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Sample GSM7457656 Query DataSets for GSM7457656
Status Public on Jan 01, 2024
Title p53-cas9_dsRNA-3
Sample type SRA
 
Source name whole embryo
Organism Danio rerio
Characteristics tissue: whole embryo
genotype: MZtp53
time: 6 hpf
treatment: dsRNA
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)
GSE234229 Double-stranded RNA triggers a distinct integrated stress response in the early embryo [dsRNA tp53]
GSE234230 Double-stranded RNA triggers a distinct integrated stress response in the early embryo
Relations
BioSample SAMN35639682
SRA SRX20599746

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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