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coding sequence cds region  (Addgene inc)


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    Addgene inc coding sequence cds region
    Coding Sequence Cds Region, supplied by Addgene inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/coding+sequence+cds+region/mCitrine_CD+Part+type+CDS+(Plasmid+%2358578)/pm39693003-48-22-40
    Average 94 stars, based on 1 article reviews
    coding sequence cds region - by Bioz Stars, 2026-11
    94/100 stars

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    Related Articles

    Over Expression:

    Article Title: Microtubule acetylation and PERK activation facilitate eribulin-induced mitochondrial calcium accumulation and cell death
    Article Snippet: These shRNA oligos were cloned into the pLKO.1-blast vector (#26655; Addgene). .. For ATAT1 overexpression, the coding sequence (CDS) of ATAT1 was obtained by PCR using pEF5B-FRT-GFP-αTAT1 (#20799, Addgene), and cloned into the pcDNA6/myc-His A expression vector (#V22120; Invitrogen). ..

    Article Title: ADAR1 Promotes NUPR1 A-to-I RNA Editing to Exacerbate Ischemic Brain Injury by Microglia Mediated Neuroinflammation.
    Article Snippet: Microglial cells occupy a crucial position as potential therapeutic targets in the context of ischemic stroke (IS).. Nonetheless, the intrinsic mechanisms that govern microglial activation in the aftermath of IS remain incompletely elucidated.. ADAR1 p150 plays a significant role in immune regulation and stress responses; however, the specific pathways through which it modulates microglial activation and the subsequent mechanisms that unfold following IS have yet to be clearly delineated.

    Article Title: Loss of YTHDC1 m 6 A reading function promotes invasiveness in urothelial carcinoma of the bladder
    Article Snippet: .. For YTHDC1 overexpression, the coding sequence (CDS) was amplified via PCR from the cDNA of WT UROtsa cells and subsequently cloned and inserted into a modified pN251 plasmid, which was originally a gift from Le Cong (Addgene plasmid #188471) . .. For SMAD6 overexpression, the CDS was PCR amplified from the cDNA of WT UROtsa cells with an HA tag and subsequently cloned and inserted into the pLVX-IRES-tdTomato (Clontech) vector.

    Article Title: Loss of YTHDC1 m 6 A reading function promotes invasiveness in urothelial carcinoma of the bladder.
    Article Snippet: .. For YTHDC1 overexpression, the coding sequence (CDS) was amplified via PCR from the cDNA of WT UROtsa cells and subsequently cloned and inserted into a modified pN251 plasmid, which was originally a gift from Le Cong (Addgene plasmid #188471)29. .. For SMAD6 overexpression, the CDS was PCR amplified from the cDNA of WT UROtsa cells with an HA tag and subsequently cloned and inserted into the pLVX-IRES-tdTomato (Clontech) vector.

    Sequencing:

    Article Title: Microtubule acetylation and PERK activation facilitate eribulin-induced mitochondrial calcium accumulation and cell death
    Article Snippet: These shRNA oligos were cloned into the pLKO.1-blast vector (#26655; Addgene). .. For ATAT1 overexpression, the coding sequence (CDS) of ATAT1 was obtained by PCR using pEF5B-FRT-GFP-αTAT1 (#20799, Addgene), and cloned into the pcDNA6/myc-His A expression vector (#V22120; Invitrogen). ..

    Article Title: ADAR1 Promotes NUPR1 A-to-I RNA Editing to Exacerbate Ischemic Brain Injury by Microglia Mediated Neuroinflammation.
    Article Snippet: Microglial cells occupy a crucial position as potential therapeutic targets in the context of ischemic stroke (IS).. Nonetheless, the intrinsic mechanisms that govern microglial activation in the aftermath of IS remain incompletely elucidated.. ADAR1 p150 plays a significant role in immune regulation and stress responses; however, the specific pathways through which it modulates microglial activation and the subsequent mechanisms that unfold following IS have yet to be clearly delineated.

    Article Title: Loss of YTHDC1 m 6 A reading function promotes invasiveness in urothelial carcinoma of the bladder
    Article Snippet: .. For YTHDC1 overexpression, the coding sequence (CDS) was amplified via PCR from the cDNA of WT UROtsa cells and subsequently cloned and inserted into a modified pN251 plasmid, which was originally a gift from Le Cong (Addgene plasmid #188471) . .. For SMAD6 overexpression, the CDS was PCR amplified from the cDNA of WT UROtsa cells with an HA tag and subsequently cloned and inserted into the pLVX-IRES-tdTomato (Clontech) vector.

