|
| Status |
Public on Dec 20, 2016 |
| Title |
RD Fusion Negative Rhabdomyosarcoma cell line H3K27ac |
| Sample type |
SRA |
| |
|
| Source name |
RD Fusion Negative Rhabdomyosarcoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
antibody: H3K27ac (Active Motif, 39133)
enrichment target: H3K27ac
target function: Active enhancers
|
| 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.
|
| 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.
Standard Illumina barcodes were introduced during library preparation
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
ChIP enriched DNA reads were mapped to reference genome (hg19) using BWA version 0.7.10
The ChIP-seq peaks were called by MACS2 version 2.1.0.
Genome_build: Hg19
Supplementary_files_format_and_content: peak files are tab delimited text files for each sample.
|
| |
|
| Submission date |
Jul 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Javed Khan |
| E-mail(s) |
khanjav@mail.nih.gov
|
| Phone |
2407606135
|
| 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) |
| GSE84628 |
ChIP-seq of Active Histone Mark (H3K27ac) and Myogenic Regulatory Factors (MYF5 and MYOD) in Fusion Negative Rhabdomyosarcoma Cell Lines |
| GSE84630 |
Fusion Negative Rhabdomyosarcoma Cell Lines |
|
| Relations |
| BioSample |
SAMN05420680 |
| SRA |
SRX1962091 |
