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reverse transcription enzyme  (Thermo Fisher)


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    Structured Review

    Thermo Fisher reverse transcription enzyme
    a UMAP showing PST cells from distinct time points. b UMAP showing the fraction of labeled transcripts per cell in vivo 4sU-labeled PST cells. c UMAP showing H-PST and L-PST cell clusters. UMAP visualization of H-PST cells responded to uni-IRI for distinct time points characterized by conventional splicing-based ( d ) or metabolic labeling-based RNA velocity analysis ( e ). Cells are color-coded by treatment time. The streamlines reveal the integration paths of local projections moving from the observed state to the extrapolated future state. f UMAP visualization of L-PST cells responded to uni-IRI for distinct time points characterized by metabolic labeling-based RNA velocity analysis. g Bar plot showing the expression of Havcr1 in H-PST and L-PST cells at distinct time points. n = 2240 cells for L-PST, n = 973 for H-PST. Data shown as mean ± SD. h Phase portraits showing total-new RNA planes of Havcr1 . i UMAP plots colored by smoothed total RNA level based on local averaging. The regulon activity of <t>transcription</t> factors Jun ( j ) and Cebpb ( k ) along with the AKI progression. In new RNA-based analysis, n = 114, 870, 79, 241, and 251 cells for NC, I_30 min, I_50 min, IR_3.8 h, and IR_5.3 h groups; In old RNA-based analysis, n = 54, 708, 44, 19, and 32 cells for NC, I_30 min, I_50 min, IR_3.8 h, and IR_5.3 h groups. Data shown as mean ± SD. l Signaling pathway role heatmap showing THBS signaling pathway network in Fib, C1q- Macro, C1q+ Macro, and H-PST cells. Source data are provided as a Source Data file.
    Reverse Transcription Enzyme, 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/product/reverse+transcript+enzyme/maxima+h+minus+reverse+transcriptase/pmc11564529-242-40-43
    Average 90 stars, based on 1 article reviews
    reverse transcription enzyme - by Bioz Stars, 2026-09
    90/100 stars

    Images

    1) Product Images from "Dyna-vivo-seq unveils cellular RNA dynamics during acute kidney injury via in vivo metabolic RNA labeling-based scRNA-seq"

    Article Title: Dyna-vivo-seq unveils cellular RNA dynamics during acute kidney injury via in vivo metabolic RNA labeling-based scRNA-seq

    Journal: Nature Communications

    doi: 10.1038/s41467-024-54202-4

    a UMAP showing PST cells from distinct time points. b UMAP showing the fraction of labeled transcripts per cell in vivo 4sU-labeled PST cells. c UMAP showing H-PST and L-PST cell clusters. UMAP visualization of H-PST cells responded to uni-IRI for distinct time points characterized by conventional splicing-based ( d ) or metabolic labeling-based RNA velocity analysis ( e ). Cells are color-coded by treatment time. The streamlines reveal the integration paths of local projections moving from the observed state to the extrapolated future state. f UMAP visualization of L-PST cells responded to uni-IRI for distinct time points characterized by metabolic labeling-based RNA velocity analysis. g Bar plot showing the expression of Havcr1 in H-PST and L-PST cells at distinct time points. n = 2240 cells for L-PST, n = 973 for H-PST. Data shown as mean ± SD. h Phase portraits showing total-new RNA planes of Havcr1 . i UMAP plots colored by smoothed total RNA level based on local averaging. The regulon activity of transcription factors Jun ( j ) and Cebpb ( k ) along with the AKI progression. In new RNA-based analysis, n = 114, 870, 79, 241, and 251 cells for NC, I_30 min, I_50 min, IR_3.8 h, and IR_5.3 h groups; In old RNA-based analysis, n = 54, 708, 44, 19, and 32 cells for NC, I_30 min, I_50 min, IR_3.8 h, and IR_5.3 h groups. Data shown as mean ± SD. l Signaling pathway role heatmap showing THBS signaling pathway network in Fib, C1q- Macro, C1q+ Macro, and H-PST cells. Source data are provided as a Source Data file.
    Figure Legend Snippet: a UMAP showing PST cells from distinct time points. b UMAP showing the fraction of labeled transcripts per cell in vivo 4sU-labeled PST cells. c UMAP showing H-PST and L-PST cell clusters. UMAP visualization of H-PST cells responded to uni-IRI for distinct time points characterized by conventional splicing-based ( d ) or metabolic labeling-based RNA velocity analysis ( e ). Cells are color-coded by treatment time. The streamlines reveal the integration paths of local projections moving from the observed state to the extrapolated future state. f UMAP visualization of L-PST cells responded to uni-IRI for distinct time points characterized by metabolic labeling-based RNA velocity analysis. g Bar plot showing the expression of Havcr1 in H-PST and L-PST cells at distinct time points. n = 2240 cells for L-PST, n = 973 for H-PST. Data shown as mean ± SD. h Phase portraits showing total-new RNA planes of Havcr1 . i UMAP plots colored by smoothed total RNA level based on local averaging. The regulon activity of transcription factors Jun ( j ) and Cebpb ( k ) along with the AKI progression. In new RNA-based analysis, n = 114, 870, 79, 241, and 251 cells for NC, I_30 min, I_50 min, IR_3.8 h, and IR_5.3 h groups; In old RNA-based analysis, n = 54, 708, 44, 19, and 32 cells for NC, I_30 min, I_50 min, IR_3.8 h, and IR_5.3 h groups. Data shown as mean ± SD. l Signaling pathway role heatmap showing THBS signaling pathway network in Fib, C1q- Macro, C1q+ Macro, and H-PST cells. Source data are provided as a Source Data file.

