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Sample GSM1120300 Query DataSets for GSM1120300
Status Public on Jun 04, 2013
Title AML daunorubicin FAIRE-Seq
Sample type SRA
Source name AML blasts, 90 mg of daunorubicin
Organism Homo sapiens
Characteristics cell type: acute myeloid leukemia
treatment: 90 mg of daunorubicin
time point: 2 hours post infusion
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
SRA SRX263855
BioSample SAMN02029049

Supplementary file Size Download File type/resource
GSM1120300_fseq_600_2029_6_no_form_GCCAATA-s-uniq-q37.bed.gz 4.1 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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