovaSeq 6000 Illumina machine.
ChIP-seq reads were trimmed using BBDuk from BBTools suite version 37.36 with suggested settings (ktrim=r k=23 mink=11 hdist=1).
ChIP-seq reads were aligned to the UCSC hg38 genome using BWA-MEM version 0.7.12-r1039 . Uniquely mapped reads were selected with MarkDuplicates from Picard Tools version 1.104
Filtering was done on reads mapping in regions present in the ENCODE hg38 blacklist and regions flagged as not primary alignment or with mapping quality score less than 15.
For H3K4me3 and H3K27ac ChIP-seq peaks were detected using MACS2 v2.2.7.1. For PML, LMNB1, H3K9me3 and H3K27me3 mapped reads were used to call domain using the Enriched Domain Detector.
Assembly: bigWig files were generated using bamCompare from Deeptools.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak (except for H3K27me3 samples) , EDD peaks (except for Input samples)
|
| |
|
| Submission date |
Feb 24, 2023 |
| Last update date |
Sep 07, 2023 |
| Contact name |
Rosa Bernardi |
| E-mail(s) |
bernardi.rosa@hsr.it
|
| Organization name |
San Raffaele Scientific Institute
|
| Street address |
via Olgettina 60
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE226060 |
PML modulates epigenetic composition of chromatin to regulate expression of pro-metastatic genes in triple-negative breast cancer [ChIP-seq] |
| GSE226210 |
PML modulates epigenetic composition of chromatin to regulate expression of pro-metastatic genes in triple-negative breast cancer |
|
| Relations |
| BioSample |
SAMN33435750 |
| SRA |
SRX19495901 |
