Additional file 3 of Microglial transcriptome analysis in the rNLS8 mouse model of TDP-43 proteinopathy reveals discrete expression profiles associated with neurodegenerative progression and recovery

Mandana Hunter (11304267)
Krista J. Spiller (11304270)
Myrna A. Dominique (11304273)
Hong Xu (71477)
Francis W. Hunter (7353059)
Terry C. Fang (3115434)
Rebecca G. Canter (11304276)
Christopher J. Roberts (1321347)
Richard M. Ransohoff (7224881)
John Q. Trojanowski (136910)
Virginia M.-Y. Lee (158420)

Publication date

August 2021

DOI

10.6084/m9.figshare.15569205.v1

Abstract

Additional file 3. Relative abundances of genes differentially expressed in microglia isolated from the spinal cord and cortex of rNLS8 control mice

Extracted data

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Additional file 3 of Microglial transcriptome analysis in the rNLS8 mouse model of TDP-43 proteinopathy reveals discrete expression profiles associated with neurodegenerative progression and recovery

Mandana Hunter (11304267)
Krista J. Spiller (11304270)
Myrna A. Dominique (11304273)
Hong Xu (71477)
Francis W. Hunter (7353059)
Terry C. Fang (3115434)
Rebecca G. Canter (11304276)
Christopher J. Roberts (1321347)
Richard M. Ransohoff (7224881)
John Q. Trojanowski (136910)
Virginia M.-Y. Lee (158420)

Open link

Publication date

August 2021

DOI

10.6084/m9.figshare.15569205.v1

Abstract

Additional file 3. Relative abundances of genes differentially expressed in microglia isolated from the spinal cord and cortex of rNLS8 control mice

Extracted data

Alexandre Amlie-Wolf (819213)
Paul Ryvkin (241021)
Rui Tong (416741)
Isabelle Dragomir (241023)
EunRan Suh (819214)
Yan Xu (14594)
Vivianna M. Van Deerlin (158410)
Brian D. Gregory (241031)
Linda K. Kwong (819215)
John Q. Trojanowski (136910)
Virginia M.-Y. Lee (158420)
Li-San Wang (10922)
Edward B. Lee (819216)

October 2015

(A), Comparison of normalized mean of read counts with log2(fold change) shows no bias...

Additional file 5: of RNA sequencing analysis reveals quiescent microglia isolation methods from postnatal mouse brains and limitations of BV2 cells

Yingbo He (2886041)
Xiang Yao (499265)
Natalie Taylor (227095)
Yuchen Bai (238875)
Timothy Lovenberg (654883)
Anindya Bhattacharya (127895)

May 2018

Fold changes and average expression level of all transcripts among all groups in LPS, AÎ˛, and aging...

Additional file 2 of Microglial transcriptome analysis in the rNLS8 mouse model of TDP-43 proteinopathy reveals discrete expression profiles associated with neurodegenerative progression and recovery

Mandana Hunter (11304267)
Krista J. Spiller (11304270)
Myrna A. Dominique (11304273)
Hong Xu (71477)
Francis W. Hunter (7353059)
Terry C. Fang (3115434)
Rebecca G. Canter (11304276)
Christopher J. Roberts (1321347)
Richard M. Ransohoff (7224881)
John Q. Trojanowski (136910)
Virginia M.-Y. Lee (158420)

August 2021

Additional file 2. Comparison of principal component scores between male and female rNLS8 control mi...

Microglial transcriptome analysis in the rNLS8 mouse model of TDP-43 proteinopathy reveals discrete expression profiles associated with neurodegenerative progression and recovery

Mandana Hunter
Krista J. Spiller
Myrna A. Dominique
Hong Xu
Francis W. Hunter
Terry C. Fang
Rebecca G. Canter
Christopher J. Roberts
Richard M. Ransohoff
John Q. Trojanowski
Virginia M.-Y. Lee

August 2021

Abstract The microglial reaction is a hallmark of neurodegenerative conditions, and elements thereof...

Additional file 3: of Transcriptomopathies of pre- and post-symptomatic frontotemporal dementia-like mice with TDP-43 depletion in forebrain neurons

Lien-Szu Wu (6526166)
Wei-Cheng Cheng (6526169)
Chia-Ying Chen (435740)
Ming-Che Wu (6526172)
Yi-Chi Wang (4966093)
Yu-Hsiang Tseng (6526175)
Trees-Juen Chuang (17657)
C.-K. Shen (6526178)

March 2019

Table S2. Changes of the mRNA levels of social behaviour-related genes in the neocortex of TDP-43 cK...

