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Sample GSM4591066 Query DataSets for GSM4591066
Status Public on Oct 01, 2020
Title small_RNA_oblong_2
Sample type SRA
 
Source name oblong
Organism Danio rerio
Characteristics tissue: oblong
rna fraction: whole cell RNA depleted for rRNA and size selected for RNA < 200 nt
Extracted molecule total RNA
Extraction protocol Tissues were homogenized and whole cell RNA was extracted using Qiazol (Qiagen) according to the manufacturer.
For small RNA library construction, one ug of whole-cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 (Invitrogen), and small RNA libraries were constructed using Ion Total RNA-Seq Kit v2 (ThermoFisher Scientific) with minor modifications. In short, the rRNA-depleted RNA samples were enriched for small RNA (<200 nt) using the magnetic bead clean-up module supplied with the kit or MonarchR RNA Cleanup Kit (New England Biolabs), adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV (ThermoFisher Scientific). The cDNA was purified using the magnetic bead clean-up module, without size-selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System (ThermoFisher Scientific) and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Ion Torrent S5
 
Description Whole cell RNA from tissue
Ion GeneStudio S5
There is no processed data for the small_RNA*fastq samples. Reads were used directly from the fastq file to search for genomic genes.
Data processing Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 2.0
Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1
Counting read ends and calculating RiboMeth-seq scores using python scripts
The output FASTA files from small RNA-seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially, SNORDs were identified by running the merged FASTA file through snoScan (Schattner et al. 2005) against zebrafish early- and late-rRNA reference sequences (Locati et al. 2017).
Genome_build: early and late zebrafish rRNA (locati et al). The reference sequences are available in the FASTA file on the series record.
Supplementary_files_format_and_content: MS Excel file contains 5' and 3' read count and calculated RiboMeth-seq score at all positions in the rRNA sequence.
 
Submission date Jun 04, 2020
Last update date Oct 01, 2020
Contact name Nicolai Krogh
E-mail(s) nicolaikj@sund.ku.dk
Organization name University of Copenhagen
Department Department of Cellular and Molecular Medicine
Lab RNA Group - Prof. Henrik Nielsen
Street address Blegdamsvej 3B
City Copenhagen
ZIP/Postal code 2200
Country Denmark
 
Platform ID GPL28630
Series (1)
GSE151797 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2’-O-Me sites
Relations
BioSample SAMN15099682
SRA SRX8469999

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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