 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 25, 2024 |
| Title |
Precise RNA knockdown of smn1,or tardbp and tarbpl by CRISPR-QKD and transcription activation of lin28a and sox9b by CRISPR-Qa in zebrafish |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
CRISPR-Cas systems have revolutionized gene regulation technologies in various organisms, including zebrafish. However, most zebrafish studies rely on transient injections of CRISPR components, with limited use of transgenic models, primarily for Cas9-mediated knockouts. This is largely due to challenges in achieving sustained and effective expression of Cas effectors. To address these challenges, we introduce the CRISPR-Q system, which integrates the QFvpr/QUAS binary expression system with CRISPR-Cas effectors. This approach overcomes limitations associated with transient mRNA or protein delivery and circumvents the toxicity and silencing issues typical of other binary systems, such as Gal4/UAS. The CRISPR-Q system enables robust expression of CasRx or dCas9vpr, facilitating efficient transcript knockdown (CRISPR-QKD) and gene activation (CRISPR-Qa). Using this system, we successfully achieved significant knockdown of smn1 and the simultaneous knockdown of the paralogs tardbp and tardbpl, modeling phenotypes of spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS), respectively. Furthermore, CRISPR-Qa effectively activated the endogenous genes lin28a and sox9b, demonstrating the system's broad applicability. The CRISPR-Q system represents a significant advancement in zebrafish genetic manipulation, providing a robust and versatile platform for studying gene function and modeling human diseases, with potential extensions to other model organisms
|
| |
|
| Overall design |
To investigate the efficiency and specificity of CRISPR-Q induced KD or transcriptional activation, we established triple transgenic (3Tg) zebrafish which contains CRISPR-Q components and guide RNAs (gRNAs or sgRNAs), and double transgenic (2Tg) zebrafish which lacks gRNA, served as a control. gRNA targeting smn1 and gRNA array targeting tardbp and tardbpl were used to test CRISPR-QKD, while sgRNAs targeting lin28a and sox9b were used for CRISPR-Qa. We then performed RNA-seq analysis for smn1, tardbp, lin28a and sox9b from 3Tg embryos and their respective 2Tg siblings.
|
| |
|
| Contributor(s) |
Jin YN, Shi M, Ge W, Bin L, Deng X, Liu C, Zheng M, Zhang P, Lei L, Li C, Guo Y, Yu YV |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
May 26, 2024 |
| Last update date |
Jun 25, 2024 |
| Contact name |
Youngnam N Jin |
| E-mail(s) |
ynjin.neo@gmail.com
|
| Phone |
13628627281
|
| Organization name |
Wuhan University
|
| Department |
Medical Research Institute
|
| Street address |
115 Donghu Road, Wuchang District
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430071 |
| Country |
China |
| |
|
| Platforms (1) |
| GPL24995 |
Illumina NovaSeq 6000 (Danio rerio) |
|
| Samples (24)
|
| GSM8290346 |
smn1, 3TG, rep1 |
| GSM8290347 |
smn1, 3TG, rep2 |
| GSM8290348 |
smn1, 3TG, rep3 |
| GSM8290349 |
tardbp, 2TG, rep1 |
| GSM8290350 |
tardbp, 2TG, rep2 |
| GSM8290351 |
tardbp, 2TG, rep3 |
| GSM8290352 |
tardbp, 3TG, rep1 |
| GSM8290353 |
tardbp, 3TG, rep2 |
| GSM8290354 |
tardbp, 3TG, rep3 |
| GSM8290355 |
lin28a, 2TG, rep1 |
| GSM8290356 |
lin28a, 2TG, rep2 |
| GSM8290357 |
lin28a, 2TG, rep3 |
| GSM8290358 |
lin28a, 3TG, rep1 |
| GSM8290359 |
lin28a, 3TG, rep2 |
| GSM8290360 |
lin28a, 3TG, rep3 |
| GSM8290361 |
sox9b, 2TG, rep1 |
| GSM8290362 |
sox9b, 2TG, rep2 |
| GSM8290363 |
sox9b, 2TG, rep3 |
| GSM8290364 |
sox9b, 3TG, rep1 |
| GSM8290365 |
sox9b, 3TG, rep2 |
| GSM8290366 |
sox9b, 3TG, rep3 |
|
| Relations |
| BioProject |
PRJNA1116733 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE268371_salmon.merged.gene.tpm_lin28a-Tg.xlsx |
3.4 Mb |
(ftp)(http) |
XLSX |
| GSE268371_salmon.merged.gene.tpm_smn1-Tg.xlsx |
3.1 Mb |
(ftp)(http) |
XLSX |
| GSE268371_salmon.merged.gene.tpm_sox9b-Tg.xlsx |
2.0 Mb |
(ftp)(http) |
XLSX |
| GSE268371_salmon.merged.gene.tpm_tardbp-Tg.xlsx |
3.5 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
Less...
More...