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Synthego Inc ice 105 webtool
Ice 105 Webtool, supplied by Synthego Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/webtools/analysis+crispr+ice+tool/pm41713797-78-16-19
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ice 105 webtool - by Bioz Stars, 2026-11
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Related Articles

Polymerase Chain Reaction:

Article Title: IMP1 is a novel Post-Transcriptional Regulator of Early Erythroid Development and Embryonic Globin output.
Article Snippet: .. Clone screening was 154 performed by PCR, purifica on, and Sanger sequencing, with inser ons and dele ons (indels) analyzed 155 using Benchling and the Synthego ICE tool. .. 156 157 PCR and RT-qPCR analysis 158 Genomic DNA was extracted and IMP1 fragments amplified using GoTaq polymerase (Thermo 159 Scien fic).

Sequencing:

Article Title: IMP1 is a novel Post-Transcriptional Regulator of Early Erythroid Development and Embryonic Globin output.
Article Snippet: .. Clone screening was 154 performed by PCR, purifica on, and Sanger sequencing, with inser ons and dele ons (indels) analyzed 155 using Benchling and the Synthego ICE tool. .. 156 157 PCR and RT-qPCR analysis 158 Genomic DNA was extracted and IMP1 fragments amplified using GoTaq polymerase (Thermo 159 Scien fic).

Analysis:

Article Title: Protocol for enhancing CRISPR-Cas9 genome editing using histone deacetylase inhibition and engineered virus-like particle delivery
Article Snippet: .. Synthego Performance Analysis, ICE Analysis. v3.0 , Synthego , https://ice.editco.bio/#/. ..

Knock-Out:

Article Title: Aging restricts maturation of CXCL13 + T follicular helper cells in human immunity.
Article Snippet: 18 Cell Reports 45, 117423, June 23, 2026 Knockout of transcription factors using CRISPR/Cas9 Cryopreserved tonsil cells were thawed in a 37◦C water bath into serum-free medium containing 10 μg/mL DNAse (Roche) and incubated for ∼1 h at 37◦C and 5% CO2. .. Knockout was performed using chemically modified synthetic single guide RNAs (gRNAs) formulated in proprietary gene knockout kits (Synthego/EditCo; Table S2) targeting genes encoding the selected transcription factors. ..

Article Title: PHGDH loss promotes hypoxia tolerance through glycolytic reprogramming and enhanced HIF-1 activity.
Article Snippet: Additional media HPLM (A4899101, Gibco) and MEM (21090022, Gibco). .. PHGDH knockout clones were generated using a CRISPR-Cas9 ribonucleoprotein-based genome editing approach in accordance with Synthego’s single-cell cloning workflow (guide sequences Table S1). .. Cells were regularly checked for mycoplasma (Mycoalert mycoplasma detection kit, Lonza).

Modification:

Article Title: Aging restricts maturation of CXCL13 + T follicular helper cells in human immunity.
Article Snippet: 18 Cell Reports 45, 117423, June 23, 2026 Knockout of transcription factors using CRISPR/Cas9 Cryopreserved tonsil cells were thawed in a 37◦C water bath into serum-free medium containing 10 μg/mL DNAse (Roche) and incubated for ∼1 h at 37◦C and 5% CO2. .. Knockout was performed using chemically modified synthetic single guide RNAs (gRNAs) formulated in proprietary gene knockout kits (Synthego/EditCo; Table S2) targeting genes encoding the selected transcription factors. ..

Gene Knockout:

Article Title: Aging restricts maturation of CXCL13 + T follicular helper cells in human immunity.
Article Snippet: 18 Cell Reports 45, 117423, June 23, 2026 Knockout of transcription factors using CRISPR/Cas9 Cryopreserved tonsil cells were thawed in a 37◦C water bath into serum-free medium containing 10 μg/mL DNAse (Roche) and incubated for ∼1 h at 37◦C and 5% CO2. .. Knockout was performed using chemically modified synthetic single guide RNAs (gRNAs) formulated in proprietary gene knockout kits (Synthego/EditCo; Table S2) targeting genes encoding the selected transcription factors. ..

