|
| Status |
Public on Sep 14, 2023 |
| Title |
ChIP, V5, LNCaP, EHMT1-K451R, Dox-rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: prostate cancer cell
cell line: LNCaP-tet-EHMT1
treatment: 0.5μg/ml doxycycline for 2 days
chip antibody: anti-V5 (Invitrogen)
|
| Growth protocol |
In RPMI 1640 medium with 10% FBS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed using the SMARTer ThruPLEX DNA-Seq Prep Kit (Takara Bio USA).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ChIP_V5_LNCaP_EHMT1_K451R_Dox.bw
ChIP_V5_LNCaP_EHMT1_K451R_Dox_peaks.narrowPeak.gz
|
| Data processing |
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were mapped to the hg19 human genome using bwa (version 0.7.9a) with aln and samse sub-commands.
Samtools (version 1.2) was used to convert sam files to bam format.
MACS2 (version 2.1.0) was used to call peak on the bam files.
bedGraph files generated from MACS2 were converted into bigwig files with UCSC tools (version 369).
Assembly: hg19
Supplementary files format and content: bw, narrowPeak
|
| |
|
| Submission date |
Apr 28, 2022 |
| Last update date |
Sep 14, 2023 |
| 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 |
MA |
| ZIP/Postal code |
02125 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE201769 |
Lysine methylation of EHMT1/GLP as a molecular switch to reprogram transcription networks in prostate cancer [ChIP-seq] |
| GSE201771 |
Lysine methylation of EHMT1/GLP as a molecular switch to reprogram transcription networks in prostate cancer |
|
| Relations |
| BioSample |
SAMN27926369 |
| SRA |
SRX15038486 |