    Article Title: The alternative polyadenylation regulator CFIm25 promotes macrophage differentiation and activates the NF-κB pathway.
    Article Snippet: .. It was generated by cloning the coding sequence (CDS) of human CFIm25 into the pLV-EF1a-IRES-Puro Vector (Addgene) that contains an EF-1a promoter upstream of an IRES element to co-express the puromycin marker. ..

    Article Title: Tissue Fluidity: A Double-Edged Sword for Multicellular Patterning
    Article Snippet: First, the pLJM1–EGFP lentiviral transfer vector (Addgene; plasmid #19319) was corrected by adding a stop codon (TAA) downstream of the EGFP ORF, thereby preventing the erroneous inclusion of 39 additional back-bone derived codons in our expression constructs. .. This resultant plasmid (pLJM-EGFP_v2) was then used to generate a pLJM1-mRFP plasmid by replacing the EGFP coding sequence (CDS) with the mRFP CDS, obtained by PCR-amplification from the pcDNA-mRFP plasmid (Addgene; plasmid #13032). ..

    Article Title: Loss of YTHDC1 m 6 A reading function promotes invasiveness in urothelial carcinoma of the bladder.
    Article Snippet: .. For YTHDC1 overexpression, the coding sequence (CDS) was amplified via PCR from the cDNA of WT UROtsa cells and subsequently cloned and inserted into a modified pN251 plasmid, which was originally a gift from Le Cong (Addgene plasmid #188471)29. .. For SMAD6 overexpression, the CDS was PCR amplified from the cDNA of WT UROtsa cells with an HA tag and subsequently cloned and inserted into the pLVX-IRES-tdTomato (Clontech) vector.

    Article Title: Dual-specificity phosphatase 23 functions as a promising prognostic biomarker in non-small cell lung cancer.
    Article Snippet: cell carcinoma (LCC) (Hendriks et al. 2024).. Notably, the mechanical property of the tumor microenvironment (TME), particularly extracellular matrix (ECM) stiffening, undergoes significantly changes during NSCLC progression.. The alternation is recognized as one of cancer hallmarks (Lim et al. 2017; Mancini et al. 2024).

    Article Title: The alternative polyadenylation regulator CFIm25 promotes macrophage differentiation and activates the NF-κB pathway
    Article Snippet: .. It was generated by cloning the coding sequence (CDS) of human CFIm25 into the pLV-EF1a-IRES-Puro Vector (Addgene) that contains an EF-1a promoter upstream of an IRES element to co-express the puromycin marker. ..

    Polymerase Chain Reaction:

    Article Title: Microtubule acetylation and PERK activation facilitate eribulin-induced mitochondrial calcium accumulation and cell death
    Article Snippet: These shRNA oligos were cloned into the pLKO.1-blast vector (#26655; Addgene). .. For ATAT1 overexpression, the coding sequence (CDS) of ATAT1 was obtained by PCR using pEF5B-FRT-GFP-αTAT1 (#20799, Addgene), and cloned into the pcDNA6/myc-His A expression vector (#V22120; Invitrogen). ..

    Article Title: Loss of YTHDC1 m 6 A reading function promotes invasiveness in urothelial carcinoma of the bladder
    Article Snippet: .. For YTHDC1 overexpression, the coding sequence (CDS) was amplified via PCR from the cDNA of WT UROtsa cells and subsequently cloned and inserted into a modified pN251 plasmid, which was originally a gift from Le Cong (Addgene plasmid #188471) . .. For SMAD6 overexpression, the CDS was PCR amplified from the cDNA of WT UROtsa cells with an HA tag and subsequently cloned and inserted into the pLVX-IRES-tdTomato (Clontech) vector.

    Article Title: Tissue Fluidity: A Double-Edged Sword for Multicellular Patterning
    Article Snippet: First, the pLJM1–EGFP lentiviral transfer vector (Addgene; plasmid #19319) was corrected by adding a stop codon (TAA) downstream of the EGFP ORF, thereby preventing the erroneous inclusion of 39 additional back-bone derived codons in our expression constructs. .. This resultant plasmid (pLJM-EGFP_v2) was then used to generate a pLJM1-mRFP plasmid by replacing the EGFP coding sequence (CDS) with the mRFP CDS, obtained by PCR-amplification from the pcDNA-mRFP plasmid (Addgene; plasmid #13032). ..

