Sequencing:Article Title: Metabolic reprogramming of macrophage-specific transketolase orchestrates angiogenesis in diabetic wounds
Article Snippet: .. Cluster generation was performed on a cBot system, followed by paired-end sequencing (2 × 150bp) on an Illumina NovaSeq 6000 platformusing the TruSeq RNA Sample Preparation Kit. ..
Article Title: Hearing Loss and Parkinson's Disease: Insights From Human and Animal Studies
Article Snippet: RNA integrity and concentration were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). .. High‐quality RNA samples were used to construct sequencing libraries with the TruSeq RNA Sample Preparation Kit (Illumina, USA). .. Libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150 bp paired‐end reads.
Sample Prep:Article Title: Metabolic reprogramming of macrophage-specific transketolase orchestrates angiogenesis in diabetic wounds
Article Snippet: .. Cluster generation was performed on a cBot system, followed by paired-end sequencing (2 × 150bp) on an Illumina NovaSeq 6000 platformusing the TruSeq RNA Sample Preparation Kit. ..
Article Title: Hearing Loss and Parkinson's Disease: Insights From Human and Animal Studies
Article Snippet: RNA integrity and concentration were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). .. High‐quality RNA samples were used to construct sequencing libraries with the TruSeq RNA Sample Preparation Kit (Illumina, USA). .. Libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150 bp paired‐end reads.
Article Title: SF3B1 mutation generates novel peptides from long non-coding RNAs
Article Snippet: .. Libraries were prepared using the TruSeq Small RNA Sample Preparation Kit (Illumina) according to the manufacturer’s protocol, with modifications for RPFs. .. Libraries were quantified with a Bioanalyzer (Agilent Technologies) and sequenced on an Illumina NovaSeq platform to generate single-end 50 nt reads.
RNA Sequencing:
Article Title: TDP2-mediated DNA repair regulates the dynamics of neuronal early response gene transcription and cortical neuron connectivity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TruSeq RNA Library Preparation Kit v2 Illumina CatRS-122–2001 Nick translation DNA labeling system 2.0 ENZO Cat#ENZ-GEN111-0050 Go-Script Promega Cat#A2791 PowerUp SYBR Thermo Fisher Scientific Cat#A25918 Deposited data yH2AX ChIP-seq GEO GSE155095 RNA-seq in WT and Tdp2cKO mice This paper GSE305228 Raw Data Mendeley Data https://doi.org/10.17632/7rz5gb477c.1, https://doi.org/ 10.17632/7tzm667fkb.1, https://doi.org/10.17632/ 7cjjdxpkmh.1, https://doi.org/10.17632/ny2c8fz2fp.1, https://doi.org/10.17632/sjvscj5mng.1, https://doi.org/ 10.17632/tz6tm3mfb4.1 Experimental models: Cell lines NIH-3T3 ATCC CRL-1658 HEK-293T ATCC CRL-3216 Experimental models: Organisms/strains Swiss Webster mouse Jackson Laboratory Strain#000689; RRID: IMSR_JAX:000689 CamKII:Cre mouse (B6.FVB-Tg (Camk2a-cre)2Gsc/Cnrm, Cassanova et al., 200151) Jackson Laboratory IMSR#01153 TDP2fl/fl mouse for conditional knockout of TDP2 This paper N/A Oligonucleotides Primers used for RT-qPCR (see Table S1) This paper N/A Primers used for ChIP-qPCR (see Table S1) This paper N/A Primers used for mouse genotyping (see Table S1) This paper N/A Tbp primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Actb primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Cell Reports 45, 118152, October 27, 2026 19 Coulter). ..
cDNA Library Assay:
Construct:
Article Title: Hearing Loss and Parkinson's Disease: Insights From Human and Animal Studies
Article Snippet: RNA integrity and concentration were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). .. High‐quality RNA samples were used to construct sequencing libraries with the TruSeq RNA Sample Preparation Kit (Illumina, USA). .. Libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150 bp paired‐end reads.
