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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
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
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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