|
| Status |
Public on Oct 03, 2024 |
| Title |
Whole embryo, disome footprints, 4 hpf rep1 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryo
genotype: Wild type AB strain
treatment: injected with sfGFP mRNAs at 1-cell stage
|
| Treatment protocol |
Reporter mRNA mix was injected in 1-cell stage embryos.
|
| Growth protocol |
Fertilized eggs were obtained by natural breeding and developed in system water at 28.5ºC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos were lysed in cycloheximide-containing buffer and treated with RNase I. Ribosomes were isolated using MicroSpin S-400 HR column (Cytiva). Ribosome footprints were extracted using Trizol reagent (Thermo Fisher Scientific), Direct-zol RNA Microprep Kit (Zymo Research) and size selection by gel electrophoresis.
preadenylated linker ligation, rRNA depletion, reverse transcription, cDNA circularization, PCR amplification for ribosome profiling
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Ribosome profiling
|
| Data processing |
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a with --outFilterMismatchNmax 1 --outFilterMultimapNmax 1 options
Read quantitation using custom scripts
Assembly: GRCz11
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Library strategy: Ribosome profiling
|
| |
|
| Submission date |
Jun 29, 2023 |
| Last update date |
Oct 03, 2024 |
| Contact name |
Kota Ishibashi |
| E-mail(s) |
ishibash@cc.kyoto-su.ac.jp
|
| Phone |
+81-75-705-1943
|
| Organization name |
Kyoto Sangyo University
|
| Department |
Department of Frontier Life Sciences
|
| Street address |
Kamigamo-motoyama
|
| City |
Kita-ku, Kyoto |
| State/province |
Kyoto |
| ZIP/Postal code |
603-8555 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21741 |
| Series (2) |
| GSE236144 |
Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish [Ribo-seq] |
| GSE236146 |
Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish |
|
| Relations |
| BioSample |
SAMN36072246 |
| SRA |
SRX20825804 |
