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| Status |
Public on Nov 03, 2019 |
| Title |
SKNSH CMYC ChIP-Seq |
| Sample type |
SRA |
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| Source name |
neuroblastoma-derived cell line
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| Organism |
Homo sapiens |
| Characteristics |
growth media: RPMI 1640, 10% FBS, 1% Penicillin/Streptomycin, 2mM L-Glutamine
cell line: SKNSH
mycn status: non-amp
chip antibody: C-MYC (Santa Cruz N262, #sc-764)
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| Treatment protocol |
N/A
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| Growth protocol |
Cells were grown up to 150 mm plates with the appropriate media.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked, flash frozen, and sent to Active Motif. According to Active Motif protocol, cells were lysed, sonicated, and then DNA-protein complexes were isolated with antibodies. Samples were reverse-crosslinked and DNA was purified.
Illumina libraries were prepared by Active Motif using standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After 15 cycles of PCR amplification, the resulting DNA libraries were quantified and sequenced on Illumina NextSeq 500.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
FASTQ sequences were adapter and quality trimmed using TrimGalore.
Phred scores were calculated per sample and used during hg19 alignment with bwa samse.
Picard tools was used to remove duplicate reads.
Fragment sizes were estimated using MaSC and these values were used as input into MACS2 for narrow peak calling.
Peaks were called significant using a q-value cut off of 0.05 and results were returned in units of signal per million reads.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig
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| Submission date |
Oct 02, 2019 |
| Last update date |
Nov 05, 2019 |
| Contact name |
Jo Lynne Rokita |
| E-mail(s) |
rokita@chop.edu
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| Organization name |
Children's Hospital of Philadelphia
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| Street address |
3501 Civic Center Blvd
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE138295 |
MYCN and MYC ChIP-Seq profiling in neuroblastoma cell lines |
| GSE138315 |
Epigenomic profiling of neuroblastoma cell lines |
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| Relations |
| BioSample |
SAMN12889043 |
| SRA |
SRX6935383 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4104637_SKNSH-CMYC-20171205.macs2.SPMR.Input.sorted.bw |
333.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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