Next-Generation Sequencing:
RNA Library Preparation:Article Title: TDP2-mediated DNA repair regulates the dynamics of neuronal early response gene transcription and cortical neuron connectivity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TruSeq RNA Library Preparation Kit v2 Illumina CatRS-122–2001 Nick translation DNA labeling system 2.0 ENZO Cat#ENZ-GEN111-0050 Go-Script Promega Cat#A2791 PowerUp SYBR Thermo Fisher Scientific Cat#A25918 Deposited data yH2AX ChIP-seq GEO GSE155095 RNA-seq in WT and Tdp2cKO mice This paper GSE305228 Raw Data Mendeley Data https://doi.org/10.17632/7rz5gb477c.1, https://doi.org/ 10.17632/7tzm667fkb.1, https://doi.org/10.17632/ 7cjjdxpkmh.1, https://doi.org/10.17632/ny2c8fz2fp.1, https://doi.org/10.17632/sjvscj5mng.1, https://doi.org/ 10.17632/tz6tm3mfb4.1 Experimental models: Cell lines NIH-3T3 ATCC CRL-1658 HEK-293T ATCC CRL-3216 Experimental models: Organisms/strains Swiss Webster mouse Jackson Laboratory Strain#000689; RRID: IMSR_JAX:000689 CamKII:Cre mouse (B6.FVB-Tg (Camk2a-cre)2Gsc/Cnrm, Cassanova et al., 200151) Jackson Laboratory IMSR#01153 TDP2fl/fl mouse for conditional knockout of TDP2 This paper N/A Oligonucleotides Primers used for RT-qPCR (see Table S1) This paper N/A Primers used for ChIP-qPCR (see Table S1) This paper N/A Primers used for mouse genotyping (see Table S1) This paper N/A Tbp primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Actb primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Cell Reports 45, 118152, October 27, 2026 19 Coulter). ..
Nick Translation:Article Title: TDP2-mediated DNA repair regulates the dynamics of neuronal early response gene transcription and cortical neuron connectivity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TruSeq RNA Library Preparation Kit v2 Illumina CatRS-122–2001 Nick translation DNA labeling system 2.0 ENZO Cat#ENZ-GEN111-0050 Go-Script Promega Cat#A2791 PowerUp SYBR Thermo Fisher Scientific Cat#A25918 Deposited data yH2AX ChIP-seq GEO GSE155095 RNA-seq in WT and Tdp2cKO mice This paper GSE305228 Raw Data Mendeley Data https://doi.org/10.17632/7rz5gb477c.1, https://doi.org/ 10.17632/7tzm667fkb.1, https://doi.org/10.17632/ 7cjjdxpkmh.1, https://doi.org/10.17632/ny2c8fz2fp.1, https://doi.org/10.17632/sjvscj5mng.1, https://doi.org/ 10.17632/tz6tm3mfb4.1 Experimental models: Cell lines NIH-3T3 ATCC CRL-1658 HEK-293T ATCC CRL-3216 Experimental models: Organisms/strains Swiss Webster mouse Jackson Laboratory Strain#000689; RRID: IMSR_JAX:000689 CamKII:Cre mouse (B6.FVB-Tg (Camk2a-cre)2Gsc/Cnrm, Cassanova et al., 200151) Jackson Laboratory IMSR#01153 TDP2fl/fl mouse for conditional knockout of TDP2 This paper N/A Oligonucleotides Primers used for RT-qPCR (see Table S1) This paper N/A Primers used for ChIP-qPCR (see Table S1) This paper N/A Primers used for mouse genotyping (see Table S1) This paper N/A Tbp primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Actb primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Cell Reports 45, 118152, October 27, 2026 19 Coulter). ..
DNA Labeling:Article Title: TDP2-mediated DNA repair regulates the dynamics of neuronal early response gene transcription and cortical neuron connectivity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TruSeq RNA Library Preparation Kit v2 Illumina CatRS-122–2001 Nick translation DNA labeling system 2.0 ENZO Cat#ENZ-GEN111-0050 Go-Script Promega Cat#A2791 PowerUp SYBR Thermo Fisher Scientific Cat#A25918 Deposited data yH2AX ChIP-seq GEO GSE155095 RNA-seq in WT and Tdp2cKO mice This paper GSE305228 Raw Data Mendeley Data https://doi.org/10.17632/7rz5gb477c.1, https://doi.org/ 10.17632/7tzm667fkb.1, https://doi.org/10.17632/ 7cjjdxpkmh.1, https://doi.org/10.17632/ny2c8fz2fp.1, https://doi.org/10.17632/sjvscj5mng.1, https://doi.org/ 10.17632/tz6tm3mfb4.1 Experimental models: Cell lines NIH-3T3 ATCC CRL-1658 HEK-293T ATCC CRL-3216 Experimental models: Organisms/strains Swiss Webster mouse Jackson Laboratory Strain#000689; RRID: IMSR_JAX:000689 CamKII:Cre mouse (B6.FVB-Tg (Camk2a-cre)2Gsc/Cnrm, Cassanova et al., 200151) Jackson Laboratory IMSR#01153 TDP2fl/fl mouse for conditional knockout of TDP2 This paper N/A Oligonucleotides Primers used for RT-qPCR (see Table S1) This paper N/A Primers used for ChIP-qPCR (see Table S1) This paper N/A Primers used for mouse genotyping (see Table S1) This paper N/A Tbp primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Actb primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Cell Reports 45, 118152, October 27, 2026 19 Coulter). ..
