|
| Status |
Public on May 02, 2023 |
| Title |
1729802 |
| 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 |
SAMN31576489 |
| SRA |
SRX18127647 |
