|
Status |
Public on Jun 01, 2024 |
Title |
Fish3 zAcaa2-sg1 |
Sample type |
SRA |
|
|
Source name |
melanoma
|
Organism |
Danio rerio |
Characteristics |
cell type: melanoma knockout: Acaa2
|
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 |
Fish3 zAcaa2-sg1
|
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 |
SAMN28571102 |
SRA |
SRX15399814 |