|
| Status |
Public on Aug 18, 2020 |
| Title |
Human_436_20A_1_H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-436
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: TNBC
paclitaxel sensitivity: Taxol-resistant
replicate: GD_ChIP_45
antibody: H3K4me3 (Millipore 05-1339)
agent: paclitaxel
cell line: MDA-MB-436
|
| Treatment protocol |
Taxol-resistant cells were grown in presence of 20nM of Paclitaxel at all time. Parental cells (MDA-MB-436 and Hs 578T) were grown in DMEM with 1:1000 DMSO at all time.
|
| Growth protocol |
MDA-MB-436 and HS 578T cells were grown in DMSO supplemented with 10%FBS and Penicilin/Streptomycin (100 U/mL Penicilium and 100 μg/mL. Streptomycin). Taxane-resistant cells were generated upon long-term exposure to increasing concentrations of paclitaxel at a starting concentration 0.05 nM with increments (dose and time adjusted to the growth and survival of adapting cells), until the cytotoxic concentration of 10 to 20 nM was reached with the resistant cells growing at a similar rate than the parental cells (>6 months).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ChIP_15_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw
|
| Data processing |
Reads were filtered for quality (phred33 score >=30) and length (n>=32) trimming using FASTX Toolkit 0.0.13.1
Filtered reads were aligned to the reference assembly hg19 using bwa v.0.5.9. Only uniquely mapped reads were retained for further analysis. Redundant reads were removed using SAMtools v0.1.18
Number of reads were downsampled to the lowest number of reads of the samples to be compared together
Peaks were called using MACS2.0 with default values (mfold[10,30], p-value 1e-03) and BigWig files were obtained with MACS2.0 default.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig (bw) files showig average reads intensity to be displayed in the genome browser
|
| |
|
| Submission date |
Apr 25, 2018 |
| Last update date |
Aug 18, 2020 |
| Contact name |
Genevieve Deblois |
| E-mail(s) |
[email protected]
|
| Organization name |
University Health Network, University of Toronto
|
| Department |
Medical Biophysics
|
| Lab |
Mathieu Lupien
|
| Street address |
101 College street
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 1L7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE113684 |
Metabolic adaptations underlie epigenetic vulnerabilities in chemoresistant breast cancer. [ChIP-Seq] |
| GSE113687 |
Metabolic adaptations underlie epigenetic vulnerabilities in chemoresistant breast cancer |
|
| Relations |
| BioSample |
SAMN08982642 |
| SRA |
SRX3995688 |
