customized automated software pipeline Search Results


highcontent analysis hca pipeline  (Revvity)
96
Revvity highcontent analysis hca pipeline
Highcontent Analysis Hca Pipeline, supplied by Revvity, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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image analysis software imaris  (Oxford Instruments)
99
Oxford Instruments image analysis software imaris
CFIm KD increases the activity of miRNAs. ( A ) Genome browser tracks showing the coverage of DICER1 TE (bottom track) by RNA-seq reads from two replicate experiments for each condition, with the two PAS that were quantified for this gene marked by black lines. The conditions are color-coded (as in Figure ) and also indicated on the y-axis. Y-axis shows the smoothened number of reads mapping along the TE, calculated by the GViz R package. ( B ) RNA fluorescence in situ imaging of DICER1 isoforms in Control and CFIm25 KD HEK293 cells with probes corresponding to the common region of the long and short 3′ UTRs (red) or to the region between the proximal and distal cleavage sites, thus present exclusively in the long 3′ UTR (green). Nuclei are marked with DAPI. Zoom-ins of the regions marked with dashed boxes are further shown both with the individual and merged channels. A snapshot of a digital representation of the actual <t>image</t> as processed in <t>IMARIS</t> is also depicted for reference. ( C ) Quantification of the copy number of the long and short 3′ UTR isoforms of DICER1 in the nucleus (left plot) and cytoplasm (right plot) of Control, CFIm25 and CFIm68 KD cells. Colocalization of the red and green signals reveals the presence of the long 3′ UTR isoform (yellow) whereas the signal from the red probe only reveals the presence of the shorter 3′ UTR isoform. mRNA copy numbers were estimated separately from the nucleus (overlapping with DAPI) and cytosol. Segregation of the signal was performed with IMARIS (see Methods). ( D ) Representative western blot showing the DICER1 expression in the Control, CFIm25 and CFIm68 KD cells. The quantification is relative to GAPDH. ( E ) qPCR measurements of let-7, miR-92a, miR-16 and miR-19b expression in CFIm25/68 KD cells relative to Control. ΔΔct values were calculated relative to U6 snRNA and then relative to the Control cells (where the ratio was set to 1). ( F ) Normalized Renilla luciferase expression of reporter mRNAs carrying binding sites for miR-16 and miR-92a in their 3′ UTRs, in Control, CFIm25 and CFIm68 KD cells, respectively. The Firefly luciferase expressed from the same construct was used as normalization control.
Image Analysis Software Imaris, supplied by Oxford Instruments, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 99 stars, based on 1 article reviews
image analysis software imaris - by Bioz Stars, 2026-03
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lemna launcher  (LemnaTec Inc)
90
LemnaTec Inc lemna launcher
CFIm KD increases the activity of miRNAs. ( A ) Genome browser tracks showing the coverage of DICER1 TE (bottom track) by RNA-seq reads from two replicate experiments for each condition, with the two PAS that were quantified for this gene marked by black lines. The conditions are color-coded (as in Figure ) and also indicated on the y-axis. Y-axis shows the smoothened number of reads mapping along the TE, calculated by the GViz R package. ( B ) RNA fluorescence in situ imaging of DICER1 isoforms in Control and CFIm25 KD HEK293 cells with probes corresponding to the common region of the long and short 3′ UTRs (red) or to the region between the proximal and distal cleavage sites, thus present exclusively in the long 3′ UTR (green). Nuclei are marked with DAPI. Zoom-ins of the regions marked with dashed boxes are further shown both with the individual and merged channels. A snapshot of a digital representation of the actual <t>image</t> as processed in <t>IMARIS</t> is also depicted for reference. ( C ) Quantification of the copy number of the long and short 3′ UTR isoforms of DICER1 in the nucleus (left plot) and cytoplasm (right plot) of Control, CFIm25 and CFIm68 KD cells. Colocalization of the red and green signals reveals the presence of the long 3′ UTR isoform (yellow) whereas the signal from the red probe only reveals the presence of the shorter 3′ UTR isoform. mRNA copy numbers were estimated separately from the nucleus (overlapping with DAPI) and cytosol. Segregation of the signal was performed with IMARIS (see Methods). ( D ) Representative western blot showing the DICER1 expression in the Control, CFIm25 and CFIm68 KD cells. The quantification is relative to GAPDH. ( E ) qPCR measurements of let-7, miR-92a, miR-16 and miR-19b expression in CFIm25/68 KD cells relative to Control. ΔΔct values were calculated relative to U6 snRNA and then relative to the Control cells (where the ratio was set to 1). ( F ) Normalized Renilla luciferase expression of reporter mRNAs carrying binding sites for miR-16 and miR-92a in their 3′ UTRs, in Control, CFIm25 and CFIm68 KD cells, respectively. The Firefly luciferase expressed from the same construct was used as normalization control.
