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Sample GSM2769598 Query DataSets for GSM2769598
Status Public on May 24, 2018
Title biotin-dCTP HEK293T PD 2
Sample type SRA
 
Source name HEK293T
Organism Homo sapiens
Characteristics cell line: HEK293T
atcc number: CRL-3216
enrichment: biotin-dCTP labeling and enrichment
genotype: wild-type
Treatment protocol None
None
Growth protocol cells was maintained in DMEM with 10% FBS and penicillin/streptomycin.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted by Universal Genomic DNA Kit (CWbiotech, CW2298).
Genomic DNA was digested to 100-500 bp and purified with Agencourt AMPure XP beads (BECKMAN COULTER) following Spin-6 column (Bio-rad) purification. 2 μg DNA fragments and 15 pg spike_in sequences were used for end repair with NEBNext® End Repair Module (NEB, E6050) and 1 μl E.coli ligase was added to repair nicks in DNA. DNA was then purified with 1.8×AMPure XP beads. dA was added to the 3’ end of double-stranded DNA by NEBNext® dA-Tailing Module (NEB, E6053) and purified with 1.8×AMPure XP beads.
Damages that may interfere the following labeling step were repaired. DNA was purified and subjected to in vitro BER labeling. For samples named "biotin-dCTP", biotin-dCTP was utilized in the in vitro BER labeling;other samples utilized biotin-dUTP. After purification, fragments labeled with biotin were enriched by streptavidin C1 beads (Invitrogen) following the manufacturer’s guidelines.
Y adaptor was ligated to double-stranded DNA on streptavidin C1 beads so that free adaptor can be removed by beads washing. DNA was then eluted from beads by 95 °C 3 min using deionized water. Eluted DNA was subjected to PCR amplification and sequencing.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Description biotin-dCTP_293TPD.uniq.peaks.bed
Data processing 150bp pairend Raw reads were firstly sent for adaptor and quality trimming using trim_galore, and reads shorter than 25 nt after trimming were excluded. For spike-in DNA sequences calculation, bowtie2 was used to reads mapping to corresponding sequences. For genome-wide dU sites identification, processed reads mapped to spike- in sequence were discarded, and then mapped to human reference genome (hg38) using bowtie2. By default, bowtie2 searches for multiple alignments bowtie2 search and only reports a random one in the best matches; for repeat sequences, bowtie reports the best matched locus or random one from the best-matched loci. After alignment, peaks were called using model-based analysis of ChIP-Seq (MACS2) using nonredundant reads. Peaks overlap with that in the control sample were removed. Genomic annotations were performed using Homer software. Gene annotations(RefSeq) were download from UCSC.
Genome_build: hg38
Supplementary_files_format_and_content: bed
 
Submission date Sep 01, 2017
Last update date May 15, 2019
Contact name zhike lu
E-mail(s) zhikelu@gmail.com
Organization name University of Chicago
Department department of chemistry
Street address 5801 South Ellis Avenue
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL20795
Series (1)
GSE99011 Genome-wide mapping reveals that deoxyuridine is enriched in the human centromeric DNA
Relations
BioSample SAMN07594254
SRA SRX3153901

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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