|
| Status |
Public on May 31, 2018 |
| Title |
SYO1 shCt H3K27ac |
| Sample type |
SRA |
| |
|
| Source name |
SYO1 (SS)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SYO1 (SS)
shRNA: shCt
antibody: anti-H3K27ac
antibody vendor: Abcam
antibody catalog: ab4729
antibody lot#: GR238071-1
|
| Treatment protocol |
Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). The cells were harvested following 48-hour exposure to the lenti-virus and 5-day selection with 2 μg/ml of puromycin.
|
| Growth protocol |
All cell lines were cultured in DMEM medium (Gibco, Grand Island, NY, USA), supplemented with 10-20% fetal bovine serum, 1% Glutamax (Gibco), 1% Sodium Pyruvate (Gibco) and 1% Penicillin-Streptomycin (Gibco).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation (ChIP) experiments were performed per standard protocols (Millipore, Billerica, MA) with minor modifications. Briefly, 10M cells were crosslinked with 1% formaldehyde for 10 min at 37 °C. This reaction was subsequently quenched with 0.125M glycine.
All library prep and sequencing were 75bp single end on Illuminia Nextseq 500
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
SYO1 shCt anti-H3K27ac ChIP-seq
|
| Data processing |
ChIP-seq reads were mapped to the human reference genome (hg19) using Bowtie2(Langmead and Salzberg, 2012) version 2.1.0 with parameters –k 1.
Peaks were called against input reads using MACS2(Zhang et al., 2008) version 2.1.0 at q=1e-3.
Peaks were filtered to remove peaks that overlap with ENCODE blacklisted regions, as well as peaks mapped to unmappable chromosomes (only chr1-22,X,Y included). Duplicate reads were removed using samtools rmdup for all downstream analyses.
ChIP-seq track densities were generated per million mapped reads with MACS2 2.1.0 using parameters –B –SPMR.
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak
|
| |
|
| Submission date |
Dec 13, 2017 |
| Last update date |
May 31, 2018 |
| Contact name |
Cigall Kadoch |
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Lab |
Kadoch Lab
|
| Street address |
450 Brookline Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE108025 |
The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma [ChIP-Seq] |
| GSE108028 |
The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma |
|
| Relations |
| BioSample |
SAMN08172273 |
| SRA |
SRX3468037 |
