|
| Status |
Public on Jul 13, 2023 |
| Title |
Mcpip1 WT_replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
embryo (6 hpf)
|
| Organism |
Danio rerio |
| Characteristics |
tissue: embryo (6 hpf)
genotype: AB/TL
treatment: microinjection with mRNA encoding zebrafish Mcpip1
|
| Treatment protocol |
Zebrafish eggs at 1-cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.
|
| Growth protocol |
AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28°C according to standard protocols.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Zebrafish embryos were collected in Fenozol (A&A Biotechnology, Gdansk, Polska) and stored at -80°C prior to analysis. For RNA isolation, the samples were homogenized in Fenozol using a tissue homogenizer (OMNI International, Kennesaw, GA, USA).
The poly (A) mRNA fraction from total RNA was isolated with Dynabeads® mRNA DIRECT™ Micro Kit (Thermo). The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA-Seq Kit v2 (Thermo). The libraries were generated from 1-15 ng of mRNA by fragmenting the mRNA with RNaseIII, purifying the fragmented RNA, and hybridizing and ligating it with Ion adaptors. Subsequently, the RNA products were reverse transcribed and amplified to double-stranded cDNA, and then purified using a magnetic bead-based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 (Agilent). Each library was diluted to ~53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument (Thermo) using reagents from the Ion PI Hi-Q 200 Kit (Thermo) and Ion PI v3 Proton Chip.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Signal processing and basecalling was performed with Torrent Suite version 5.14.0.
Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR (version 2.7.10a) (PMID: 23104886) and bowtie2 (version 2.4.4) (PMID: 22388286) for unmapped reads.
Gene counts were created with htseq-count (PMID: 25260700), using Ensembl gene model.
Differential expression was tested with DESeq2 version (version 1.40.1) (PMID: 2551628)
Assembly: Danio rerio Ensembl genome version GRCz11
Supplementary files format and content: DESeq2 normalized count
|
| |
|
| Submission date |
May 10, 2023 |
| Last update date |
Jul 13, 2023 |
| Contact name |
Michał Mikula |
| E-mail(s) |
[email protected]
|
| Phone |
+48225462655
|
| Organization name |
Maria Skłodowska-Curie National Research Institute of Oncology
|
| Department |
Genetics
|
| Street address |
Roentgena 5
|
| City |
Warsaw |
| ZIP/Postal code |
02781 |
| Country |
Poland |
| |
|
| Platform ID |
GPL24059 |
| Series (1) |
| GSE232220 |
MCPIP1 functions as a safeguard of early embryonic development |
|
| Relations |
| BioSample |
SAMN35027579 |
| SRA |
SRX20282370 |