Lemna Launcher, supplied by LemnaTec Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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ucsc goldenpath database  (Biotechnology Information)
90
Biotechnology Information ucsc goldenpath database
CFIm KD increases the activity of miRNAs. ( A ) Genome browser tracks showing the coverage of DICER1 TE (bottom track) by RNA-seq reads from two replicate experiments for each condition, with the two PAS that were quantified for this gene marked by black lines. The conditions are color-coded (as in Figure ) and also indicated on the y-axis. Y-axis shows the smoothened number of reads mapping along the TE, calculated by the GViz R package. ( B ) RNA fluorescence in situ imaging of DICER1 isoforms in Control and CFIm25 KD HEK293 cells with probes corresponding to the common region of the long and short 3′ UTRs (red) or to the region between the proximal and distal cleavage sites, thus present exclusively in the long 3′ UTR (green). Nuclei are marked with DAPI. Zoom-ins of the regions marked with dashed boxes are further shown both with the individual and merged channels. A snapshot of a digital representation of the actual <t>image</t> as processed in <t>IMARIS</t> is also depicted for reference. ( C ) Quantification of the copy number of the long and short 3′ UTR isoforms of DICER1 in the nucleus (left plot) and cytoplasm (right plot) of Control, CFIm25 and CFIm68 KD cells. Colocalization of the red and green signals reveals the presence of the long 3′ UTR isoform (yellow) whereas the signal from the red probe only reveals the presence of the shorter 3′ UTR isoform. mRNA copy numbers were estimated separately from the nucleus (overlapping with DAPI) and cytosol. Segregation of the signal was performed with IMARIS (see Methods). ( D ) Representative western blot showing the DICER1 expression in the Control, CFIm25 and CFIm68 KD cells. The quantification is relative to GAPDH. ( E ) qPCR measurements of let-7, miR-92a, miR-16 and miR-19b expression in CFIm25/68 KD cells relative to Control. ΔΔct values were calculated relative to U6 snRNA and then relative to the Control cells (where the ratio was set to 1). ( F ) Normalized Renilla luciferase expression of reporter mRNAs carrying binding sites for miR-16 and miR-92a in their 3′ UTRs, in Control, CFIm25 and CFIm68 KD cells, respectively. The Firefly luciferase expressed from the same construct was used as normalization control.
Ucsc Goldenpath Database, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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illumina metagenomic application  (Illumina Inc)
90
Illumina Inc illumina metagenomic application
CFIm KD increases the activity of miRNAs. ( A ) Genome browser tracks showing the coverage of DICER1 TE (bottom track) by RNA-seq reads from two replicate experiments for each condition, with the two PAS that were quantified for this gene marked by black lines. The conditions are color-coded (as in Figure ) and also indicated on the y-axis. Y-axis shows the smoothened number of reads mapping along the TE, calculated by the GViz R package. ( B ) RNA fluorescence in situ imaging of DICER1 isoforms in Control and CFIm25 KD HEK293 cells with probes corresponding to the common region of the long and short 3′ UTRs (red) or to the region between the proximal and distal cleavage sites, thus present exclusively in the long 3′ UTR (green). Nuclei are marked with DAPI. Zoom-ins of the regions marked with dashed boxes are further shown both with the individual and merged channels. A snapshot of a digital representation of the actual <t>image</t> as processed in <t>IMARIS</t> is also depicted for reference. ( C ) Quantification of the copy number of the long and short 3′ UTR isoforms of DICER1 in the nucleus (left plot) and cytoplasm (right plot) of Control, CFIm25 and CFIm68 KD cells. Colocalization of the red and green signals reveals the presence of the long 3′ UTR isoform (yellow) whereas the signal from the red probe only reveals the presence of the shorter 3′ UTR isoform. mRNA copy numbers were estimated separately from the nucleus (overlapping with DAPI) and cytosol. Segregation of the signal was performed with IMARIS (see Methods). ( D ) Representative western blot showing the DICER1 expression in the Control, CFIm25 and CFIm68 KD cells. The quantification is relative to GAPDH. ( E ) qPCR measurements of let-7, miR-92a, miR-16 and miR-19b expression in CFIm25/68 KD cells relative to Control. ΔΔct values were calculated relative to U6 snRNA and then relative to the Control cells (where the ratio was set to 1). ( F ) Normalized Renilla luciferase expression of reporter mRNAs carrying binding sites for miR-16 and miR-92a in their 3′ UTRs, in Control, CFIm25 and CFIm68 KD cells, respectively. The Firefly luciferase expressed from the same construct was used as normalization control.
