|
| Status |
Public on Apr 27, 2017 |
| Title |
RH4 CTCF rep1 |
| Sample type |
SRA |
| |
|
| Source name |
RMS cell line, PAX3-FOXO1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RH4
cell type: rhabdomyosarcoma
antibody: CTCF, EMD Millipore (cat07-729 lot2628833 pAb)
enrichment target: CTCF
target function: Domain Insulator
|
| Treatment protocol |
ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies. DNase samples were treated with DNaseI (fresh growing cells, without fixation). DNaseI (Roche 04-716-728-001) was added to the cells (0.25 to 0.5 units) and incubated for 5 minutes at 37 ˚C. The digestion was halted with 50 µL of stop buffer (9.5 mL H2O + 100 µL 1M TrisHCl pH 7.4 + 20µL 5M NaCl + 200µL 0.5 M EDTA, with 150 µL 10% SDS and 125 µL proteinase K added just before use). Proteinase K activation at 55 ˚C for 1 hour was followed by DNA purification by column (MiniElute PCR purification kit, Qiagen).
|
| Growth protocol |
Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol. DNase DNA purification was performed by column (MiniElute PCR purification kit, Qiagen).
Standard Illumina barcodes were introduced during library preparation
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
DNA (ChIP-enriched)
|
| Data processing |
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10
The ChIP-seq and DNase-seq peaks were called by MACS2 version 2.1.0. DNase was run in paired-end mode
The enhancers were identified using ROSE2 pipeline in bamliquidator 1.3
Enrichment of known and de novo motifs were found using HOMER version 4.8.2
Chromatin states were learned using ChromeHMM version 1.10
Genome_build: Hg19
Supplementary_files_format_and_content: peak files are tab delimited text files for each sample.
|
| |
|
| Submission date |
Jun 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ashish Lal |
| E-mail(s) |
ashish.lal@nih.gov
|
| Phone |
2407607396
|
| Organization name |
NCI, NIH
|
| Department |
Genetics Branch
|
| Lab |
Javed Khan
|
| Street address |
37 Convent Dr.
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE83726 |
PAX3-FOXO1 establishes myogenic super enhancers [RMS Chip-seq] |
| GSE83728 |
Epigenetic Lanscape and BRD4 Transcriptional Dependency of PAX3-FOXO1 Driven Rhabdomyosarcoma |
|
| Relations |
| BioSample |
SAMN05293573 |
| SRA |
SRX1878889 |