Clone Assay:

Article Title: PHGDH loss promotes hypoxia tolerance through glycolytic reprogramming and enhanced HIF-1 activity.
Article Snippet: Additional media HPLM (A4899101, Gibco) and MEM (21090022, Gibco). .. PHGDH knockout clones were generated using a CRISPR-Cas9 ribonucleoprotein-based genome editing approach in accordance with Synthego’s single-cell cloning workflow (guide sequences Table S1). .. Cells were regularly checked for mycoplasma (Mycoalert mycoplasma detection kit, Lonza).

Generated:

Article Title: PHGDH loss promotes hypoxia tolerance through glycolytic reprogramming and enhanced HIF-1 activity.
Article Snippet: Additional media HPLM (A4899101, Gibco) and MEM (21090022, Gibco). .. PHGDH knockout clones were generated using a CRISPR-Cas9 ribonucleoprotein-based genome editing approach in accordance with Synthego’s single-cell cloning workflow (guide sequences Table S1). .. Cells were regularly checked for mycoplasma (Mycoalert mycoplasma detection kit, Lonza).

CRISPR:

Article Title: PHGDH loss promotes hypoxia tolerance through glycolytic reprogramming and enhanced HIF-1 activity.
Article Snippet: Additional media HPLM (A4899101, Gibco) and MEM (21090022, Gibco). .. PHGDH knockout clones were generated using a CRISPR-Cas9 ribonucleoprotein-based genome editing approach in accordance with Synthego’s single-cell cloning workflow (guide sequences Table S1). .. Cells were regularly checked for mycoplasma (Mycoalert mycoplasma detection kit, Lonza).

Single Cell:

Article Title: PHGDH loss promotes hypoxia tolerance through glycolytic reprogramming and enhanced HIF-1 activity.
Article Snippet: Additional media HPLM (A4899101, Gibco) and MEM (21090022, Gibco). .. PHGDH knockout clones were generated using a CRISPR-Cas9 ribonucleoprotein-based genome editing approach in accordance with Synthego’s single-cell cloning workflow (guide sequences Table S1). .. Cells were regularly checked for mycoplasma (Mycoalert mycoplasma detection kit, Lonza).

Cloning:

Article Title: PHGDH loss promotes hypoxia tolerance through glycolytic reprogramming and enhanced HIF-1 activity.
Article Snippet: Additional media HPLM (A4899101, Gibco) and MEM (21090022, Gibco). .. PHGDH knockout clones were generated using a CRISPR-Cas9 ribonucleoprotein-based genome editing approach in accordance with Synthego’s single-cell cloning workflow (guide sequences Table S1). .. Cells were regularly checked for mycoplasma (Mycoalert mycoplasma detection kit, Lonza).

other:

Article Title: Aging restricts maturation of CXCL13 + T follicular helper cells in human immunity.
Article Snippet: Genomic DNA was extracted using the QuickExtract solution (LGC Biosearch Technologies).

Article Title: Expansion and CAR engineering of granulocyte-monocyte progenitors for cellular immunotherapy.
Article Snippet: The 10× Genomics libraries were first sequenced on an Illumina NextSeq 500 aiming at a coverage of 5,000 raw reads per cell to estimate the cell numbers, before being sequenced deeper on an Illumina HiSeq 2500 aiming at a coverage of 50,000 raw reads per cell (paired-end; read1: 26 cycles; i7 index: 8 cycles; read 2: 98 cycles).



