Additional file 5: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Additional file 1: Figure S2. of Distinct pattern of enteric phospho-alpha-synuclein aggregates and gene expression profiles in patients with Parkinson’s disease

Martina Barrenschee (359697)
Dimitri Zorenkov (425145)
Martina Böttner (425141)
Christina Lange (184185)
François Cossais (3620387)
Amelie Scharf (3620393)
Günther Deuschl (58204)
Susanne Schneider (28500)
Mark Ellrichmann (3138195)
Annette Fritscher-Ravens (3620390)
Thilo Wedel (374098)

January 2017

Mean ganglionic area, mean neuronal area and % p-a-syn positive aggregates per neuron of patients wi...

Additional file 10: of Blood transcriptomics of drug-naĂŻve sporadic Parkinsonâs disease patients

Raffaella Calligaris (3538310)
Mihaela Banica (3538313)
Paola Roncaglia (268638)
Elisa Robotti (2656801)
Sara Finaurini (3538325)
Christina Vlachouli (3538328)
Lucia Antonutti (3538319)
Francesco Iorio (408438)
Annamaria Carissimo (310106)
Tatiana Cattaruzza (3538304)
Andrea Ceiner (3538316)
Dejan Lazarevic (2541580)
Alberto Cucca (3538322)
Nicola Pangher (3538307)
Emilio Marengo (2656810)
Diego di Bernardo (5572)
Gilberto Pizzolato (374225)
Stefano Gustincich (169690)

October 2015

List of common genes between A9 DA neurons of the SN in the mouse and differentially expressed trans...

Additional file 1: Table S1. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

Alexandra Dumitriu (129081)
Javad Golji (264013)
Adam Labadorf (205504)
Benbo Gao (707290)
Thomas Beach (559420)
Richard Myers (179413)
Kenneth Longo (3579509)
Jeanne Latourelle (3579512)

January 2016

Detailed information for the entire set of 29 PD cases and 44 controls studied by MS3 proteomics, RN...

Additional file 4: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Table S2. Differential expression analysis for mRNAs in fibroblasts, iPSCs/ESCs and neurons for the ...

Additional file 8: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Table S5. Differential expression analysis for piRNAs/piRNA-like molecules in fibroblasts, iPSCs/ESC...

Additional file 11: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Figure S5. Analysis of cell type abundance and marker genes in tissues. (TIF 524 kb

Additional file 12: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Table S7. Differential expression analysis for mRNAs, mature miRNAs and piRNAs/piRNA-like molecules ...

Additional file 1: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Table S1. Cohort statistics with details about age, gender and all other covariates used for differe...

Additional file 7: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Table S4. Differential expression analysis for mature miRNAs in fibroblasts, iPSCs/ESCs and neurons ...

Additional file 10: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Table S6. Differential expression analysis for piRNAs/piRNA-like molecues and mature miRNAs for the ...

Additional file 13: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Figure S6. Global statistics on RRBS and analysis of differential methylation. (TIF 351 kb

Additional file 14: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Figure S7. Immunohistochemical staining for methyl-cytosine in all eight control- and PD-patients. (...

Additional file 5: Table S5. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

Alexandra Dumitriu (129081)
Javad Golji (264013)
Adam Labadorf (205504)
Benbo Gao (707290)
Thomas Beach (559420)
Richard Myers (179413)
Kenneth Longo (3579509)
Jeanne Latourelle (3579512)

January 2016

Results for the mRNA abundance comparison between 19 PD and 24 control samples present in the microa...

Additional file 3: Table S3. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

Alexandra Dumitriu (129081)
Javad Golji (264013)
Adam Labadorf (205504)
Benbo Gao (707290)
Thomas Beach (559420)
Richard Myers (179413)
Kenneth Longo (3579509)
Jeanne Latourelle (3579512)

January 2016

Results for the mRNA abundance comparison between 29 PD and 44 control samples for the 17,580 protei...

Additional file 4: of The SH-SY5Y cell line in Parkinson’s disease research: a systematic review

Helena Xicoy (3693394)
Bé Wieringa (42792)
Gerard Martens (3693397)

January 2017

Alternative neuronal (−like) cell lines used to validate the findings in SH-SY5Y cells. The table co...

Additional file 1: Figure S2. of Distinct pattern of enteric phospho-alpha-synuclein aggregates and gene expression profiles in patients with Parkinson’s disease

Martina Barrenschee (359697)
Dimitri Zorenkov (425145)
Martina Böttner (425141)
Christina Lange (184185)
François Cossais (3620387)
Amelie Scharf (3620393)
Günther Deuschl (58204)
Susanne Schneider (28500)
Mark Ellrichmann (3138195)
Annette Fritscher-Ravens (3620390)
Thilo Wedel (374098)

January 2017

Mean ganglionic area, mean neuronal area and % p-a-syn positive aggregates per neuron of patients wi...

Additional file 10: of Blood transcriptomics of drug-naĂŻve sporadic Parkinsonâs disease patients

Raffaella Calligaris (3538310)
Mihaela Banica (3538313)
Paola Roncaglia (268638)
Elisa Robotti (2656801)
Sara Finaurini (3538325)
Christina Vlachouli (3538328)
Lucia Antonutti (3538319)
Francesco Iorio (408438)
Annamaria Carissimo (310106)
Tatiana Cattaruzza (3538304)
Andrea Ceiner (3538316)
Dejan Lazarevic (2541580)
Alberto Cucca (3538322)
Nicola Pangher (3538307)
Emilio Marengo (2656810)
Diego di Bernardo (5572)
Gilberto Pizzolato (374225)
Stefano Gustincich (169690)

October 2015

List of common genes between A9 DA neurons of the SN in the mouse and differentially expressed trans...

