|
| Status |
Public on Jun 04, 2013 |
| Title |
AML un-treated FAIRE-Seq |
| Sample type |
SRA |
| |
|
| Source name |
AML blasts, untreated
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: acute myeloid leukemia
treatment: Un-treated
time point: Before treatment
|
| Treatment protocol |
AML blasts were isolated from patients’ blood with a BD Vacutainer CPT Cell Preparation Tube according to the manufacturer’s protocol. Mononuclear blasts cells were washed once with cold PBS and counted. Then cells were fixed and processed according to the FAIRE-seq protocol used for cell lines. 1x108 blast cells before and 2 hrs post Daun administration were used for FAIRE experiments.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After fixation, lysates were cleared from sonicated nuclei and histone-free DNA were isolated by phenol-chloroform extraction. Libraries were prepared according to the provider’s kits and protocols for ChIP samples.
Libraries were prepared according to the provider’s kits and protocols for ChIP samples.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
FAIRE-enriched DNA
|
| Data processing |
Reads were aligned to hg19 using BWA, duplicates and reads with mapping quality less than 37 were removed.
Peaks: Peak regions were called by using F-seq package.
Genome_build: hg19
Supplementary_files_format_and_content: bed files indicate the peak regions.
|
| |
|
| Submission date |
Apr 10, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Baoxu Pang |
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Lab |
Michael Snyder
|
| Street address |
3165 Porter Drive
|
| City |
Palo Alto |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
94304 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE33632 |
Genome-wide analysis of histone eviction by FAIRE-Seq |
|
| Relations |
| SRA |
SRX263854 |
| BioSample |
SAMN02029048 |
