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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 01, 2021 |
| Title |
circNick-LRS_human_brain |
| Sample type |
SRA |
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| Source name |
Human cortex
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| Organism |
Homo sapiens |
| Characteristics |
source: Agilent Technologies, cat: 540143
tissue: cortex
genotype: wild type
age: 25 and 50 years mix
molecule subtype: enriched circRNA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total human brain RNA was derived from post mortem cortex and provided by Agilent (Agilent Technologies, cat: 540143). For the preparation of mouse brain RNA, a male mouse (strain 129S2/SV) was sacrificed, and the entire brain was harvested and grained in Trizol (Thermo Fisher Scientific). Total RNA was obtained according to the manufacture’s protocol.
After rRNA and linear RNA depletion the enriched circRNA linearized and polyadenylated. Later, the protocol, SQK-PCS108, version PCS_9035_v108_revF_26Jun2017, provided by ONT was applied to prepare the library and run it on the MinION flow cells.
Sequencing of circular RNA
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
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| Data processing |
Nanopore data was basecalled using Guppy (v 3.4.5)
filtered using NanoFilt (v 2.6.0) allowing only reads with average base quality of 7 or more and a read length of 250 bp or more
mapped to the human genome (hg19) or mouse genome (mm10) using a parallelized version of Blat
Detetion of circular RNA (circRNA) using custom scripts
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: Tab-delimited text files list all detected circRNAs, including genomic coordinates, number of reads spanning backsplice junction (BSJ), host gene that circRNAs originates from and circRNA ID from circBase, circAtlas and CIRCpedia.
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| Submission date |
Dec 09, 2020 |
| Last update date |
Jun 01, 2021 |
| Contact name |
Morten T Veno |
| E-mail(s) |
morten.veno@omiics.com
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| Phone |
+45 28727107
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| Organization name |
Omiics ApS
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| Street address |
Aabogade 15
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| City |
Aarhus N |
| State/province |
DK |
| ZIP/Postal code |
8200 |
| Country |
Denmark |
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| Platform ID |
GPL24106 |
| Series (1) |
| GSE127059 |
CircRNAs full-length sequencing in the human and mouse brain samples using Oxford Nanopore Technology |
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| Relations |
| BioSample |
SAMN17038213 |
| SRA |
SRX9657937 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4966278_circNick-LRS_human_brain_candidates.annotated.txt.gz |
753.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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