cDNA Synthesis:
Article Title: Processing of lysophosphatidylcholines by ExoU secreted by P. aeruginosa leads to inflammasome activation and cell death.
Article Snippet: RNA extraction and quantitative reverse transcription PCR (RT-qPCR) analysis THP-1 macrophages and THP-1 monocytes were infected with PA14, PA14 exoU::tn, PAO1+vector, and PAO1+ExoU for 1 h. RNA extractions were conducted using an RNeasy Mini Kit (Qiagen, 74004) and eluted RNA was stored at -80◦C prior to use. .. cDNA was synthesized using the iScript cDNA Synthesis Kit (Bio-Rad, 1708890). .. Quantitative real-time PCR (qPCR) reactions were conducted in triplicates with a total volume of 20 μl per reaction using: 2 μl cDNA, 10 μl SYBR green PCR master mix (Bio-Rad), and 100 pmol of forward and reverse primers.
Article Title: Disruption of local CTCF binding impairs renin expression and blood pressure response in Dahl salt-sensitive rats.
Article Snippet: 1 in Dahl salt-sensitive rats 2 Mark Vanden Avond, Michael N. Grzybowski, Terry Kurth, Chun Yang, Jason Klotz, Ana 3 Hantke Guixa, Andrew Greene, Sridhar Rao, Qiongzi Qiu, Pengyuan Liu 7, , Yong Liu, 4 Mingyu Liang, Allen W. Cowley Jr., Aron M. Geurts 5 Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA 6 The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA 7 Department of Pediatrics, Division of Hematology, Oncology, and Bone Marrow 8 Transplantation, Medical College of Wisconsin, Milwaukee, WI, USA.. 9 Versiti Blood Research Institute, Milwaukee, WI, USA.. 10 Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 11 Milwaukee, WI, USA.
Article Title: Salivary miRNAs along with p53 and EGFR in oral exfoliated cells: a pilot study on candidate noninvasive biomarkers for the early detection of oral cancer in tobacco users.
Article Snippet: 1 Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, Haryana 124001, India 2 Swami Shraddhanand College, University of Delhi, New Delhi 110036, India 3 Dept.. of Oral Pathology, Postgraduate Institute of Dental Sciences, Rohtak, Haryana 124001, India Abstract Background The low 5-year survival rate for Oral Squamous Cell Carcinoma (OSCC) is largely attributed to the limitations of current invasive diagnostic procedures and diagnosis at a late stage.. Biomarkers from saliva and exfoliated oral cells could be used to diagnose oral cancer as the malignancy begins in the epithelium and would be particularly useful for screening patients in high-risk categories like tobacco users.
Article Title: Macrophages modulate ovarian cancer progression by regulating epithelial-mesenchymal transition.
Article Snippet: The isolated RNA was dissolved in nuclease-free water and quantified using a NanoDrop spectrophotometer (Implen). .. cDNA synthesis was carried out using the iScript cDNA Synthesis Kit (Bio-Rad, Cat. No. 1708890) according to the manufacturer’s instructions under the following cycling conditions: 25 ◦C for 5 min, 46 ◦C for 20 min, and 95 ◦C for 5 min. Quantitative PCR was performed using SYBR Green Supermix (Bio-Rad, Cat. No. 171–5121) on the QuantStudio 5 Real-Time PCR System. .. The expression levels of M1 and M2 markers (CD206, CD163, ARG1, iNOS and CD86) whereas EMT-related genes (E-cadherin, N-cadherin, Snail, Slug, MMP-2, Twist, Vimentin, and ZEB) were analysed, with GAPDH serving as the endogenous control.
Article Title: Aire is a cell-intrinsic regulator of natural IgM-secreting cells.
