|
| Status |
Public on Oct 25, 2013 |
| Title |
Ion_H3K4me3_melanoma_tumor_3 |
| Sample type |
SRA |
| |
|
| Source name |
Melanoma tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
antibody concentration (ug/ml): 1
cell type: Melanoma tumor tissue
|
| 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 |
SAMN02298830 |
| SRA |
SRX330707 |