    Article Title: Loss of YTHDC1 m 6 A reading function promotes invasiveness in urothelial carcinoma of the bladder.
    Article Snippet: .. For YTHDC1 overexpression, the coding sequence (CDS) was amplified via PCR from the cDNA of WT UROtsa cells and subsequently cloned and inserted into a modified pN251 plasmid, which was originally a gift from Le Cong (Addgene plasmid #188471)29. .. For SMAD6 overexpression, the CDS was PCR amplified from the cDNA of WT UROtsa cells with an HA tag and subsequently cloned and inserted into the pLVX-IRES-tdTomato (Clontech) vector.

    Clone Assay:

    Article Title: Microtubule acetylation and PERK activation facilitate eribulin-induced mitochondrial calcium accumulation and cell death
    Article Snippet: These shRNA oligos were cloned into the pLKO.1-blast vector (#26655; Addgene). .. For ATAT1 overexpression, the coding sequence (CDS) of ATAT1 was obtained by PCR using pEF5B-FRT-GFP-αTAT1 (#20799, Addgene), and cloned into the pcDNA6/myc-His A expression vector (#V22120; Invitrogen). ..

    Article Title: Loss of YTHDC1 m 6 A reading function promotes invasiveness in urothelial carcinoma of the bladder
    Article Snippet: .. For YTHDC1 overexpression, the coding sequence (CDS) was amplified via PCR from the cDNA of WT UROtsa cells and subsequently cloned and inserted into a modified pN251 plasmid, which was originally a gift from Le Cong (Addgene plasmid #188471) . .. For SMAD6 overexpression, the CDS was PCR amplified from the cDNA of WT UROtsa cells with an HA tag and subsequently cloned and inserted into the pLVX-IRES-tdTomato (Clontech) vector.

    Article Title: Loss of YTHDC1 m 6 A reading function promotes invasiveness in urothelial carcinoma of the bladder.
    Article Snippet: .. For YTHDC1 overexpression, the coding sequence (CDS) was amplified via PCR from the cDNA of WT UROtsa cells and subsequently cloned and inserted into a modified pN251 plasmid, which was originally a gift from Le Cong (Addgene plasmid #188471)29. .. For SMAD6 overexpression, the CDS was PCR amplified from the cDNA of WT UROtsa cells with an HA tag and subsequently cloned and inserted into the pLVX-IRES-tdTomato (Clontech) vector.

    Expressing:

    Article Title: Microtubule acetylation and PERK activation facilitate eribulin-induced mitochondrial calcium accumulation and cell death
    Article Snippet: These shRNA oligos were cloned into the pLKO.1-blast vector (#26655; Addgene). .. For ATAT1 overexpression, the coding sequence (CDS) of ATAT1 was obtained by PCR using pEF5B-FRT-GFP-αTAT1 (#20799, Addgene), and cloned into the pcDNA6/myc-His A expression vector (#V22120; Invitrogen). ..

    Plasmid Preparation:

    Article Title: Microtubule acetylation and PERK activation facilitate eribulin-induced mitochondrial calcium accumulation and cell death
    Article Snippet: These shRNA oligos were cloned into the pLKO.1-blast vector (#26655; Addgene). .. For ATAT1 overexpression, the coding sequence (CDS) of ATAT1 was obtained by PCR using pEF5B-FRT-GFP-αTAT1 (#20799, Addgene), and cloned into the pcDNA6/myc-His A expression vector (#V22120; Invitrogen). ..

    Article Title: ADAR1 Promotes NUPR1 A-to-I RNA Editing to Exacerbate Ischemic Brain Injury by Microglia Mediated Neuroinflammation.
    Article Snippet: Microglial cells occupy a crucial position as potential therapeutic targets in the context of ischemic stroke (IS).. Nonetheless, the intrinsic mechanisms that govern microglial activation in the aftermath of IS remain incompletely elucidated.. ADAR1 p150 plays a significant role in immune regulation and stress responses; however, the specific pathways through which it modulates microglial activation and the subsequent mechanisms that unfold following IS have yet to be clearly delineated.

