Additional file 8: of Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimerâs disease

Additional file 3: of Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimerâs disease

Qi Zhang (28502)
Cheng Ma (298689)
Marla Gearing (1939525)
Peng Wang (34436)
Lih-Shen Chin (62183)
Lian Li (49049)

March 2018

Table S3. List of novel proteins with altered abundances in AD identified in the present study. The ...

Additional file 1: of Quantitative proteomics of acutely-isolated mouse microglia identifies novel immune Alzheimerâs disease-related proteins

Srikant Rangaraju (4174204)
Eric Dammer (4174213)
Syed Ali Raza (4905754)
Tianwen Gao (262800)
Hailian Xiao (36120)
Ranjita Betarbet (4174207)
Duc Duong (4174198)
James Webster (3633883)
Chadwick Hales (3491627)
James Lah (3504050)
Allan Levey (3504062)
Nicholas Seyfried (3504065)

June 2018

Table S1. Log2 transformed protein abundance data and differential expression analyses. (XLSX 1522 k...

Additional file 5: of Quantitative proteomics of acutely-isolated mouse microglia identifies novel immune Alzheimerâs disease-related proteins

Srikant Rangaraju (4174204)
Eric Dammer (4174213)
Syed Ali Raza (4905754)
Tianwen Gao (262800)
Hailian Xiao (36120)
Ranjita Betarbet (4174207)
Duc Duong (4174198)
James Webster (3633883)
Chadwick Hales (3491627)
James Lah (3504050)
Allan Levey (3504062)
Nicholas Seyfried (3504065)

June 2018

Table S4. Pathway analysis of proteins differentially increased in 5xFAD (vs. WT) microglia. (XLSX 1...

Additional file 1: of Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimerâs disease

David Hondius (5332583)
Kristel Eigenhuis (5332589)
Tjado Morrema (3491993)
Roel van der Schors (5332592)
Pim van Nierop (518817)
Marianna Bugiani (490560)
Ka Li (399537)
Jeroen Hoozemans (3417251)
August Smit (5332586)
Annemieke Rozemuller (3417257)

June 2018

Figure S1. Coomassie blue staining of the SDS PAGE gels containing the microdissected tissue lysates...

Additional file 5: of Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimer’s disease

David Hondius (5332583)
Kristel Eigenhuis (5332589)
Tjado Morrema (3491993)
Roel van der Schors (5332592)
Pim van Nierop (518817)
Marianna Bugiani (490560)
Ka Li (399537)
Jeroen Hoozemans (3417251)
August Smit (5332586)
Annemieke Rozemuller (3417257)

June 2018

Figure S4. Clustering analysis of experimental groups and individual cases. Clustering analysis and ...

Additional file 2: of Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimerâs disease

David Hondius (5332583)
Kristel Eigenhuis (5332589)
Tjado Morrema (3491993)
Roel van der Schors (5332592)
Pim van Nierop (518817)
Marianna Bugiani (490560)
Ka Li (399537)
Jeroen Hoozemans (3417251)
August Smit (5332586)
Annemieke Rozemuller (3417257)

June 2018

Figure S2. Total protein fluorescent signal from blots used for immunoblot analysis. Total protein l...

Additional file 7: of Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimerâs disease

David Hondius (5332583)
Kristel Eigenhuis (5332589)
Tjado Morrema (3491993)
Roel van der Schors (5332592)
Pim van Nierop (518817)
Marianna Bugiani (490560)
Ka Li (399537)
Jeroen Hoozemans (3417251)
August Smit (5332586)
Annemieke Rozemuller (3417257)

June 2018

Figure S6. Protein expression of males versus females. Quantitative data on several CAA selective da...

Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimer’s disease

David C. Hondius
Kristel N. Eigenhuis
Tjado H. J. Morrema
Roel C. van der Schors
Pim van Nierop
Marianna Bugiani
Ka Wan Li
Jeroen J. M. Hoozemans
August B. Smit
Annemieke J. M. Rozemuller

June 2018

Abstract Alzheimer’s disease (AD) is characterized by amyloid beta (Aβ) deposits as plaques in the p...