    Techniques Used: Labeling, In Vivo, Expressing, Activity Assay

    Related Articles

    Reverse Transcription:

    Article Title: Optogenetic Clustering of Human IRE1 Reveals Differential Regulation of Transcription and mRNA Splice Isoform Abundance by the UPR
    Article Snippet: .. The reaction was then quickly mixed with 0.5 μl RNaseOUT (Thermo Fisher #10777019), 1 μl of 20mM strand-switching primer, 1 μl Maxima H Minus Reverse Transcriptase (Thermo Fisher EP0751), and 4 μl Maxima H Minus buffer. ..

    Article Title: Deciphering direct transcriptional effects of epigenetic compounds through large-scale new RNA profiling
    Article Snippet: Briefly, 2 μl purified RNA from each sample was transferred to a 384 well plate and 2 μl alkylation mix (50 mM Tris-HCl pH 8.4, 45% DMSO (Sigma), 200 mM iodoacetamide (Sigma)) was added to each well and the plate was incubated at 50 °C for 15 min. To quench the alkylation reaction, 2 μl quenching mix (35 mM DTT (Thermo Scientific), 0.5 mM dNTPs (Thermo Scientific), 0.5 μM Smart-seq3 oligo-dT primer (5′-biotin-ACGAGCATCAGCAGCATACGA T30VN-3′; IDT), 0.4 U/μl RRI (Takara)) was added and the plate was incubated for 5 min at 21 °C, then 10 min at 72 °C to denature any RNA secondary structures. .. Reverse transcription master mix (25 mM Tris-HCl pH 8.0, 35 mM NaCl (Sigma), 1 mM GTP (Thermo Scientific), 3.6 mM MgCl 2 (invitrogen), 5% PEG (Sigma), 2 mM DTT (Thermo Scientific), 0,4 U/μl RNase Inhibitor (Takara), Smart-seq3 TSO oligo (5′-biotin-AGAGACAGATTGCGCAATGNNNNNNNNrGrGrG-3′; IDT), 2 U/μl Maxima H Minus Reverse Transcriptase (Thermo Scientific)) was then added at a volume of 6 μl to each well and the plate was incubated in a thermocycler using the same RT protocol as in NASC-seq2. .. After reverse transcription, 6 μl PCR mix (1X KAPA HiFi buffer containing 2 mM MgCl 2 (Roche), 0.02 U/μl KAPA HotStart DNA polymerase (Roche), Smart-seq3 forward PCR primer (5′-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATTGCGCAATG-3′; IDT), Smart-seq3 reverse PCR primer (5′-ACGAGCATCAGCAGCATACGA-3′; IDT), 0.3 mM dNTPs (Thermo Scientific), 0.5 μM MgCl 2 (invitrogen)) was added to each well and PCR was performed as follows: 3 min at 98 °C for initial denaturation, 17 cycles of 20 s at 98 °C, 30 s at 65 °C and 6 min at 72 °C.

