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| Status |
Public on Apr 05, 2022 |
| Title |
501-KO5-2-MITF |
| Sample type |
SRA |
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| Source name |
501mel ARID2 KO
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| Organism |
Homo sapiens |
| Characteristics |
construct: Lenti-CRISPR V2 Cas9 + sgRNA
disease state: metastatic melanoma
melanoma molecular subtype: BRAFV600E
antibody: MITF - Sigma A. #HPA003259
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
XL ChIP-seq: For ARID2, SS18, BRG1, TEAD4, FOSL2, CTCF, and MITF cells were cross-linked with 2 mM disuccinimidyl glutarate (DSG, Pierce 20593) in PBS for 45 min followed by 1% FA for 10 min at RT. For H3K27ac and H3K27me3 cells were cross-linked with 1% FA for 10 min at RT. ChIP was performed as previously described (Fontanals-Cirera B, Hasson D, Vardabasso C, Di Micco R et al. Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene. Mol Cell 2017 Nov 16;68(4):731-744.e9)
ChIP-seq: Libraries for ChIP-seq were done as previously described (Fontanals-Cirera B, Hasson D, Vardabasso C, Di Micco R et al. Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene. Mol Cell 2017 Nov 16;68(4):731-744.e9)
ATAC-seq: For all ATAC-seq libraries, 50k cells were harvested, tagmented with 2.5-5uL Nextera Tn5 Transposes from nextera for 30 min, amplified up to 10 cycles and purified essentially as previously described in ATAC protocols. Purified libraries were then size selected on 2% agarose gel (150-700bp).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
single end
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| Data processing |
XL ChIP-seq: Reads were aligned using Bowtie (version 0.12.7) with parameters -k 1 -m 1 --best -S -n 2 -l 65 -q. BAM files were generated using SAMtools. duplicated reads were removed using SAMtools. bigwig files were generated from BAM files using deepTools bamCoverage (version 2.4.1) with parameters –normalizeUsingRPKM –binsize 10. Significant peaks were called using MACS2 callpeak (version 2.1.1.2) with parameters -f BAM -g 2.7e9 -s 100 --bw 200 —slocal 1000 -q 0.01.
ATAC-seq: Reads (40bp Paired-end) were aligned using Bowtie2 (version 2.1.0) with parameters -q -X 2000. BAM files were generated using SAMtools. Reads that align to mtDNA, with quality value Q<30, as well as duplicated reads, were discarded using in-house scripts and Samtools.. bigwig files were generated from BAM files using deepTools bamCoverage (version 2.4.1) with parameters –normalizeUsingRPKM –binsize 10. Significant peaks were called using MACS2 callpeak (version 2.1.1.2) with parameters –nomodel –nolambada –keepdup all –slocal 10000
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: fastq - raw illumina reads. bigwig - aligned reads pileup with deeptools
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| Submission date |
Apr 20, 2021 |
| Last update date |
Apr 05, 2022 |
| Contact name |
Emily Bernstein |
| E-mail(s) |
emily.bernstein@mssm.edu
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| Phone |
(212) 824-9335
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| Organization name |
Mount Sinai School of Medicine
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| Department |
Oncological Sciences
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| Lab |
Bernstein Lab
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| Street address |
1470 Madison Avenue, 6th floor Rm 302
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE172383 |
PBAF complex deficiency in melanoma mediates BAF occupancy and transcription factor dynamics (Chromatin) |
| GSE172386 |
PBAF complex deficiency in melanoma mediates BAF occupancy and transcription factor dynamics |
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| Relations |
| BioSample |
SAMN18806628 |
| SRA |
SRX10640875 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5253865_501-KO5-2-MITF_S12_R1_001.bw |
143.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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