    Article Title: Loss of YTHDC1 m 6 A reading function promotes invasiveness in urothelial carcinoma of the bladder
    Article Snippet: .. For YTHDC1 overexpression, the coding sequence (CDS) was amplified via PCR from the cDNA of WT UROtsa cells and subsequently cloned and inserted into a modified pN251 plasmid, which was originally a gift from Le Cong (Addgene plasmid #188471) . .. For SMAD6 overexpression, the CDS was PCR amplified from the cDNA of WT UROtsa cells with an HA tag and subsequently cloned and inserted into the pLVX-IRES-tdTomato (Clontech) vector.

    Article Title: Tissue Fluidity: A Double-Edged Sword for Multicellular Patterning
    Article Snippet: First, the pLJM1–EGFP lentiviral transfer vector (Addgene; plasmid #19319) was corrected by adding a stop codon (TAA) downstream of the EGFP ORF, thereby preventing the erroneous inclusion of 39 additional back-bone derived codons in our expression constructs. .. This resultant plasmid (pLJM-EGFP_v2) was then used to generate a pLJM1-mRFP plasmid by replacing the EGFP coding sequence (CDS) with the mRFP CDS, obtained by PCR-amplification from the pcDNA-mRFP plasmid (Addgene; plasmid #13032). ..

    Article Title: Loss of YTHDC1 m 6 A reading function promotes invasiveness in urothelial carcinoma of the bladder.
    Article Snippet: .. For YTHDC1 overexpression, the coding sequence (CDS) was amplified via PCR from the cDNA of WT UROtsa cells and subsequently cloned and inserted into a modified pN251 plasmid, which was originally a gift from Le Cong (Addgene plasmid #188471)29. .. For SMAD6 overexpression, the CDS was PCR amplified from the cDNA of WT UROtsa cells with an HA tag and subsequently cloned and inserted into the pLVX-IRES-tdTomato (Clontech) vector.

    Synthesized:

    Article Title: ADAR1 Promotes NUPR1 A-to-I RNA Editing to Exacerbate Ischemic Brain Injury by Microglia Mediated Neuroinflammation.
    Article Snippet: Microglial cells occupy a crucial position as potential therapeutic targets in the context of ischemic stroke (IS).. Nonetheless, the intrinsic mechanisms that govern microglial activation in the aftermath of IS remain incompletely elucidated.. ADAR1 p150 plays a significant role in immune regulation and stress responses; however, the specific pathways through which it modulates microglial activation and the subsequent mechanisms that unfold following IS have yet to be clearly delineated.

    Cloning:

    Article Title: ADAR1 Promotes NUPR1 A-to-I RNA Editing to Exacerbate Ischemic Brain Injury by Microglia Mediated Neuroinflammation.
    Article Snippet: Microglial cells occupy a crucial position as potential therapeutic targets in the context of ischemic stroke (IS).. Nonetheless, the intrinsic mechanisms that govern microglial activation in the aftermath of IS remain incompletely elucidated.. ADAR1 p150 plays a significant role in immune regulation and stress responses; however, the specific pathways through which it modulates microglial activation and the subsequent mechanisms that unfold following IS have yet to be clearly delineated.

    Article Title: The alternative polyadenylation regulator CFIm25 promotes macrophage differentiation and activates the NF-κB pathway.
    Article Snippet: .. It was generated by cloning the coding sequence (CDS) of human CFIm25 into the pLV-EF1a-IRES-Puro Vector (Addgene) that contains an EF-1a promoter upstream of an IRES element to co-express the puromycin marker. ..

    Article Title: The alternative polyadenylation regulator CFIm25 promotes macrophage differentiation and activates the NF-κB pathway
    Article Snippet: .. It was generated by cloning the coding sequence (CDS) of human CFIm25 into the pLV-EF1a-IRES-Puro Vector (Addgene) that contains an EF-1a promoter upstream of an IRES element to co-express the puromycin marker. ..