    Article Title: Nucleosome Positioning Shapes Cryptic Antisense Transcription
    Article Snippet: .. Reverse transcription was then performed using Maxima H Minus RT (Thermo Fisher Cat. No. EP0753) by adding 6.5 μl RT master mix (4 μl 5X RT buffer, 1 μl DEPC water, 0.5 μl RiboLick RNAse inhibitor, 1 μl Maxima H Minus RT), then cycling as follows: 50 °C for 30 min, 65 °C for 15 min, 85 °C for 5 min. 2.5 μl of indexed RPI-n primer (10 μM) were then added to each RT reaction, then PCR was performed as a 100 μl reaction using the Q5 polymerase (NEB) with the included high GC content enhancer. ..

    Article Title: The rewiring of cAMP/cGMP and LDH signalling drives cardiac hypertrophy in Pde5a -/- mice.
    Article Snippet: The yield and purity of RNA was determined with the NanoDrop OneC microvolume UV-Vis Spectrophotometer (Thermo Fisher Scientific). .. RNA was reverse transcribed by Maxima H Minus Reverse Transcriptase (cat. EP0751; Thermo Fisher Scientific) according to the manufacturer’s protocol and then processed for quantitative PCR (qPCR). qPCR reaction was carried out by using PowerUp SYBR green Master Mix (cat. A25743; Thermo Fisher Scientific). .. Target transcripts were analysed using QuantStudio 7 Flex RT–PCR System (Thermo Fisher Scientific).

    Article Title: Genetically encoded and modular subcellular organelle probes reveal dysfunction in lysosomes and mitochondria driven by PRKN knockout
    Article Snippet: RNA extraction kit , Zymo , Cat# R2062. .. Maxima H Minus Reverse Transcriptase , Thermo Scientific , Cat# EP0752. .. 2x PowerUp SYBR Green Master Mix , Applied Biosystems , Cat#A25741.

    Article Title: Genetically encoded and modular subcellular organelle probes reveal dysfunction in lysosomes and mitochondria driven by PRKN knockout
    Article Snippet: RNA was extracted from samples using TRIzol (Invitrogen 15596018) and an RNA extraction kit following the manufacturer’s recommended protocol (Zymo R2062). .. RNA concentration and purity were measured on a spectrophotometer. cDNA was produced from 1 μg of RNA per sample, using Maxima H Minus Reverse Transcriptase (Thermo Scientific EP0752) and following the manufacturer’s recommendations. qPCR reactions were prepared in a 384-well plate (Applied Biosystems 4309849) with 1:10 dilution of cDNA, 2x PowerUp SYBR Green Master Mix (Applied Biosystems A25741) and 1 μM each of forward and reverse primers. qPCRs were run on QuantStudio 7 (Applied Biosystems 4485701) and analyzed using the ΔΔCt method, normalized to ACTB and S18 rRNA. ..

    Article Title: Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ
    Article Snippet: .. At this point, 1 μl of this sample was set-aside for quality control. ssDNA amplification from template RNA was performed by reverse transcription, using: 150 μl of unpurified in vitro transcription reaction, 1.7 mM dNTP mix, 19 μM forward primer, 240 U RNAsin Plus RNAse inhibitor (Promega), 1200 U Maxima H Minus Reverse Transcriptase (ThermoFisher), 60 μl of 5x Maxima Buffer and water up to 300 μl. ..

    Incubation:

