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EZ-editor™ Gene Knockout Cell Line Strategy

HDAC6 Gene Knockout Strategy

EZ-editor™ technology (CRISPR based), developed by Ubigene, is more efficient than general CRISPR/Cas9 technology in double-strand breaking and homologous recombination. With EZ-editor™, Ubigene has successfully edited over 10000 genes on more than 500 types of cell lines.
Objective
To create a Human HDAC6 Knockout model in cell line by EZ-editor™-mediated genome engineering.
Target gene info
Official symbol
HDAC6
Gene id
10013
Organism
Homo sapiens
Gene type
protein-coding
Official full symbol
histone deacetylase 6
Also known as
CPBHM, HD6, JM21, PPP1R90
Genomic regions
Chromosome X
Summary
Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene belongs to class II of the histone deacetylase/acuc/apha family. It contains an internal duplication of two catalytic domains which appear to function independently of each other. This protein possesses histone deacetylase activity and represses transcription.
Strategy Summary
This gene has 13 protein coding transcripts：
Transcript Length(nt) Protein Length(aa) Protein name Transcript type Transcript name ccds
XM_047441703 4595 XP_047297659 1261 protein deacetylase HDAC6 3 transcript variant X1
XM_047441704 4473 XP_047297660 1229 protein deacetylase HDAC6 3 transcript variant X2
NM_001321225 4147 NP_001308154 1229 protein deacetylase HDAC6 3 transcript variant 1
XM_047441707 2691 XP_047297663 715 protein deacetylase HDAC6 3 transcript variant X6
XM_047441705 2829 XP_047297661 747 protein deacetylase HDAC6 3 transcript variant X4
XM_047441706 2746 XP_047297662 747 protein deacetylase HDAC6 3 transcript variant X5
NM_001321229 4122 NP_001308158 1215 protein deacetylase HDAC6 3 transcript variant 6 CCDS14306.1
NM_001321226 4527 NP_001308155 1215 protein deacetylase HDAC6 3 transcript variant 2 CCDS14306.1
NM_001321227 4248 NP_001308156 1215 protein deacetylase HDAC6 3 transcript variant 3 CCDS14306.1
NM_001321228 4211 NP_001308157 1215 protein deacetylase HDAC6 3 transcript variant 4 CCDS14306.1
NM_006044 4118 NP_006035 1215 protein deacetylase HDAC6 3 transcript variant 5 CCDS14306.1
NM_001321231 2241 NP_001308160 146 protein deacetylase HDAC6 3 transcript variant 8 CCDS87740.1
NM_001321230 1962 NP_001308159 146 protein deacetylase HDAC6 3 transcript variant 7 CCDS87740.1
Frame-shift
Fragment A
Fragment B
Strategy

Project Comprehensive Difficulty Assessment

According to the Red Cotton database: the CRISPR gene-editing strategy design is Unknown.
Knockout project comprehensive difficulty is thus assessed as Unknown.
Red Cotton™ Notes Gene HDAC6 had been KO in hela cell line.
EZ-editor™ Gene Dependency
EZ-editor™ Gene Expression Level

EZ-editor™ Gene Dependency

Result

The HDAC6 gene you inquire is evaluated as high risk in 0% cell line. Cell line is not selected, unable to assess the accurate risk level, for reference only.

Gene lethality score

Dependent Cell Lines Gene Dependency 0 0.5 1

Lethality score of HDAC6 in different cells

0.0%>0.5
All cells
0
Non-essential gene
0.5
Boundary score
1
Essential gene
More details

EZ-editor™ Gene Expression Level

Result

In all cell lines, there is 4.8% cells with low expression level, 95.2% cells with medium expression level of HDAC6 gene. Cell line is not selected, unable to assess the accurate expression level, for reference only.

Gene Expression

Cell Lines Frequency log2(TPM+1) 0 2 4 6 8 10 12

TPM of HDAC6 in different cells

4.8%95.2%
All cells
0~0.5
Below cutoff
0.5~10
Low
10~1000
Medium
>1000
High
More details
Work flow
Ubigene Red Cotton Workflow

Ubigene - Make genome editing easier

Ubigene is an international high-technology enterprise focused on gene-editing cells. Our exclusive EZ-editor™ technology has 10-20 times more efficient editing than traditional methods, easily achieving gene knockout, point mutation, and knock-in. Based on EZ-editor™ technology, Ubigene has accumulated over 6000 successful gene-editing cases from more than 300 cell lines including iPSC and ESC, and has established a KO Cell Line Bank with 5000+ KO cell lines and Red Cotton™ gRNA Plasmid Bank with 10000+ gRNA plasmids available in stock.

Ubigene focuses on technological innovation and product development, of which EZ-editor™ series products that cover the whole workflow of gene-editing keep improving. Ubigene will move on toward our goal of "Make genome editing easier" and we won't stop!

Cell products

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红棉系统新技能上线啦！基因风险评估：“火眼金睛”辨基因，致死风险一秒知。评估结果可在Red Cotton Assessment模块查看哦。

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