|
| Status |
Public on Oct 23, 2018 |
| Title |
Control shRNA [ChIP] |
| Sample type |
SRA |
| |
|
| Source name |
PC-3 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC-3 cell line
genotype: KMT2D normal
cell type: Prostate cancer cell line
antibody: H3K4me1 (Abcam, ab8895)
|
| Treatment protocol |
PC-3 cells (3×105/well) were seeded in 6-well plates and transfected with shRNA expressing lentivirus for 1 week
|
| Growth protocol |
Human prostate cancer cells PC-3 were cultured in RPMI1640 medium supplemented with 10% FBS and incubated at 37℃ in a humidified atmosphere with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We performed H3K4me1 ChIP using a Pierce Agarose ChIP Kit.PC-3 cells were fixed with 1% formaldehyde, lysed and digested by micrococcal nuclease leading to a DNA size range from 100-500bp. 4 ul of H3K4me1 antibody was added to the precleared sample and incubated overnight at 4 °C. The complexes were purified using ChIP Grade Protein A/G Plus Agarose followed by elution from the beads and reverse cross-linking. DNA was purified by DNA Clean-Up Column.
CHIP product was quantified by BioAnalyzer 2100 and Qubit fluorimeter. Then performed DNA-end repair and ligation of methylated sequencing adaptor. Then DNA was amplified by PCR and selected size at 100-300bp. Finally, prepared libraries were sequenced by BGISEQ-500.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
BGISEQ-500
|
| Data processing |
The data was filtered and removed low quality reads, N reads and adaptor sequences.
ChIP-seq reads were aligned to the hg19 genome assembly using SOAP2 (Version: 2.21t)
The alignment results were used for peaks calling by SICER.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using SICER
|
| |
|
| Submission date |
Feb 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shidong Lv |
| E-mail(s) |
lsd990@163.com
|
| Phone |
02061641114
|
| Organization name |
Nanfang Hospital
|
| Street address |
1838 Guangzhou North Ave.
|
| City |
Guangzhou |
| State/province |
State... |
| ZIP/Postal code |
510515 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (2) |
| GSE94816 |
Genome-wide maps of chromatin state difference in KMT2D Knockdown/Control PC-3 Cells |
| GSE94817 |
Analysis of KMT2D Knockdown/Control PC-3 Cell Line |
|
| Relations |
| BioSample |
SAMN06324257 |
| SRA |
SRX2600817 |