    Article Title: Deciphering direct transcriptional effects of epigenetic compounds through large-scale new RNA profiling
    Article Snippet: Briefly, 2 μl purified RNA from each sample was transferred to a 384 well plate and 2 μl alkylation mix (50 mM Tris-HCl pH 8.4, 45% DMSO (Sigma), 200 mM iodoacetamide (Sigma)) was added to each well and the plate was incubated at 50 °C for 15 min. To quench the alkylation reaction, 2 μl quenching mix (35 mM DTT (Thermo Scientific), 0.5 mM dNTPs (Thermo Scientific), 0.5 μM Smart-seq3 oligo-dT primer (5′-biotin-ACGAGCATCAGCAGCATACGA T30VN-3′; IDT), 0.4 U/μl RRI (Takara)) was added and the plate was incubated for 5 min at 21 °C, then 10 min at 72 °C to denature any RNA secondary structures. .. Reverse transcription master mix (25 mM Tris-HCl pH 8.0, 35 mM NaCl (Sigma), 1 mM GTP (Thermo Scientific), 3.6 mM MgCl 2 (invitrogen), 5% PEG (Sigma), 2 mM DTT (Thermo Scientific), 0,4 U/μl RNase Inhibitor (Takara), Smart-seq3 TSO oligo (5′-biotin-AGAGACAGATTGCGCAATGNNNNNNNNrGrGrG-3′; IDT), 2 U/μl Maxima H Minus Reverse Transcriptase (Thermo Scientific)) was then added at a volume of 6 μl to each well and the plate was incubated in a thermocycler using the same RT protocol as in NASC-seq2. .. After reverse transcription, 6 μl PCR mix (1X KAPA HiFi buffer containing 2 mM MgCl 2 (Roche), 0.02 U/μl KAPA HotStart DNA polymerase (Roche), Smart-seq3 forward PCR primer (5′-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATTGCGCAATG-3′; IDT), Smart-seq3 reverse PCR primer (5′-ACGAGCATCAGCAGCATACGA-3′; IDT), 0.3 mM dNTPs (Thermo Scientific), 0.5 μM MgCl 2 (invitrogen)) was added to each well and PCR was performed as follows: 3 min at 98 °C for initial denaturation, 17 cycles of 20 s at 98 °C, 30 s at 65 °C and 6 min at 72 °C.

    Polymerase Chain Reaction:

    Article Title: Nucleosome Positioning Shapes Cryptic Antisense Transcription
    Article Snippet: .. Reverse transcription was then performed using Maxima H Minus RT (Thermo Fisher Cat. No. EP0753) by adding 6.5 μl RT master mix (4 μl 5X RT buffer, 1 μl DEPC water, 0.5 μl RiboLick RNAse inhibitor, 1 μl Maxima H Minus RT), then cycling as follows: 50 °C for 30 min, 65 °C for 15 min, 85 °C for 5 min. 2.5 μl of indexed RPI-n primer (10 μM) were then added to each RT reaction, then PCR was performed as a 100 μl reaction using the Q5 polymerase (NEB) with the included high GC content enhancer. ..

    other:

    Article Title: Deciphering direct transcriptional effects of epigenetic compounds through large-scale new RNA profiling
    Article Snippet: Following the quenching reaction, the cells were denatured at 72 °C for 10 min and 3 μl RT reaction (2 μl TSO (5’-Biotin-AGAGACAGATTGCGCAATGNNNNNNNNrGrGrG-3’; IDT), 25 mM Tris-HCl (pH 8.0), 35 mM NaCl, 1 mM GTP (tris-buffered, Thermo Fisher Scientific), 2.5 mM MgCl2, 5 % PEG, 2 mM DTT, 0.4 U/μl RRI, 2 μM TSO and 2 U/μl Maxima H-minus reverse transcriptase (Thermo Fisher Scientific)) was added and the plates were incubated at 42 °C for 90 min followed by 10 cycles of 50 °C and 42 °C for 2 min each, and final denaturation for 5 min at 85 °C.

    Real-time Polymerase Chain Reaction:

    Article Title: The rewiring of cAMP/cGMP and LDH signalling drives cardiac hypertrophy in Pde5a -/- mice.
    Article Snippet: The yield and purity of RNA was determined with the NanoDrop OneC microvolume UV-Vis Spectrophotometer (Thermo Fisher Scientific). .. RNA was reverse transcribed by Maxima H Minus Reverse Transcriptase (cat. EP0751; Thermo Fisher Scientific) according to the manufacturer’s protocol and then processed for quantitative PCR (qPCR). qPCR reaction was carried out by using PowerUp SYBR green Master Mix (cat. A25743; Thermo Fisher Scientific). .. Target transcripts were analysed using QuantStudio 7 Flex RT–PCR System (Thermo Fisher Scientific).