Additional file 2: of Transcriptomopathies of pre- and post-symptomatic frontotemporal dementia-like mice with TDP-43 depletion in forebrain neurons

Lien-Szu Wu (6526166)
Wei-Cheng Cheng (6526169)
Chia-Ying Chen (435740)
Ming-Che Wu (6526172)
Yi-Chi Wang (4966093)
Yu-Hsiang Tseng (6526175)
Trees-Juen Chuang (17657)
C.-K. Shen (6526178)

March 2019

Table S1. List of the chromosome numbers, donor positions, acceptors positions and gene names of the...

Additional file 1: of Genome-wide RNAseq study of the molecular mechanisms underlying microglia activation in response to pathological tau perturbation in the rTg4510 tau transgenic animal model

Hong Wang (13528)
Yupeng Li (507508)
John Ryder (6092906)
Justin Hole (6092909)
Philip Ebert (6092912)
David Airey (513432)
Hui-Rong Qian (18854)
Benjamin Logsdon (3491201)
Alice Fisher (6092915)
Zeshan Ahmed (6092918)
Tracey Murray (5632871)
Annalisa Cavallini (6092921)
Suchira Bose (6092924)
Brian Eastwood (6092927)
David Collier (231300)
Jeffrey Dage (729068)
Bradley Miller (1869454)
Kalpana Merchant (6092930)
Michael O’Neill (2179246)
Ronald Demattos (6092933)

December 2018

Figure S1. Microglia isolation from adult mouse brain and validation by q-RT-PCR and FACS analysis. ...

Additional file 1: of Transcriptomopathies of pre- and post-symptomatic frontotemporal dementia-like mice with TDP-43 depletion in forebrain neurons

Lien-Szu Wu (6526166)
Wei-Cheng Cheng (6526169)
Chia-Ying Chen (435740)
Ming-Che Wu (6526172)
Yi-Chi Wang (4966093)
Yu-Hsiang Tseng (6526175)
Trees-Juen Chuang (17657)
C.-K. Shen (6526178)

March 2019

Figure S1. Altered activity of daily living (ADL) of TDP-43 cKO mice. Figure S2. Immunohistochemistr...

Additional file 1: of Znf179 E3 ligase-mediated TDP-43 polyubiquitination is involved in TDP-43- ubiquitinated inclusions (UBI) (+)-related neurodegenerative pathology

Yi-Chao Lee (157380)
Wan-Chen Huang (561431)
Jiann-Her Lin (5944379)
Tzu-Jen Kao (244247)
Hui-Ching Lin (286355)
Kuen-Haur Lee (4405330)
Hsin-Chuan Lin (5944382)
Che-Kun Shen (5944385)
Wen-Chang Chang (13410)
Chi-Chen Huang (4405333)

November 2018

Figure S1. (A) Analysis the microarray data from GEO (GDS717), Znf179 mRNA expression in the whole b...

Additional file 4: Figure S2. of Transcriptome analysis of microglia in a mouse model of Rett syndrome: differential expression of genes associated with microglia/macrophage activation and cellular stress

Dejian Zhao (552133)
Ryan Mokhtari (3876916)
Erika Pedrosa (139072)
Rayna Birnbaum (3876919)
Deyou Zheng (7943)
Herbert Lachman (3505484)

March 2017

Principal components analysis (PCA) was carried out on the top 5000 most variable genes as defined b...

Additional file 3: of Genome-wide RNAseq study of the molecular mechanisms underlying microglia activation in response to pathological tau perturbation in the rTg4510 tau transgenic animal model

Hong Wang (13528)
Yupeng Li (507508)
John Ryder (6092906)
Justin Hole (6092909)
Philip Ebert (6092912)
David Airey (513432)
Hui-Rong Qian (18854)
Benjamin Logsdon (3491201)
Alice Fisher (6092915)
Zeshan Ahmed (6092918)
Tracey Murray (5632871)
Annalisa Cavallini (6092921)
Suchira Bose (6092924)
Brian Eastwood (6092927)
David Collier (231300)
Jeffrey Dage (729068)
Bradley Miller (1869454)
Kalpana Merchant (6092930)
Michael OâNeill (6094406)
Ronald Demattos (6092933)

December 2018

Table S2. The list of DEGs in three microglia transcriptomic studies. (XLSX 240 kb

Additional file 1: of Identification and therapeutic modulation of a pro-inflammatory subset of disease-associated-microglia in Alzheimerâs disease

Srikant Rangaraju (4174204)
Eric Dammer (4174213)
Syed Raza (4174210)
Priyadharshini Rathakrishnan (5245535)
Hailian Xiao (36120)
Tianwen Gao (262800)
Duc Duong (4174198)
Michael Pennington (1343655)
James Lah (3504050)
Nicholas Seyfried (3504065)
Allan Levey (3504062)

May 2018

Table S1. Mouse microglial transcriptomic modules identified by Weighted Correlation Network Analysi...