Chromatin Immunoprecipitation:Article Title: TDP2-mediated DNA repair regulates the dynamics of neuronal early response gene transcription and cortical neuron connectivity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TruSeq RNA Library Preparation Kit v2 Illumina CatRS-122–2001 Nick translation DNA labeling system 2.0 ENZO Cat#ENZ-GEN111-0050 Go-Script Promega Cat#A2791 PowerUp SYBR Thermo Fisher Scientific Cat#A25918 Deposited data yH2AX ChIP-seq GEO GSE155095 RNA-seq in WT and Tdp2cKO mice This paper GSE305228 Raw Data Mendeley Data https://doi.org/10.17632/7rz5gb477c.1, https://doi.org/ 10.17632/7tzm667fkb.1, https://doi.org/10.17632/ 7cjjdxpkmh.1, https://doi.org/10.17632/ny2c8fz2fp.1, https://doi.org/10.17632/sjvscj5mng.1, https://doi.org/ 10.17632/tz6tm3mfb4.1 Experimental models: Cell lines NIH-3T3 ATCC CRL-1658 HEK-293T ATCC CRL-3216 Experimental models: Organisms/strains Swiss Webster mouse Jackson Laboratory Strain#000689; RRID: IMSR_JAX:000689 CamKII:Cre mouse (B6.FVB-Tg (Camk2a-cre)2Gsc/Cnrm, Cassanova et al., 200151) Jackson Laboratory IMSR#01153 TDP2fl/fl mouse for conditional knockout of TDP2 This paper N/A Oligonucleotides Primers used for RT-qPCR (see Table S1) This paper N/A Primers used for ChIP-qPCR (see Table S1) This paper N/A Primers used for mouse genotyping (see Table S1) This paper N/A Tbp primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Actb primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Cell Reports 45, 118152, October 27, 2026 19 Coulter). ..
Gene Knockout:Article Title: TDP2-mediated DNA repair regulates the dynamics of neuronal early response gene transcription and cortical neuron connectivity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TruSeq RNA Library Preparation Kit v2 Illumina CatRS-122–2001 Nick translation DNA labeling system 2.0 ENZO Cat#ENZ-GEN111-0050 Go-Script Promega Cat#A2791 PowerUp SYBR Thermo Fisher Scientific Cat#A25918 Deposited data yH2AX ChIP-seq GEO GSE155095 RNA-seq in WT and Tdp2cKO mice This paper GSE305228 Raw Data Mendeley Data https://doi.org/10.17632/7rz5gb477c.1, https://doi.org/ 10.17632/7tzm667fkb.1, https://doi.org/10.17632/ 7cjjdxpkmh.1, https://doi.org/10.17632/ny2c8fz2fp.1, https://doi.org/10.17632/sjvscj5mng.1, https://doi.org/ 10.17632/tz6tm3mfb4.1 Experimental models: Cell lines NIH-3T3 ATCC CRL-1658 HEK-293T ATCC CRL-3216 Experimental models: Organisms/strains Swiss Webster mouse Jackson Laboratory Strain#000689; RRID: IMSR_JAX:000689 CamKII:Cre mouse (B6.FVB-Tg (Camk2a-cre)2Gsc/Cnrm, Cassanova et al., 200151) Jackson Laboratory IMSR#01153 TDP2fl/fl mouse for conditional knockout of TDP2 This paper N/A Oligonucleotides Primers used for RT-qPCR (see Table S1) This paper N/A Primers used for ChIP-qPCR (see Table S1) This paper N/A Primers used for mouse genotyping (see Table S1) This paper N/A Tbp primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Actb primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Cell Reports 45, 118152, October 27, 2026 19 Coulter). ..