    Article Title: Genetically encoded and modular subcellular organelle probes reveal dysfunction in lysosomes and mitochondria driven by PRKN knockout
    Article Snippet: RNA was extracted from samples using TRIzol (Invitrogen 15596018) and an RNA extraction kit following the manufacturer’s recommended protocol (Zymo R2062). .. RNA concentration and purity were measured on a spectrophotometer. cDNA was produced from 1 μg of RNA per sample, using Maxima H Minus Reverse Transcriptase (Thermo Scientific EP0752) and following the manufacturer’s recommendations. qPCR reactions were prepared in a 384-well plate (Applied Biosystems 4309849) with 1:10 dilution of cDNA, 2x PowerUp SYBR Green Master Mix (Applied Biosystems A25741) and 1 μM each of forward and reverse primers. qPCRs were run on QuantStudio 7 (Applied Biosystems 4485701) and analyzed using the ΔΔCt method, normalized to ACTB and S18 rRNA. ..

    SYBR Green Assay:

    Article Title: The rewiring of cAMP/cGMP and LDH signalling drives cardiac hypertrophy in Pde5a -/- mice.
    Article Snippet: The yield and purity of RNA was determined with the NanoDrop OneC microvolume UV-Vis Spectrophotometer (Thermo Fisher Scientific). .. RNA was reverse transcribed by Maxima H Minus Reverse Transcriptase (cat. EP0751; Thermo Fisher Scientific) according to the manufacturer’s protocol and then processed for quantitative PCR (qPCR). qPCR reaction was carried out by using PowerUp SYBR green Master Mix (cat. A25743; Thermo Fisher Scientific). .. Target transcripts were analysed using QuantStudio 7 Flex RT–PCR System (Thermo Fisher Scientific).

    Article Title: Genetically encoded and modular subcellular organelle probes reveal dysfunction in lysosomes and mitochondria driven by PRKN knockout
    Article Snippet: RNA was extracted from samples using TRIzol (Invitrogen 15596018) and an RNA extraction kit following the manufacturer’s recommended protocol (Zymo R2062). .. RNA concentration and purity were measured on a spectrophotometer. cDNA was produced from 1 μg of RNA per sample, using Maxima H Minus Reverse Transcriptase (Thermo Scientific EP0752) and following the manufacturer’s recommendations. qPCR reactions were prepared in a 384-well plate (Applied Biosystems 4309849) with 1:10 dilution of cDNA, 2x PowerUp SYBR Green Master Mix (Applied Biosystems A25741) and 1 μM each of forward and reverse primers. qPCRs were run on QuantStudio 7 (Applied Biosystems 4485701) and analyzed using the ΔΔCt method, normalized to ACTB and S18 rRNA. ..

    Concentration Assay:

    Article Title: Genetically encoded and modular subcellular organelle probes reveal dysfunction in lysosomes and mitochondria driven by PRKN knockout
    Article Snippet: RNA was extracted from samples using TRIzol (Invitrogen 15596018) and an RNA extraction kit following the manufacturer’s recommended protocol (Zymo R2062). .. RNA concentration and purity were measured on a spectrophotometer. cDNA was produced from 1 μg of RNA per sample, using Maxima H Minus Reverse Transcriptase (Thermo Scientific EP0752) and following the manufacturer’s recommendations. qPCR reactions were prepared in a 384-well plate (Applied Biosystems 4309849) with 1:10 dilution of cDNA, 2x PowerUp SYBR Green Master Mix (Applied Biosystems A25741) and 1 μM each of forward and reverse primers. qPCRs were run on QuantStudio 7 (Applied Biosystems 4485701) and analyzed using the ΔΔCt method, normalized to ACTB and S18 rRNA. ..

    Spectrophotometry:

    Article Title: Genetically encoded and modular subcellular organelle probes reveal dysfunction in lysosomes and mitochondria driven by PRKN knockout
    Article Snippet: RNA was extracted from samples using TRIzol (Invitrogen 15596018) and an RNA extraction kit following the manufacturer’s recommended protocol (Zymo R2062). .. RNA concentration and purity were measured on a spectrophotometer. cDNA was produced from 1 μg of RNA per sample, using Maxima H Minus Reverse Transcriptase (Thermo Scientific EP0752) and following the manufacturer’s recommendations. qPCR reactions were prepared in a 384-well plate (Applied Biosystems 4309849) with 1:10 dilution of cDNA, 2x PowerUp SYBR Green Master Mix (Applied Biosystems A25741) and 1 μM each of forward and reverse primers. qPCRs were run on QuantStudio 7 (Applied Biosystems 4485701) and analyzed using the ΔΔCt method, normalized to ACTB and S18 rRNA. ..

