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Sample GSM6705467 Query DataSets for GSM6705467
Status Public on May 02, 2023
Title BC3-716
Sample type SRA
 
Source name Guthrie cards/neonatal blood spots
Organism Homo sapiens
Characteristics tissue: Guthrie cards/neonatal blood spots
disease state: Leukemia
Extracted molecule total RNA
Extraction protocol RNA was extracted from one-half a spot from each Guthrie card with TRIzol
TrioRNA-seq library preparation with custom anydeplete to remove ribosomal RNA and adult and fetal hemoglobin transcripts
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
 
Data processing Raw reads were trimmed off adapter and low quality reads in the sequencer and generated FASTQ files
The FASTQ files were mapped aganist the human refrence genome (hg19) using STAR spliced alignment algorithm (versions 2.7.0)
Aligned with parameters and –chimericSegmentMin 20, --quantMode GeneCounts
The resulting STAR prduced chemiric junction file for each sample processed by CIRCexplorer2 (version 2.3.3) to estimate circRNA abundance
Alignments were visualised and interrogated using the Integrative Genomics Viewer v2.3.80 (Thorvaldsdóttir et al., 2013).
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include gene counts for each sample
Supplementary files format and content: Tab-delimited text files include CIRCexplorer2 produced number of Junction reads for each sample
 
Submission date Nov 02, 2022
Last update date May 02, 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)
GSE125986 Circular RNAs drive oncogenic chromosomal translocations through R-loop-mediated genome instability
GSE217126 Circular RNAs drive oncogenic chromosomal translocations through R-loop-mediated genome instability [ncRNA-seq]
Relations
BioSample SAMN31576488
SRA SRX18127648

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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