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Sample GSM1720619 Query DataSets for GSM1720619
Status Public on Jun 30, 2016
Title K562 DRIP-seq
Sample type SRA
Source name erythromyeloblastoid leukemia cell line
Organism Homo sapiens
Characteristics cell line: K562
Extracted molecule genomic DNA
Extraction protocol Standard Illumina protocols.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
Description RNA/DNA hybrids
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.
Data processing Library strategy: DRIP-Seq
DRIPc-seq, DRIP-seq, MethylC-seq, RNA-seq: All fastq files were trimmed with FastqMcf before mapping.
DRIPc-seq, DRIP-seq: Trimmed fastq reads were mapped to hg19 or mm9 using BWA 0.6.1 and Bowtie2.2.1. Peak calling was performed using a custom HMM algorithm.
RNA-seq: Trimmed fastq reads were mapped to hg19 using TopHat 2.0.5.
MethylC-seq: Trimmed fastq reads were mapped to hg19 using Bismark 0.7.7.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: wig files, bed files, bedGraph files.
Submission date Jun 23, 2015
Last update date May 15, 2019
Contact name Yoong Wearn Lim
Organization name University of California, Davis
Department Molecular and Cellular Biology
Lab Chedin
Street address One Shields Avenue
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
Platform ID GPL11154
Series (1)
GSE70189 Human and mouse DRIP-seq and DRIPc-seq
BioSample SAMN03787480
SRA SRX1070682

Supplementary file Size Download File type/resource
GSM1720619_K562_DRIP.wig.gz 245.4 Mb (ftp)(http) WIG
GSM1720619_K562_DRIP_peaks.bed.gz 417.1 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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