Article Snippet: Flowjo 10 (Trees- tar) software was used for analysis. .. REAGENT or RESOURCE SOURCE IDENTIFIER iScript cDNA Synthesis BioRad Cat# 1708890 TaqMan Fast Advanced Master Mix Thermo Fisher Scientific Cat# 4444557 NEBNext Ultra II New England Biolabs Cat# E7103L OneStep Ahead RT- PCR kit Qiagen Cat# 220211 Deposited data Single cell RNA-seq analysis of mature thymic epithelial cells Sansom et al. GEO: GSE53111 Differential features of Aire-induced and Aire-independent promiscuous gene expression in thymic epithelial cells St. Pierre et al. GEO: GSE65617 RNA sequencing of Aire-reporter-positive CD138+IgM+ cells from Aire+/+ and Aire–/– Aire-HCO mice This paper GEO: GSE310317 Bulk immunoglobulin heavy-chain repertoire sequencing This paper GEO: GSE332886 Experimental models: Organisms/strains Mus musculus (BALB/c): Aire- HCOTG: Aire-HCO4 Aschenbrenner et al.81 N/A Mus musculus (C57BL/6): AdigTG: Tg(Aire-G6pc2/GFP)1Mand Gardner et al.18 N/A Mus musculus (C57BL/6): Tcra -/-: Tcratm1Mom Mombaerts et al.82 N/A Mus musculus (C57BL/6): Cd40-/-: B6.129P2-Cd40tm1Kik/J Kawabe et al.83 N/A Mus musculus (C57BL/6): Airef/f: B6.Cg-Airetm1Dfil/J Dobes et al.52 N/A Mus musculus(BALB/c): Ciita-/-: C.129S2(B6)-Ciitatm1Ccum/J Chang et al.84 N/A Mus musculus (C57BL/6): Mb1-Cre: Cd79atm1(cre)Reth Hobeika et al.53 N/A Mus musculus (C57BL/6): Foxn1-Cre: Tg(Foxn1-cre)8Ghr Rossi et al.54 N/A Mus musculus (C57BL/6); Aire-/-; B6.129S2-Airetm1.1Doi Anderson et al.2 N/A Mus musculus (BALB/c): Aire-/-: C.Cg-Airetm1Pltn Ramsey et al.3 N/A Software and algorithms FlowJo software 10.7.2 Tree Star https://www.flowjo.com GraphPad PRISM 7.0 Graphpad Software https://www.graphpad.com/ NDP.view2 Hamamatsu Photonics https://www.hamamatsu.com/ Image J National Institute of Health https://imagej.net/ LEGENDplex Data Analysis Software Suite BioLegend https://www.biolegend.com/ ll OPEN ACCESS Article e3 Immunity 59, 1–19.e1–e6, December 8, 2026 .. Total RNA was isolated using the RNeasy RNA Isolation Kit (Qiagen).
Reverse Transcription:
Article Title: Disruption of local CTCF binding impairs renin expression and blood pressure response in Dahl salt-sensitive rats.
Article Snippet: 1 in Dahl salt-sensitive rats 2 Mark Vanden Avond, Michael N. Grzybowski, Terry Kurth, Chun Yang, Jason Klotz, Ana 3 Hantke Guixa, Andrew Greene, Sridhar Rao, Qiongzi Qiu, Pengyuan Liu 7, , Yong Liu, 4 Mingyu Liang, Allen W. Cowley Jr., Aron M. Geurts 5 Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA 6 The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA 7 Department of Pediatrics, Division of Hematology, Oncology, and Bone Marrow 8 Transplantation, Medical College of Wisconsin, Milwaukee, WI, USA.. 9 Versiti Blood Research Institute, Milwaukee, WI, USA.. 10 Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 11 Milwaukee, WI, USA.
Synthesized:Article Title: Processing of lysophosphatidylcholines by ExoU secreted by P. aeruginosa leads to inflammasome activation and cell death.
Article Snippet: RNA extraction and quantitative reverse transcription PCR (RT-qPCR) analysis THP-1 macrophages and THP-1 monocytes were infected with PA14, PA14 exoU::tn, PAO1+vector, and PAO1+ExoU for 1 h. RNA extractions were conducted using an RNeasy Mini Kit (Qiagen, 74004) and eluted RNA was stored at -80◦C prior to use. .. cDNA was synthesized using the iScript cDNA Synthesis Kit (Bio-Rad, 1708890). .. Quantitative real-time PCR (qPCR) reactions were conducted in triplicates with a total volume of 20 μl per reaction using: 2 μl cDNA, 10 μl SYBR green PCR master mix (Bio-Rad), and 100 pmol of forward and reverse primers.
