Result

Search results for the GEO ID: GSE41600

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Title

Source name

Description

Characteristics

GSM1019957

GPL570

BEAS-2B cells_DMSO+4% NaOAc treatment_3 h_rep1

Bronchial epithelial cells, treated with 1% DMSO and 4% NaOAc for 3 h

cell type: Bronchial epithelial cells treatment: treated with 1% DMSO and 4% NaOAc for 3 h

Sample_geo_accession	GSM1019957
Sample_status	Public on Jan 28 2013
Sample_submission_date	Oct 15 2012
Sample_last_update_date	Jan 28 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	A total of 1.2 x 106 BEAS-2B cells were seeded in 10-cm dishes and incubated further for 24 h in supplement-free medium prior to treatment.
Sample_growth_protocol_ch1	Bronchial epithelial cells (BEAS-2B, ATCC) were grown in bronchial epithelial basal media (BEBM, Lonza) supplemented with bronchial epithelial growth factors (Lonza) under a humidified environment with 5% CO2 at 37 °C. All culture plates and flasks were coated with collagen before use.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated after 3 h of treatment using the Qiagen RNEasy kit
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3' IVT Express Kit).
Sample_hyb_protocol	The labeled RNA was further purified, fragmented and hybridized with rotation at 45 °C for 16 h to the Affymetrix GeneChip Human Genome U133 plus 2.0 arrays. The arrays were washed and stained using the GeneChip Hybridization Wash and Stain kit on an Affymetrix Fluidics Station 450.
Sample_scan_protocol	The chips were scanned using a GeneChip 7G Scanner.
Sample_data_processing	Raw data was normalized using the Robust Multichip Analysis approach and statistical analysis was done using the Bioconductor statistical software and R program. The probe set’s detection call was estimated using the Wilcoxon signed rank-based algorithm. Probe sets that are absent in all of the study samples were removed from further analyses. Differential expression analysis was performed using a linear modeling approach and the empirical Bayes statistics as implemented in the limma package of the R software. The P values obtained were controlled for multiple testing (false discovery rate) using the Benjamini-Hochberg method. P value and fold induction were calculated. Differentially expressed transcripts were ranked by P values, and P < 0.05 and fold induction >1.5 were considered at a statistically significant level. Hierarchical clustering of the data was computed on log-transformed and normalized data by using complete linkage and Pearson correlation distances. Computation and visualization was done with R packages.
Sample_platform_id	GPL570
Sample_contact_name	Lilibeth,A,Salvador
Sample_contact_department	Medicinal Chemistry
Sample_contact_institute	University of Florida
Sample_contact_address	1600 SW Archer Road
Sample_contact_city	Gainesville
Sample_contact_state	Fl
Sample_contact_zip/postal_code	32610
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1019nnn/GSM1019957/suppl/GSM1019957_8866.CEL.gz
Sample_series_id	GSE41600
Sample_data_row_count	54675

GSM1019958

GPL570

BEAS-2B cells_DMSO+4% NaOAc treatment_3 h_rep2

Bronchial epithelial cells, treated with 1% DMSO and 4% NaOAc for 3 h

cell type: Bronchial epithelial cells treatment: treated with 1% DMSO and 4% NaOAc for 3 h

Sample_geo_accession	GSM1019958
Sample_status	Public on Jan 28 2013
Sample_submission_date	Oct 15 2012
Sample_last_update_date	Jan 28 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	A total of 1.2 x 106 BEAS-2B cells were seeded in 10-cm dishes and incubated further for 24 h in supplement-free medium prior to treatment.
Sample_growth_protocol_ch1	Bronchial epithelial cells (BEAS-2B, ATCC) were grown in bronchial epithelial basal media (BEBM, Lonza) supplemented with bronchial epithelial growth factors (Lonza) under a humidified environment with 5% CO2 at 37 °C. All culture plates and flasks were coated with collagen before use.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated after 3 h of treatment using the Qiagen RNEasy kit
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3' IVT Express Kit).
Sample_hyb_protocol	The labeled RNA was further purified, fragmented and hybridized with rotation at 45 °C for 16 h to the Affymetrix GeneChip Human Genome U133 plus 2.0 arrays. The arrays were washed and stained using the GeneChip Hybridization Wash and Stain kit on an Affymetrix Fluidics Station 450.
Sample_scan_protocol	The chips were scanned using a GeneChip 7G Scanner.
Sample_data_processing	Raw data was normalized using the Robust Multichip Analysis approach and statistical analysis was done using the Bioconductor statistical software and R program. The probe set’s detection call was estimated using the Wilcoxon signed rank-based algorithm. Probe sets that are absent in all of the study samples were removed from further analyses. Differential expression analysis was performed using a linear modeling approach and the empirical Bayes statistics as implemented in the limma package of the R software. The P values obtained were controlled for multiple testing (false discovery rate) using the Benjamini-Hochberg method. P value and fold induction were calculated. Differentially expressed transcripts were ranked by P values, and P < 0.05 and fold induction >1.5 were considered at a statistically significant level. Hierarchical clustering of the data was computed on log-transformed and normalized data by using complete linkage and Pearson correlation distances. Computation and visualization was done with R packages.
Sample_platform_id	GPL570
Sample_contact_name	Lilibeth,A,Salvador
Sample_contact_department	Medicinal Chemistry
Sample_contact_institute	University of Florida
Sample_contact_address	1600 SW Archer Road
Sample_contact_city	Gainesville
Sample_contact_state	Fl
Sample_contact_zip/postal_code	32610
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1019nnn/GSM1019958/suppl/GSM1019958_8870.CEL.gz
Sample_series_id	GSE41600
Sample_data_row_count	54675

