|
| Status |
Public on Jul 14, 2020 |
| Title |
LN_HOXB13_GSK_S6_L001 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: prostate cancer cell
antibody: HOXB13
cell line: LNCaP
|
| Treatment protocol |
LNCaP cells grown in RPMI1640 with 5% CSS were treated with 50μM GSK2879552 for 4 hours
|
| Growth protocol |
LNCaP cells were maintained in RPMI-1640 with 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries construction was performed using ThruPLEX DNA-seq 48D Kit (Rubicon Genomics)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
technical replicate for HOXB13 ChIP-Seq after treated with GSK
LN_HOXB13_GSK_S6_peaks.narrowPeak
LN_HOXB13_GSK_S6.bw
|
| Data processing |
Raw reads were aligned to hg19 using bwa (version 0.7.2)
sam files are converted to bam with samtools (version 0.1.18 )
MACS2 (version 2.1.2) was used to call peak on the bam files
bedGraph files containing signal per million reads produced from MACS2 was converted to bigwig files with ucsctool kit (315)
Genome_build: GRCh37
Supplementary_files_format_and_content: bigWig and narrowPeak files containing normalized signal and peak intervals
|
| |
|
| Submission date |
Apr 20, 2020 |
| Last update date |
Jul 14, 2020 |
| Contact name |
Changmeng Cai |
| E-mail(s) |
changmeng.cai@umb.edu
|
| Organization name |
University of Massachusetts Boston
|
| Street address |
100 William T. Morrissey Blvd.
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02125 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE148928 |
ChIP-Seq for HOXB13 in LNCaP cell line with GSK treatment and VEH control |
| GSE149007 |
Lineage-specific chromatin binding of FOXA1 is regulated by LSD1-mediated demethylation |
|
| Relations |
| BioSample |
SAMN14651591 |
| SRA |
SRX8147142 |