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<t>CRISPR/Cas9-mediated</t> knockout of Mcu in RBL-2H3 cells. A , exon structure of rat Mcu indicating the target sites of guide RNA1 and guide RNA2. B , quantitative real-time PCR analysis of Mcu mRNA expression in wild-type (WT) RBL-2H3 cells and Mcu knockout (KO) clones A4 and D10 (n = 30 wells; 3 biological replicates). Medians ( bars ) with 95% confidence intervals (error bars ) are displayed on the scatter dot plots. C , immunoblot analysis of WT and Mcu KO clones A4 and D10 using MCU antibodies raised against either the C terminus or N terminus. Vinculin served as a loading control. Molecular weights are indicated in kilodaltons (kDa). MCU, mitochondrial Ca 2+ uniporter.
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<t>CRISPR/Cas9-mediated</t> knockout of Mcu in RBL-2H3 cells. A , exon structure of rat Mcu indicating the target sites of guide RNA1 and guide RNA2. B , quantitative real-time PCR analysis of Mcu mRNA expression in wild-type (WT) RBL-2H3 cells and Mcu knockout (KO) clones A4 and D10 (n = 30 wells; 3 biological replicates). Medians ( bars ) with 95% confidence intervals (error bars ) are displayed on the scatter dot plots. C , immunoblot analysis of WT and Mcu KO clones A4 and D10 using MCU antibodies raised against either the C terminus or N terminus. Vinculin served as a loading control. Molecular weights are indicated in kilodaltons (kDa). MCU, mitochondrial Ca 2+ uniporter.
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Image Search Results


CRISPR/Cas9-mediated knockout of Mcu in RBL-2H3 cells. A , exon structure of rat Mcu indicating the target sites of guide RNA1 and guide RNA2. B , quantitative real-time PCR analysis of Mcu mRNA expression in wild-type (WT) RBL-2H3 cells and Mcu knockout (KO) clones A4 and D10 (n = 30 wells; 3 biological replicates). Medians ( bars ) with 95% confidence intervals (error bars ) are displayed on the scatter dot plots. C , immunoblot analysis of WT and Mcu KO clones A4 and D10 using MCU antibodies raised against either the C terminus or N terminus. Vinculin served as a loading control. Molecular weights are indicated in kilodaltons (kDa). MCU, mitochondrial Ca 2+ uniporter.

Journal: The Journal of Biological Chemistry

Article Title: Deletion of mitochondrial calcium uniporter enhances calcium signals by slowing calcium clearance and triggers adaptive transcriptomic remodeling

doi: 10.1016/j.jbc.2026.111473

Figure Lengend Snippet: CRISPR/Cas9-mediated knockout of Mcu in RBL-2H3 cells. A , exon structure of rat Mcu indicating the target sites of guide RNA1 and guide RNA2. B , quantitative real-time PCR analysis of Mcu mRNA expression in wild-type (WT) RBL-2H3 cells and Mcu knockout (KO) clones A4 and D10 (n = 30 wells; 3 biological replicates). Medians ( bars ) with 95% confidence intervals (error bars ) are displayed on the scatter dot plots. C , immunoblot analysis of WT and Mcu KO clones A4 and D10 using MCU antibodies raised against either the C terminus or N terminus. Vinculin served as a loading control. Molecular weights are indicated in kilodaltons (kDa). MCU, mitochondrial Ca 2+ uniporter.

Article Snippet: Two different guide (g)RNAs targeting rat Mcu (Ensembl Gene ID: ENSRNOG00000045920 ; chromosomal location chr20 29,038,480—29,199,224 [-]; genome: Rnor_6.0 (rn6, Rattus norvegicus )) were designed using the Benchling CRISPR design webtool ( https://benchling.com/crispr ).

