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| Status |
Public on Jul 08, 2024 |
| Title |
P0 Pitx3-GFP+ 2 |
| Sample type |
SRA |
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| Source name |
primary
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| Organism |
Mus musculus |
| Characteristics |
cell line: primary
cell type: dopamine neurons
genotype: Pitx3-GFP
treatment: purification by FACS
age: P0
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy micro kit (Qiagen). 10 to 50 ng of total RNA was used for the construction of sequencing libraries.
Nanopore libraries were constructed using the circPanel-LRS method described in a previous paper (PMID: 34571139). Briefly, CircPanel-LRS uses circRNA-specific primers (CSP) for cDNA synthesis and an adjacent outward pointing primer for second strand cDNA synthesis. CSP primers are modified at the 5′ end to be compatible with ONT-cPRM-adaptor primers for library amplification and nanopore long-read sequencing.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
MinION |
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| Description |
Long-read circRNA-seq
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| Data processing |
Basecalling and demultiplexing was done using Guppy (version 5.0.11+2b6dbff)
Fastq files were analyzed using https://github.com/omiics-dk/long_read_circRNA. This tool was specifically designed to analyze circRNA ONT data generated using the method used in this study. This tool does quality filtering, genome mapping, circRNA detetction, quantification and annotation.
Assembly: mm10
Supplementary files format and content: Tab delimited txt file. Contains the genomic coordininates of detected circRNAs. Also has tabs showing host gene, matching annotation from circBase, circAtlas and CIRCpedia. Columns with the total number of reads spanning back splice junctions (bsj) and the bsj spanning read numbers for the individual samples.
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| Submission date |
Apr 13, 2023 |
| Last update date |
Jul 08, 2024 |
| Contact name |
Morten T Veno |
| E-mail(s) |
[email protected]
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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 |
GPL24973 |
| Series (1) |
| GSE229597 |
Transcriptomic profiling of long non-coding RNAs identifies circRmst as a regulator of midbrain dopamine neuron migration |
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| Relations |
| SRA |
SRX19950982 |
| BioSample |
SAMN34164454 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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