GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM8228800

Query DataSets for GSM8228800

Status

Public on Apr 26, 2024

Title

Zebrafish, Riboseq, low dose, dsRNA2

Sample type

SRA

Source name

whole embryo

Organism

Danio rerio

Characteristics

tissue: whole embryo
developmental stage: 50% epi stage
cell type: embryonic cell
genotype: wild type
treatment: dsRNA

Extracted molecule

total RNA

Extraction protocol

Both control group and dsRNA-injected embryos at 5 hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4°C for 10 minutes to remove cellular components, including undigested material such as cell nuclei.Then, RNaseI was added to the supernatant and incubated at 25°C for 30 minutes to digest RNA, while the RNA fragments protected by ribosomes were preserved. Subsequently, an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation, and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction.
RNA fragments within the size range of 26-34nt was separated using polyacrylamide gel electrophoresis without RNase, and the corresponding bands were collected. The recovered bands were subjected to ligation reaction, where a preadenylylated and 3’-blocked linker (5’ rApp-CTGTAGGCACCATCAAT-NH2 3’) was attached to the 3' end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently, the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase (Epicentre, CL4111K), resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA, a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR, and barcode sequences were incorporated.

Library strategy

OTHER

Library source

transcriptomic

Library selection

other

Instrument model

Illumina NovaSeq 6000

Description

dsR_2
low-dose-ribo-density.tsv
RIBOseq-low dose-RPF count.xls

Data processing

The library underwent quality control assessment, and was subjected to Illumina Novaseq 6000 sequencing.
Bio-informatics analysis of RIBOseq profilling was performed to analyze the library data.
Assembly: GRCz10
Supplementary files format and content: Excel file includes raw counts for each Sample
Library strategy: Ribo-seq

Submission date

Apr 24, 2024

Last update date

Apr 26, 2024

Contact name

tong lu

E-mail(s)

202020327@mail.sdu.edu.cn

Organization name

ShanDong University

Street address

72, binghai rd