Real-time Polymerase Chain Reaction:Article Title: Disruption of local CTCF binding impairs renin expression and blood pressure response in Dahl salt-sensitive rats.
Article Snippet: 1 in Dahl salt-sensitive rats 2 Mark Vanden Avond, Michael N. Grzybowski, Terry Kurth, Chun Yang, Jason Klotz, Ana 3 Hantke Guixa, Andrew Greene, Sridhar Rao, Qiongzi Qiu, Pengyuan Liu 7, , Yong Liu, 4 Mingyu Liang, Allen W. Cowley Jr., Aron M. Geurts 5 Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA 6 The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA 7 Department of Pediatrics, Division of Hematology, Oncology, and Bone Marrow 8 Transplantation, Medical College of Wisconsin, Milwaukee, WI, USA.. 9 Versiti Blood Research Institute, Milwaukee, WI, USA.. 10 Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 11 Milwaukee, WI, USA.
Article Title: Macrophages modulate ovarian cancer progression by regulating epithelial-mesenchymal transition.
Article Snippet: The isolated RNA was dissolved in nuclease-free water and quantified using a NanoDrop spectrophotometer (Implen). .. cDNA synthesis was carried out using the iScript cDNA Synthesis Kit (Bio-Rad, Cat. No. 1708890) according to the manufacturer’s instructions under the following cycling conditions: 25 ◦C for 5 min, 46 ◦C for 20 min, and 95 ◦C for 5 min. Quantitative PCR was performed using SYBR Green Supermix (Bio-Rad, Cat. No. 171–5121) on the QuantStudio 5 Real-Time PCR System. .. The expression levels of M1 and M2 markers (CD206, CD163, ARG1, iNOS and CD86) whereas EMT-related genes (E-cadherin, N-cadherin, Snail, Slug, MMP-2, Twist, Vimentin, and ZEB) were analysed, with GAPDH serving as the endogenous control.
Incubation:Article Title: Salivary miRNAs along with p53 and EGFR in oral exfoliated cells: a pilot study on candidate noninvasive biomarkers for the early detection of oral cancer in tobacco users.
Article Snippet: 1 Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, Haryana 124001, India 2 Swami Shraddhanand College, University of Delhi, New Delhi 110036, India 3 Dept.. of Oral Pathology, Postgraduate Institute of Dental Sciences, Rohtak, Haryana 124001, India Abstract Background The low 5-year survival rate for Oral Squamous Cell Carcinoma (OSCC) is largely attributed to the limitations of current invasive diagnostic procedures and diagnosis at a late stage.. Biomarkers from saliva and exfoliated oral cells could be used to diagnose oral cancer as the malignancy begins in the epithelium and would be particularly useful for screening patients in high-risk categories like tobacco users.
SYBR Green Assay:Article Title: Macrophages modulate ovarian cancer progression by regulating epithelial-mesenchymal transition.
Article Snippet: The isolated RNA was dissolved in nuclease-free water and quantified using a NanoDrop spectrophotometer (Implen). .. cDNA synthesis was carried out using the iScript cDNA Synthesis Kit (Bio-Rad, Cat. No. 1708890) according to the manufacturer’s instructions under the following cycling conditions: 25 ◦C for 5 min, 46 ◦C for 20 min, and 95 ◦C for 5 min. Quantitative PCR was performed using SYBR Green Supermix (Bio-Rad, Cat. No. 171–5121) on the QuantStudio 5 Real-Time PCR System. .. The expression levels of M1 and M2 markers (CD206, CD163, ARG1, iNOS and CD86) whereas EMT-related genes (E-cadherin, N-cadherin, Snail, Slug, MMP-2, Twist, Vimentin, and ZEB) were analysed, with GAPDH serving as the endogenous control.
Reverse Transcription Polymerase Chain Reaction:Article Title: Aire is a cell-intrinsic regulator of natural IgM-secreting cells.
