|
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 |