|
| Status |
Public on Feb 11, 2017 |
| Title |
Input, SAOS2 |
| Sample type |
SRA |
| |
|
| Source name |
SAOS2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SAOS2
cell type: osteosarcoma cell line
passage number: less than 20 passages
chip antibody vendor: No antibody
|
| Treatment protocol |
No treatment
|
| Growth protocol |
SAOS2 cells were grown in DMEM, 10% Fetal Bovine Serum, 2mM L-glutamine and 1X penicillin-streptomycin (All from Invitrogen) and split every three days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP DNA was extracted by standard phenol approach.
NEB ChIP-seq prep kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Input DNA
|
| Data processing |
Base calling: RTA 1.12.4.2 and sequencing chemistry: Illumina TruSeq 3.0. All raw files were generated using this method.
Alignment: Illumina Casava 1.8.2. All processed data files were generated using this method.
Processed files are peak files. Peak calling was performed using MACS (version 1.4.1 2011_06_27; band width = 300; model fold = 10,30; pvalue cutoff = 1.00e-05)
Genome_build: hg19
Supplementary_files_format_and_content: peak file
|
| |
|
| Submission date |
Jan 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jing Huang |
| E-mail(s) |
huangj3@mail.nih.gov
|
| Organization name |
National Cancer Institute
|
| Lab |
Cancer Biology and Genetics
|
| Street address |
37 Convent Dr. 37/3140
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
MD 20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE76937 |
RUNX2 and CBFB genome-wide binding in osteosarcoma SAOS2 cells |
|
| Relations |
| BioSample |
SAMN04420268 |
| SRA |
SRX1533881 |