Quantitative RT-PCR:Article Title: TDP2-mediated DNA repair regulates the dynamics of neuronal early response gene transcription and cortical neuron connectivity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TruSeq RNA Library Preparation Kit v2 Illumina CatRS-122–2001 Nick translation DNA labeling system 2.0 ENZO Cat#ENZ-GEN111-0050 Go-Script Promega Cat#A2791 PowerUp SYBR Thermo Fisher Scientific Cat#A25918 Deposited data yH2AX ChIP-seq GEO GSE155095 RNA-seq in WT and Tdp2cKO mice This paper GSE305228 Raw Data Mendeley Data https://doi.org/10.17632/7rz5gb477c.1, https://doi.org/ 10.17632/7tzm667fkb.1, https://doi.org/10.17632/ 7cjjdxpkmh.1, https://doi.org/10.17632/ny2c8fz2fp.1, https://doi.org/10.17632/sjvscj5mng.1, https://doi.org/ 10.17632/tz6tm3mfb4.1 Experimental models: Cell lines NIH-3T3 ATCC CRL-1658 HEK-293T ATCC CRL-3216 Experimental models: Organisms/strains Swiss Webster mouse Jackson Laboratory Strain#000689; RRID: IMSR_JAX:000689 CamKII:Cre mouse (B6.FVB-Tg (Camk2a-cre)2Gsc/Cnrm, Cassanova et al., 200151) Jackson Laboratory IMSR#01153 TDP2fl/fl mouse for conditional knockout of TDP2 This paper N/A Oligonucleotides Primers used for RT-qPCR (see Table S1) This paper N/A Primers used for ChIP-qPCR (see Table S1) This paper N/A Primers used for mouse genotyping (see Table S1) This paper N/A Tbp primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Actb primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Cell Reports 45, 118152, October 27, 2026 19 Coulter). ..
ChIP-qPCR:Article Title: TDP2-mediated DNA repair regulates the dynamics of neuronal early response gene transcription and cortical neuron connectivity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TruSeq RNA Library Preparation Kit v2 Illumina CatRS-122–2001 Nick translation DNA labeling system 2.0 ENZO Cat#ENZ-GEN111-0050 Go-Script Promega Cat#A2791 PowerUp SYBR Thermo Fisher Scientific Cat#A25918 Deposited data yH2AX ChIP-seq GEO GSE155095 RNA-seq in WT and Tdp2cKO mice This paper GSE305228 Raw Data Mendeley Data https://doi.org/10.17632/7rz5gb477c.1, https://doi.org/ 10.17632/7tzm667fkb.1, https://doi.org/10.17632/ 7cjjdxpkmh.1, https://doi.org/10.17632/ny2c8fz2fp.1, https://doi.org/10.17632/sjvscj5mng.1, https://doi.org/ 10.17632/tz6tm3mfb4.1 Experimental models: Cell lines NIH-3T3 ATCC CRL-1658 HEK-293T ATCC CRL-3216 Experimental models: Organisms/strains Swiss Webster mouse Jackson Laboratory Strain#000689; RRID: IMSR_JAX:000689 CamKII:Cre mouse (B6.FVB-Tg (Camk2a-cre)2Gsc/Cnrm, Cassanova et al., 200151) Jackson Laboratory IMSR#01153 TDP2fl/fl mouse for conditional knockout of TDP2 This paper N/A Oligonucleotides Primers used for RT-qPCR (see Table S1) This paper N/A Primers used for ChIP-qPCR (see Table S1) This paper N/A Primers used for mouse genotyping (see Table S1) This paper N/A Tbp primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Actb primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Cell Reports 45, 118152, October 27, 2026 19 Coulter). ..
Genotyping:Article Title: TDP2-mediated DNA repair regulates the dynamics of neuronal early response gene transcription and cortical neuron connectivity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER TruSeq RNA Library Preparation Kit v2 Illumina CatRS-122–2001 Nick translation DNA labeling system 2.0 ENZO Cat#ENZ-GEN111-0050 Go-Script Promega Cat#A2791 PowerUp SYBR Thermo Fisher Scientific Cat#A25918 Deposited data yH2AX ChIP-seq GEO GSE155095 RNA-seq in WT and Tdp2cKO mice This paper GSE305228 Raw Data Mendeley Data https://doi.org/10.17632/7rz5gb477c.1, https://doi.org/ 10.17632/7tzm667fkb.1, https://doi.org/10.17632/ 7cjjdxpkmh.1, https://doi.org/10.17632/ny2c8fz2fp.1, https://doi.org/10.17632/sjvscj5mng.1, https://doi.org/ 10.17632/tz6tm3mfb4.1 Experimental models: Cell lines NIH-3T3 ATCC CRL-1658 HEK-293T ATCC CRL-3216 Experimental models: Organisms/strains Swiss Webster mouse Jackson Laboratory Strain#000689; RRID: IMSR_JAX:000689 CamKII:Cre mouse (B6.FVB-Tg (Camk2a-cre)2Gsc/Cnrm, Cassanova et al., 200151) Jackson Laboratory IMSR#01153 TDP2fl/fl mouse for conditional knockout of TDP2 This paper N/A Oligonucleotides Primers used for RT-qPCR (see Table S1) This paper N/A Primers used for ChIP-qPCR (see Table S1) This paper N/A Primers used for mouse genotyping (see Table S1) This paper N/A Tbp primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Actb primer assay, ready-made 20X primer mix Integrated DNA Technologies N/A Cell Reports 45, 118152, October 27, 2026 19 Coulter). ..
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