Article Snippet: Flowjo 10 (Trees- tar) software was used for analysis. .. REAGENT or RESOURCE SOURCE IDENTIFIER iScript cDNA Synthesis BioRad Cat# 1708890 TaqMan Fast Advanced Master Mix Thermo Fisher Scientific Cat# 4444557 NEBNext Ultra II New England Biolabs Cat# E7103L OneStep Ahead RT- PCR kit Qiagen Cat# 220211 Deposited data Single cell RNA-seq analysis of mature thymic epithelial cells Sansom et al. GEO: GSE53111 Differential features of Aire-induced and Aire-independent promiscuous gene expression in thymic epithelial cells St. Pierre et al. GEO: GSE65617 RNA sequencing of Aire-reporter-positive CD138+IgM+ cells from Aire+/+ and Aire–/– Aire-HCO mice This paper GEO: GSE310317 Bulk immunoglobulin heavy-chain repertoire sequencing This paper GEO: GSE332886 Experimental models: Organisms/strains Mus musculus (BALB/c): Aire- HCOTG: Aire-HCO4 Aschenbrenner et al.81 N/A Mus musculus (C57BL/6): AdigTG: Tg(Aire-G6pc2/GFP)1Mand Gardner et al.18 N/A Mus musculus (C57BL/6): Tcra -/-: Tcratm1Mom Mombaerts et al.82 N/A Mus musculus (C57BL/6): Cd40-/-: B6.129P2-Cd40tm1Kik/J Kawabe et al.83 N/A Mus musculus (C57BL/6): Airef/f: B6.Cg-Airetm1Dfil/J Dobes et al.52 N/A Mus musculus(BALB/c): Ciita-/-: C.129S2(B6)-Ciitatm1Ccum/J Chang et al.84 N/A Mus musculus (C57BL/6): Mb1-Cre: Cd79atm1(cre)Reth Hobeika et al.53 N/A Mus musculus (C57BL/6): Foxn1-Cre: Tg(Foxn1-cre)8Ghr Rossi et al.54 N/A Mus musculus (C57BL/6); Aire-/-; B6.129S2-Airetm1.1Doi Anderson et al.2 N/A Mus musculus (BALB/c): Aire-/-: C.Cg-Airetm1Pltn Ramsey et al.3 N/A Software and algorithms FlowJo software 10.7.2 Tree Star https://www.flowjo.com GraphPad PRISM 7.0 Graphpad Software https://www.graphpad.com/ NDP.view2 Hamamatsu Photonics https://www.hamamatsu.com/ Image J National Institute of Health https://imagej.net/ LEGENDplex Data Analysis Software Suite BioLegend https://www.biolegend.com/ ll OPEN ACCESS Article e3 Immunity 59, 1–19.e1–e6, December 8, 2026 .. Total RNA was isolated using the RNeasy RNA Isolation Kit (Qiagen).
Single Cell RNA-Seq:Article Title: Aire is a cell-intrinsic regulator of natural IgM-secreting cells.
Article Snippet: Flowjo 10 (Trees- tar) software was used for analysis. .. REAGENT or RESOURCE SOURCE IDENTIFIER iScript cDNA Synthesis BioRad Cat# 1708890 TaqMan Fast Advanced Master Mix Thermo Fisher Scientific Cat# 4444557 NEBNext Ultra II New England Biolabs Cat# E7103L OneStep Ahead RT- PCR kit Qiagen Cat# 220211 Deposited data Single cell RNA-seq analysis of mature thymic epithelial cells Sansom et al. GEO: GSE53111 Differential features of Aire-induced and Aire-independent promiscuous gene expression in thymic epithelial cells St. Pierre et al. GEO: GSE65617 RNA sequencing of Aire-reporter-positive CD138+IgM+ cells from Aire+/+ and Aire–/– Aire-HCO mice This paper GEO: GSE310317 Bulk immunoglobulin heavy-chain repertoire sequencing This paper GEO: GSE332886 Experimental models: Organisms/strains Mus musculus (BALB/c): Aire- HCOTG: Aire-HCO4 Aschenbrenner et al.81 N/A Mus musculus (C57BL/6): AdigTG: Tg(Aire-G6pc2/GFP)1Mand Gardner et al.18 N/A Mus musculus (C57BL/6): Tcra -/-: Tcratm1Mom Mombaerts et al.82 N/A Mus musculus (C57BL/6): Cd40-/-: B6.129P2-Cd40tm1Kik/J Kawabe et al.83 N/A Mus musculus (C57BL/6): Airef/f: B6.Cg-Airetm1Dfil/J Dobes et al.52 N/A Mus musculus(BALB/c): Ciita-/-: C.129S2(B6)-Ciitatm1Ccum/J Chang et al.84 N/A Mus musculus (C57BL/6): Mb1-Cre: Cd79atm1(cre)Reth Hobeika et al.53 N/A Mus musculus (C57BL/6): Foxn1-Cre: Tg(Foxn1-cre)8Ghr Rossi et al.54 N/A Mus musculus (C57BL/6); Aire-/-; B6.129S2-Airetm1.1Doi Anderson et al.2 N/A Mus musculus (BALB/c): Aire-/-: C.Cg-Airetm1Pltn Ramsey et al.3 N/A Software and algorithms FlowJo software 10.7.2 Tree Star https://www.flowjo.com GraphPad PRISM 7.0 Graphpad Software https://www.graphpad.com/ NDP.view2 Hamamatsu Photonics https://www.hamamatsu.com/ Image J National Institute of Health https://imagej.net/ LEGENDplex Data Analysis Software Suite BioLegend https://www.biolegend.com/ ll OPEN ACCESS Article e3 Immunity 59, 1–19.e1–e6, December 8, 2026 .. Total RNA was isolated using the RNeasy RNA Isolation Kit (Qiagen).
Analysis:Article Title: Aire is a cell-intrinsic regulator of natural IgM-secreting cells.
Article Snippet: Flowjo 10 (Trees- tar) software was used for analysis. .. REAGENT or RESOURCE SOURCE IDENTIFIER iScript cDNA Synthesis BioRad Cat# 1708890 TaqMan Fast Advanced Master Mix Thermo Fisher Scientific Cat# 4444557 NEBNext Ultra II New England Biolabs Cat# E7103L OneStep Ahead RT- PCR kit Qiagen Cat# 220211 Deposited data Single cell RNA-seq analysis of mature thymic epithelial cells Sansom et al. GEO: GSE53111 Differential features of Aire-induced and Aire-independent promiscuous gene expression in thymic epithelial cells St. Pierre et al. GEO: GSE65617 RNA sequencing of Aire-reporter-positive CD138+IgM+ cells from Aire+/+ and Aire–/– Aire-HCO mice This paper GEO: GSE310317 Bulk immunoglobulin heavy-chain repertoire sequencing This paper GEO: GSE332886 Experimental models: Organisms/strains Mus musculus (BALB/c): Aire- HCOTG: Aire-HCO4 Aschenbrenner et al.81 N/A Mus musculus (C57BL/6): AdigTG: Tg(Aire-G6pc2/GFP)1Mand Gardner et al.18 N/A Mus musculus (C57BL/6): Tcra -/-: Tcratm1Mom Mombaerts et al.82 N/A Mus musculus (C57BL/6): Cd40-/-: B6.129P2-Cd40tm1Kik/J Kawabe et al.83 N/A Mus musculus (C57BL/6): Airef/f: B6.Cg-Airetm1Dfil/J Dobes et al.52 N/A Mus musculus(BALB/c): Ciita-/-: C.129S2(B6)-Ciitatm1Ccum/J Chang et al.84 N/A Mus musculus (C57BL/6): Mb1-Cre: Cd79atm1(cre)Reth Hobeika et al.53 N/A Mus musculus (C57BL/6): Foxn1-Cre: Tg(Foxn1-cre)8Ghr Rossi et al.54 N/A Mus musculus (C57BL/6); Aire-/-; B6.129S2-Airetm1.1Doi Anderson et al.2 N/A Mus musculus (BALB/c): Aire-/-: C.Cg-Airetm1Pltn Ramsey et al.3 N/A Software and algorithms FlowJo software 10.7.2 Tree Star https://www.flowjo.com GraphPad PRISM 7.0 Graphpad Software https://www.graphpad.com/ NDP.view2 Hamamatsu Photonics https://www.hamamatsu.com/ Image J National Institute of Health https://imagej.net/ LEGENDplex Data Analysis Software Suite BioLegend https://www.biolegend.com/ ll OPEN ACCESS Article e3 Immunity 59, 1–19.e1–e6, December 8, 2026 .. Total RNA was isolated using the RNeasy RNA Isolation Kit (Qiagen).