    Produced:

    Article Title: Genetically encoded and modular subcellular organelle probes reveal dysfunction in lysosomes and mitochondria driven by PRKN knockout
    Article Snippet: RNA was extracted from samples using TRIzol (Invitrogen 15596018) and an RNA extraction kit following the manufacturer’s recommended protocol (Zymo R2062). .. RNA concentration and purity were measured on a spectrophotometer. cDNA was produced from 1 μg of RNA per sample, using Maxima H Minus Reverse Transcriptase (Thermo Scientific EP0752) and following the manufacturer’s recommendations. qPCR reactions were prepared in a 384-well plate (Applied Biosystems 4309849) with 1:10 dilution of cDNA, 2x PowerUp SYBR Green Master Mix (Applied Biosystems A25741) and 1 μM each of forward and reverse primers. qPCRs were run on QuantStudio 7 (Applied Biosystems 4485701) and analyzed using the ΔΔCt method, normalized to ACTB and S18 rRNA. ..

    Control:

    Article Title: Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ
    Article Snippet: .. At this point, 1 μl of this sample was set-aside for quality control. ssDNA amplification from template RNA was performed by reverse transcription, using: 150 μl of unpurified in vitro transcription reaction, 1.7 mM dNTP mix, 19 μM forward primer, 240 U RNAsin Plus RNAse inhibitor (Promega), 1200 U Maxima H Minus Reverse Transcriptase (ThermoFisher), 60 μl of 5x Maxima Buffer and water up to 300 μl. ..

    Amplification:

    Article Title: Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ
    Article Snippet: .. At this point, 1 μl of this sample was set-aside for quality control. ssDNA amplification from template RNA was performed by reverse transcription, using: 150 μl of unpurified in vitro transcription reaction, 1.7 mM dNTP mix, 19 μM forward primer, 240 U RNAsin Plus RNAse inhibitor (Promega), 1200 U Maxima H Minus Reverse Transcriptase (ThermoFisher), 60 μl of 5x Maxima Buffer and water up to 300 μl. ..

    In Vitro:

    Article Title: Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ
    Article Snippet: .. At this point, 1 μl of this sample was set-aside for quality control. ssDNA amplification from template RNA was performed by reverse transcription, using: 150 μl of unpurified in vitro transcription reaction, 1.7 mM dNTP mix, 19 μM forward primer, 240 U RNAsin Plus RNAse inhibitor (Promega), 1200 U Maxima H Minus Reverse Transcriptase (ThermoFisher), 60 μl of 5x Maxima Buffer and water up to 300 μl. ..



