|
| Status |
Public on Apr 08, 2021 |
| Title |
PC3_ecDNA_positive_ChIP_PolII.umi |
| Sample type |
SRA |
| |
|
| Source name |
PC3 from NCI60
|
| Organism |
Homo sapiens |
| Characteristics |
source: The PC3 was initiated from a bone metastasis of a grade IV prostatic adenocarcinoma from a 62-year-old male Caucasian.
ip antibody: RNA polymerase II (920102, Biolegend)
|
| Growth protocol |
Tumor specimens were dissociated and cultured as neurospheres in DMEM/F12 medium (11330-032, Gibco) supplemented with N-2 supplement (17502-048, Gibco) and growth factors (EGF and FGF-basic). Cells with passages between 15 and 26 were used for experiments.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
2 million cells were crosslinked and lysed in the same way as ChIA-PET. After lysis, the nuclei pellets were sonicated and immunoprecipitated with anti-RNApolII antibody (920102, Biolegend) or anti-H3K27ac antibody (39133, Active Motif).
4 ng of ChIPped DNA or input DNA were subjected to end-repair, A-tailing and adaptor ligation (IDT xGen Dual Index UMI Adapters) with the KAPA Hyper Prep Kit (KK8505, KAPA Biosystems). Adaptor-ligated DNA fragments were PCR amplified with the KAPA Library Amplification ReadyMix (KK2612, Kapa Biosystems) and sequenced on Illumina platform.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ChIP-seq
|
| Data processing |
The raw reads were quality trimmed using Trim Galore version 0.4.3 (options: --stringency 3 -q 30 -e .20 --length 15) and mapped to the hg19 genome using BWA 0.7.12 (command: mem). Reads with mapping quality greater than 30 were retained, de-duplicated. Only reads share the same mapping coordinate and UMI barcodes will be removed. The high quality non-redundant reads were used to call peaks with MACS2.1.0.20151222 (macs2 callpeak options: --nomodel --extsize 250 -B --SPMR -g hs --keep-dup all). Fold enrichment was computed with MACS2 bdgcmp and the output bedgraph file was converted to bigWig with bedGraphToBigWig.
Illumina RTA-1.18 software used for basecalling
Genome_build: hg19
|
| |
|
| Submission date |
Apr 22, 2020 |
| Last update date |
Apr 08, 2021 |
| Contact name |
Chia-Lin Wei |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Washington
|
| Department |
The Northwest Genomics Center (NWGC)
|
| Lab |
Genome Sciences
|
| Street address |
3720 15th Ave NE
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195-5065 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE124769 |
Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription |
|
| Relations |
| BioSample |
SAMN14671440 |
| SRA |
SRX8158052 |
