Result

Search results for the GEO ID: GSE38031

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM932772

GPL1261

ctrl_rep1

NSC not irradiated

cell type: Murine ES-derived neural stem cells (NSC)

Sample_geo_accession	GSM932772
Sample_status	Public on Jul 25 2013
Sample_submission_date	May 17 2012
Sample_last_update_date	Jul 25 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	10Gy irradiation (Faxitron RX-650 device at 2Gy/min for 5 min)
Sample_growth_protocol_ch1	Euromed-N cell culture medium (Euroclone), supplemented with L-Gln and P/S, 1x N2 supplement (Invitrogen), 20ng/ml each murine EGF and FGF2 at 5% CO2 and 37° C.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction, Qiagen RNA mini column purification, isopropanol precipitation.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	cRNA was hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 430 2.0 Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000 7G.
Sample_data_processing	Cell intensity values and probe detection calls were computed from the raw array data using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment using packages from BioConductor. Robust Multi-Array Average (RMA) normalization was applied. Normalized data were then filtered based on the Affymetrix detection call, so that only probes that had a Present call in at least one of the arrays were retained. Probes with low intensity values (less than 100) in all arrays were also excluded from statistical analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Paola,,Roncaglia
Sample_contact_department	Neurobiology
Sample_contact_institute	SISSA/ISAS (International School for Advanced Studies)
Sample_contact_address	via Bonomea 265
Sample_contact_city	Trieste
Sample_contact_state	TS
Sample_contact_zip/postal_code	34136
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM932nnn/GSM932772/suppl/GSM932772_C1.CEL.gz
Sample_series_id	GSE38031
Sample_data_row_count	45101

GSM932773

GPL1261

ctrl_rep2

NSC not irradiated

cell type: Murine ES-derived neural stem cells (NSC)

Sample_geo_accession	GSM932773
Sample_status	Public on Jul 25 2013
Sample_submission_date	May 17 2012
Sample_last_update_date	Jul 25 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	10Gy irradiation (Faxitron RX-650 device at 2Gy/min for 5 min)
Sample_growth_protocol_ch1	Euromed-N cell culture medium (Euroclone), supplemented with L-Gln and P/S, 1x N2 supplement (Invitrogen), 20ng/ml each murine EGF and FGF2 at 5% CO2 and 37° C.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction, Qiagen RNA mini column purification, isopropanol precipitation.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	cRNA was hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 430 2.0 Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000 7G.
Sample_data_processing	Cell intensity values and probe detection calls were computed from the raw array data using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment using packages from BioConductor. Robust Multi-Array Average (RMA) normalization was applied. Normalized data were then filtered based on the Affymetrix detection call, so that only probes that had a Present call in at least one of the arrays were retained. Probes with low intensity values (less than 100) in all arrays were also excluded from statistical analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Paola,,Roncaglia
Sample_contact_department	Neurobiology
Sample_contact_institute	SISSA/ISAS (International School for Advanced Studies)
Sample_contact_address	via Bonomea 265
Sample_contact_city	Trieste
Sample_contact_state	TS
Sample_contact_zip/postal_code	34136
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM932nnn/GSM932773/suppl/GSM932773_C2.CEL.gz
Sample_series_id	GSE38031
Sample_data_row_count	45101

GSM932774

GPL1261

ctrl_rep3

NSC not irradiated

cell type: Murine ES-derived neural stem cells (NSC)

Sample_geo_accession	GSM932774
Sample_status	Public on Jul 25 2013
Sample_submission_date	May 17 2012
Sample_last_update_date	Jul 25 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	10Gy irradiation (Faxitron RX-650 device at 2Gy/min for 5 min)
Sample_growth_protocol_ch1	Euromed-N cell culture medium (Euroclone), supplemented with L-Gln and P/S, 1x N2 supplement (Invitrogen), 20ng/ml each murine EGF and FGF2 at 5% CO2 and 37° C.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction, Qiagen RNA mini column purification, isopropanol precipitation.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	cRNA was hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 430 2.0 Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000 7G.
Sample_data_processing	Cell intensity values and probe detection calls were computed from the raw array data using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment using packages from BioConductor. Robust Multi-Array Average (RMA) normalization was applied. Normalized data were then filtered based on the Affymetrix detection call, so that only probes that had a Present call in at least one of the arrays were retained. Probes with low intensity values (less than 100) in all arrays were also excluded from statistical analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Paola,,Roncaglia
Sample_contact_department	Neurobiology
Sample_contact_institute	SISSA/ISAS (International School for Advanced Studies)
Sample_contact_address	via Bonomea 265
Sample_contact_city	Trieste
Sample_contact_state	TS
Sample_contact_zip/postal_code	34136
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM932nnn/GSM932774/suppl/GSM932774_C3.CEL.gz
Sample_series_id	GSE38031
Sample_data_row_count	45101

