|
| Status |
Public on Jan 21, 2022 |
| Title |
Cas13d_6h_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
6hours_Zebrafish_embryos
|
| Organism |
Danio rerio |
| Characteristics |
developmental stage: embryos
treatment: injected with RfxCas13d mRNA (200-250 pg/embryo).
|
| Treatment protocol |
Zebrafish embryos were injected with the indicated mRNA and/or guideRNAs and after 6 hours post injection.
|
| Growth protocol |
Transgenic zebrafish were kept according to the National Research Council’s and IACUC approved protocol 2016-1059 at the Stowers Institute for Medical Research zebrafish facility.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol
mRNAseq libraries were generated from 500 ng of high-quality total RNA, as assessed using the Bioanalyzer (Agilent). Libraries were made according to the manufacturer’s directions for the TruSeq Stranded mRNA LP Sample Prep Kit (Illumina, Cat. No. 20020594) with TruSeq RNA Single Indexes Set A and B (Illumina, Cat. No. 20020492 and 20020493). Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer (Agilent) and Qubit Fluorometer (Life Technologies). Libraries were pooled, re-quantified and sequenced as 75bp single reads on a high-output flowcell using the Illumina NextSeq instrument.
Poly(A)_enrichment
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Single cell transgenic zebrafish embryos expressing RFP (maternally provided) were injected with RfxCas13d mRNA (200-250 pg/embryo).
|
| Data processing |
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome danRer11 with STAR aligner (version STAR_2.6.1c ), using projects gene models. TPM values were generated using RSEM (version v1.3.0 ).
Genome_build: danRer11 with RFP mRNA sequence
Supplementary_files_format_and_content: TPM gene expression in excel file
|
| |
|
| Submission date |
Aug 15, 2019 |
| Last update date |
Jan 21, 2022 |
| Contact name |
Huzaifa Hassan |
| Organization name |
Stowers Institute for Medical Research
|
| Street address |
1000 E 50th St
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL20828 |
| Series (1) |
| GSE135884 |
CRISPR-Cas13d induces efficient mRNA knock-down in animal embryos |
|
| Relations |
| BioSample |
SAMN12585554 |
| SRA |
SRX6721804 |
