|
| Status |
Public on Jun 01, 2024 |
| Title |
Fish2 zTLR4bb-sg2 |
| Sample type |
SRA |
| |
|
| Source name |
melanoma
|
| Organism |
Danio rerio |
| Characteristics |
cell type: melanoma
knockout: TLR4
|
| Growth protocol |
Tumors generated by TEAZ were dissected out from randomly picked fish.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mince the tumor tissue into small sizes with a razor and transfer the pieces immediately to a 15 ml conical tube containing tissue digestion buffer. After tissue dissociation, suspension cells were filtered through a 70 mm strainer to remove tissue debris followed by counterstaining with Hoechst 33342. After FACS, tdTomato and Hoechst double positive melanomas were lysed for phenol-chloroform based whole genome extraction. To validate gene editing using CRISPR-seq, primer pairs were set to flank 200-280 bp of the sequence that should encompass mutation sites within 100 bp from the beginning or end of it.
The sequence was amplified from 50-100 ng of genomic DNA using Phusion High-Fidelity DNA Polymerase master mix PCR protocol.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Fish2
zTLR4bb-sg2
|
| Data processing |
The results of the amplicon were aligned and percent of indels at the target site was quantified using R version 4.0.5 and CrispRVariants 1.18.0 as previously described (Linsay et. al. 2016).
Assembly: GRCz10
Library strategy: CRISPR-Seq
|
| |
|
| Submission date |
May 20, 2022 |
| Last update date |
Jun 01, 2024 |
| Contact name |
Ting-Hsiang Huang |
| E-mail(s) |
thuang316@gmail.com
|
| Organization name |
Memorial Sloan Ketteting Cancer Center
|
| Lab |
Richard White
|
| Street address |
417 E68th
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL24995 |
| Series (1) |
| GSE203490 |
Validation of sgRNAs against acaa2 and tlr4 in zebrafish. |
|
| Relations |
| BioSample |
SAMN28571087 |
| SRA |
SRX15399829 |