    Amplification:

    Article Title: Loss of YTHDC1 m 6 A reading function promotes invasiveness in urothelial carcinoma of the bladder
    Article Snippet: .. For YTHDC1 overexpression, the coding sequence (CDS) was amplified via PCR from the cDNA of WT UROtsa cells and subsequently cloned and inserted into a modified pN251 plasmid, which was originally a gift from Le Cong (Addgene plasmid #188471) . .. For SMAD6 overexpression, the CDS was PCR amplified from the cDNA of WT UROtsa cells with an HA tag and subsequently cloned and inserted into the pLVX-IRES-tdTomato (Clontech) vector.

    Article Title: Loss of YTHDC1 m 6 A reading function promotes invasiveness in urothelial carcinoma of the bladder.
    Article Snippet: .. For YTHDC1 overexpression, the coding sequence (CDS) was amplified via PCR from the cDNA of WT UROtsa cells and subsequently cloned and inserted into a modified pN251 plasmid, which was originally a gift from Le Cong (Addgene plasmid #188471)29. .. For SMAD6 overexpression, the CDS was PCR amplified from the cDNA of WT UROtsa cells with an HA tag and subsequently cloned and inserted into the pLVX-IRES-tdTomato (Clontech) vector.

    Modification:

    Article Title: Loss of YTHDC1 m 6 A reading function promotes invasiveness in urothelial carcinoma of the bladder
    Article Snippet: .. For YTHDC1 overexpression, the coding sequence (CDS) was amplified via PCR from the cDNA of WT UROtsa cells and subsequently cloned and inserted into a modified pN251 plasmid, which was originally a gift from Le Cong (Addgene plasmid #188471) . .. For SMAD6 overexpression, the CDS was PCR amplified from the cDNA of WT UROtsa cells with an HA tag and subsequently cloned and inserted into the pLVX-IRES-tdTomato (Clontech) vector.

    Article Title: Loss of YTHDC1 m 6 A reading function promotes invasiveness in urothelial carcinoma of the bladder.
    Article Snippet: .. For YTHDC1 overexpression, the coding sequence (CDS) was amplified via PCR from the cDNA of WT UROtsa cells and subsequently cloned and inserted into a modified pN251 plasmid, which was originally a gift from Le Cong (Addgene plasmid #188471)29. .. For SMAD6 overexpression, the CDS was PCR amplified from the cDNA of WT UROtsa cells with an HA tag and subsequently cloned and inserted into the pLVX-IRES-tdTomato (Clontech) vector.

    Generated:

    Article Title: The alternative polyadenylation regulator CFIm25 promotes macrophage differentiation and activates the NF-κB pathway.
    Article Snippet: .. It was generated by cloning the coding sequence (CDS) of human CFIm25 into the pLV-EF1a-IRES-Puro Vector (Addgene) that contains an EF-1a promoter upstream of an IRES element to co-express the puromycin marker. ..

    Article Title: Dual-specificity phosphatase 23 functions as a promising prognostic biomarker in non-small cell lung cancer.
    Article Snippet: cell carcinoma (LCC) (Hendriks et al. 2024).. Notably, the mechanical property of the tumor microenvironment (TME), particularly extracellular matrix (ECM) stiffening, undergoes significantly changes during NSCLC progression.. The alternation is recognized as one of cancer hallmarks (Lim et al. 2017; Mancini et al. 2024).

    Article Title: The alternative polyadenylation regulator CFIm25 promotes macrophage differentiation and activates the NF-κB pathway
    Article Snippet: .. It was generated by cloning the coding sequence (CDS) of human CFIm25 into the pLV-EF1a-IRES-Puro Vector (Addgene) that contains an EF-1a promoter upstream of an IRES element to co-express the puromycin marker. ..

    Marker:

    Article Title: The alternative polyadenylation regulator CFIm25 promotes macrophage differentiation and activates the NF-κB pathway.
    Article Snippet: .. It was generated by cloning the coding sequence (CDS) of human CFIm25 into the pLV-EF1a-IRES-Puro Vector (Addgene) that contains an EF-1a promoter upstream of an IRES element to co-express the puromycin marker. ..

    Article Title: The alternative polyadenylation regulator CFIm25 promotes macrophage differentiation and activates the NF-κB pathway
    Article Snippet: .. It was generated by cloning the coding sequence (CDS) of human CFIm25 into the pLV-EF1a-IRES-Puro Vector (Addgene) that contains an EF-1a promoter upstream of an IRES element to co-express the puromycin marker. ..

