|
| Status |
Public on Feb 24, 2020 |
| Title |
BPLER_MS275_H3K27ac_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
stem-like breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BPLER2
cell type: a stem-like breast cancer (BrCa) cell model
transforming gene: TERT; SV40-LT/st; HRASV12
treatment: MS-275 (Entinostat)
chip antibody: H3K27ac - ChIP grade (Abcam, ab4729)
|
| Treatment protocol |
BPLER2 cells were plated in 15cm petri dish at 3.3x10e6 cell/plate in BMI-T medium. The day after, cells were treated with 1 mM (f.c.) MS-275 for 24 hours. After treatment, cells were formaldehyde cross-linked, harvested and processed for chromatin immunoprecipitation (ChIP)-sequencing analysis.
|
| Growth protocol |
BPLER2 cells were described before (Cancer Cell 12, 160-170, 2007). Both cells and BPLER culture medium (BMI-T) are available from Live Tissue Culture Service Center, University if Miami (contact LTCC@med.miami.edu).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates from formaldehyde cross-linked cells were clarified from sonicated nuclei and histone-DNA complexes were immunoprecipitated with antibody. Cross-links were reversed and DNA extracted for library construction.
Libraries for paired-end sequencing and alignment were prepared according to NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® according to manufacturer instructions (New England BioLabs).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
CC14_S2
|
| Data processing |
Base calling, data filtering and read alignment performed on BaseSpace Illumina platform.
Broad peak calling was performed using SICER (v.0.1.1) with default parameters. Peak regions were further filtered after SICER peak calling with adjusted p-value (FDR)<0.01 and fold change >2.5.
Identification of super-enhancers was done using ROSE algorithm (Cell 153, 307-319, 2013; Cell 153, 320-334, 2013).
Genome_build: hs19
Supplementary_files_format_and_content: bigWig files were generated from bed files using the Wig/BedGraph-to-bigWig converter (Galaxy Version 1.1.1)
Supplementary_files_format_and_content: tab-delimited text files include: Stitched enhancer ID; chromosome; stitched enhancer start; stitched enhancer end; number of constituent stitched; size of constituents stitched together; signal(s) of ranking_bam, rank of ranking bam, binary of super-enhancer (1) vs. typical (0). Signal of ranking bam is density times length.
|
| |
|
| Submission date |
May 17, 2019 |
| Last update date |
Feb 24, 2020 |
| Contact name |
Corrado Caslini |
| E-mail(s) |
ccaslini@med.miami.edu
|
| Organization name |
University of Miami
|
| Street address |
1501 NW 10th Avenue
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE131436 |
Genome-wide analysis of histone 3 lysine K27 acetylation in stem-like breast cancer cells in response to HDAC1/3/7 inhibition. |
| GSE131632 |
Genome-wide analysis of histone 3 lysine K27 acetylation and differential expression analysis in stem-like breast cancer cells in response to HDAC1/3/7 inhibition or knockdown |
|
| Relations |
| BioSample |
SAMN11730020 |
| SRA |
SRX5862441 |