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    a UMAP showing PST cells from distinct time points. b UMAP showing the fraction of labeled transcripts per cell in vivo 4sU-labeled PST cells. c UMAP showing H-PST and L-PST cell clusters. UMAP visualization of H-PST cells responded to uni-IRI for distinct time points characterized by conventional splicing-based ( d ) or metabolic labeling-based RNA velocity analysis ( e ). Cells are color-coded by treatment time. The streamlines reveal the integration paths of local projections moving from the observed state to the extrapolated future state. f UMAP visualization of L-PST cells responded to uni-IRI for distinct time points characterized by metabolic labeling-based RNA velocity analysis. g Bar plot showing the expression of Havcr1 in H-PST and L-PST cells at distinct time points. n = 2240 cells for L-PST, n = 973 for H-PST. Data shown as mean ± SD. h Phase portraits showing total-new RNA planes of Havcr1 . i UMAP plots colored by smoothed total RNA level based on local averaging. The regulon activity of <t>transcription</t> factors Jun ( j ) and Cebpb ( k ) along with the AKI progression. In new RNA-based analysis, n = 114, 870, 79, 241, and 251 cells for NC, I_30 min, I_50 min, IR_3.8 h, and IR_5.3 h groups; In old RNA-based analysis, n = 54, 708, 44, 19, and 32 cells for NC, I_30 min, I_50 min, IR_3.8 h, and IR_5.3 h groups. Data shown as mean ± SD. l Signaling pathway role heatmap showing THBS signaling pathway network in Fib, C1q- Macro, C1q+ Macro, and H-PST cells. Source data are provided as a Source Data file.
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    a UMAP showing PST cells from distinct time points. b UMAP showing the fraction of labeled transcripts per cell in vivo 4sU-labeled PST cells. c UMAP showing H-PST and L-PST cell clusters. UMAP visualization of H-PST cells responded to uni-IRI for distinct time points characterized by conventional splicing-based ( d ) or metabolic labeling-based RNA velocity analysis ( e ). Cells are color-coded by treatment time. The streamlines reveal the integration paths of local projections moving from the observed state to the extrapolated future state. f UMAP visualization of L-PST cells responded to uni-IRI for distinct time points characterized by metabolic labeling-based RNA velocity analysis. g Bar plot showing the expression of Havcr1 in H-PST and L-PST cells at distinct time points. n = 2240 cells for L-PST, n = 973 for H-PST. Data shown as mean ± SD. h Phase portraits showing total-new RNA planes of Havcr1 . i UMAP plots colored by smoothed total RNA level based on local averaging. The regulon activity of transcription factors Jun ( j ) and Cebpb ( k ) along with the AKI progression. In new RNA-based analysis, n = 114, 870, 79, 241, and 251 cells for NC, I_30 min, I_50 min, IR_3.8 h, and IR_5.3 h groups; In old RNA-based analysis, n = 54, 708, 44, 19, and 32 cells for NC, I_30 min, I_50 min, IR_3.8 h, and IR_5.3 h groups. Data shown as mean ± SD. l Signaling pathway role heatmap showing THBS signaling pathway network in Fib, C1q- Macro, C1q+ Macro, and H-PST cells. Source data are provided as a Source Data file.

    Journal: Nature Communications

    Article Title: Dyna-vivo-seq unveils cellular RNA dynamics during acute kidney injury via in vivo metabolic RNA labeling-based scRNA-seq

    doi: 10.1038/s41467-024-54202-4

    Figure Lengend Snippet: a UMAP showing PST cells from distinct time points. b UMAP showing the fraction of labeled transcripts per cell in vivo 4sU-labeled PST cells. c UMAP showing H-PST and L-PST cell clusters. UMAP visualization of H-PST cells responded to uni-IRI for distinct time points characterized by conventional splicing-based ( d ) or metabolic labeling-based RNA velocity analysis ( e ). Cells are color-coded by treatment time. The streamlines reveal the integration paths of local projections moving from the observed state to the extrapolated future state. f UMAP visualization of L-PST cells responded to uni-IRI for distinct time points characterized by metabolic labeling-based RNA velocity analysis. g Bar plot showing the expression of Havcr1 in H-PST and L-PST cells at distinct time points. n = 2240 cells for L-PST, n = 973 for H-PST. Data shown as mean ± SD. h Phase portraits showing total-new RNA planes of Havcr1 . i UMAP plots colored by smoothed total RNA level based on local averaging. The regulon activity of transcription factors Jun ( j ) and Cebpb ( k ) along with the AKI progression. In new RNA-based analysis, n = 114, 870, 79, 241, and 251 cells for NC, I_30 min, I_50 min, IR_3.8 h, and IR_5.3 h groups; In old RNA-based analysis, n = 54, 708, 44, 19, and 32 cells for NC, I_30 min, I_50 min, IR_3.8 h, and IR_5.3 h groups. Data shown as mean ± SD. l Signaling pathway role heatmap showing THBS signaling pathway network in Fib, C1q- Macro, C1q+ Macro, and H-PST cells. Source data are provided as a Source Data file.

    Article Snippet: The barcoded beads were then resuspended in a reverse transcription mix, consisting of 1× RT buffer, 1 mM dNTP (TransGen Biotech, cat# AD101-12), 2.5 μM Template Switch Oligo (Sangon, 5’-AAGCAGTGGTATCAACGCAGAGTGAATrGrGrG-3’), 1U/μL Recombination RNase Inhibitor (TaKaRa, cat# 2313 A), 10 U/μL reverse transcription enzyme (Thermo Fisher, cat# EP0753), 1 mM GTP (Thermo Fisher, cat# R0461), and 5% PEG-8000 (Beyotime, cat# R0056).

    Techniques: Labeling, In Vivo, Expressing, Activity Assay