Transcriptomic analysis of ΔNLS-hTDP-43 expressing mice.

Alexandre Amlie-Wolf (819213)
Paul Ryvkin (241021)
Rui Tong (416741)
Isabelle Dragomir (241023)
EunRan Suh (819214)
Yan Xu (14594)
Vivianna M. Van Deerlin (158410)
Brian D. Gregory (241031)
Linda K. Kwong (819215)
John Q. Trojanowski (136910)
Virginia M.-Y. Lee (158420)
Li-San Wang (10922)
Edward B. Lee (819216)

October 2015

(A), Comparison of normalized mean of read counts with log2(fold change) shows no bias...

Additional file 5: of RNA sequencing analysis reveals quiescent microglia isolation methods from postnatal mouse brains and limitations of BV2 cells

Yingbo He (2886041)
Xiang Yao (499265)
Natalie Taylor (227095)
Yuchen Bai (238875)
Timothy Lovenberg (654883)
Anindya Bhattacharya (127895)

May 2018

Fold changes and average expression level of all transcripts among all groups in LPS, AÎ˛, and aging...

Additional file 2 of Microglial transcriptome analysis in the rNLS8 mouse model of TDP-43 proteinopathy reveals discrete expression profiles associated with neurodegenerative progression and recovery

Mandana Hunter (11304267)
Krista J. Spiller (11304270)
Myrna A. Dominique (11304273)
Hong Xu (71477)
Francis W. Hunter (7353059)
Terry C. Fang (3115434)
Rebecca G. Canter (11304276)
Christopher J. Roberts (1321347)
Richard M. Ransohoff (7224881)
John Q. Trojanowski (136910)
Virginia M.-Y. Lee (158420)

August 2021

Additional file 2. Comparison of principal component scores between male and female rNLS8 control mi...

Microglial transcriptome analysis in the rNLS8 mouse model of TDP-43 proteinopathy reveals discrete expression profiles associated with neurodegenerative progression and recovery

Mandana Hunter
Krista J. Spiller
Myrna A. Dominique
Hong Xu
Francis W. Hunter
Terry C. Fang
Rebecca G. Canter
Christopher J. Roberts
Richard M. Ransohoff
John Q. Trojanowski
Virginia M.-Y. Lee

August 2021

Abstract The microglial reaction is a hallmark of neurodegenerative conditions, and elements thereof...

Additional file 3: of Transcriptomopathies of pre- and post-symptomatic frontotemporal dementia-like mice with TDP-43 depletion in forebrain neurons

Lien-Szu Wu (6526166)
Wei-Cheng Cheng (6526169)
Chia-Ying Chen (435740)
Ming-Che Wu (6526172)
Yi-Chi Wang (4966093)
Yu-Hsiang Tseng (6526175)
Trees-Juen Chuang (17657)
C.-K. Shen (6526178)

March 2019

Table S2. Changes of the mRNA levels of social behaviour-related genes in the neocortex of TDP-43 cK...

Additional file 2: of Transcriptomopathies of pre- and post-symptomatic frontotemporal dementia-like mice with TDP-43 depletion in forebrain neurons

Lien-Szu Wu (6526166)
Wei-Cheng Cheng (6526169)
Chia-Ying Chen (435740)
Ming-Che Wu (6526172)
Yi-Chi Wang (4966093)
Yu-Hsiang Tseng (6526175)
Trees-Juen Chuang (17657)
C.-K. Shen (6526178)

March 2019

Table S1. List of the chromosome numbers, donor positions, acceptors positions and gene names of the...

Additional file 1: of Genome-wide RNAseq study of the molecular mechanisms underlying microglia activation in response to pathological tau perturbation in the rTg4510 tau transgenic animal model

Hong Wang (13528)
Yupeng Li (507508)
John Ryder (6092906)
Justin Hole (6092909)
Philip Ebert (6092912)
David Airey (513432)
Hui-Rong Qian (18854)
Benjamin Logsdon (3491201)
Alice Fisher (6092915)
Zeshan Ahmed (6092918)
Tracey Murray (5632871)
Annalisa Cavallini (6092921)
Suchira Bose (6092924)
Brian Eastwood (6092927)
David Collier (231300)
Jeffrey Dage (729068)
Bradley Miller (1869454)
Kalpana Merchant (6092930)
Michael O’Neill (2179246)
Ronald Demattos (6092933)

December 2018

Figure S1. Microglia isolation from adult mouse brain and validation by q-RT-PCR and FACS analysis. ...