Illumina Metagenomic Application, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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illumina metagenomic application - by Bioz Stars, 2026-03
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somatic pipeline  (Sophia Genetics)
97
Sophia Genetics somatic pipeline
CFIm KD increases the activity of miRNAs. ( A ) Genome browser tracks showing the coverage of DICER1 TE (bottom track) by RNA-seq reads from two replicate experiments for each condition, with the two PAS that were quantified for this gene marked by black lines. The conditions are color-coded (as in Figure ) and also indicated on the y-axis. Y-axis shows the smoothened number of reads mapping along the TE, calculated by the GViz R package. ( B ) RNA fluorescence in situ imaging of DICER1 isoforms in Control and CFIm25 KD HEK293 cells with probes corresponding to the common region of the long and short 3′ UTRs (red) or to the region between the proximal and distal cleavage sites, thus present exclusively in the long 3′ UTR (green). Nuclei are marked with DAPI. Zoom-ins of the regions marked with dashed boxes are further shown both with the individual and merged channels. A snapshot of a digital representation of the actual <t>image</t> as processed in <t>IMARIS</t> is also depicted for reference. ( C ) Quantification of the copy number of the long and short 3′ UTR isoforms of DICER1 in the nucleus (left plot) and cytoplasm (right plot) of Control, CFIm25 and CFIm68 KD cells. Colocalization of the red and green signals reveals the presence of the long 3′ UTR isoform (yellow) whereas the signal from the red probe only reveals the presence of the shorter 3′ UTR isoform. mRNA copy numbers were estimated separately from the nucleus (overlapping with DAPI) and cytosol. Segregation of the signal was performed with IMARIS (see Methods). ( D ) Representative western blot showing the DICER1 expression in the Control, CFIm25 and CFIm68 KD cells. The quantification is relative to GAPDH. ( E ) qPCR measurements of let-7, miR-92a, miR-16 and miR-19b expression in CFIm25/68 KD cells relative to Control. ΔΔct values were calculated relative to U6 snRNA and then relative to the Control cells (where the ratio was set to 1). ( F ) Normalized Renilla luciferase expression of reporter mRNAs carrying binding sites for miR-16 and miR-92a in their 3′ UTRs, in Control, CFIm25 and CFIm68 KD cells, respectively. The Firefly luciferase expressed from the same construct was used as normalization control.
Somatic Pipeline, supplied by Sophia Genetics, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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novoalign  (Thermo Fisher)
90
Thermo Fisher novoalign
CFIm KD increases the activity of miRNAs. ( A ) Genome browser tracks showing the coverage of DICER1 TE (bottom track) by RNA-seq reads from two replicate experiments for each condition, with the two PAS that were quantified for this gene marked by black lines. The conditions are color-coded (as in Figure ) and also indicated on the y-axis. Y-axis shows the smoothened number of reads mapping along the TE, calculated by the GViz R package. ( B ) RNA fluorescence in situ imaging of DICER1 isoforms in Control and CFIm25 KD HEK293 cells with probes corresponding to the common region of the long and short 3′ UTRs (red) or to the region between the proximal and distal cleavage sites, thus present exclusively in the long 3′ UTR (green). Nuclei are marked with DAPI. Zoom-ins of the regions marked with dashed boxes are further shown both with the individual and merged channels. A snapshot of a digital representation of the actual <t>image</t> as processed in <t>IMARIS</t> is also depicted for reference. ( C ) Quantification of the copy number of the long and short 3′ UTR isoforms of DICER1 in the nucleus (left plot) and cytoplasm (right plot) of Control, CFIm25 and CFIm68 KD cells. Colocalization of the red and green signals reveals the presence of the long 3′ UTR isoform (yellow) whereas the signal from the red probe only reveals the presence of the shorter 3′ UTR isoform. mRNA copy numbers were estimated separately from the nucleus (overlapping with DAPI) and cytosol. Segregation of the signal was performed with IMARIS (see Methods). ( D ) Representative western blot showing the DICER1 expression in the Control, CFIm25 and CFIm68 KD cells. The quantification is relative to GAPDH. ( E ) qPCR measurements of let-7, miR-92a, miR-16 and miR-19b expression in CFIm25/68 KD cells relative to Control. ΔΔct values were calculated relative to U6 snRNA and then relative to the Control cells (where the ratio was set to 1). ( F ) Normalized Renilla luciferase expression of reporter mRNAs carrying binding sites for miR-16 and miR-92a in their 3′ UTRs, in Control, CFIm25 and CFIm68 KD cells, respectively. The Firefly luciferase expressed from the same construct was used as normalization control.