Additional file 8: of Deep proteomic network analysis of Alzheimer’s disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease

Erik Johnson (528214)
Eric Dammer (4174213)
Duc Duong (4174198)
Luming Yin (5821523)
Madhav Thambisetty (133912)
Juan Troncoso (249012)
James Lah (3504050)
Allan Levey (3504062)
Nicholas Seyfried (3504065)

October 2018

Figure S1. SDS-PAGE of Brain Homogenates. Dorsolateral prefrontal cortex (DLPFC) brain tissue homoge...

Additional file 1: of Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimerâs disease

Qi Zhang (28502)
Cheng Ma (298689)
Marla Gearing (1939525)
Peng Wang (34436)
Lih-Shen Chin (62183)
Lian Li (49049)

March 2018

Table S1. Demographic and neuropathological data of human AD patient and control cases. For each cas...

Additional file 13: of Deep proteomic network analysis of Alzheimerâs disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease

Erik Johnson (528214)
Eric Dammer (4174213)
Duc Duong (4174198)
Luming Yin (5821523)
Madhav Thambisetty (133912)
Juan Troncoso (249012)
James Lah (3504050)
Allan Levey (3504062)
Nicholas Seyfried (3504065)

October 2018

Figure S6. Cell Type Population Changes Associated with AD and Correlation with Amyloid and Tau Path...

Additional file 6: of Glycoprotein NMB: a novel Alzheimerâs disease associated marker expressed in a subset of activated microglia

Melanie HĂźttenrauch (5875208)
Isabella Ogorek (528694)
Hans Klafki (1735903)
Markus Otto (120832)
Christine Stadelmann (137943)
Sascha Weggen (185102)
Jens Wiltfang (44073)
Oliver Wirths (3554801)

October 2018

High magnification of an amyloid plaque surrounded by GPNMB-positive microglia. (PDF 481 kb

Additional file 1: of Deep proteomic network analysis of Alzheimer’s disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease

Erik Johnson (528214)
Eric Dammer (4174213)
Duc Duong (4174198)
Luming Yin (5821523)
Madhav Thambisetty (133912)
Juan Troncoso (249012)
James Lah (3504050)
Allan Levey (3504062)
Nicholas Seyfried (3504065)

October 2018

Table S1. Sample List. AD, Alzheimer’s disease; AS, asymptomatic Alzheimer’s disease; CT, control; M...

Additional file 2: of Deep proteomic network analysis of Alzheimer’s disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease

Erik Johnson (528214)
Eric Dammer (4174213)
Duc Duong (4174198)
Luming Yin (5821523)
Madhav Thambisetty (133912)
Juan Troncoso (249012)
James Lah (3504050)
Allan Levey (3504062)
Nicholas Seyfried (3504065)

October 2018

Table S2. Case Characteristics. Values shown are means ± SD. AD, Alzheimer’s disease; AsymAD, asympt...

Additional file 7: of Glycoprotein NMB: a novel Alzheimerâs disease associated marker expressed in a subset of activated microglia

Melanie HĂźttenrauch (5875208)
Isabella Ogorek (528694)
Hans Klafki (1735903)
Markus Otto (120832)
Christine Stadelmann (137943)
Sascha Weggen (185102)
Jens Wiltfang (44073)
Oliver Wirths (3554801)

October 2018

Correlation analysis between GPNMB gene expression levels and microglia markers measured by RT-PCR. ...

Additional file 3: of Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimerâs disease

Qi Zhang (28502)
Cheng Ma (298689)
Marla Gearing (1939525)
Peng Wang (34436)
Lih-Shen Chin (62183)
Lian Li (49049)

March 2018

Table S3. List of novel proteins with altered abundances in AD identified in the present study. The ...

Additional file 1: of Quantitative proteomics of acutely-isolated mouse microglia identifies novel immune Alzheimerâs disease-related proteins

Srikant Rangaraju (4174204)
Eric Dammer (4174213)
Syed Ali Raza (4905754)
Tianwen Gao (262800)
Hailian Xiao (36120)
Ranjita Betarbet (4174207)
Duc Duong (4174198)
James Webster (3633883)
Chadwick Hales (3491627)
James Lah (3504050)
Allan Levey (3504062)
Nicholas Seyfried (3504065)

June 2018

Table S1. Log2 transformed protein abundance data and differential expression analyses. (XLSX 1522 k...

