|
| Status |
Public on Aug 01, 2019 |
| Title |
ChIP-Seq_PC3_KDM2B |
| Sample type |
SRA |
| |
|
| Source name |
Human prostatic adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC3
tissue: prostate; derived from metastatic site: bone
disease: grade IV, adenocarcinoma
age: 62 years adult
chip antibody: millipore, 09-864
|
| Growth protocol |
PC3 cells were obtained from ATCC and cultured according to the manufacturers' instructions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell nuclei from approximately 20 million formaldehyde crosslinked (1%; 10 minutes at room temperature) were isolated and chromatin was fragmented using sonicator (bioruptor). Lysate were cleared and protein-DNA complexes were isolated using target antibodies and protein-G coated magnetic beads. Chromatin IP was conducted following the standard protocol from ActiveMotif ChIP-IT High Sensitivity® (HS) Kit.
Libraries were prepared according to standard Illumina HiSeq 3000 protocol/Illumina HiSeq 4000. Samples were sequenced at Integrated Genomics Operation Core at UT MD Anderson Cancer Center.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Reads were trimmed by trimmomatic prior to alignment, as recommended by the ChIP kit manufacturer.
The trimmed reads were then aligned to the hg19 reference genome using bowtie2.
Only uniquely aligned reads were kept for downstream 45 analysis, with duplicate reads removed by the same tools software v1.9.
To visualize ChIP-seq signal at individual genomic regions, we generated bedGraph file by using HOMER software v4.10.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph
|
| |
|
| Submission date |
May 28, 2019 |
| Last update date |
Aug 01, 2019 |
| Contact name |
Filippo Giancotti |
| E-mail(s) |
[email protected]
|
| Organization name |
UT MD Anderson Cancer Center
|
| Department |
Cancer Biology
|
| Lab |
Dr. Giancotti Lab
|
| Street address |
1881 East Road
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE131829 |
Genome-wide maps of chromatin state in PC3 cells |
| GSE131830 |
Transcriptomic data and Genome-wide maps of chromatin state in prostate cancer |
|
| Relations |
| BioSample |
SAMN11505995 |
| SRA |
SRX5735030 |