Novoalign, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/novoalign/product/Thermo Fisher
Average 90 stars, based on 1 article reviews
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automated software pipelines  (Partek)
90
Partek automated software pipelines
CFIm KD increases the activity of miRNAs. ( A ) Genome browser tracks showing the coverage of DICER1 TE (bottom track) by RNA-seq reads from two replicate experiments for each condition, with the two PAS that were quantified for this gene marked by black lines. The conditions are color-coded (as in Figure ) and also indicated on the y-axis. Y-axis shows the smoothened number of reads mapping along the TE, calculated by the GViz R package. ( B ) RNA fluorescence in situ imaging of DICER1 isoforms in Control and CFIm25 KD HEK293 cells with probes corresponding to the common region of the long and short 3′ UTRs (red) or to the region between the proximal and distal cleavage sites, thus present exclusively in the long 3′ UTR (green). Nuclei are marked with DAPI. Zoom-ins of the regions marked with dashed boxes are further shown both with the individual and merged channels. A snapshot of a digital representation of the actual <t>image</t> as processed in <t>IMARIS</t> is also depicted for reference. ( C ) Quantification of the copy number of the long and short 3′ UTR isoforms of DICER1 in the nucleus (left plot) and cytoplasm (right plot) of Control, CFIm25 and CFIm68 KD cells. Colocalization of the red and green signals reveals the presence of the long 3′ UTR isoform (yellow) whereas the signal from the red probe only reveals the presence of the shorter 3′ UTR isoform. mRNA copy numbers were estimated separately from the nucleus (overlapping with DAPI) and cytosol. Segregation of the signal was performed with IMARIS (see Methods). ( D ) Representative western blot showing the DICER1 expression in the Control, CFIm25 and CFIm68 KD cells. The quantification is relative to GAPDH. ( E ) qPCR measurements of let-7, miR-92a, miR-16 and miR-19b expression in CFIm25/68 KD cells relative to Control. ΔΔct values were calculated relative to U6 snRNA and then relative to the Control cells (where the ratio was set to 1). ( F ) Normalized Renilla luciferase expression of reporter mRNAs carrying binding sites for miR-16 and miR-92a in their 3′ UTRs, in Control, CFIm25 and CFIm68 KD cells, respectively. The Firefly luciferase expressed from the same construct was used as normalization control.
