 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 28, 2020 |
| Title |
liver2 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Homo sapiens |
| Characteristics |
technology: 5hmC-Seal
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified using Qiagen's Puregene kit and sonicated to about 200 bp.
Fragmented DNA was purified by Zymo DNA Clean and Concentration Kit. Then, the selective 5hmC chemical labeling was performed in glucosylation buffer (50 mM HEPES buffer pH 8.0, 25 mM MgCl2) containing above fragmented DNA, βGT, N3-UDP-Glc, and incubated at 37°C for 2 hr. After DNA purification in ddH2O, DBCO-PEG4-Biotin (Click Chemistry Tools) was added and incubated at 37°C for 2 hr. The biotin labeled DNA was pulled down by C1 Streptavidin beads (Life Technologies) for 15 min at room temperature. Next, the captured DNA fragments were subjected to PCR amplification using Nextera DNA sample preparation kit. The resulting amplified product was purified by 1.0X AMPure XP beads. Input library was made by direct PCR from fragmented DNA directly without labeling and pull-down. The libraries were quantified by a Qubit fluorometer (Life Technologies) and sequenced on NextSeq 500.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
High-quality reads were then mapped to hg19 reference genome by Bowtie with uniquely mapped reads retained for the following analyses.
PCR duplicates were removed by Samtools.
Normalization were performed by Deeptools.
Peak calling was performed with MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 output narrowPeak file
|
| |
|
| Submission date |
Jan 30, 2020 |
| Last update date |
Oct 29, 2020 |
| Contact name |
Xiaolong Cui |
| E-mail(s) |
xiaolong.cui@northwestern.edu
|
| Organization name |
Northwestern University
|
| Department |
Department of Preventive Medicine
|
| Street address |
680 N Lake Shore Drive
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE144530 |
A human tissue map of 5-hydroxymethylcytosines exhibits tissue specificity through gene and enhancer modulation |
|
| Relations |
| BioSample |
SAMN13944779 |
| SRA |
SRX7651220 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4290214_liver2_peaks.narrowPeak.gz |
873.7 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