GSM1019959

GPL570

BEAS-2B cells_DMSO+100 nM human neutrophil elastase treatment_3 h_rep1

Bronchial epithelial cells, treated with 1% DMSO and 100 nM elastase for 3 h

cell type: Bronchial epithelial cells treatment: treated with 1% DMSO and 100 nM elastase (prepared in 4% NaOAc) for 3 h

Sample_geo_accession	GSM1019959
Sample_status	Public on Jan 28 2013
Sample_submission_date	Oct 15 2012
Sample_last_update_date	Jan 28 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	A total of 1.2 x 106 BEAS-2B cells were seeded in 10-cm dishes and incubated further for 24 h in supplement-free medium prior to treatment.
Sample_growth_protocol_ch1	Bronchial epithelial cells (BEAS-2B, ATCC) were grown in bronchial epithelial basal media (BEBM, Lonza) supplemented with bronchial epithelial growth factors (Lonza) under a humidified environment with 5% CO2 at 37 °C. All culture plates and flasks were coated with collagen before use.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated after 3 h of treatment using the Qiagen RNEasy kit
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3' IVT Express Kit).
Sample_hyb_protocol	The labeled RNA was further purified, fragmented and hybridized with rotation at 45 °C for 16 h to the Affymetrix GeneChip Human Genome U133 plus 2.0 arrays. The arrays were washed and stained using the GeneChip Hybridization Wash and Stain kit on an Affymetrix Fluidics Station 450.
Sample_scan_protocol	The chips were scanned using a GeneChip 7G Scanner.
Sample_data_processing	Raw data was normalized using the Robust Multichip Analysis approach and statistical analysis was done using the Bioconductor statistical software and R program. The probe set’s detection call was estimated using the Wilcoxon signed rank-based algorithm. Probe sets that are absent in all of the study samples were removed from further analyses. Differential expression analysis was performed using a linear modeling approach and the empirical Bayes statistics as implemented in the limma package of the R software. The P values obtained were controlled for multiple testing (false discovery rate) using the Benjamini-Hochberg method. P value and fold induction were calculated. Differentially expressed transcripts were ranked by P values, and P < 0.05 and fold induction >1.5 were considered at a statistically significant level. Hierarchical clustering of the data was computed on log-transformed and normalized data by using complete linkage and Pearson correlation distances. Computation and visualization was done with R packages.
Sample_platform_id	GPL570
Sample_contact_name	Lilibeth,A,Salvador
Sample_contact_department	Medicinal Chemistry
Sample_contact_institute	University of Florida
Sample_contact_address	1600 SW Archer Road
Sample_contact_city	Gainesville
Sample_contact_state	Fl
Sample_contact_zip/postal_code	32610
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1019nnn/GSM1019959/suppl/GSM1019959_8865.CEL.gz
Sample_series_id	GSE41600
Sample_data_row_count	54675

GSM1019960

GPL570

BEAS-2B cells_DMSO+100 nM human neutrophil elastase treatment_3 h_rep2

Bronchial epithelial cells, treated with 1% DMSO and 100 nM elastase for 3 h

cell type: Bronchial epithelial cells treatment: treated with 1% DMSO and 100 nM elastase (prepared in 4% NaOAc) for 3 h

Sample_geo_accession	GSM1019960
Sample_status	Public on Jan 28 2013
Sample_submission_date	Oct 15 2012
Sample_last_update_date	Jan 28 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	A total of 1.2 x 106 BEAS-2B cells were seeded in 10-cm dishes and incubated further for 24 h in supplement-free medium prior to treatment.
Sample_growth_protocol_ch1	Bronchial epithelial cells (BEAS-2B, ATCC) were grown in bronchial epithelial basal media (BEBM, Lonza) supplemented with bronchial epithelial growth factors (Lonza) under a humidified environment with 5% CO2 at 37 °C. All culture plates and flasks were coated with collagen before use.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated after 3 h of treatment using the Qiagen RNEasy kit
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3' IVT Express Kit).
Sample_hyb_protocol	The labeled RNA was further purified, fragmented and hybridized with rotation at 45 °C for 16 h to the Affymetrix GeneChip Human Genome U133 plus 2.0 arrays. The arrays were washed and stained using the GeneChip Hybridization Wash and Stain kit on an Affymetrix Fluidics Station 450.
Sample_scan_protocol	The chips were scanned using a GeneChip 7G Scanner.
Sample_data_processing	Raw data was normalized using the Robust Multichip Analysis approach and statistical analysis was done using the Bioconductor statistical software and R program. The probe set’s detection call was estimated using the Wilcoxon signed rank-based algorithm. Probe sets that are absent in all of the study samples were removed from further analyses. Differential expression analysis was performed using a linear modeling approach and the empirical Bayes statistics as implemented in the limma package of the R software. The P values obtained were controlled for multiple testing (false discovery rate) using the Benjamini-Hochberg method. P value and fold induction were calculated. Differentially expressed transcripts were ranked by P values, and P < 0.05 and fold induction >1.5 were considered at a statistically significant level. Hierarchical clustering of the data was computed on log-transformed and normalized data by using complete linkage and Pearson correlation distances. Computation and visualization was done with R packages.
Sample_platform_id	GPL570
Sample_contact_name	Lilibeth,A,Salvador
Sample_contact_department	Medicinal Chemistry
Sample_contact_institute	University of Florida
Sample_contact_address	1600 SW Archer Road
Sample_contact_city	Gainesville
Sample_contact_state	Fl
Sample_contact_zip/postal_code	32610
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1019nnn/GSM1019960/suppl/GSM1019960_8869.CEL.gz
Sample_series_id	GSE41600
Sample_data_row_count	54675

GSM1019961

GPL570

BEAS-2B cells_10 μM symplostatin 5 + 100 nM human neutrophil elastase treatment_3 h_rep1

Bronchial epithelial cells, treated with 10 μM symplostatin 5 and 100 nM elastase for 3 h

cell type: Bronchial epithelial cells treatment: treated with 10 μM symplostatin 5 (prepared in DMSO) and 100 nM elastase (prepared in 4% NaOAc) for 3 h

Sample_geo_accession	GSM1019961
Sample_status	Public on Jan 28 2013
Sample_submission_date	Oct 15 2012
Sample_last_update_date	Jan 28 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	A total of 1.2 x 106 BEAS-2B cells were seeded in 10-cm dishes and incubated further for 24 h in supplement-free medium prior to treatment.
Sample_growth_protocol_ch1	Bronchial epithelial cells (BEAS-2B, ATCC) were grown in bronchial epithelial basal media (BEBM, Lonza) supplemented with bronchial epithelial growth factors (Lonza) under a humidified environment with 5% CO2 at 37 °C. All culture plates and flasks were coated with collagen before use.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated after 3 h of treatment using the Qiagen RNEasy kit
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3' IVT Express Kit).
Sample_hyb_protocol	The labeled RNA was further purified, fragmented and hybridized with rotation at 45 °C for 16 h to the Affymetrix GeneChip Human Genome U133 plus 2.0 arrays. The arrays were washed and stained using the GeneChip Hybridization Wash and Stain kit on an Affymetrix Fluidics Station 450.
Sample_scan_protocol	The chips were scanned using a GeneChip 7G Scanner.
Sample_data_processing	Raw data was normalized using the Robust Multichip Analysis approach and statistical analysis was done using the Bioconductor statistical software and R program. The probe set’s detection call was estimated using the Wilcoxon signed rank-based algorithm. Probe sets that are absent in all of the study samples were removed from further analyses. Differential expression analysis was performed using a linear modeling approach and the empirical Bayes statistics as implemented in the limma package of the R software. The P values obtained were controlled for multiple testing (false discovery rate) using the Benjamini-Hochberg method. P value and fold induction were calculated. Differentially expressed transcripts were ranked by P values, and P < 0.05 and fold induction >1.5 were considered at a statistically significant level. Hierarchical clustering of the data was computed on log-transformed and normalized data by using complete linkage and Pearson correlation distances. Computation and visualization was done with R packages.
Sample_platform_id	GPL570
Sample_contact_name	Lilibeth,A,Salvador
Sample_contact_department	Medicinal Chemistry
Sample_contact_institute	University of Florida
Sample_contact_address	1600 SW Archer Road
Sample_contact_city	Gainesville
Sample_contact_state	Fl
Sample_contact_zip/postal_code	32610
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1019nnn/GSM1019961/suppl/GSM1019961_8864.CEL.gz
Sample_series_id	GSE41600
Sample_data_row_count	54675

GSM1019962

GPL570

BEAS-2B cells_10 μM symplostatin 5 + 100 nM human neutrophil elastase treatment_3 h_rep2

Bronchial epithelial cells, treated with 10 μM symplostatin 5 and 100 nM elastase for 3 h

cell type: Bronchial epithelial cells treatment: treated with 10 μM symplostatin 5 (prepared in DMSO) and 100 nM elastase (prepared in 4% NaOAc) for 3 h

Sample_geo_accession	GSM1019962
Sample_status	Public on Jan 28 2013
Sample_submission_date	Oct 15 2012
Sample_last_update_date	Jan 28 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	A total of 1.2 x 106 BEAS-2B cells were seeded in 10-cm dishes and incubated further for 24 h in supplement-free medium prior to treatment.
Sample_growth_protocol_ch1	Bronchial epithelial cells (BEAS-2B, ATCC) were grown in bronchial epithelial basal media (BEBM, Lonza) supplemented with bronchial epithelial growth factors (Lonza) under a humidified environment with 5% CO2 at 37 °C. All culture plates and flasks were coated with collagen before use.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated after 3 h of treatment using the Qiagen RNEasy kit
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3' IVT Express Kit).
Sample_hyb_protocol	The labeled RNA was further purified, fragmented and hybridized with rotation at 45 °C for 16 h to the Affymetrix GeneChip Human Genome U133 plus 2.0 arrays. The arrays were washed and stained using the GeneChip Hybridization Wash and Stain kit on an Affymetrix Fluidics Station 450.
Sample_scan_protocol	The chips were scanned using a GeneChip 7G Scanner.
Sample_data_processing	Raw data was normalized using the Robust Multichip Analysis approach and statistical analysis was done using the Bioconductor statistical software and R program. The probe set’s detection call was estimated using the Wilcoxon signed rank-based algorithm. Probe sets that are absent in all of the study samples were removed from further analyses. Differential expression analysis was performed using a linear modeling approach and the empirical Bayes statistics as implemented in the limma package of the R software. The P values obtained were controlled for multiple testing (false discovery rate) using the Benjamini-Hochberg method. P value and fold induction were calculated. Differentially expressed transcripts were ranked by P values, and P < 0.05 and fold induction >1.5 were considered at a statistically significant level. Hierarchical clustering of the data was computed on log-transformed and normalized data by using complete linkage and Pearson correlation distances. Computation and visualization was done with R packages.
Sample_platform_id	GPL570
Sample_contact_name	Lilibeth,A,Salvador
Sample_contact_department	Medicinal Chemistry
Sample_contact_institute	University of Florida
Sample_contact_address	1600 SW Archer Road
Sample_contact_city	Gainesville
Sample_contact_state	Fl
Sample_contact_zip/postal_code	32610
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1019nnn/GSM1019962/suppl/GSM1019962_8868.CEL.gz
Sample_series_id	GSE41600
Sample_data_row_count	54675

GSM1019963

GPL570

BEAS-2B cells_10 μM symplostatin 5 + 4% NaOAc treatment_3 h_rep1

Bronchial epithelial cells, treated with 10 μM symplostatin 5 and 4% NaOAc for 3 h

cell type: Bronchial epithelial cells treatment: treated with 10 μM symplostatin 5 (prepared in DMSO) and 4% NaOAc for 3 h

Sample_geo_accession	GSM1019963
Sample_status	Public on Jan 28 2013
Sample_submission_date	Oct 15 2012
Sample_last_update_date	Jan 28 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	A total of 1.2 x 106 BEAS-2B cells were seeded in 10-cm dishes and incubated further for 24 h in supplement-free medium prior to treatment.
Sample_growth_protocol_ch1	Bronchial epithelial cells (BEAS-2B, ATCC) were grown in bronchial epithelial basal media (BEBM, Lonza) supplemented with bronchial epithelial growth factors (Lonza) under a humidified environment with 5% CO2 at 37 °C. All culture plates and flasks were coated with collagen before use.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated after 3 h of treatment using the Qiagen RNEasy kit
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3' IVT Express Kit).
Sample_hyb_protocol	The labeled RNA was further purified, fragmented and hybridized with rotation at 45 °C for 16 h to the Affymetrix GeneChip Human Genome U133 plus 2.0 arrays. The arrays were washed and stained using the GeneChip Hybridization Wash and Stain kit on an Affymetrix Fluidics Station 450.
Sample_scan_protocol	The chips were scanned using a GeneChip 7G Scanner.
Sample_data_processing	Raw data was normalized using the Robust Multichip Analysis approach and statistical analysis was done using the Bioconductor statistical software and R program. The probe set’s detection call was estimated using the Wilcoxon signed rank-based algorithm. Probe sets that are absent in all of the study samples were removed from further analyses. Differential expression analysis was performed using a linear modeling approach and the empirical Bayes statistics as implemented in the limma package of the R software. The P values obtained were controlled for multiple testing (false discovery rate) using the Benjamini-Hochberg method. P value and fold induction were calculated. Differentially expressed transcripts were ranked by P values, and P < 0.05 and fold induction >1.5 were considered at a statistically significant level. Hierarchical clustering of the data was computed on log-transformed and normalized data by using complete linkage and Pearson correlation distances. Computation and visualization was done with R packages.
Sample_platform_id	GPL570
Sample_contact_name	Lilibeth,A,Salvador
Sample_contact_department	Medicinal Chemistry
Sample_contact_institute	University of Florida
Sample_contact_address	1600 SW Archer Road
Sample_contact_city	Gainesville
Sample_contact_state	Fl
Sample_contact_zip/postal_code	32610
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1019nnn/GSM1019963/suppl/GSM1019963_8863.CEL.gz
Sample_series_id	GSE41600
Sample_data_row_count	54675

GSM1019964

GPL570

BEAS-2B cells_10 μM symplostatin 5 + 4% NaOAc treatment_3 h_rep2

Bronchial epithelial cells, treated with 10 μM symplostatin 5 and 4% NaOAc for 3 h

cell type: Bronchial epithelial cells treatment: treated with 10 μM symplostatin 5 (prepared in DMSO) and 4% NaOAc for 3 h

Sample_geo_accession	GSM1019964
Sample_status	Public on Jan 28 2013
Sample_submission_date	Oct 15 2012
Sample_last_update_date	Jan 28 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	A total of 1.2 x 106 BEAS-2B cells were seeded in 10-cm dishes and incubated further for 24 h in supplement-free medium prior to treatment.
Sample_growth_protocol_ch1	Bronchial epithelial cells (BEAS-2B, ATCC) were grown in bronchial epithelial basal media (BEBM, Lonza) supplemented with bronchial epithelial growth factors (Lonza) under a humidified environment with 5% CO2 at 37 °C. All culture plates and flasks were coated with collagen before use.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was isolated after 3 h of treatment using the Qiagen RNEasy kit
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3' IVT Express Kit).
Sample_hyb_protocol	The labeled RNA was further purified, fragmented and hybridized with rotation at 45 °C for 16 h to the Affymetrix GeneChip Human Genome U133 plus 2.0 arrays. The arrays were washed and stained using the GeneChip Hybridization Wash and Stain kit on an Affymetrix Fluidics Station 450.
Sample_scan_protocol	The chips were scanned using a GeneChip 7G Scanner.
Sample_data_processing	Raw data was normalized using the Robust Multichip Analysis approach and statistical analysis was done using the Bioconductor statistical software and R program. The probe set’s detection call was estimated using the Wilcoxon signed rank-based algorithm. Probe sets that are absent in all of the study samples were removed from further analyses. Differential expression analysis was performed using a linear modeling approach and the empirical Bayes statistics as implemented in the limma package of the R software. The P values obtained were controlled for multiple testing (false discovery rate) using the Benjamini-Hochberg method. P value and fold induction were calculated. Differentially expressed transcripts were ranked by P values, and P < 0.05 and fold induction >1.5 were considered at a statistically significant level. Hierarchical clustering of the data was computed on log-transformed and normalized data by using complete linkage and Pearson correlation distances. Computation and visualization was done with R packages.
Sample_platform_id	GPL570
Sample_contact_name	Lilibeth,A,Salvador
Sample_contact_department	Medicinal Chemistry
Sample_contact_institute	University of Florida
Sample_contact_address	1600 SW Archer Road
Sample_contact_city	Gainesville
Sample_contact_state	Fl
Sample_contact_zip/postal_code	32610
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1019nnn/GSM1019964/suppl/GSM1019964_8867.CEL.gz
Sample_series_id	GSE41600
Sample_data_row_count	54675

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