Gene Expression:Article Title: Aire is a cell-intrinsic regulator of natural IgM-secreting cells.
Article Snippet: Flowjo 10 (Trees- tar) software was used for analysis. .. REAGENT or RESOURCE SOURCE IDENTIFIER iScript cDNA Synthesis BioRad Cat# 1708890 TaqMan Fast Advanced Master Mix Thermo Fisher Scientific Cat# 4444557 NEBNext Ultra II New England Biolabs Cat# E7103L OneStep Ahead RT- PCR kit Qiagen Cat# 220211 Deposited data Single cell RNA-seq analysis of mature thymic epithelial cells Sansom et al. GEO: GSE53111 Differential features of Aire-induced and Aire-independent promiscuous gene expression in thymic epithelial cells St. Pierre et al. GEO: GSE65617 RNA sequencing of Aire-reporter-positive CD138+IgM+ cells from Aire+/+ and Aire–/– Aire-HCO mice This paper GEO: GSE310317 Bulk immunoglobulin heavy-chain repertoire sequencing This paper GEO: GSE332886 Experimental models: Organisms/strains Mus musculus (BALB/c): Aire- HCOTG: Aire-HCO4 Aschenbrenner et al.81 N/A Mus musculus (C57BL/6): AdigTG: Tg(Aire-G6pc2/GFP)1Mand Gardner et al.18 N/A Mus musculus (C57BL/6): Tcra -/-: Tcratm1Mom Mombaerts et al.82 N/A Mus musculus (C57BL/6): Cd40-/-: B6.129P2-Cd40tm1Kik/J Kawabe et al.83 N/A Mus musculus (C57BL/6): Airef/f: B6.Cg-Airetm1Dfil/J Dobes et al.52 N/A Mus musculus(BALB/c): Ciita-/-: C.129S2(B6)-Ciitatm1Ccum/J Chang et al.84 N/A Mus musculus (C57BL/6): Mb1-Cre: Cd79atm1(cre)Reth Hobeika et al.53 N/A Mus musculus (C57BL/6): Foxn1-Cre: Tg(Foxn1-cre)8Ghr Rossi et al.54 N/A Mus musculus (C57BL/6); Aire-/-; B6.129S2-Airetm1.1Doi Anderson et al.2 N/A Mus musculus (BALB/c): Aire-/-: C.Cg-Airetm1Pltn Ramsey et al.3 N/A Software and algorithms FlowJo software 10.7.2 Tree Star https://www.flowjo.com GraphPad PRISM 7.0 Graphpad Software https://www.graphpad.com/ NDP.view2 Hamamatsu Photonics https://www.hamamatsu.com/ Image J National Institute of Health https://imagej.net/ LEGENDplex Data Analysis Software Suite BioLegend https://www.biolegend.com/ ll OPEN ACCESS Article e3 Immunity 59, 1–19.e1–e6, December 8, 2026 .. Total RNA was isolated using the RNeasy RNA Isolation Kit (Qiagen).
RNA Sequencing:Article Title: Aire is a cell-intrinsic regulator of natural IgM-secreting cells.