Additional file 5: of Quantitative proteomics of acutely-isolated mouse microglia identifies novel immune Alzheimerâs disease-related proteins

Srikant Rangaraju (4174204)
Eric Dammer (4174213)
Syed Ali Raza (4905754)
Tianwen Gao (262800)
Hailian Xiao (36120)
Ranjita Betarbet (4174207)
Duc Duong (4174198)
James Webster (3633883)
Chadwick Hales (3491627)
James Lah (3504050)
Allan Levey (3504062)
Nicholas Seyfried (3504065)

June 2018

Table S4. Pathway analysis of proteins differentially increased in 5xFAD (vs. WT) microglia. (XLSX 1...

Additional file 1: of Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimerâs disease

David Hondius (5332583)
Kristel Eigenhuis (5332589)
Tjado Morrema (3491993)
Roel van der Schors (5332592)
Pim van Nierop (518817)
Marianna Bugiani (490560)
Ka Li (399537)
Jeroen Hoozemans (3417251)
August Smit (5332586)
Annemieke Rozemuller (3417257)

June 2018

Figure S1. Coomassie blue staining of the SDS PAGE gels containing the microdissected tissue lysates...

Additional file 5: of Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimer’s disease

David Hondius (5332583)
Kristel Eigenhuis (5332589)
Tjado Morrema (3491993)
Roel van der Schors (5332592)
Pim van Nierop (518817)
Marianna Bugiani (490560)
Ka Li (399537)
Jeroen Hoozemans (3417251)
August Smit (5332586)
Annemieke Rozemuller (3417257)

June 2018

Figure S4. Clustering analysis of experimental groups and individual cases. Clustering analysis and ...

Additional file 2: of Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimerâs disease

David Hondius (5332583)
Kristel Eigenhuis (5332589)
Tjado Morrema (3491993)
Roel van der Schors (5332592)
Pim van Nierop (518817)
Marianna Bugiani (490560)
Ka Li (399537)
Jeroen Hoozemans (3417251)
August Smit (5332586)
Annemieke Rozemuller (3417257)

June 2018

Figure S2. Total protein fluorescent signal from blots used for immunoblot analysis. Total protein l...

Additional file 7: of Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimerâs disease

David Hondius (5332583)
Kristel Eigenhuis (5332589)
Tjado Morrema (3491993)
Roel van der Schors (5332592)
Pim van Nierop (518817)
Marianna Bugiani (490560)
Ka Li (399537)
Jeroen Hoozemans (3417251)
August Smit (5332586)
Annemieke Rozemuller (3417257)

June 2018

Figure S6. Protein expression of males versus females. Quantitative data on several CAA selective da...

Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimer’s disease

David C. Hondius
Kristel N. Eigenhuis
Tjado H. J. Morrema
Roel C. van der Schors
Pim van Nierop
Marianna Bugiani
Ka Wan Li
Jeroen J. M. Hoozemans
August B. Smit
Annemieke J. M. Rozemuller

June 2018

Abstract Alzheimer’s disease (AD) is characterized by amyloid beta (Aβ) deposits as plaques in the p...

Additional file 8: of Deep proteomic network analysis of Alzheimer’s disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease

Erik Johnson (528214)
Eric Dammer (4174213)
Duc Duong (4174198)
Luming Yin (5821523)
Madhav Thambisetty (133912)
Juan Troncoso (249012)
James Lah (3504050)
Allan Levey (3504062)
Nicholas Seyfried (3504065)

October 2018

Figure S1. SDS-PAGE of Brain Homogenates. Dorsolateral prefrontal cortex (DLPFC) brain tissue homoge...

Additional file 1: of Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimerâs disease

Qi Zhang (28502)
Cheng Ma (298689)
Marla Gearing (1939525)
Peng Wang (34436)
Lih-Shen Chin (62183)
Lian Li (49049)

March 2018

Table S1. Demographic and neuropathological data of human AD patient and control cases. For each cas...

Additional file 13: of Deep proteomic network analysis of Alzheimerâs disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease

Erik Johnson (528214)
Eric Dammer (4174213)
Duc Duong (4174198)
Luming Yin (5821523)
Madhav Thambisetty (133912)
Juan Troncoso (249012)
James Lah (3504050)
Allan Levey (3504062)
Nicholas Seyfried (3504065)

October 2018

Figure S6. Cell Type Population Changes Associated with AD and Correlation with Amyloid and Tau Path...