GSM932775

GPL1261

ctrl_rep4

NSC not irradiated

cell type: Murine ES-derived neural stem cells (NSC)

Sample_geo_accession	GSM932775
Sample_status	Public on Jul 25 2013
Sample_submission_date	May 17 2012
Sample_last_update_date	Jul 25 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	10Gy irradiation (Faxitron RX-650 device at 2Gy/min for 5 min)
Sample_growth_protocol_ch1	Euromed-N cell culture medium (Euroclone), supplemented with L-Gln and P/S, 1x N2 supplement (Invitrogen), 20ng/ml each murine EGF and FGF2 at 5% CO2 and 37° C.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction, Qiagen RNA mini column purification, isopropanol precipitation.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	cRNA was hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 430 2.0 Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000 7G.
Sample_data_processing	Cell intensity values and probe detection calls were computed from the raw array data using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment using packages from BioConductor. Robust Multi-Array Average (RMA) normalization was applied. Normalized data were then filtered based on the Affymetrix detection call, so that only probes that had a Present call in at least one of the arrays were retained. Probes with low intensity values (less than 100) in all arrays were also excluded from statistical analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Paola,,Roncaglia
Sample_contact_department	Neurobiology
Sample_contact_institute	SISSA/ISAS (International School for Advanced Studies)
Sample_contact_address	via Bonomea 265
Sample_contact_city	Trieste
Sample_contact_state	TS
Sample_contact_zip/postal_code	34136
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM932nnn/GSM932775/suppl/GSM932775_C4.CEL.gz
Sample_series_id	GSE38031
Sample_data_row_count	45101

GSM932776

GPL1261

irr_rep1

NSC 10Gy, d7

cell type: Murine ES-derived neural stem cells (NSC)

Sample_geo_accession	GSM932776
Sample_status	Public on Jul 25 2013
Sample_submission_date	May 17 2012
Sample_last_update_date	Jul 25 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	10Gy irradiation (Faxitron RX-650 device at 2Gy/min for 5 min)
Sample_growth_protocol_ch1	Euromed-N cell culture medium (Euroclone), supplemented with L-Gln and P/S, 1x N2 supplement (Invitrogen), 20ng/ml each murine EGF and FGF2 at 5% CO2 and 37° C.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction, Qiagen RNA mini column purification, isopropanol precipitation.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	cRNA was hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 430 2.0 Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000 7G.
Sample_data_processing	Cell intensity values and probe detection calls were computed from the raw array data using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment using packages from BioConductor. Robust Multi-Array Average (RMA) normalization was applied. Normalized data were then filtered based on the Affymetrix detection call, so that only probes that had a Present call in at least one of the arrays were retained. Probes with low intensity values (less than 100) in all arrays were also excluded from statistical analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Paola,,Roncaglia
Sample_contact_department	Neurobiology
Sample_contact_institute	SISSA/ISAS (International School for Advanced Studies)
Sample_contact_address	via Bonomea 265
Sample_contact_city	Trieste
Sample_contact_state	TS
Sample_contact_zip/postal_code	34136
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM932nnn/GSM932776/suppl/GSM932776_I1.CEL.gz
Sample_series_id	GSE38031
Sample_data_row_count	45101

GSM932777

GPL1261

irr_rep2

NSC 10Gy, d7

cell type: Murine ES-derived neural stem cells (NSC)

