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| Status |
Public on Jun 30, 2016 |
| Title |
K562 DRIP-seq |
| Sample type |
SRA |
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| Source name |
erythromyeloblastoid leukemia cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard Illumina protocols.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
RNA/DNA hybrids
Genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI.
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| 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.
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| Submission date |
Jun 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yoong Wearn Lim |
| E-mail(s) |
ywlim@ucdavis.edu
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| Organization name |
University of California, Davis
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| Department |
Molecular and Cellular Biology
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| Lab |
Chedin
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| Street address |
One Shields Avenue
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE70189 |
Human and mouse DRIP-seq and DRIPc-seq |
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| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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