|
| Status |
Public on Jan 01, 2024 |
| Title |
TP450-3 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryo
cell type: wide type
time: 6 hpf
treatment: tol2 mRNA
|
| Treatment protocol |
Zebrafish embryos injected with cas9 mRNA, tol2 mRNA or dsRNA were maintained in 1/3x Ringer's at 28.5C
|
| Growth protocol |
Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs were extracted from 6 hpf embryos using TRIzol reagent (Invitrogen), and were precipitated by cold isopropanol (50%, v/v) in the presence of carrier glycogen (20 µg/each sample). Polyadenylated mRNAs were purified by the poly(A) mRNA Magnetic Isolation Module (NEB).
The mRNA libraries were then generated using NEBNext Ultra RNA Library Prep Kit for lllumina following manufacturer’s instruction. Briefly, mRNA fragmentation and priming were carried out via NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. ProtoScript II Reverse Transcriptase and Second Strand Synthesis Enzyme Mix were used to synthesize first and second strand cDNAs. AxyPrep Mag PCR Clean-up (Axygen) kit were then used to purify the cDNAs. After that, cDNAs were treated with End Prep Enzyme Mix to repair 3’ and 5’ ends, followed by dA-tailing and adaptor ligation. Following size selection by AxyPrep Mag PCR Clean-up (Axygen) kit, fragments haboring around 300 bp inserts were recovered.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
50% epi stage
|
| Data processing |
Each library was amplified by a 11-cycle PCR, and 150 bp paired-end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data.
The quality was examined by Cutadapt and FastQC.
Sequencing results from three biological repeat samples were assembled and aligned using StringTi.
Differential expression was calculated with DESeq2 and edgeR.
Assembly: GRCz10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample
|
| |
|
| Submission date |
Jun 06, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
tong lu |
| E-mail(s) |
202020327@mail.sdu.edu.cn
|
| Organization name |
ShanDong University
|
| Street address |
72, binghai rd
|
| City |
Qingdao |
| ZIP/Postal code |
266207 |
| Country |
China |
| |
|
| Platform ID |
GPL14875 |
| Series (2) |
| GSE234227 |
Double-stranded RNA triggers a distinct integrated stress response in the early embryo [cas9 tol2] |
| GSE234230 |
Double-stranded RNA triggers a distinct integrated stress response in the early embryo |
|
| Relations |
| BioSample |
SAMN35639464 |
| SRA |
SRX20599697 |
