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Sample GSM4490619 Query DataSets for GSM4490619
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
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
BioSample SAMN14668653
SRA SRX8237442

Supplementary file Size Download File type/resource
GSM4490619_LYC_unmod-fastq.tar.gz 13.2 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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