Additional file 6: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Additional file 2 of Early transcriptional responses of bronchial epithelial cells to whole cigarette smoke mirror those of in-vivo exposed human bronchial mucosa

van der Does, Anne M.
Mahbub, Rashad M.
Ninaber, Dennis K.
Rathnayake, Senani N. H.
Timens, Wim
van den Berge, Maarten
Aliee, Hananeh
Theis, Fabian J.
Nawijn, Martijn C.
Hiemstra, Pieter S.
Faiz, Alen
Guided Treatment in Optimal Selected Cancer Patients (GUTS)
Groningen Research Institute for Asthma and COPD (GRIAC)
Leiden University Medical Center
University of Technology Sydney
Institute of Epidemiology 2

January 2022

Additional file 2. List of differentially expressed genes and associated pathways after cigarette sm...

Additional file 1 of Cytotoxicity analysis of biomass combustion particles in human pulmonary alveolar epithelial cells on an air–liquid interface/dynamic culture platform

Shaorui Ke (11310402)
Qi Liu (33068)
Xinlian Zhang (3998450)
Yuhan Yao (8755512)
Xudong Yang (355575)
Guodong Sui (1956631)

August 2021

Additional file 1: The chemicals and reagents, cell viability assay, apoptosis assay, detection of m...

Additional file 1: Tables S1 and S2. of Morphometric analysis of inflammation in bronchial biopsies following exposure to inhaled diesel exhaust and allergen challenge in atopic subjects

Ali Hosseini (383134)
Jeremy Hirota (3420404)
Tillie Hackett (3420401)
Kelly McNagny (244257)
Susan Wilson (134263)
Chris Carlsten (71596)

January 2016

Pearson correlation coefficients matrix for inflammatory biomarkersâ expression in the lung submuc...

Additional file 5: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Table S2. FC and p-value of the genes differentially expressed after exposure to UFP from diesel com...

Additional file 11: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Table S7. Genes identified by maSigPro as differentially modulated in time during the exposure to bi...

Additional file 8: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Figure S4. Temporal variation of fold changes for the 11 genes that displayed a statistically signif...

Additional file 9: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Table S5. Functional enrichment of gene sets from GSEA Hallmarks collection in cells exposed to dies...

Additional file 12: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Figure S5. Expression profiles of genes showing statistically significant expression changes over ti...

Additional file 3: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Table S1. Total number of reads and number and percentage of reads mapped by TopHat in each analyzed...

Additional file 1: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Figure S1. TEM image of diesel particles before (A) and after (B) sonication and resuspension. (PDF ...

Additional file 4: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Figure S3. Distributions of normalized cpm counts (in log2) for the 13.309 genes passing the express...

Additional file 13: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Table S8. Detail of the filtering criteria for each of the DEGs from network analysis (Fig. 4); for ...

Additional file 14: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Table S9. Biological interactions of genes from network analysis (Fig. 4 and AdditionalÂ fileÂ 15: F...

Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Grilli, Andrea
Bengalli, Rossella
Longhin, Eleonora
Capasso, Laura
Proverbio, Maria Carla
Forcato, Mattia
Bicciato, Silvio
Gualtieri, Maurizio
Battaglia, Cristina
Camatini, Marina

January 2018

Background: Emissions from diesel vehicles and biomass burning are the principal sources of primary ...

Additional file 1: of Multi-cellular human bronchial models exposed to diesel exhaust particles: assessment of inflammation, oxidative stress and macrophage polarization

Jie Ji (423886)
Swapna Upadhyay (4166407)
Xiaomiao Xiong (5162510)
Maria Malmlรถf (5162531)
Thomas Sandstrรถm (3430388)
Per Gerde (2180934)
Lena Palmberg (332871)

May 2018

Supplement. Table S1. Primer Used for Quantitative Real-Time PCR (qPCR). Figure S1. Positive control...

Additional file 2 of Early transcriptional responses of bronchial epithelial cells to whole cigarette smoke mirror those of in-vivo exposed human bronchial mucosa

van der Does, Anne M.
Mahbub, Rashad M.
Ninaber, Dennis K.
Rathnayake, Senani N. H.
Timens, Wim
van den Berge, Maarten
Aliee, Hananeh
Theis, Fabian J.
Nawijn, Martijn C.
Hiemstra, Pieter S.
Faiz, Alen
Guided Treatment in Optimal Selected Cancer Patients (GUTS)
Groningen Research Institute for Asthma and COPD (GRIAC)
Leiden University Medical Center
University of Technology Sydney
Institute of Epidemiology 2

January 2022

Additional file 2. List of differentially expressed genes and associated pathways after cigarette sm...

Additional file 1 of Cytotoxicity analysis of biomass combustion particles in human pulmonary alveolar epithelial cells on an air–liquid interface/dynamic culture platform

Shaorui Ke (11310402)
Qi Liu (33068)
Xinlian Zhang (3998450)
Yuhan Yao (8755512)
Xudong Yang (355575)
Guodong Sui (1956631)

August 2021

Additional file 1: The chemicals and reagents, cell viability assay, apoptosis assay, detection of m...