Techniques: CRISPR, Knock-Out, Real-time Polymerase Chain Reaction, Expressing, Clone Assay, Western Blot, Control

Mcu knockout by CRISPR/Cas9 causes widespread and divergent transcriptomic changes across clones generated using distinct guide RNAs. A and B , volcano plots showing differentially expressed genes (DEGs) in Mcu −/− clones A4 ( A ) and D10 ( B ) relative to WT cells. Red and blue dots represent significantly upregulated and downregulated genes, respectively. Mcu is shown as a green dot . Gray dots indicate unchanged genes, either with below absolute fold change 2.0 cutoff ( light gray ) or having false discovery rate(FDR) higher than 0.05 ( dark gray ). C , volcano plot comparing A4 and D10 clones directly. D and E , Venn diagrams of downregulated genes ( D ) and upregulated genes ( E ) in A4 versus WT and D10 versus WT, highlighting both overlapping and clone-specific expression changes. F , ingenuity pathway analysis (IPA) of the 213 DEGs common to both clones (64 downregulated and 149 upregulated) with a z-score cutoff of 1.0. G , bubble plot displays enriched canonical pathways predicted by IPA. The y -axis on the right shows enriched pathway names ordered according to hierarchical clustering of their z-scores across two conditions (A4 versus WT and D10 versus WT), with the corresponding dendrogram displayed on the left . The x -axis labels the two conditions. Each pathway is represented by two circles , one for each condition. Circle size corresponds to the gene ratio for that pathway in the given condition. The fill color of each circle reflects the z-score: red for positive z-scores (activation), blue for negative z-scores (inhibition), transparent for values near zero, and gray where the z-score is NA. Threshold of z-score was set to absolute z-score ≥ 1.5. Below cutoff p values ( i.e. , p value > 0.05) are indicated by small lines on the right of the bubble. MCU, mitochondrial Ca 2+ uniporter.

Journal: The Journal of Biological Chemistry

Article Title: Deletion of mitochondrial calcium uniporter enhances calcium signals by slowing calcium clearance and triggers adaptive transcriptomic remodeling

doi: 10.1016/j.jbc.2026.111473

Figure Lengend Snippet: Mcu knockout by CRISPR/Cas9 causes widespread and divergent transcriptomic changes across clones generated using distinct guide RNAs. A and B , volcano plots showing differentially expressed genes (DEGs) in Mcu −/− clones A4 ( A ) and D10 ( B ) relative to WT cells. Red and blue dots represent significantly upregulated and downregulated genes, respectively. Mcu is shown as a green dot . Gray dots indicate unchanged genes, either with below absolute fold change 2.0 cutoff ( light gray ) or having false discovery rate(FDR) higher than 0.05 ( dark gray ). C , volcano plot comparing A4 and D10 clones directly. D and E , Venn diagrams of downregulated genes ( D ) and upregulated genes ( E ) in A4 versus WT and D10 versus WT, highlighting both overlapping and clone-specific expression changes. F , ingenuity pathway analysis (IPA) of the 213 DEGs common to both clones (64 downregulated and 149 upregulated) with a z-score cutoff of 1.0. G , bubble plot displays enriched canonical pathways predicted by IPA. The y -axis on the right shows enriched pathway names ordered according to hierarchical clustering of their z-scores across two conditions (A4 versus WT and D10 versus WT), with the corresponding dendrogram displayed on the left . The x -axis labels the two conditions. Each pathway is represented by two circles , one for each condition. Circle size corresponds to the gene ratio for that pathway in the given condition. The fill color of each circle reflects the z-score: red for positive z-scores (activation), blue for negative z-scores (inhibition), transparent for values near zero, and gray where the z-score is NA. Threshold of z-score was set to absolute z-score ≥ 1.5. Below cutoff p values ( i.e. , p value > 0.05) are indicated by small lines on the right of the bubble. MCU, mitochondrial Ca 2+ uniporter.

Article Snippet: Two different guide (g)RNAs targeting rat Mcu (Ensembl Gene ID: ENSRNOG00000045920 ; chromosomal location chr20 29,038,480—29,199,224 [-]; genome: Rnor_6.0 (rn6, Rattus norvegicus )) were designed using the Benchling CRISPR design webtool ( https://benchling.com/crispr ).

Techniques: Knock-Out, CRISPR, Clone Assay, Generated, Expressing, Activation Assay, Inhibition