    Stable Transfection:

    Article Title: Dual-specificity phosphatase 23 functions as a promising prognostic biomarker in non-small cell lung cancer.
    Article Snippet: cell carcinoma (LCC) (Hendriks et al. 2024).. Notably, the mechanical property of the tumor microenvironment (TME), particularly extracellular matrix (ECM) stiffening, undergoes significantly changes during NSCLC progression.. The alternation is recognized as one of cancer hallmarks (Lim et al. 2017; Mancini et al. 2024).

    shRNA:

    Article Title: Dual-specificity phosphatase 23 functions as a promising prognostic biomarker in non-small cell lung cancer.
    Article Snippet: cell carcinoma (LCC) (Hendriks et al. 2024).. Notably, the mechanical property of the tumor microenvironment (TME), particularly extracellular matrix (ECM) stiffening, undergoes significantly changes during NSCLC progression.. The alternation is recognized as one of cancer hallmarks (Lim et al. 2017; Mancini et al. 2024).

    Construct:

    Article Title: Dual-specificity phosphatase 23 functions as a promising prognostic biomarker in non-small cell lung cancer.
    Article Snippet: cell carcinoma (LCC) (Hendriks et al. 2024).. Notably, the mechanical property of the tumor microenvironment (TME), particularly extracellular matrix (ECM) stiffening, undergoes significantly changes during NSCLC progression.. The alternation is recognized as one of cancer hallmarks (Lim et al. 2017; Mancini et al. 2024).

    Transfection:

    Article Title: Dual-specificity phosphatase 23 functions as a promising prognostic biomarker in non-small cell lung cancer.
    Article Snippet: cell carcinoma (LCC) (Hendriks et al. 2024).. Notably, the mechanical property of the tumor microenvironment (TME), particularly extracellular matrix (ECM) stiffening, undergoes significantly changes during NSCLC progression.. The alternation is recognized as one of cancer hallmarks (Lim et al. 2017; Mancini et al. 2024).



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    95
    Twist Bioscience coding sequence cds region
    SQANTI3 categories and framework for annotating NNC (novel not in catalog) features. A , Seven features of NNC isoforms that create a novel junction (or two). Multiple features can be observed in a single transcript, but only one is necessary to assign the isoform to the NNC category. Dotted line indicates the new junction. Black (UTR) and gray <t>(CDS)</t> bars represent the reference annotation with the spaces indicating introns. Yellow bars represent examples of NNC isoforms. B , New categorization of spliced transcripts that map to a gene with a single exon. C , Example gene with multiple reference isoforms and a novel isoform with a new splice site that occurs in the CDS of one reference isoform and UTR of the other reference isoform. D , Novel isoform with a new splice site that occurs in the intron of one reference isoform of the gene and the CDS of the other reference isoform.
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    A)ALKBH5 upregulated FBXL5 expression by m 6 A demethylation. We performed m 6 A sequencing in A549 cells and identified m 6 A peaks across different regions in negative control (EV) and ALKBH5 overexpressed (ALKBH5 OE) cells; B) Volcano plot displayed significant m 6 A methylation peaks that were upregulated and downregulated by ALKBH5; C) We observed decreased m 6 A methylation (m 6 A demethylation) in the genomic CDS region; D) Cumulative percent and E) quantified changes for methylation indicated overall decreased methylation by ALKBH5 overexpression; F) Specific decreased m 6 A peak of the CDS region in FBXL5 mRNA in the presence of ALKBH5 overexpression in A549 cells; G) IHC staining of NSCLC tissue microarray indicated a positive correlation between ALKBH5 and FBXL5 protein expression; H) Western blot revealed upregulated FBXL5 by ALKBH5 overexpression in A549 and H226 NSCLC cells; I) Graphical interpretation of FBXL5 and ALKBH5 mutations stably transfected into NSCLC cells; J) m 6 A‐RIP‐qPCR demonstrated m 6 A methylation in FBXL5 mRNA; K) Common RIP‐qPCR demonstrated binding of ALKBH5 to FBXL5 mRNA. Western blot was presented for quality control in protein extracted from the input group and the groups immunoprecipitated by IgG and ALKBH5 antibody; L) ALKBH5 H204A mutation impaired the binding of ALKBH5 to FBXL5 mRNA as indicated by RIP‐qPCR. Western blot was performed for quality control using protein extracted from the corresponding groups; M) Western blot in NSCLC cells indicated that wild‐type ALKBH5 could upregulate wild‐type FBXL5, but this regulation was attenuated in the presence of ALKBH5 H204A mutation or FBLX5 synonymous mutation in potentially m 6 A sites.

