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Sample GSM3587363 Query DataSets for GSM3587363
Status Public on May 01, 2023
Title HEK293T_Nuc_rep2
Sample type SRA
 
Source name HEK293T_Nuc
Organism Homo sapiens
Characteristics cell line: HEK293
passages: 8-10
molecule subtype: rRNA depleted, RNase R treated, nuclear RNA
Treatment protocol Cell were harvested at maximum 90% confluency after transfection. Cell were transfected in 6-well trays with 2.5ug of plasmid DNA, 5ul Lipofectamine 2000 with Optimem. Cells were collected 24hrs 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 total RNA
Extraction protocol RNA was harvested by Trizol (ThermoFisher Scientific) or, for nuclear/cytosolic fractionation, using the PARIS kit (ThermoFisher Scientific)
KAPA RNA HyperPrep kit with RIboErase (Roche)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Nuc_2_8R.trimmed_kapa
Data processing Whole transcriptome RNA, or nuclear and cytoplasmic-fractionated RNA from ribo-depleted (total RNA-seq) or RNase R treated (circular RNA-seq) samples, respectively, were multiplexed and sequenced separately on the Illumina NextSeq 500 platform (high output mode) using the stranded, single end protocol with a read length of 150.
Raw reads were adaptor trimmed and filtered for short sequences using cutadapt v1.8.13, setting minimum-length option to 18, error-rate 0.2 and overlap 5.
The resulting FASTQ files were mapped against the human reference genome (Hg19) using the STAR spliced alignment algorithm (version 2.5.3a with default parameters and --chimSegmentMin 20)
The resulting STAR produced Chimeric.out.junction file for each sample was parsed and annotated for circRNA prediction and backsplice abundance using CIRCexplorer2
Genome_build: hg19
Supplementary_files_format_and_content: CircExplorer2 circRNA detection and abundandce estimation
 
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)
GSE125984 Circular RNAs drive oncogenic chromosomal translocations through R-loop-mediated genome instability [RNA-seq]
GSE125986 Circular RNAs drive oncogenic chromosomal translocations through R-loop-mediated genome instability
Relations
BioSample SAMN10856060
SRA SRX5320581

Supplementary file Size Download File type/resource
GSM3587363_Nuc_2_8R.trimmed_kapa.fastq.gz_CIRCexplorer_circ.tsv.gz 418.7 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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