Article Snippet: Flowjo 10 (Trees- tar) software was used for analysis. .. REAGENT or RESOURCE SOURCE IDENTIFIER iScript cDNA Synthesis BioRad Cat# 1708890 TaqMan Fast Advanced Master Mix Thermo Fisher Scientific Cat# 4444557 NEBNext Ultra II New England Biolabs Cat# E7103L OneStep Ahead RT- PCR kit Qiagen Cat# 220211 Deposited data Single cell RNA-seq analysis of mature thymic epithelial cells Sansom et al. GEO: GSE53111 Differential features of Aire-induced and Aire-independent promiscuous gene expression in thymic epithelial cells St. Pierre et al. GEO: GSE65617 RNA sequencing of Aire-reporter-positive CD138+IgM+ cells from Aire+/+ and Aire–/– Aire-HCO mice This paper GEO: GSE310317 Bulk immunoglobulin heavy-chain repertoire sequencing This paper GEO: GSE332886 Experimental models: Organisms/strains Mus musculus (BALB/c): Aire- HCOTG: Aire-HCO4 Aschenbrenner et al.81 N/A Mus musculus (C57BL/6): AdigTG: Tg(Aire-G6pc2/GFP)1Mand Gardner et al.18 N/A Mus musculus (C57BL/6): Tcra -/-: Tcratm1Mom Mombaerts et al.82 N/A Mus musculus (C57BL/6): Cd40-/-: B6.129P2-Cd40tm1Kik/J Kawabe et al.83 N/A Mus musculus (C57BL/6): Airef/f: B6.Cg-Airetm1Dfil/J Dobes et al.52 N/A Mus musculus(BALB/c): Ciita-/-: C.129S2(B6)-Ciitatm1Ccum/J Chang et al.84 N/A Mus musculus (C57BL/6): Mb1-Cre: Cd79atm1(cre)Reth Hobeika et al.53 N/A Mus musculus (C57BL/6): Foxn1-Cre: Tg(Foxn1-cre)8Ghr Rossi et al.54 N/A Mus musculus (C57BL/6); Aire-/-; B6.129S2-Airetm1.1Doi Anderson et al.2 N/A Mus musculus (BALB/c): Aire-/-: C.Cg-Airetm1Pltn Ramsey et al.3 N/A Software and algorithms FlowJo software 10.7.2 Tree Star https://www.flowjo.com GraphPad PRISM 7.0 Graphpad Software https://www.graphpad.com/ NDP.view2 Hamamatsu Photonics https://www.hamamatsu.com/ Image J National Institute of Health https://imagej.net/ LEGENDplex Data Analysis Software Suite BioLegend https://www.biolegend.com/ ll OPEN ACCESS Article e3 Immunity 59, 1–19.e1–e6, December 8, 2026 .. Total RNA was isolated using the RNeasy RNA Isolation Kit (Qiagen).
Sequencing:Article Title: Aire is a cell-intrinsic regulator of natural IgM-secreting cells.
Article Snippet: Flowjo 10 (Trees- tar) software was used for analysis. .. REAGENT or RESOURCE SOURCE IDENTIFIER iScript cDNA Synthesis BioRad Cat# 1708890 TaqMan Fast Advanced Master Mix Thermo Fisher Scientific Cat# 4444557 NEBNext Ultra II New England Biolabs Cat# E7103L OneStep Ahead RT- PCR kit Qiagen Cat# 220211 Deposited data Single cell RNA-seq analysis of mature thymic epithelial cells Sansom et al. GEO: GSE53111 Differential features of Aire-induced and Aire-independent promiscuous gene expression in thymic epithelial cells St. Pierre et al. GEO: GSE65617 RNA sequencing of Aire-reporter-positive CD138+IgM+ cells from Aire+/+ and Aire–/– Aire-HCO mice This paper GEO: GSE310317 Bulk immunoglobulin heavy-chain repertoire sequencing This paper GEO: GSE332886 Experimental models: Organisms/strains Mus musculus (BALB/c): Aire- HCOTG: Aire-HCO4 Aschenbrenner et al.81 N/A Mus musculus (C57BL/6): AdigTG: Tg(Aire-G6pc2/GFP)1Mand Gardner et al.18 N/A Mus musculus (C57BL/6): Tcra -/-: Tcratm1Mom Mombaerts et al.82 N/A Mus musculus (C57BL/6): Cd40-/-: B6.129P2-Cd40tm1Kik/J Kawabe et al.83 N/A Mus musculus (C57BL/6): Airef/f: B6.Cg-Airetm1Dfil/J Dobes et al.52 N/A Mus musculus(BALB/c): Ciita-/-: C.129S2(B6)-Ciitatm1Ccum/J Chang et al.84 N/A Mus musculus (C57BL/6): Mb1-Cre: Cd79atm1(cre)Reth Hobeika et al.53 N/A Mus musculus (C57BL/6): Foxn1-Cre: Tg(Foxn1-cre)8Ghr Rossi et al.54 N/A Mus musculus (C57BL/6); Aire-/-; B6.129S2-Airetm1.1Doi Anderson et al.2 N/A Mus musculus (BALB/c): Aire-/-: C.Cg-Airetm1Pltn Ramsey et al.3 N/A Software and algorithms FlowJo software 10.7.2 Tree Star https://www.flowjo.com GraphPad PRISM 7.0 Graphpad Software https://www.graphpad.com/ NDP.view2 Hamamatsu Photonics https://www.hamamatsu.com/ Image J National Institute of Health https://imagej.net/ LEGENDplex Data Analysis Software Suite BioLegend https://www.biolegend.com/ ll OPEN ACCESS Article e3 Immunity 59, 1–19.e1–e6, December 8, 2026 .. Total RNA was isolated using the RNeasy RNA Isolation Kit (Qiagen).
