|
| Status |
Public on Nov 04, 2018 |
| Title |
SYO1_Input_shControl_ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
SYO1 (Synovial Sarcoma)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Synovial Sarcoma
cell line: SYO1
chip antibody: none (Input)
antibody manufacturer: -
antibody catalog number: -
antibody lot number: -
|
| Treatment protocol |
EoL-1 and JURKAT cells were untreated. MOLM-13 cells were treated with 1:10,000 DMSO for 48hr. SYO-1 cells were lentivirally infected with either shControl or shSSX vector, selected with puromycin for 48h, and then cultured for 5 days. Cells were harvested for ChIP-seq 7 days post infection. TTC1240 cells were lentivirally infected with empty vector control or vector containing SMARCB1.
|
| Growth protocol |
HEK293T cells and malignant rhabdoid tumor cell line TTC1240 were grown in DMEM (Gibco) supplemented with 10% FBS, 1% GlutaMAX (Gibco), and 1% penicillin-streptomycin (Gibco). Acute myeloid leukemia cell lines EoL-1 and MOLM-13 were grown in RPMI (Gibco) supplemented with 10% FBS, 1% GlutaMAX (Gibco), and 1% penicillin-streptomycin (Gibco). Synovial sarcoma cell line SYO-1 was grown in DMEM without sodium pyruvate (Gibco) supplemented with 10% FBS, 1% GlutaMAX (Gibco), and 1% penicillin-streptomycin (Gibco).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq was performed using standard protocols (Millipore, Billerica, MA). Specifically, cells were fixed in 1% formaldehyde (Sigma Aldrich, F8775) for 10min at 37C and quenched with 125mM glycine for 5min at 37C. After washing, nuclei were sonicated using Covaris Sonicator, and the supernatant was used for immunoprecipitation with the indicated antibody.
ChIP-sequencing libraries were prepared with the Rubicon Thruplex DNAseq prep kit using standard protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
SYO1_Input_shControl_ChIP-Seq
|
| Data processing |
Basecalls were performed using bcl2fastq v2.19.1 for NextSeq output.
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 2.1.0, reporting only the highest scoring alignment for each sequence.
To create ChIP-seq coverage plots, bedGraph plots were created using MACS2 callpeak, sorted and then converted to bigWig format
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using bedGraphToBigWig script downloaded from UCSC
|
| |
|
| Submission date |
Apr 12, 2018 |
| Last update date |
Nov 04, 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 |
Massachusetts |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE113040 |
A non-canonical SWI/SNF complex underlies synthetic lethality in cancers driven by BAF complex perturbation [ChIP-seq] |
| GSE113042 |
A non-canonical SWI/SNF complex underlies synthetic lethality in cancers driven by BAF complex perturbation |
|
| Relations |
| BioSample |
SAMN08918719 |
| SRA |
SRX3927302 |