Automated Software Pipelines, supplied by Partek, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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algorithm custom computational pipeline  (Thermo Fisher)
98
Thermo Fisher algorithm custom computational pipeline
CFIm KD increases the activity of miRNAs. ( A ) Genome browser tracks showing the coverage of DICER1 TE (bottom track) by RNA-seq reads from two replicate experiments for each condition, with the two PAS that were quantified for this gene marked by black lines. The conditions are color-coded (as in Figure ) and also indicated on the y-axis. Y-axis shows the smoothened number of reads mapping along the TE, calculated by the GViz R package. ( B ) RNA fluorescence in situ imaging of DICER1 isoforms in Control and CFIm25 KD HEK293 cells with probes corresponding to the common region of the long and short 3′ UTRs (red) or to the region between the proximal and distal cleavage sites, thus present exclusively in the long 3′ UTR (green). Nuclei are marked with DAPI. Zoom-ins of the regions marked with dashed boxes are further shown both with the individual and merged channels. A snapshot of a digital representation of the actual <t>image</t> as processed in <t>IMARIS</t> is also depicted for reference. ( C ) Quantification of the copy number of the long and short 3′ UTR isoforms of DICER1 in the nucleus (left plot) and cytoplasm (right plot) of Control, CFIm25 and CFIm68 KD cells. Colocalization of the red and green signals reveals the presence of the long 3′ UTR isoform (yellow) whereas the signal from the red probe only reveals the presence of the shorter 3′ UTR isoform. mRNA copy numbers were estimated separately from the nucleus (overlapping with DAPI) and cytosol. Segregation of the signal was performed with IMARIS (see Methods). ( D ) Representative western blot showing the DICER1 expression in the Control, CFIm25 and CFIm68 KD cells. The quantification is relative to GAPDH. ( E ) qPCR measurements of let-7, miR-92a, miR-16 and miR-19b expression in CFIm25/68 KD cells relative to Control. ΔΔct values were calculated relative to U6 snRNA and then relative to the Control cells (where the ratio was set to 1). ( F ) Normalized Renilla luciferase expression of reporter mRNAs carrying binding sites for miR-16 and miR-92a in their 3′ UTRs, in Control, CFIm25 and CFIm68 KD cells, respectively. The Firefly luciferase expressed from the same construct was used as normalization control.
Algorithm Custom Computational Pipeline, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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custom matlab code (bramila pipeline v2.0)  (MathWorks Inc)
90
MathWorks Inc custom matlab code (bramila pipeline v2.0)
CFIm KD increases the activity of miRNAs. ( A ) Genome browser tracks showing the coverage of DICER1 TE (bottom track) by RNA-seq reads from two replicate experiments for each condition, with the two PAS that were quantified for this gene marked by black lines. The conditions are color-coded (as in Figure ) and also indicated on the y-axis. Y-axis shows the smoothened number of reads mapping along the TE, calculated by the GViz R package. ( B ) RNA fluorescence in situ imaging of DICER1 isoforms in Control and CFIm25 KD HEK293 cells with probes corresponding to the common region of the long and short 3′ UTRs (red) or to the region between the proximal and distal cleavage sites, thus present exclusively in the long 3′ UTR (green). Nuclei are marked with DAPI. Zoom-ins of the regions marked with dashed boxes are further shown both with the individual and merged channels. A snapshot of a digital representation of the actual <t>image</t> as processed in <t>IMARIS</t> is also depicted for reference. ( C ) Quantification of the copy number of the long and short 3′ UTR isoforms of DICER1 in the nucleus (left plot) and cytoplasm (right plot) of Control, CFIm25 and CFIm68 KD cells. Colocalization of the red and green signals reveals the presence of the long 3′ UTR isoform (yellow) whereas the signal from the red probe only reveals the presence of the shorter 3′ UTR isoform. mRNA copy numbers were estimated separately from the nucleus (overlapping with DAPI) and cytosol. Segregation of the signal was performed with IMARIS (see Methods). ( D ) Representative western blot showing the DICER1 expression in the Control, CFIm25 and CFIm68 KD cells. The quantification is relative to GAPDH. ( E ) qPCR measurements of let-7, miR-92a, miR-16 and miR-19b expression in CFIm25/68 KD cells relative to Control. ΔΔct values were calculated relative to U6 snRNA and then relative to the Control cells (where the ratio was set to 1). ( F ) Normalized Renilla luciferase expression of reporter mRNAs carrying binding sites for miR-16 and miR-92a in their 3′ UTRs, in Control, CFIm25 and CFIm68 KD cells, respectively. The Firefly luciferase expressed from the same construct was used as normalization control.
