Result

Search results for the GEO ID: GSE23888

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Characteristics

GSM589102

GPL1261

THz irradiated group vs. Control group

Mouse mesenchymal stem cells Mouse mesenchymal stem cells

cell type: mesenchymal stem cells treatment group: 9 hours of THz irradiation cell type: mesenchymal stem cells treatment group: control

ch1: Mouse mesenchymal stem cells after 9 hours of THz irradiation ch2: Mouse mesenchymal stem cells control group ch1 CEL file: 19_Mouse430_2.CEL ch2 CEL file: 29_Mouse430_2.CEL

Sample_geo_accession	GSM589102
Sample_status	Public on Dec 28 2010
Sample_submission_date	Aug 31 2010
Sample_last_update_date	Dec 28 2010
Sample_type	RNA
Sample_channel_count	2
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells are irradiated for 9 hours with high-energy (~1 µJ, pulsewidth 35 fsi.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 were cultured on tissue-culture treated flasks. Once the cells reached 80–90% confluence, they were sub-cultured in supplemented medium (95% α-MEM, 5% FBS, and antibiotics) for THz irradiation treatment. Roziglitazone (1µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100µM), and dexamethasone (1µM) were added to the medium 24 hours before irradiation. Roziglitazone (1µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100µM), and dexamethasone (1µM) were added to the medium 24 hours before 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 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_organism_ch2	Mus musculus
Sample_taxid_ch2	10090
Sample_treatment_protocol_ch2	Cells are irradiated for 9 hours with high-energy (~1 µJ, pulsewidth 35 fsi.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_ch2	Mouse mesenchymal stem cells were cultured on tissue-culture treated flasks. Once the cells reached 80–90% confluence, they were sub-cultured in supplemented medium (95% α-MEM, 5% FBS, and antibiotics) for THz irradiation treatment. Roziglitazone (1µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100µM), and dexamethasone (1µM) were added to the medium 24 hours before irradiation. Roziglitazone (1µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100µM), and dexamethasone (1µM) were added to the medium 24 hours before irradiation.
Sample_molecule_ch2	total RNA
Sample_extract_protocol_ch2	Cellular RNA was extracted using the RNeasy Mini kit (Qiagen) following the manufacturer's instructions.
Sample_label_ch2	biotin
Sample_label_protocol_ch2	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 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 400.
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Statistically significant differentially expressed genes in the Affymetrix GeneChip® microarray data were identified via the Bioconductor software framework and the Significance Score (S-Score) algorithm version 1.20.0.
Sample_data_processing	SScore is an R package that facilitates the comparison of gene expression between Affymetrix GeneChips using the S-score algorithm. The S-score algorithm uses probe level data directly to assess differences in gene expression, without preliminary separate step of probe set expression summary estimation. Therefore, the algorithm avoids introduction of error associated with the expression summary estimation process and has been demonstrated to improve the accuracy of identifying differentially expressed genes. The S-score produces accurate results even when few or no replicates are available.
Sample_data_processing	Reference: Kennedy RE, Kerns RT, Kong X, Archer KJ, Miles MF. SScore: an R package for detecting differential gene expression without gene expression summaries. Bioinformatics. 2006;22:1272–1274
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/GSM589nnn/GSM589102/suppl/GSM589102_19_Mouse430_2.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM589nnn/GSM589102/suppl/GSM589102_29_Mouse430_2.CEL.gz
Sample_series_id	GSE23888
Sample_data_row_count	45037

GSM589102

GPL1261

THz irradiated group vs. Control group

Mouse mesenchymal stem cells Mouse mesenchymal stem cells

cell type: mesenchymal stem cells treatment group: 9 hours of THz irradiation cell type: mesenchymal stem cells treatment group: control

ch1: Mouse mesenchymal stem cells after 9 hours of THz irradiation ch2: Mouse mesenchymal stem cells control group ch1 CEL file: 19_Mouse430_2.CEL ch2 CEL file: 29_Mouse430_2.CEL

Sample_geo_accession	GSM589102
Sample_status	Public on Dec 28 2010
Sample_submission_date	Aug 31 2010
Sample_last_update_date	Dec 28 2010
Sample_type	RNA
Sample_channel_count	2
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Cells are irradiated for 9 hours with high-energy (~1 µJ, pulsewidth 35 fsi.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 were cultured on tissue-culture treated flasks. Once the cells reached 80–90% confluence, they were sub-cultured in supplemented medium (95% α-MEM, 5% FBS, and antibiotics) for THz irradiation treatment. Roziglitazone (1µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100µM), and dexamethasone (1µM) were added to the medium 24 hours before irradiation. Roziglitazone (1µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100µM), and dexamethasone (1µM) were added to the medium 24 hours before 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 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_organism_ch2	Mus musculus
Sample_taxid_ch2	10090
Sample_treatment_protocol_ch2	Cells are irradiated for 9 hours with high-energy (~1 µJ, pulsewidth 35 fsi.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_ch2	Mouse mesenchymal stem cells were cultured on tissue-culture treated flasks. Once the cells reached 80–90% confluence, they were sub-cultured in supplemented medium (95% α-MEM, 5% FBS, and antibiotics) for THz irradiation treatment. Roziglitazone (1µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100µM), and dexamethasone (1µM) were added to the medium 24 hours before irradiation. Roziglitazone (1µM), insulin (5 µg/ml), 3-Isobutyl-1-methylxanthine (100µM), and dexamethasone (1µM) were added to the medium 24 hours before irradiation.
Sample_molecule_ch2	total RNA
Sample_extract_protocol_ch2	Cellular RNA was extracted using the RNeasy Mini kit (Qiagen) following the manufacturer's instructions.
Sample_label_ch2	biotin
Sample_label_protocol_ch2	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 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 400.
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Statistically significant differentially expressed genes in the Affymetrix GeneChip® microarray data were identified via the Bioconductor software framework and the Significance Score (S-Score) algorithm version 1.20.0.
Sample_data_processing	SScore is an R package that facilitates the comparison of gene expression between Affymetrix GeneChips using the S-score algorithm. The S-score algorithm uses probe level data directly to assess differences in gene expression, without preliminary separate step of probe set expression summary estimation. Therefore, the algorithm avoids introduction of error associated with the expression summary estimation process and has been demonstrated to improve the accuracy of identifying differentially expressed genes. The S-score produces accurate results even when few or no replicates are available.
Sample_data_processing	Reference: Kennedy RE, Kerns RT, Kong X, Archer KJ, Miles MF. SScore: an R package for detecting differential gene expression without gene expression summaries. Bioinformatics. 2006;22:1272–1274
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/GSM589nnn/GSM589102/suppl/GSM589102_19_Mouse430_2.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM589nnn/GSM589102/suppl/GSM589102_29_Mouse430_2.CEL.gz
Sample_series_id	GSE23888
Sample_data_row_count	45037

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