|
| Status |
Public on Oct 01, 2020 |
| Title |
PM_2 |
| Sample type |
SRA |
| |
|
| Source name |
protruding-mouth stage
|
| Organism |
Danio rerio |
| Characteristics |
tissue: protruding-mouth stage
rna fraction: size fractionated (20-40 nt) whole cell RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were homogenized and whole cell RNA was extracted using Qiazol (Qiagen) according to the manufacturer.
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Whole cell RNA from tissue
Ribo_meth_seq_results.xlsx
|
| 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) |
[email protected]
|
| 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 |
GPL24059 |
| 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 |
SAMN15099689 |
| SRA |
SRX8469992 |
