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Status |
Public on Oct 01, 2020 |
Title |
small_RNA_oblong_2 |
Sample type |
SRA |
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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.
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Ion Torrent S5 |
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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.
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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.
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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 |
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|
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 |
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Relations |
BioSample |
SAMN15099682 |
SRA |
SRX8469999 |