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Status |
Public on Feb 11, 2023 |
Title |
SMARCA4_786O PBRM1KO_ATPasei_24hr_ChIPSeq_rep1 |
Sample type |
SRA |
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Source name |
Cancer cell line
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Organism |
Homo sapiens |
Characteristics |
source: 786-O (ATCC CRL1932) protein: SMARCA4 treatment: SMARCA2/4 ATPase inhibitor, 10uM, 24 hr chip antibody: SMARCA4(AbCAM, ab110641, lot GR3375498-10)
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Treatment protocol |
Cells were treated with DMSO control or 5nM bortezomib for 9 hours prior to ChIP-seq. Cells were treated with DMSO control or 10uM SMARCA2/4 ATPase inhibitor (BRM014) for 24 hours prior to ChIPseq.
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Growth protocol |
Cells were grown in RPMI-1640 medium (Sigma) supplemented with 10% fetal bovine serum (Gibco). Cells were maintained in a 5% CO2-humidified incubator at 37°C.
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Extracted molecule |
genomic DNA |
Extraction protocol |
For each protein of interest, approximately 2x107 cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and stopped by adding glycine to a final concentration of 0.2M. Chromatin was extracted and sonicated to ~500bp (Vibra cell, SONICS). The total volume of immunoprecipitation was 2 ml and the amount of antibody used was 20 µg. The input DNA was precleared with protein G Dynabeads (LifeTechnologies) for 2 hours at 4°C and then incubated with antibodies overnight at 4°C. Protein G beads were added the following day and mixture was nutated for 3 hours at 4°C. The beads were washed 6 times with wash buffer at room temperature. At least 10 ng of the amplified DNA was used with NEBNext ChIP-Seq library prep reagent set (NEB). Each library was sequenced to an average depth of 30-50 million reads on Novaseq
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NovaSeq 6000 |
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Data processing |
Sequencing reads were mapped against human genome reference hg19 using the Burrows-Wheeler Aligner (BWA) (version 0.6.2) 'mem' algorithm. Only reads with mapQ >10 and with duplicate removed by rmdup were used in the subsequent analysis Significant peaks were called using MACS2 24 (q-value < 0.01). Assembly: hg19 Supplementary files format and content: ChIP-seq peaks are in macs2 narrowPeak format, including 10 columns: "chromosome" "start coordinate" "end coordinate" "name" "score" "strand" "signalValue" "pValue" "qValue" "peak"
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Submission date |
Jan 05, 2023 |
Last update date |
Feb 11, 2023 |
Contact name |
Xiaosai Yao |
E-mail(s) |
xiaosai.yao@gmail.com, yao.xiaosai@gene.com
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Phone |
+65 68088271
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Organization name |
Genome Institute of Singapore
|
Street address |
60 Biopolis Street, Genome, #02-01
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City |
Singapore |
ZIP/Postal code |
138672 |
Country |
Singapore |
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Platform ID |
GPL24676 |
Series (2) |
GSE152735 |
Genome-wide chromatin profiles of PBRM1 |
GSE222244 |
Genome-wide chromatin profiles of PBRM1 Drug treatment [ChIP-Seq] |
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Relations |
BioSample |
SAMN32602228 |
SRA |
SRX18945317 |