Software:Article Title: Aire is a cell-intrinsic regulator of natural IgM-secreting cells.
Article Snippet: Flowjo 10 (Trees- tar) software was used for analysis. .. REAGENT or RESOURCE SOURCE IDENTIFIER iScript cDNA Synthesis BioRad Cat# 1708890 TaqMan Fast Advanced Master Mix Thermo Fisher Scientific Cat# 4444557 NEBNext Ultra II New England Biolabs Cat# E7103L OneStep Ahead RT- PCR kit Qiagen Cat# 220211 Deposited data Single cell RNA-seq analysis of mature thymic epithelial cells Sansom et al. GEO: GSE53111 Differential features of Aire-induced and Aire-independent promiscuous gene expression in thymic epithelial cells St. Pierre et al. GEO: GSE65617 RNA sequencing of Aire-reporter-positive CD138+IgM+ cells from Aire+/+ and Aire–/– Aire-HCO mice This paper GEO: GSE310317 Bulk immunoglobulin heavy-chain repertoire sequencing This paper GEO: GSE332886 Experimental models: Organisms/strains Mus musculus (BALB/c): Aire- HCOTG: Aire-HCO4 Aschenbrenner et al.81 N/A Mus musculus (C57BL/6): AdigTG: Tg(Aire-G6pc2/GFP)1Mand Gardner et al.18 N/A Mus musculus (C57BL/6): Tcra -/-: Tcratm1Mom Mombaerts et al.82 N/A Mus musculus (C57BL/6): Cd40-/-: B6.129P2-Cd40tm1Kik/J Kawabe et al.83 N/A Mus musculus (C57BL/6): Airef/f: B6.Cg-Airetm1Dfil/J Dobes et al.52 N/A Mus musculus(BALB/c): Ciita-/-: C.129S2(B6)-Ciitatm1Ccum/J Chang et al.84 N/A Mus musculus (C57BL/6): Mb1-Cre: Cd79atm1(cre)Reth Hobeika et al.53 N/A Mus musculus (C57BL/6): Foxn1-Cre: Tg(Foxn1-cre)8Ghr Rossi et al.54 N/A Mus musculus (C57BL/6); Aire-/-; B6.129S2-Airetm1.1Doi Anderson et al.2 N/A Mus musculus (BALB/c): Aire-/-: C.Cg-Airetm1Pltn Ramsey et al.3 N/A Software and algorithms FlowJo software 10.7.2 Tree Star https://www.flowjo.com GraphPad PRISM 7.0 Graphpad Software https://www.graphpad.com/ NDP.view2 Hamamatsu Photonics https://www.hamamatsu.com/ Image J National Institute of Health https://imagej.net/ LEGENDplex Data Analysis Software Suite BioLegend https://www.biolegend.com/ ll OPEN ACCESS Article e3 Immunity 59, 1–19.e1–e6, December 8, 2026 .. Total RNA was isolated using the RNeasy RNA Isolation Kit (Qiagen).
|