|
Status |
Public on Oct 25, 2013 |
Title |
Ion_WM266-4_H3K4me3 |
Sample type |
SRA |
|
|
Source name |
Melanoma derived cell line
|
Organism |
Homo sapiens |
Characteristics |
cell line: WM266-4 chip antibody: H3K4me3 antibody concentration (ug/ml): 1 cell type: Melanoma derived cell line
|
Treatment protocol |
mouse dendritic cells were treated with 0.1ug/ml LPS
|
Growth protocol |
Mouse dendritic cells were isolated from wild type C57BL/6 mice and cultured as previously published. Melanoma tumor derived cell lines were culturedin 10% FCS medium.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were constructed according to Illumina or Ion Torrent protocols.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Ion Torrent PGM |
|
|
Data processing |
alignment were performed using BWA aligner ChIP-seq peak calling was performed using the contiguous segmentation algorithm as part of the Scripture package (http://www.broadinstitute.org/software/scripture/) Genome_build: mm9, hg19 Supplementary_files_format_and_content: bed files are output from scripture program, which identify ChIP-seq regions that have enriched peaks
|
|
|
Submission date |
Aug 01, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Christine S Cheng |
Organization name |
Broad Institute of MIT and Harvard
|
Street address |
7 Cambridge Center
|
City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02142 |
Country |
USA |
|
|
Platform ID |
GPL17301 |
Series (1) |
GSE49477 |
Semiconductor based DNA sequencing of histone modification states |
|
Relations |
BioSample |
SAMN02298823 |
SRA |
SRX330703 |