|
| Status |
Public on Feb 01, 2017 |
| Title |
input DNA |
| Sample type |
SRA |
| |
|
| Source name |
input DNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC3
tissue: prostate; derived from metastatic site: bone
chip antibody: none
|
| Treatment protocol |
no treatment
|
| Growth protocol |
RPMI1640 supplied with 10% fetal bovine serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The chromatin was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against H3K36me2( Millipore).
Libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) were mapped to the genome using the BWA algorithm with default settings.
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome were used in the subsequent analysis
Tags were extended in silico (using Active Motif software) at their 3´- ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp). To identify the density of fragments (extended tags) along the genome, the genome was divided into 32-nt bins and the number of fragments in each bin was determined.
Peaks were called using SICER.
Tag Normalization: tag number of all samples was reduced (by random sampling) to the number of tags present in the smallest sample.
"Active Regions" were used when comparing different amples.
Genome_build: hg19
Supplementary_files_format_and_content: The number of fragments in each bin is stored in a bigWig file.
|
| |
|
| Submission date |
Jul 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ni Li |
| E-mail(s) |
lini@sibs.ac.cn
|
| Organization name |
Institute of Health Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences
|
| Lab |
Laboratory of Tumor Progression and Metastasis
|
| Street address |
320 Yueyang Road, Shanghai, 200025 P.R. China
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE84869 |
H3K36me2 occupancy profiling by high throughput sequencing from control and WHSC1 knockdown PC3 cells. |
|
| Relations |
| BioSample |
SAMN05441420 |
| SRA |
SRX1978386 |
