|
| Status |
Public on Dec 31, 2022 |
| Title |
4.0hpf (+4sU) injection replicate 2 Inj_R2_TP6 |
| Sample type |
SRA |
| |
|
| Source name |
Zebrafish embryos
|
| Organism |
Danio rerio |
| Characteristics |
cell type: Whole embryos
strain: TLAB (TL X AB)
chip antibody: SLAMseq combined with 3' end RNAseq
treatment: Injected with 4sU, SLAMseq at 4hpf
|
| Treatment protocol |
Zebrafish embryos were injected with 4sU or incubated in 4sU
|
| Growth protocol |
Zebrafish (Danio rerio) were raised according to standard protocols (28°C water temperature; 14 hour light/10 hour dark cycle). TLAB fish were generated by crossing zebrafish AB and the natural variant TL (Tupfel Longfin) stocks, and used for all experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
QuantSeq 3' end sequencing was used to prepare libraries for SLAMseq as well as oocyte samples. TTSLAMseq libraries were generated using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina®. (NEB). Other RNAseq libraries were generated using using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) and indexed with NEBNext Multiplex Oligos for Illumina (Dual Index Primer Set I) (New England Biolabs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
4.0hpf (+4sU) injection replicate 2
Polyadenylated RNA
|
| Data processing |
3' end sequencing data were used to creat custom annotations using 3' GAmES
SLAMseq was mapped and counted using SLAMdunk 3.4.1. Reads were alingned to the dr11 genome
Additional SNP filtering was performed using samtools pileup
TTSLAMseq data were sequentially mapped to rRNA sequences, mitochondrial sequences and then the genome.
other RNAseq data were mapped to dr11 using STAR and counted using featureCounts
Genome_build: dr11
Supplementary_files_format_and_content: count files of SLAMseq data were created using custom scripts after SNP filtering
Supplementary_files_format_and_content: bedgraph files were genererated using deeptools
Supplementary_files_format_and_content: Count files of TTSLAmseq data were obtained from SLAMdunk
|
| |
|
| Submission date |
Oct 04, 2021 |
| Last update date |
Dec 31, 2022 |
| Contact name |
Stefan Ludwig Ameres |
| E-mail(s) |
stefan.ameres@imba.oeaw.ac.at
|
| Organization name |
Institute of Molecular Biotechnology
|
| Street address |
Dr.-Bohr-Gasse 3
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL18413 |
| Series (1) |
| GSE185283 |
Time-resolved RNA sequencing reveals distinct post-transcriptional regimes during zebrafish embryogenesis |
|
| Relations |
| BioSample |
SAMN22044440 |
| SRA |
SRX12479946 |