Custom Matlab Code (Bramila Pipeline V2.0), supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/custom matlab code (bramila pipeline v2.0)/product/MathWorks Inc
Average 90 stars, based on 1 article reviews
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nikon nis elements software  (Nikon)
99
Nikon nikon nis elements software
CFIm KD increases the activity of miRNAs. ( A ) Genome browser tracks showing the coverage of DICER1 TE (bottom track) by RNA-seq reads from two replicate experiments for each condition, with the two PAS that were quantified for this gene marked by black lines. The conditions are color-coded (as in Figure ) and also indicated on the y-axis. Y-axis shows the smoothened number of reads mapping along the TE, calculated by the GViz R package. ( B ) RNA fluorescence in situ imaging of DICER1 isoforms in Control and CFIm25 KD HEK293 cells with probes corresponding to the common region of the long and short 3′ UTRs (red) or to the region between the proximal and distal cleavage sites, thus present exclusively in the long 3′ UTR (green). Nuclei are marked with DAPI. Zoom-ins of the regions marked with dashed boxes are further shown both with the individual and merged channels. A snapshot of a digital representation of the actual <t>image</t> as processed in <t>IMARIS</t> is also depicted for reference. ( C ) Quantification of the copy number of the long and short 3′ UTR isoforms of DICER1 in the nucleus (left plot) and cytoplasm (right plot) of Control, CFIm25 and CFIm68 KD cells. Colocalization of the red and green signals reveals the presence of the long 3′ UTR isoform (yellow) whereas the signal from the red probe only reveals the presence of the shorter 3′ UTR isoform. mRNA copy numbers were estimated separately from the nucleus (overlapping with DAPI) and cytosol. Segregation of the signal was performed with IMARIS (see Methods). ( D ) Representative western blot showing the DICER1 expression in the Control, CFIm25 and CFIm68 KD cells. The quantification is relative to GAPDH. ( E ) qPCR measurements of let-7, miR-92a, miR-16 and miR-19b expression in CFIm25/68 KD cells relative to Control. ΔΔct values were calculated relative to U6 snRNA and then relative to the Control cells (where the ratio was set to 1). ( F ) Normalized Renilla luciferase expression of reporter mRNAs carrying binding sites for miR-16 and miR-92a in their 3′ UTRs, in Control, CFIm25 and CFIm68 KD cells, respectively. The Firefly luciferase expressed from the same construct was used as normalization control.
Nikon Nis Elements Software, supplied by Nikon, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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matlab software pipeline  (MathWorks Inc)
90
MathWorks Inc matlab software pipeline
CFIm KD increases the activity of miRNAs. ( A ) Genome browser tracks showing the coverage of DICER1 TE (bottom track) by RNA-seq reads from two replicate experiments for each condition, with the two PAS that were quantified for this gene marked by black lines. The conditions are color-coded (as in Figure ) and also indicated on the y-axis. Y-axis shows the smoothened number of reads mapping along the TE, calculated by the GViz R package. ( B ) RNA fluorescence in situ imaging of DICER1 isoforms in Control and CFIm25 KD HEK293 cells with probes corresponding to the common region of the long and short 3′ UTRs (red) or to the region between the proximal and distal cleavage sites, thus present exclusively in the long 3′ UTR (green). Nuclei are marked with DAPI. Zoom-ins of the regions marked with dashed boxes are further shown both with the individual and merged channels. A snapshot of a digital representation of the actual <t>image</t> as processed in <t>IMARIS</t> is also depicted for reference. ( C ) Quantification of the copy number of the long and short 3′ UTR isoforms of DICER1 in the nucleus (left plot) and cytoplasm (right plot) of Control, CFIm25 and CFIm68 KD cells. Colocalization of the red and green signals reveals the presence of the long 3′ UTR isoform (yellow) whereas the signal from the red probe only reveals the presence of the shorter 3′ UTR isoform. mRNA copy numbers were estimated separately from the nucleus (overlapping with DAPI) and cytosol. Segregation of the signal was performed with IMARIS (see Methods). ( D ) Representative western blot showing the DICER1 expression in the Control, CFIm25 and CFIm68 KD cells. The quantification is relative to GAPDH. ( E ) qPCR measurements of let-7, miR-92a, miR-16 and miR-19b expression in CFIm25/68 KD cells relative to Control. ΔΔct values were calculated relative to U6 snRNA and then relative to the Control cells (where the ratio was set to 1). ( F ) Normalized Renilla luciferase expression of reporter mRNAs carrying binding sites for miR-16 and miR-92a in their 3′ UTRs, in Control, CFIm25 and CFIm68 KD cells, respectively. The Firefly luciferase expressed from the same construct was used as normalization control.
