|
| Status |
Public on Sep 09, 2020 |
| Title |
LYC_unmod |
| Sample type |
SRA |
| |
|
| Source name |
Unmodified IVT
|
| Organism |
Bacillus subtilis |
| Characteristics |
modifications: None
|
| Treatment protocol |
single transcripts unmodified samples are folded in vitro and treated with DMSO
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Purified with columns or extracted with TRIzol with or without RNA with poly A tail
Purified RNA was ligated with a adpator at the 3' end and followed by a motor protein or adaptors were ligated at the 5' end and 3' end of the product from fragmented reversed transcribed RNA
Oxford Nanopore direct RNA sequencing or RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Data processing |
Basecall samples with Albacore version 2.3.3 no filtering
Aligned samples with Graphmap 0.5.2
Aligned raw signal to sequence with Nanopolish 10.2
Calculated reactivity with PORE-cupine
Genome_build: GRCh38
SRA_file_format: Fast5
Processed_files_format_and_content: CSV files were generated, higher peaks represent a higher possibiilty for single stranded regions
|
| |
|
| Submission date |
Apr 22, 2020 |
| Last update date |
Apr 20, 2021 |
| Contact name |
Aw Jong Ghut Ashley |
| E-mail(s) |
awjga1@gis.a-star.edu.sg
|
| Organization name |
Genome Institute of Singapore
|
| Street address |
60 Biopolis St
|
| City |
singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL26847 |
| Series (1) |
| GSE133361 |
Determination of isoform-specific RNA structure with nanopore long reads |
|
| Relations |
| BioSample |
SAMN14668653 |
| SRA |
SRX8237442 |