Additional file 1: Table S1. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

Alexandra Dumitriu (129081)
Javad Golji (264013)
Adam Labadorf (205504)
Benbo Gao (707290)
Thomas Beach (559420)
Richard Myers (179413)
Kenneth Longo (3579509)
Jeanne Latourelle (3579512)

January 2016

Detailed information for the entire set of 29 PD cases and 44 controls studied by MS3 proteomics, RN...

Additional file 4: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Table S2. Differential expression analysis for mRNAs in fibroblasts, iPSCs/ESCs and neurons for the ...

Additional file 8: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Table S5. Differential expression analysis for piRNAs/piRNA-like molecules in fibroblasts, iPSCs/ESC...

Additional file 11: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Figure S5. Analysis of cell type abundance and marker genes in tissues. (TIF 524 kb

Additional file 12: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Table S7. Differential expression analysis for mRNAs, mature miRNAs and piRNAs/piRNA-like molecules ...

Additional file 1: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Table S1. Cohort statistics with details about age, gender and all other covariates used for differe...

Additional file 7: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Table S4. Differential expression analysis for mature miRNAs in fibroblasts, iPSCs/ESCs and neurons ...

Additional file 10: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Table S6. Differential expression analysis for piRNAs/piRNA-like molecues and mature miRNAs for the ...

Additional file 13: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Figure S6. Global statistics on RRBS and analysis of differential methylation. (TIF 351 kb

Additional file 14: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Markus Schulze (5173634)
Annika Sommer (3451856)
Sonja Plötz (5495657)
Michaela Farrell (5495660)
Beate Winner (602511)
Janina Grosch (5495654)
Jürgen Winkler (208179)
Markus Riemenschneider (5173637)

July 2018

Figure S7. Immunohistochemical staining for methyl-cytosine in all eight control- and PD-patients. (...

Additional file 5: Table S5. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

Alexandra Dumitriu (129081)
Javad Golji (264013)
Adam Labadorf (205504)
Benbo Gao (707290)
Thomas Beach (559420)
Richard Myers (179413)
Kenneth Longo (3579509)
Jeanne Latourelle (3579512)

January 2016

Results for the mRNA abundance comparison between 19 PD and 24 control samples present in the microa...

Additional file 3: Table S3. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

Alexandra Dumitriu (129081)
Javad Golji (264013)
Adam Labadorf (205504)
Benbo Gao (707290)
Thomas Beach (559420)
Richard Myers (179413)
Kenneth Longo (3579509)
Jeanne Latourelle (3579512)

January 2016

Results for the mRNA abundance comparison between 29 PD and 44 control samples for the 17,580 protei...

Additional file 4: of The SH-SY5Y cell line in Parkinson’s disease research: a systematic review

Helena Xicoy (3693394)
Bé Wieringa (42792)
Gerard Martens (3693397)

January 2017

Alternative neuronal (−like) cell lines used to validate the findings in SH-SY5Y cells. The table co...

Additional file 1: Figure S2. of Distinct pattern of enteric phospho-alpha-synuclein aggregates and gene expression profiles in patients with Parkinson’s disease

Martina Barrenschee (359697)
Dimitri Zorenkov (425145)
Martina Böttner (425141)
Christina Lange (184185)
François Cossais (3620387)
Amelie Scharf (3620393)
Günther Deuschl (58204)
Susanne Schneider (28500)
Mark Ellrichmann (3138195)
Annette Fritscher-Ravens (3620390)
Thilo Wedel (374098)

January 2017

Mean ganglionic area, mean neuronal area and % p-a-syn positive aggregates per neuron of patients wi...

Additional file 10: of Blood transcriptomics of drug-naĂŻve sporadic Parkinsonâs disease patients

Raffaella Calligaris (3538310)
Mihaela Banica (3538313)
Paola Roncaglia (268638)
Elisa Robotti (2656801)
Sara Finaurini (3538325)
Christina Vlachouli (3538328)
Lucia Antonutti (3538319)
Francesco Iorio (408438)
Annamaria Carissimo (310106)
Tatiana Cattaruzza (3538304)
Andrea Ceiner (3538316)
Dejan Lazarevic (2541580)
Alberto Cucca (3538322)
Nicola Pangher (3538307)
Emilio Marengo (2656810)
Diego di Bernardo (5572)
Gilberto Pizzolato (374225)
Stefano Gustincich (169690)

October 2015

List of common genes between A9 DA neurons of the SN in the mouse and differentially expressed trans...

Additional file 1: Table S1. of Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

Alexandra Dumitriu (129081)
Javad Golji (264013)
Adam Labadorf (205504)
Benbo Gao (707290)
Thomas Beach (559420)
Richard Myers (179413)
Kenneth Longo (3579509)
Jeanne Latourelle (3579512)

January 2016

Detailed information for the entire set of 29 PD cases and 44 controls studied by MS3 proteomics, RN...

Additional file 5: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Abstract

Extracted data

Additional file 5: of Sporadic Parkinson’s disease derived neuronal cells show disease-specific mRNA and small RNA signatures with abundant deregulation of piRNAs

Abstract

Extracted data

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