    Journal: Advanced Science

    Article Title: Cis‐Regulation of an m 6 A Eraser by an Insertion Variant Associated with Survival of Patients With Non‐Small Cell Lung Carcinoma

    doi: 10.1002/advs.202407652

    Figure Lengend Snippet: A)ALKBH5 upregulated FBXL5 expression by m 6 A demethylation. We performed m 6 A sequencing in A549 cells and identified m 6 A peaks across different regions in negative control (EV) and ALKBH5 overexpressed (ALKBH5 OE) cells; B) Volcano plot displayed significant m 6 A methylation peaks that were upregulated and downregulated by ALKBH5; C) We observed decreased m 6 A methylation (m 6 A demethylation) in the genomic CDS region; D) Cumulative percent and E) quantified changes for methylation indicated overall decreased methylation by ALKBH5 overexpression; F) Specific decreased m 6 A peak of the CDS region in FBXL5 mRNA in the presence of ALKBH5 overexpression in A549 cells; G) IHC staining of NSCLC tissue microarray indicated a positive correlation between ALKBH5 and FBXL5 protein expression; H) Western blot revealed upregulated FBXL5 by ALKBH5 overexpression in A549 and H226 NSCLC cells; I) Graphical interpretation of FBXL5 and ALKBH5 mutations stably transfected into NSCLC cells; J) m 6 A‐RIP‐qPCR demonstrated m 6 A methylation in FBXL5 mRNA; K) Common RIP‐qPCR demonstrated binding of ALKBH5 to FBXL5 mRNA. Western blot was presented for quality control in protein extracted from the input group and the groups immunoprecipitated by IgG and ALKBH5 antibody; L) ALKBH5 H204A mutation impaired the binding of ALKBH5 to FBXL5 mRNA as indicated by RIP‐qPCR. Western blot was performed for quality control using protein extracted from the corresponding groups; M) Western blot in NSCLC cells indicated that wild‐type ALKBH5 could upregulate wild‐type FBXL5, but this regulation was attenuated in the presence of ALKBH5 H204A mutation or FBLX5 synonymous mutation in potentially m 6 A sites.

    Article Snippet: Western blot was used to detect whether the impact of ALKBH5 on FBXL5 was dependent on potential m 6 A sites in the FBXL5 coding sequence (CDS) region and ALKBH5 H204 protein region, with FLAG and HA antibody (Proteintech, China).

    Techniques: Expressing, Sequencing, Negative Control, Methylation, Over Expression, Immunohistochemistry, Microarray, Western Blot, Stable Transfection, Transfection, Binding Assay, Control, Immunoprecipitation, Mutagenesis

    A)ALKBH5‐FBXL5 axis decreased intracellular ROS and inhibited PI3K‐AKT and NF‐κB pathway activations to exert a cancer suppressor role in NSCLC. ALKBH5 overexpression and FBXL5 knockdown were performed in A549 cells and the opposite manipulation was performed in H226 cells, which was validated by western blot; B) ROS fluorescent probe staining and C) flow cytometric detection indicated decreased ROS levels by ALKBH5 overexpression, which was retrieved by FBXL5 knockdown in A549 cells, and opposite results were observed by in H226 cells with the corresponding manipulation; D) p‐AKT and p65, two key elements for PI3K and NF‐κB pathways activation, were downregulated by ALKBH5 overexpression, which could be reversed by FBXL5 downregulation in A549 cells. Conversely, PI3K and NF‐κB pathways could be activated by ALKBH5 downregulation, which was attenuated by FBXL5 upregulation in H226 cells; E,F) Colony formation and G,H) migration of A549 cells were inhibited by ALKBH5 overexpression but were retrieved by FBXL5 downregulation, and vice versa for the impact of ALKBH5‐FBXL5 axis on colony formation and migration in H226 cells I,J) Similarly, in vivo experiments demonstrated that FBXL5 was also indispensable for ALKBH5‐induced shrinkage of xenograft tumors constructed by A549 cells; K,L) IHC experiments of xenograft tumors for Ki‐67, PCNA, indicated less staining by ALKBH5 overexpression, which was partly restored in the presence of additional FBXL5 knockdown. HE was used as a background staining marker for NSCLC cells.