Additional file 6: of Glycoprotein NMB: a novel Alzheimerâs disease associated marker expressed in a subset of activated microglia

Melanie HĂźttenrauch (5875208)
Isabella Ogorek (528694)
Hans Klafki (1735903)
Markus Otto (120832)
Christine Stadelmann (137943)
Sascha Weggen (185102)
Jens Wiltfang (44073)
Oliver Wirths (3554801)

October 2018

High magnification of an amyloid plaque surrounded by GPNMB-positive microglia. (PDF 481 kb

Additional file 1: of Deep proteomic network analysis of Alzheimer’s disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease

Erik Johnson (528214)
Eric Dammer (4174213)
Duc Duong (4174198)
Luming Yin (5821523)
Madhav Thambisetty (133912)
Juan Troncoso (249012)
James Lah (3504050)
Allan Levey (3504062)
Nicholas Seyfried (3504065)

October 2018

Table S1. Sample List. AD, Alzheimer’s disease; AS, asymptomatic Alzheimer’s disease; CT, control; M...

Additional file 2: of Deep proteomic network analysis of Alzheimer’s disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease

Erik Johnson (528214)
Eric Dammer (4174213)
Duc Duong (4174198)
Luming Yin (5821523)
Madhav Thambisetty (133912)
Juan Troncoso (249012)
James Lah (3504050)
Allan Levey (3504062)
Nicholas Seyfried (3504065)

October 2018

Table S2. Case Characteristics. Values shown are means ± SD. AD, Alzheimer’s disease; AsymAD, asympt...

Additional file 7: of Glycoprotein NMB: a novel Alzheimerâs disease associated marker expressed in a subset of activated microglia

Melanie HĂźttenrauch (5875208)
Isabella Ogorek (528694)
Hans Klafki (1735903)
Markus Otto (120832)
Christine Stadelmann (137943)
Sascha Weggen (185102)
Jens Wiltfang (44073)
Oliver Wirths (3554801)

October 2018

Correlation analysis between GPNMB gene expression levels and microglia markers measured by RT-PCR. ...

Additional file 3: of Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimerâs disease

Qi Zhang (28502)
Cheng Ma (298689)
Marla Gearing (1939525)
Peng Wang (34436)
Lih-Shen Chin (62183)
Lian Li (49049)

March 2018

Table S3. List of novel proteins with altered abundances in AD identified in the present study. The ...

Additional file 1: of Quantitative proteomics of acutely-isolated mouse microglia identifies novel immune Alzheimerâs disease-related proteins

Srikant Rangaraju (4174204)
Eric Dammer (4174213)
Syed Ali Raza (4905754)
Tianwen Gao (262800)
Hailian Xiao (36120)
Ranjita Betarbet (4174207)
Duc Duong (4174198)
James Webster (3633883)
Chadwick Hales (3491627)
James Lah (3504050)
Allan Levey (3504062)
Nicholas Seyfried (3504065)

June 2018

Table S1. Log2 transformed protein abundance data and differential expression analyses. (XLSX 1522 k...

Additional file 5: of Quantitative proteomics of acutely-isolated mouse microglia identifies novel immune Alzheimerâs disease-related proteins

Srikant Rangaraju (4174204)
Eric Dammer (4174213)
Syed Ali Raza (4905754)
Tianwen Gao (262800)
Hailian Xiao (36120)
Ranjita Betarbet (4174207)
Duc Duong (4174198)
James Webster (3633883)
Chadwick Hales (3491627)
James Lah (3504050)
Allan Levey (3504062)
Nicholas Seyfried (3504065)

June 2018

Table S4. Pathway analysis of proteins differentially increased in 5xFAD (vs. WT) microglia. (XLSX 1...

Additional file 8: of Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimerâs disease

Abstract

Extracted data

Additional file 8: of Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimerâs disease

Abstract

Extracted data

Related items

Related items

Additional file 8: of Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimerâs disease

Abstract

Extracted data

Additional file 8: of Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimerâs disease

Abstract

Extracted data

Related items

Related items

Additional file 8: of Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimerâs disease

Additional file 8: of Proteomics analysis identifies new markers associated with capillary cerebral amyloid angiopathy in Alzheimerâs disease