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Sample GSM3587365 Query DataSets for GSM3587365
Status Public on May 01, 2023
Title DRIPpcDNA31_rep1
Sample type SRA
 
Source name DRIPpcDNA31
Organism Homo sapiens
Characteristics cell line: HEK293
passages: 6-8
Treatment protocol Cell were harvested at maximum 90% confluency after transfection. Cell were transfected at 60-70% confluency in 10cm dish with 6ug of plasmid DNA, 5ul Lipofectamine 2000 with Optimem. Cells were collected 3days after transfection.
Growth protocol HEK293 cells were grown in DMEM supplemented with 10% FBS and 1X penicillin-Streptomycin-Antimycotic. These were grown at 37oC and 5% carbon dioxide
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was harvested by GenElute Mammalian Genomic DNA miniprep kit (Merck)
DRIP DNA (2 ng) was used to generate DRIP-0seq libraries with NEBNext Ultra II DNA library prep kit (New England Biolabs) according to manufactureres instructions. Samples were multiplexed and sequenced on the Illumina NextSeq 500 (Illumina) using the single end protocol with 75 read length (high ouotput kit).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing library strategy: DRIP-Seq
Samples were multiplexed and sequenced on the Illumina NextSeq 500 using the stranded single end protocol with a read length of 75.
Raw reads were adaptor trimmed and filtered for short sequences using cutadapt v1.8.1 3
The resulting FASTQ files were analysed and quality checked using the FastQC program
The filtered reads were mapped against the human reference genome (Hg19) using the BWA alignment algorithm 4 (version 0.7.9a-r786 with default parameters)
Enriched regions of the genome were identified using the MACS2 peak caller 5 (version 2.1.1.20160309) using default parameters and reporting only peakswith a FDR cut-off (-q) < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 peak files
 
Submission date Jan 31, 2019
Last update date May 01, 2023
Contact name Simon Conn
E-mail(s) simon.conn@flinders.edu.au
Organization name Flinders University
Department College of Medicine and Public Health
Lab Circular RNAs in Cancer Laboratory
Street address Sturt Road, Bedford Park
City Adelaide
State/province South Australia
ZIP/Postal code 5042
Country Australia
 
Platform ID GPL18573
Series (2)
GSE125985 Circular RNAs drive oncogenic chromosomal translocations through R-loop-mediated genome instability [DRIP-seq]
GSE125986 Circular RNAs drive oncogenic chromosomal translocations through R-loop-mediated genome instability
Relations
BioSample SAMN10856058
SRA SRX5320587

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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