Sample_geo_accession	GSM932777
Sample_status	Public on Jul 25 2013
Sample_submission_date	May 17 2012
Sample_last_update_date	Jul 25 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	10Gy irradiation (Faxitron RX-650 device at 2Gy/min for 5 min)
Sample_growth_protocol_ch1	Euromed-N cell culture medium (Euroclone), supplemented with L-Gln and P/S, 1x N2 supplement (Invitrogen), 20ng/ml each murine EGF and FGF2 at 5% CO2 and 37° C.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction, Qiagen RNA mini column purification, isopropanol precipitation.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	cRNA was hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 430 2.0 Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000 7G.
Sample_data_processing	Cell intensity values and probe detection calls were computed from the raw array data using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment using packages from BioConductor. Robust Multi-Array Average (RMA) normalization was applied. Normalized data were then filtered based on the Affymetrix detection call, so that only probes that had a Present call in at least one of the arrays were retained. Probes with low intensity values (less than 100) in all arrays were also excluded from statistical analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Paola,,Roncaglia
Sample_contact_department	Neurobiology
Sample_contact_institute	SISSA/ISAS (International School for Advanced Studies)
Sample_contact_address	via Bonomea 265
Sample_contact_city	Trieste
Sample_contact_state	TS
Sample_contact_zip/postal_code	34136
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM932nnn/GSM932777/suppl/GSM932777_I2.CEL.gz
Sample_series_id	GSE38031
Sample_data_row_count	45101

GSM932778

GPL1261

irr_rep3

NSC 10Gy, d7

cell type: Murine ES-derived neural stem cells (NSC)

Sample_geo_accession	GSM932778
Sample_status	Public on Jul 25 2013
Sample_submission_date	May 17 2012
Sample_last_update_date	Jul 25 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	10Gy irradiation (Faxitron RX-650 device at 2Gy/min for 5 min)
Sample_growth_protocol_ch1	Euromed-N cell culture medium (Euroclone), supplemented with L-Gln and P/S, 1x N2 supplement (Invitrogen), 20ng/ml each murine EGF and FGF2 at 5% CO2 and 37° C.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction, Qiagen RNA mini column purification, isopropanol precipitation.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	cRNA was hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 430 2.0 Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000 7G.
Sample_data_processing	Cell intensity values and probe detection calls were computed from the raw array data using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment using packages from BioConductor. Robust Multi-Array Average (RMA) normalization was applied. Normalized data were then filtered based on the Affymetrix detection call, so that only probes that had a Present call in at least one of the arrays were retained. Probes with low intensity values (less than 100) in all arrays were also excluded from statistical analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Paola,,Roncaglia
Sample_contact_department	Neurobiology
Sample_contact_institute	SISSA/ISAS (International School for Advanced Studies)
Sample_contact_address	via Bonomea 265
Sample_contact_city	Trieste
Sample_contact_state	TS
Sample_contact_zip/postal_code	34136
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM932nnn/GSM932778/suppl/GSM932778_I3.CEL.gz
Sample_series_id	GSE38031
Sample_data_row_count	45101

GSM932779

GPL1261

irr_rep4

NSC 10Gy, d7

cell type: Murine ES-derived neural stem cells (NSC)

Sample_geo_accession	GSM932779
Sample_status	Public on Jul 25 2013
Sample_submission_date	May 17 2012
Sample_last_update_date	Jul 25 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	10Gy irradiation (Faxitron RX-650 device at 2Gy/min for 5 min)
Sample_growth_protocol_ch1	Euromed-N cell culture medium (Euroclone), supplemented with L-Gln and P/S, 1x N2 supplement (Invitrogen), 20ng/ml each murine EGF and FGF2 at 5% CO2 and 37° C.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction, Qiagen RNA mini column purification, isopropanol precipitation.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	cRNA was hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 430 2.0 Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000 7G.
Sample_data_processing	Cell intensity values and probe detection calls were computed from the raw array data using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment using packages from BioConductor. Robust Multi-Array Average (RMA) normalization was applied. Normalized data were then filtered based on the Affymetrix detection call, so that only probes that had a Present call in at least one of the arrays were retained. Probes with low intensity values (less than 100) in all arrays were also excluded from statistical analysis.
Sample_platform_id	GPL1261
Sample_contact_name	Paola,,Roncaglia
Sample_contact_department	Neurobiology
Sample_contact_institute	SISSA/ISAS (International School for Advanced Studies)
Sample_contact_address	via Bonomea 265
Sample_contact_city	Trieste
Sample_contact_state	TS
Sample_contact_zip/postal_code	34136
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM932nnn/GSM932779/suppl/GSM932779_I4.CEL.gz
Sample_series_id	GSE38031
Sample_data_row_count	45101

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