|
| Status |
Public on Feb 01, 2020 |
| Title |
ChIPseq_BrM_H3K4me3_REP2 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231 breast cancer cell line brain metastatic variant
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231 BrM2
cell type: mammary gland/breast epithelial cell
target molecule: H3K4me3
|
| Growth protocol |
Cells were grown in monolayer in DMEM + 10% FBS + Penicillin-streptomycin at 37ºC, 5% CO2 for 3 days
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed in 1% formaldehyde for 10 min. Chromatin was prepared and immunoprecipitated as previously described (Greer CB, Tanaka Y, Kim YJ, Xie P, Zhang MQ, Park IH, Kim TH: Histone Deacetylases Positively Regulate Transcription through the Elongation Machinery. Cell Rep 2015, 13(7):1444-1455.).
DNA libraries were prepared using ThruPLEX DNA-seq Kit (Takara)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
MDAMB231_BrM_H3K4me3_merge.mqsd.coverage.RPKM.bw
MDAMB231_Par_BoM_BrM_LM_H3K4me3_merge_peaks.broadPeak.unique.bed
MDAMB231_Par_BoM_BrM_LM_H3K4me3_merge_peaks.broadPeak.counts.txt
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Reads were trimmed of adapters using Trimmomatic v0.32
Trimmed reads were aligned using Bowtie2 v2.3.4.3 to hg19 using standard parameters and a maximum fragment length of 2000
Duplicate reads were determined using Picard tools v2.18.21
Bam files were filtered using samtools -F 1804
For consensus peak calling filtered bam files were merged. Peak calling was performed using MACS2 v2.1.2 with the option --broad.
Motif finding was performed using HOMER v4.10.
Reads that fell within consensus peaks were determined using featureCounts
DESeq2 was used to determine differential histone signal
Genome_build: hg19
Supplementary_files_format_and_content: bigwig (merge of replicates for each IP and input), bed (consensus peak for each IP), txt (DESeq2 results and raw counts)
|
| |
|
| Submission date |
Apr 11, 2019 |
| Last update date |
Feb 01, 2020 |
| Contact name |
Qin Yan |
| E-mail(s) |
qin.yan@yale.edu, craig.wilen@yale.edu
|
| Organization name |
Yale University
|
| Department |
Pathology
|
| Lab |
BML338
|
| Street address |
310 Cedar St.
|
| City |
New Haven |
| ZIP/Postal code |
06510 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE129645 |
Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain [ChIPseq] |
| GSE129647 |
Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain |
|
| Relations |
| BioSample |
SAMN11397960 |
| SRA |
SRX5668292 |