    Journal: Advanced Science

    Article Title: Cis‐Regulation of an m 6 A Eraser by an Insertion Variant Associated with Survival of Patients With Non‐Small Cell Lung Carcinoma

    doi: 10.1002/advs.202407652

    Figure Lengend Snippet: A)ALKBH5‐FBXL5 axis decreased intracellular ROS and inhibited PI3K‐AKT and NF‐κB pathway activations to exert a cancer suppressor role in NSCLC. ALKBH5 overexpression and FBXL5 knockdown were performed in A549 cells and the opposite manipulation was performed in H226 cells, which was validated by western blot; B) ROS fluorescent probe staining and C) flow cytometric detection indicated decreased ROS levels by ALKBH5 overexpression, which was retrieved by FBXL5 knockdown in A549 cells, and opposite results were observed by in H226 cells with the corresponding manipulation; D) p‐AKT and p65, two key elements for PI3K and NF‐κB pathways activation, were downregulated by ALKBH5 overexpression, which could be reversed by FBXL5 downregulation in A549 cells. Conversely, PI3K and NF‐κB pathways could be activated by ALKBH5 downregulation, which was attenuated by FBXL5 upregulation in H226 cells; E,F) Colony formation and G,H) migration of A549 cells were inhibited by ALKBH5 overexpression but were retrieved by FBXL5 downregulation, and vice versa for the impact of ALKBH5‐FBXL5 axis on colony formation and migration in H226 cells I,J) Similarly, in vivo experiments demonstrated that FBXL5 was also indispensable for ALKBH5‐induced shrinkage of xenograft tumors constructed by A549 cells; K,L) IHC experiments of xenograft tumors for Ki‐67, PCNA, indicated less staining by ALKBH5 overexpression, which was partly restored in the presence of additional FBXL5 knockdown. HE was used as a background staining marker for NSCLC cells.

    Article Snippet: Western blot was used to detect whether the impact of ALKBH5 on FBXL5 was dependent on potential m 6 A sites in the FBXL5 coding sequence (CDS) region and ALKBH5 H204 protein region, with FLAG and HA antibody (Proteintech, China).

    Techniques: Over Expression, Knockdown, Western Blot, Staining, Activation Assay, Migration, In Vivo, Construct, Marker

    SQANTI3 categories and framework for annotating NNC (novel not in catalog) features. A , Seven features of NNC isoforms that create a novel junction (or two). Multiple features can be observed in a single transcript, but only one is necessary to assign the isoform to the NNC category. Dotted line indicates the new junction. Black (UTR) and gray (CDS) bars represent the reference annotation with the spaces indicating introns. Yellow bars represent examples of NNC isoforms. B , New categorization of spliced transcripts that map to a gene with a single exon. C , Example gene with multiple reference isoforms and a novel isoform with a new splice site that occurs in the CDS of one reference isoform and UTR of the other reference isoform. D , Novel isoform with a new splice site that occurs in the intron of one reference isoform of the gene and the CDS of the other reference isoform.

    Journal: eNeuro

    Article Title: RNA Isoform Diversity in Human Neurodegenerative Diseases

    doi: 10.1523/ENEURO.0296-24.2024

    Figure Lengend Snippet: SQANTI3 categories and framework for annotating NNC (novel not in catalog) features. A , Seven features of NNC isoforms that create a novel junction (or two). Multiple features can be observed in a single transcript, but only one is necessary to assign the isoform to the NNC category. Dotted line indicates the new junction. Black (UTR) and gray (CDS) bars represent the reference annotation with the spaces indicating introns. Yellow bars represent examples of NNC isoforms. B , New categorization of spliced transcripts that map to a gene with a single exon. C , Example gene with multiple reference isoforms and a novel isoform with a new splice site that occurs in the CDS of one reference isoform and UTR of the other reference isoform. D , Novel isoform with a new splice site that occurs in the intron of one reference isoform of the gene and the CDS of the other reference isoform.

    Article Snippet: The amplified cDNA libraries were enriched using a custom probe panel of 50 genes targeting exons in the coding sequence (CDS) region (Twist Bioscience) with the Standard Hybridization and Wash kit (Twist Bioscience #104178).

    Techniques: