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Search results for the GEO ID: GSE41084

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Description

Characteristics

GSM1008413

GPL1261

12 hours broadband THz irradiation, biological rep1

Mouse mesenchymal stem cells

cell type: mesenchymal stem cells thz irradiation conditions: 12 hours broadband THz irradiation

Sample_geo_accession	GSM1008413
Sample_status	Public on Jul 01 2013
Sample_submission_date	Sep 21 2012
Sample_last_update_date	Jul 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells are irradiated for 12 hours with high-energy (~1 µJ, pulsewidth 35 fs i.e. high peak power per pulse ~30 MW), average density power 1mW/cm2, broadband THz radiation (~10 THz) at a high repetition rate (1 kHz).
Sample_growth_protocol_ch1	Mouse mesenchymal stem cells (MSCs) (ScienCell Research Laboratories, CA 92011, Catalog Number M7500) were cultured on tissue culture treated plastic T-75 flasks (Corning). Once the cells reached 80-90% confluence, the cells were sub-cultured in supplemented medium (95% α-MEM, 5% FBS, and antibiotics) for THz irradiation treatment. Roziglitazone (1 µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100 µM), and dexamethasone (1 µM), were added to the medium again 48 hours prior to irradiation.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cellular RNA was extracted using the RNeasy Mini kit (Qiagen) following the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA using an oligo dT-primer containing the T7 RNApolymerase promoter site and the One-Cycle Target Labeling Kit (Affymetrix). Biotin-labeled cRNA was purified and the absorbance measured at 260 nm to determine yield (NanoDrop).
Sample_hyb_protocol	Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	The raw microarray .CEL files were analyzed using R and Bioconductor. More specifically, the robust multi-array (RMA) method included in the affy package was used for preprocessing, background correction, and normalization of the raw data. Probes without Entrez identifiers or gene symbols as well as probes with small standard deviation across samples were filtered out from the analysis. Further, features mapping to the same Entrez identifier were consolidated by leaving the one with largest value and, finally, probes with standard deviation less than 0.5 across samples were filtered out from the analysis. Differentially expressed genes were identified using the Bioconductor limma package and ranked by calculating the B statistics for each gene. Gene annotation was performed using the Bioconductor mouse4302.db package, while the hypergeometric test of the Bioconductor’s GOstats package was used for identifying overrepresentation of differentially expressed genes in gene ontology terms.
Sample_platform_id	GPL1261
Sample_contact_name	Boian,S,Alexandrov
Sample_contact_email	boian@lanl.gov
Sample_contact_department	Theoretical Division
Sample_contact_institute	LANL
Sample_contact_address	Bikini Atoll Road
Sample_contact_city	Los Alamos
Sample_contact_state	NM
Sample_contact_zip/postal_code	87545
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1008nnn/GSM1008413/suppl/GSM1008413_09_Mouse430_2.CEL.gz
Sample_series_id	GSE41084
Sample_series_id	GSE41106
Sample_data_row_count	45101

GSM1008414

GPL1261

Control for 12 hours broadband THz irradiation, biological rep1

Mouse mesenchymal stem cells

cell type: mesenchymal stem cells thz irradiation conditions: none

Sample_geo_accession	GSM1008414
Sample_status	Public on Jul 01 2013
Sample_submission_date	Sep 21 2012
Sample_last_update_date	Jul 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells are irradiated for 12 hours with high-energy (~1 µJ, pulsewidth 35 fs i.e. high peak power per pulse ~30 MW), average density power 1mW/cm2, broadband THz radiation (~10 THz) at a high repetition rate (1 kHz).
Sample_growth_protocol_ch1	Mouse mesenchymal stem cells (MSCs) (ScienCell Research Laboratories, CA 92011, Catalog Number M7500) were cultured on tissue culture treated plastic T-75 flasks (Corning). Once the cells reached 80-90% confluence, the cells were sub-cultured in supplemented medium (95% α-MEM, 5% FBS, and antibiotics) for THz irradiation treatment. Roziglitazone (1 µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100 µM), and dexamethasone (1 µM), were added to the medium again 48 hours prior to irradiation.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cellular RNA was extracted using the RNeasy Mini kit (Qiagen) following the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA using an oligo dT-primer containing the T7 RNApolymerase promoter site and the One-Cycle Target Labeling Kit (Affymetrix). Biotin-labeled cRNA was purified and the absorbance measured at 260 nm to determine yield (NanoDrop).
Sample_hyb_protocol	Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	The raw microarray .CEL files were analyzed using R and Bioconductor. More specifically, the robust multi-array (RMA) method included in the affy package was used for preprocessing, background correction, and normalization of the raw data. Probes without Entrez identifiers or gene symbols as well as probes with small standard deviation across samples were filtered out from the analysis. Further, features mapping to the same Entrez identifier were consolidated by leaving the one with largest value and, finally, probes with standard deviation less than 0.5 across samples were filtered out from the analysis. Differentially expressed genes were identified using the Bioconductor limma package and ranked by calculating the B statistics for each gene. Gene annotation was performed using the Bioconductor mouse4302.db package, while the hypergeometric test of the Bioconductor’s GOstats package was used for identifying overrepresentation of differentially expressed genes in gene ontology terms.
Sample_platform_id	GPL1261
Sample_contact_name	Boian,S,Alexandrov
Sample_contact_email	boian@lanl.gov
Sample_contact_department	Theoretical Division
Sample_contact_institute	LANL
Sample_contact_address	Bikini Atoll Road
Sample_contact_city	Los Alamos
Sample_contact_state	NM
Sample_contact_zip/postal_code	87545
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1008nnn/GSM1008414/suppl/GSM1008414_10_Mouse430_2.CEL.gz
Sample_series_id	GSE41084
Sample_series_id	GSE41106
Sample_data_row_count	45101

GSM1008415

GPL1261

12 hours broadband THz irradiation, biological rep2

Mouse mesenchymal stem cells

cell type: mesenchymal stem cells thz irradiation conditions: 12 hours broadband THz irradiation

Sample_geo_accession	GSM1008415
Sample_status	Public on Jul 01 2013
Sample_submission_date	Sep 21 2012
Sample_last_update_date	Jul 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells are irradiated for 12 hours with high-energy (~1 µJ, pulsewidth 35 fs i.e. high peak power per pulse ~30 MW), average density power 1mW/cm2, broadband THz radiation (~10 THz) at a high repetition rate (1 kHz).
Sample_growth_protocol_ch1	Mouse mesenchymal stem cells (MSCs) (ScienCell Research Laboratories, CA 92011, Catalog Number M7500) were cultured on tissue culture treated plastic T-75 flasks (Corning). Once the cells reached 80-90% confluence, the cells were sub-cultured in supplemented medium (95% α-MEM, 5% FBS, and antibiotics) for THz irradiation treatment. Roziglitazone (1 µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100 µM), and dexamethasone (1 µM), were added to the medium again 48 hours prior to irradiation.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cellular RNA was extracted using the RNeasy Mini kit (Qiagen) following the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA using an oligo dT-primer containing the T7 RNApolymerase promoter site and the One-Cycle Target Labeling Kit (Affymetrix). Biotin-labeled cRNA was purified and the absorbance measured at 260 nm to determine yield (NanoDrop).
Sample_hyb_protocol	Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	The raw microarray .CEL files were analyzed using R and Bioconductor. More specifically, the robust multi-array (RMA) method included in the affy package was used for preprocessing, background correction, and normalization of the raw data. Probes without Entrez identifiers or gene symbols as well as probes with small standard deviation across samples were filtered out from the analysis. Further, features mapping to the same Entrez identifier were consolidated by leaving the one with largest value and, finally, probes with standard deviation less than 0.5 across samples were filtered out from the analysis. Differentially expressed genes were identified using the Bioconductor limma package and ranked by calculating the B statistics for each gene. Gene annotation was performed using the Bioconductor mouse4302.db package, while the hypergeometric test of the Bioconductor’s GOstats package was used for identifying overrepresentation of differentially expressed genes in gene ontology terms.
Sample_platform_id	GPL1261
Sample_contact_name	Boian,S,Alexandrov
Sample_contact_email	boian@lanl.gov
Sample_contact_department	Theoretical Division
Sample_contact_institute	LANL
Sample_contact_address	Bikini Atoll Road
Sample_contact_city	Los Alamos
Sample_contact_state	NM
Sample_contact_zip/postal_code	87545
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1008nnn/GSM1008415/suppl/GSM1008415_11_Mouse430_2.CEL.gz
Sample_series_id	GSE41084
Sample_series_id	GSE41106
Sample_data_row_count	45101

GSM1008416

GPL1261

Control for 12 hours broadband THz irradiation, biological rep2

Mouse mesenchymal stem cells

cell type: mesenchymal stem cells thz irradiation conditions: none

Sample_geo_accession	GSM1008416
Sample_status	Public on Jul 01 2013
Sample_submission_date	Sep 21 2012
Sample_last_update_date	Jul 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells are irradiated for 12 hours with high-energy (~1 µJ, pulsewidth 35 fs i.e. high peak power per pulse ~30 MW), average density power 1mW/cm2, broadband THz radiation (~10 THz) at a high repetition rate (1 kHz).
Sample_growth_protocol_ch1	Mouse mesenchymal stem cells (MSCs) (ScienCell Research Laboratories, CA 92011, Catalog Number M7500) were cultured on tissue culture treated plastic T-75 flasks (Corning). Once the cells reached 80-90% confluence, the cells were sub-cultured in supplemented medium (95% α-MEM, 5% FBS, and antibiotics) for THz irradiation treatment. Roziglitazone (1 µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100 µM), and dexamethasone (1 µM), were added to the medium again 48 hours prior to irradiation.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cellular RNA was extracted using the RNeasy Mini kit (Qiagen) following the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA using an oligo dT-primer containing the T7 RNApolymerase promoter site and the One-Cycle Target Labeling Kit (Affymetrix). Biotin-labeled cRNA was purified and the absorbance measured at 260 nm to determine yield (NanoDrop).
Sample_hyb_protocol	Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	The raw microarray .CEL files were analyzed using R and Bioconductor. More specifically, the robust multi-array (RMA) method included in the affy package was used for preprocessing, background correction, and normalization of the raw data. Probes without Entrez identifiers or gene symbols as well as probes with small standard deviation across samples were filtered out from the analysis. Further, features mapping to the same Entrez identifier were consolidated by leaving the one with largest value and, finally, probes with standard deviation less than 0.5 across samples were filtered out from the analysis. Differentially expressed genes were identified using the Bioconductor limma package and ranked by calculating the B statistics for each gene. Gene annotation was performed using the Bioconductor mouse4302.db package, while the hypergeometric test of the Bioconductor’s GOstats package was used for identifying overrepresentation of differentially expressed genes in gene ontology terms.
Sample_platform_id	GPL1261
Sample_contact_name	Boian,S,Alexandrov
Sample_contact_email	boian@lanl.gov
Sample_contact_department	Theoretical Division
Sample_contact_institute	LANL
Sample_contact_address	Bikini Atoll Road
Sample_contact_city	Los Alamos
Sample_contact_state	NM
Sample_contact_zip/postal_code	87545
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1008nnn/GSM1008416/suppl/GSM1008416_12_Mouse430_2.CEL.gz
Sample_series_id	GSE41084
Sample_series_id	GSE41106
Sample_data_row_count	45101

GSM1008417

GPL1261

12 hours broadband THz irradiation, biological rep3

Mouse mesenchymal stem cells

cell type: mesenchymal stem cells thz irradiation conditions: 12 hours broadband THz irradiation

Sample_geo_accession	GSM1008417
Sample_status	Public on Jul 01 2013
Sample_submission_date	Sep 21 2012
Sample_last_update_date	Jul 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells are irradiated for 12 hours with high-energy (~1 µJ, pulsewidth 35 fs i.e. high peak power per pulse ~30 MW), average density power 1mW/cm2, broadband THz radiation (~10 THz) at a high repetition rate (1 kHz).
Sample_growth_protocol_ch1	Mouse mesenchymal stem cells (MSCs) (ScienCell Research Laboratories, CA 92011, Catalog Number M7500) were cultured on tissue culture treated plastic T-75 flasks (Corning). Once the cells reached 80-90% confluence, the cells were sub-cultured in supplemented medium (95% α-MEM, 5% FBS, and antibiotics) for THz irradiation treatment. Roziglitazone (1 µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100 µM), and dexamethasone (1 µM), were added to the medium again 48 hours prior to irradiation.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cellular RNA was extracted using the RNeasy Mini kit (Qiagen) following the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA using an oligo dT-primer containing the T7 RNApolymerase promoter site and the One-Cycle Target Labeling Kit (Affymetrix). Biotin-labeled cRNA was purified and the absorbance measured at 260 nm to determine yield (NanoDrop).
Sample_hyb_protocol	Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	The raw microarray .CEL files were analyzed using R and Bioconductor. More specifically, the robust multi-array (RMA) method included in the affy package was used for preprocessing, background correction, and normalization of the raw data. Probes without Entrez identifiers or gene symbols as well as probes with small standard deviation across samples were filtered out from the analysis. Further, features mapping to the same Entrez identifier were consolidated by leaving the one with largest value and, finally, probes with standard deviation less than 0.5 across samples were filtered out from the analysis. Differentially expressed genes were identified using the Bioconductor limma package and ranked by calculating the B statistics for each gene. Gene annotation was performed using the Bioconductor mouse4302.db package, while the hypergeometric test of the Bioconductor’s GOstats package was used for identifying overrepresentation of differentially expressed genes in gene ontology terms.
Sample_platform_id	GPL1261
Sample_contact_name	Boian,S,Alexandrov
Sample_contact_email	boian@lanl.gov
Sample_contact_department	Theoretical Division
Sample_contact_institute	LANL
Sample_contact_address	Bikini Atoll Road
Sample_contact_city	Los Alamos
Sample_contact_state	NM
Sample_contact_zip/postal_code	87545
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1008nnn/GSM1008417/suppl/GSM1008417_19_Mouse430_2.CEL.gz
Sample_series_id	GSE41084
Sample_series_id	GSE41106
Sample_data_row_count	45101

GSM1008418

GPL1261

Control for 12 hours broadband THz irradiation, biological rep3

Mouse mesenchymal stem cells

cell type: mesenchymal stem cells thz irradiation conditions: none

Sample_geo_accession	GSM1008418
Sample_status	Public on Jul 01 2013
Sample_submission_date	Sep 21 2012
Sample_last_update_date	Jul 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells are irradiated for 12 hours with high-energy (~1 µJ, pulsewidth 35 fs i.e. high peak power per pulse ~30 MW), average density power 1mW/cm2, broadband THz radiation (~10 THz) at a high repetition rate (1 kHz).
Sample_growth_protocol_ch1	Mouse mesenchymal stem cells (MSCs) (ScienCell Research Laboratories, CA 92011, Catalog Number M7500) were cultured on tissue culture treated plastic T-75 flasks (Corning). Once the cells reached 80-90% confluence, the cells were sub-cultured in supplemented medium (95% α-MEM, 5% FBS, and antibiotics) for THz irradiation treatment. Roziglitazone (1 µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100 µM), and dexamethasone (1 µM), were added to the medium again 48 hours prior to irradiation.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cellular RNA was extracted using the RNeasy Mini kit (Qiagen) following the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA using an oligo dT-primer containing the T7 RNApolymerase promoter site and the One-Cycle Target Labeling Kit (Affymetrix). Biotin-labeled cRNA was purified and the absorbance measured at 260 nm to determine yield (NanoDrop).
Sample_hyb_protocol	Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
Sample_data_processing	The raw microarray .CEL files were analyzed using R and Bioconductor. More specifically, the robust multi-array (RMA) method included in the affy package was used for preprocessing, background correction, and normalization of the raw data. Probes without Entrez identifiers or gene symbols as well as probes with small standard deviation across samples were filtered out from the analysis. Further, features mapping to the same Entrez identifier were consolidated by leaving the one with largest value and, finally, probes with standard deviation less than 0.5 across samples were filtered out from the analysis. Differentially expressed genes were identified using the Bioconductor limma package and ranked by calculating the B statistics for each gene. Gene annotation was performed using the Bioconductor mouse4302.db package, while the hypergeometric test of the Bioconductor’s GOstats package was used for identifying overrepresentation of differentially expressed genes in gene ontology terms.
Sample_platform_id	GPL1261
Sample_contact_name	Boian,S,Alexandrov
Sample_contact_email	boian@lanl.gov
Sample_contact_department	Theoretical Division
Sample_contact_institute	LANL
Sample_contact_address	Bikini Atoll Road
Sample_contact_city	Los Alamos
Sample_contact_state	NM
Sample_contact_zip/postal_code	87545
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1008nnn/GSM1008418/suppl/GSM1008418_20_Mouse430_2.CEL.gz
Sample_series_id	GSE41084
Sample_series_id	GSE41106
Sample_data_row_count	45101

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