Additional file 1: of Transcriptomopathies of pre- and post-symptomatic frontotemporal dementia-like mice with TDP-43 depletion in forebrain neurons

Lien-Szu Wu (6526166)
Wei-Cheng Cheng (6526169)
Chia-Ying Chen (435740)
Ming-Che Wu (6526172)
Yi-Chi Wang (4966093)
Yu-Hsiang Tseng (6526175)
Trees-Juen Chuang (17657)
C.-K. Shen (6526178)

March 2019

Figure S1. Altered activity of daily living (ADL) of TDP-43 cKO mice. Figure S2. Immunohistochemistr...

Additional file 1: of Znf179 E3 ligase-mediated TDP-43 polyubiquitination is involved in TDP-43- ubiquitinated inclusions (UBI) (+)-related neurodegenerative pathology

Yi-Chao Lee (157380)
Wan-Chen Huang (561431)
Jiann-Her Lin (5944379)
Tzu-Jen Kao (244247)
Hui-Ching Lin (286355)
Kuen-Haur Lee (4405330)
Hsin-Chuan Lin (5944382)
Che-Kun Shen (5944385)
Wen-Chang Chang (13410)
Chi-Chen Huang (4405333)

November 2018

Figure S1. (A) Analysis the microarray data from GEO (GDS717), Znf179 mRNA expression in the whole b...

Dejian Zhao (552133)
Ryan Mokhtari (3876916)
Erika Pedrosa (139072)
Rayna Birnbaum (3876919)
Deyou Zheng (7943)
Herbert Lachman (3505484)

March 2017

Principal components analysis (PCA) was carried out on the top 5000 most variable genes as defined b...

Additional file 3: of Genome-wide RNAseq study of the molecular mechanisms underlying microglia activation in response to pathological tau perturbation in the rTg4510 tau transgenic animal model

Hong Wang (13528)
Yupeng Li (507508)
John Ryder (6092906)
Justin Hole (6092909)
Philip Ebert (6092912)
David Airey (513432)
Hui-Rong Qian (18854)
Benjamin Logsdon (3491201)
Alice Fisher (6092915)
Zeshan Ahmed (6092918)
Tracey Murray (5632871)
Annalisa Cavallini (6092921)
Suchira Bose (6092924)
Brian Eastwood (6092927)
David Collier (231300)
Jeffrey Dage (729068)
Bradley Miller (1869454)
Kalpana Merchant (6092930)
Michael OâNeill (6094406)
Ronald Demattos (6092933)

December 2018

Table S2. The list of DEGs in three microglia transcriptomic studies. (XLSX 240 kb

Additional file 1: of Identification and therapeutic modulation of a pro-inflammatory subset of disease-associated-microglia in Alzheimerâs disease

Srikant Rangaraju (4174204)
Eric Dammer (4174213)
Syed Raza (4174210)
Priyadharshini Rathakrishnan (5245535)
Hailian Xiao (36120)
Tianwen Gao (262800)
Duc Duong (4174198)
Michael Pennington (1343655)
James Lah (3504050)
Nicholas Seyfried (3504065)
Allan Levey (3504062)

May 2018

Table S1. Mouse microglial transcriptomic modules identified by Weighted Correlation Network Analysi...

Transcriptomic analysis of ΔNLS-hTDP-43 expressing mice.

Alexandre Amlie-Wolf (819213)
Paul Ryvkin (241021)
Rui Tong (416741)
Isabelle Dragomir (241023)
EunRan Suh (819214)
Yan Xu (14594)
Vivianna M. Van Deerlin (158410)
Brian D. Gregory (241031)
Linda K. Kwong (819215)
John Q. Trojanowski (136910)
Virginia M.-Y. Lee (158420)
Li-San Wang (10922)
Edward B. Lee (819216)

October 2015

(A), Comparison of normalized mean of read counts with log2(fold change) shows no bias...

Additional file 5: of RNA sequencing analysis reveals quiescent microglia isolation methods from postnatal mouse brains and limitations of BV2 cells

Yingbo He (2886041)
Xiang Yao (499265)
Natalie Taylor (227095)
Yuchen Bai (238875)
Timothy Lovenberg (654883)
Anindya Bhattacharya (127895)

May 2018

Fold changes and average expression level of all transcripts among all groups in LPS, AÎ˛, and aging...

Additional file 3 of Microglial transcriptome analysis in the rNLS8 mouse model of TDP-43 proteinopathy reveals discrete expression profiles associated with neurodegenerative progression and recovery

Abstract

Extracted data

Additional file 3 of Microglial transcriptome analysis in the rNLS8 mouse model of TDP-43 proteinopathy reveals discrete expression profiles associated with neurodegenerative progression and recovery

Abstract

Extracted data

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