Matlab Software Pipeline, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/matlab software pipeline/product/MathWorks Inc
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Image Search Results


CFIm KD increases the activity of miRNAs. ( A ) Genome browser tracks showing the coverage of DICER1 TE (bottom track) by RNA-seq reads from two replicate experiments for each condition, with the two PAS that were quantified for this gene marked by black lines. The conditions are color-coded (as in Figure ) and also indicated on the y-axis. Y-axis shows the smoothened number of reads mapping along the TE, calculated by the GViz R package. ( B ) RNA fluorescence in situ imaging of DICER1 isoforms in Control and CFIm25 KD HEK293 cells with probes corresponding to the common region of the long and short 3′ UTRs (red) or to the region between the proximal and distal cleavage sites, thus present exclusively in the long 3′ UTR (green). Nuclei are marked with DAPI. Zoom-ins of the regions marked with dashed boxes are further shown both with the individual and merged channels. A snapshot of a digital representation of the actual image as processed in IMARIS is also depicted for reference. ( C ) Quantification of the copy number of the long and short 3′ UTR isoforms of DICER1 in the nucleus (left plot) and cytoplasm (right plot) of Control, CFIm25 and CFIm68 KD cells. Colocalization of the red and green signals reveals the presence of the long 3′ UTR isoform (yellow) whereas the signal from the red probe only reveals the presence of the shorter 3′ UTR isoform. mRNA copy numbers were estimated separately from the nucleus (overlapping with DAPI) and cytosol. Segregation of the signal was performed with IMARIS (see Methods). ( D ) Representative western blot showing the DICER1 expression in the Control, CFIm25 and CFIm68 KD cells. The quantification is relative to GAPDH. ( E ) qPCR measurements of let-7, miR-92a, miR-16 and miR-19b expression in CFIm25/68 KD cells relative to Control. ΔΔct values were calculated relative to U6 snRNA and then relative to the Control cells (where the ratio was set to 1). ( F ) Normalized Renilla luciferase expression of reporter mRNAs carrying binding sites for miR-16 and miR-92a in their 3′ UTRs, in Control, CFIm25 and CFIm68 KD cells, respectively. The Firefly luciferase expressed from the same construct was used as normalization control.

Journal: Nucleic Acids Research

Article Title: CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis

doi: 10.1093/nar/gkac114

Figure Lengend Snippet: CFIm KD increases the activity of miRNAs. ( A ) Genome browser tracks showing the coverage of DICER1 TE (bottom track) by RNA-seq reads from two replicate experiments for each condition, with the two PAS that were quantified for this gene marked by black lines. The conditions are color-coded (as in Figure ) and also indicated on the y-axis. Y-axis shows the smoothened number of reads mapping along the TE, calculated by the GViz R package. ( B ) RNA fluorescence in situ imaging of DICER1 isoforms in Control and CFIm25 KD HEK293 cells with probes corresponding to the common region of the long and short 3′ UTRs (red) or to the region between the proximal and distal cleavage sites, thus present exclusively in the long 3′ UTR (green). Nuclei are marked with DAPI. Zoom-ins of the regions marked with dashed boxes are further shown both with the individual and merged channels. A snapshot of a digital representation of the actual image as processed in IMARIS is also depicted for reference. ( C ) Quantification of the copy number of the long and short 3′ UTR isoforms of DICER1 in the nucleus (left plot) and cytoplasm (right plot) of Control, CFIm25 and CFIm68 KD cells. Colocalization of the red and green signals reveals the presence of the long 3′ UTR isoform (yellow) whereas the signal from the red probe only reveals the presence of the shorter 3′ UTR isoform. mRNA copy numbers were estimated separately from the nucleus (overlapping with DAPI) and cytosol. Segregation of the signal was performed with IMARIS (see Methods). ( D ) Representative western blot showing the DICER1 expression in the Control, CFIm25 and CFIm68 KD cells. The quantification is relative to GAPDH. ( E ) qPCR measurements of let-7, miR-92a, miR-16 and miR-19b expression in CFIm25/68 KD cells relative to Control. ΔΔct values were calculated relative to U6 snRNA and then relative to the Control cells (where the ratio was set to 1). ( F ) Normalized Renilla luciferase expression of reporter mRNAs carrying binding sites for miR-16 and miR-92a in their 3′ UTRs, in Control, CFIm25 and CFIm68 KD cells, respectively. The Firefly luciferase expressed from the same construct was used as normalization control.

Article Snippet: Detection and analysis of spots were performed using automated pipelines developed in image analysis software IMARIS (BITPLANE).

Techniques: Activity Assay, RNA Sequencing, Fluorescence, In Situ, Imaging, Control, Western Blot, Expressing, Luciferase, Binding Assay, Construct