Additional file 1: Tables S1 and S2. of Morphometric analysis of inflammation in bronchial biopsies following exposure to inhaled diesel exhaust and allergen challenge in atopic subjects

Ali Hosseini (383134)
Jeremy Hirota (3420404)
Tillie Hackett (3420401)
Kelly McNagny (244257)
Susan Wilson (134263)
Chris Carlsten (71596)

January 2016

Pearson correlation coefficients matrix for inflammatory biomarkersâ expression in the lung submuc...

Additional file 5: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Table S2. FC and p-value of the genes differentially expressed after exposure to UFP from diesel com...

Additional file 11: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Table S7. Genes identified by maSigPro as differentially modulated in time during the exposure to bi...

Additional file 8: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Figure S4. Temporal variation of fold changes for the 11 genes that displayed a statistically signif...

Additional file 9: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Table S5. Functional enrichment of gene sets from GSEA Hallmarks collection in cells exposed to dies...

Additional file 12: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Figure S5. Expression profiles of genes showing statistically significant expression changes over ti...

Additional file 3: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Table S1. Total number of reads and number and percentage of reads mapped by TopHat in each analyzed...

Additional file 1: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Figure S1. TEM image of diesel particles before (A) and after (B) sonication and resuspension. (PDF ...

Additional file 4: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Figure S3. Distributions of normalized cpm counts (in log2) for the 13.309 genes passing the express...

Additional file 13: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Table S8. Detail of the filtering criteria for each of the DEGs from network analysis (Fig. 4); for ...

Additional file 14: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Andrea Grilli (4048408)
Rossella Bengalli (5151773)
Eleonora Longhin (5151776)
Laura Capasso (5151779)
Maria Proverbio (5151782)
Mattia Forcato (141773)
Silvio Bicciato (141776)
Maurizio Gualtieri (2049592)
Cristina Battaglia (67215)
Marina Camatini (381935)

April 2018

Table S9. Biological interactions of genes from network analysis (Fig. 4 and AdditionalÂ fileÂ 15: F...

Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Grilli, Andrea
Bengalli, Rossella
Longhin, Eleonora
Capasso, Laura
Proverbio, Maria Carla
Forcato, Mattia
Bicciato, Silvio
Gualtieri, Maurizio
Battaglia, Cristina
Camatini, Marina

January 2018

Background: Emissions from diesel vehicles and biomass burning are the principal sources of primary ...

Additional file 1: of Multi-cellular human bronchial models exposed to diesel exhaust particles: assessment of inflammation, oxidative stress and macrophage polarization

Jie Ji (423886)
Swapna Upadhyay (4166407)
Xiaomiao Xiong (5162510)
Maria Malmlรถf (5162531)
Thomas Sandstrรถm (3430388)
Per Gerde (2180934)
Lena Palmberg (332871)

May 2018

Supplement. Table S1. Primer Used for Quantitative Real-Time PCR (qPCR). Figure S1. Positive control...

Additional file 2 of Early transcriptional responses of bronchial epithelial cells to whole cigarette smoke mirror those of in-vivo exposed human bronchial mucosa

van der Does, Anne M.
Mahbub, Rashad M.
Ninaber, Dennis K.
Rathnayake, Senani N. H.
Timens, Wim
van den Berge, Maarten
Aliee, Hananeh
Theis, Fabian J.
Nawijn, Martijn C.
Hiemstra, Pieter S.
Faiz, Alen
Guided Treatment in Optimal Selected Cancer Patients (GUTS)
Groningen Research Institute for Asthma and COPD (GRIAC)
Leiden University Medical Center
University of Technology Sydney
Institute of Epidemiology 2

January 2022

Additional file 2. List of differentially expressed genes and associated pathways after cigarette sm...

Additional file 1 of Cytotoxicity analysis of biomass combustion particles in human pulmonary alveolar epithelial cells on an air–liquid interface/dynamic culture platform

Shaorui Ke (11310402)
Qi Liu (33068)
Xinlian Zhang (3998450)
Yuhan Yao (8755512)
Xudong Yang (355575)
Guodong Sui (1956631)

August 2021

Additional file 1: The chemicals and reagents, cell viability assay, apoptosis assay, detection of m...

Additional file 1: Tables S1 and S2. of Morphometric analysis of inflammation in bronchial biopsies following exposure to inhaled diesel exhaust and allergen challenge in atopic subjects

Ali Hosseini (383134)
Jeremy Hirota (3420404)
Tillie Hackett (3420401)
Kelly McNagny (244257)
Susan Wilson (134263)
Chris Carlsten (71596)

January 2016

Pearson correlation coefficients matrix for inflammatory biomarkersâ expression in the lung submuc...

Additional file 6: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Abstract

Extracted data

Additional file 6: of Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

Abstract

Extracted data

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