Result

Search results for the GEO ID: GSE14484

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Title

Source name

Description

Characteristics

GSM361568

GPL1355

Brain_BVi_1

Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of inactivated baculovirus vectors (5E7 viral particles)

strain: Wistar gender: Male weight: 250-300g age: NA tissue: Brain agent: Inactivated baculovirus vectors

GeneSpring processed/normalized data not provided by submitter

Sample_geo_accession	GSM361568
Sample_status	Public on Apr 17 2009
Sample_submission_date	Jan 20 2009
Sample_last_update_date	Apr 16 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_biomaterial_provider_ch1	Zhao Ying
Sample_treatment_protocol_ch1	Inactivated baculovirus vectors were obtained by placing 200 µl of purified baculovirus (at 107pfu/ µl) on ice at a distance of 5 cm and subjected to short wavelength UV radiation (254nm UV) for 1 hour using a HL-2000 Hybrilinker (UVP, LLC Upland, CA). The inactivation of infectivity was verified by infecting U87 glioma cells. The inactivated baculoviruses (5ul, 5E07 viral particles) were injected stereotaxically into the striatum at two injection sites (AP ±1.0mm, ML +2.5mm, and DV -5.0mm from bregma and dura) using a 10 μl Hamilton syringe connected with a 30-gauge needle, at a speed of 0.5 μl/min. The needle remained in place for another 5 min before being slowly retracted. Rats were sacrificed and the brain tissues were collected 48 hours later for analysis.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. RNA was further cleaned up using RNeasy mini kit (Qiagen). Total RNA was quantified using a Nanodrop spectrophotometer and its quality was further assessed using an RNA nanochip on a Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	One to 10 ug of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands)
Sample_label_protocol_ch1
Sample_label_protocol_ch1
Sample_hyb_protocol	Hybridization mixes with 15 ug of fragmented cRNA previously checked on the bioanalyzer were prepared according to Affymetrix’s GeneChip® Hybridization, Wash, and Stain Kit’s instruction and used to hybridize the GeneChip Rat Genome 230 2.0 for 16 hours at 45ºC. The arrays were washed and stained with phycoerythrin according to the manufacturer’s instructions.
Sample_scan_protocol	Chips were scanned using GeneChip® Scanner 3000 and data acquired using the GCOS software
Sample_data_processing	Data obtained from GCOS was exported using the Data Transfer Tool and transferred to GeneSpring and Genedata software respectively. The GC-RMA preprocessor file was used to re-process imported CEL files and to normalize the data at the probe level. Replicates (at least 3 per experiment) were grouped and data normalized using the default setting of Genespring (Data transformation: values less than 0.01 to 0.001; Global normalization function: Per Chip normalization to median or a percentile; Gene normalization function: normalize to median was used. The Genedata’s Refiner function was used to assess the overall quality of the hybridization. To analyze the data, the genes were grouped according to the cells’ or brain’s treatment (Non- infected/infected) and the log of normalized values were taken for further analysis. Data was filtered according to their flags in such a way that at least 3 out of 4 brain samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition
Sample_platform_id	GPL1355
Sample_contact_name	Jerome,,Boulaire
Sample_contact_email	jboulaire@ibn.a-star.edu.sg
Sample_contact_phone	+65 6824 7172
Sample_contact_fax	+65 6478 9083
Sample_contact_department	Gene Delivery
Sample_contact_institute	Institute of Bioengineering and Nanotechnology
Sample_contact_address	31 Biopolis Way
Sample_contact_city	Singapore
Sample_contact_zip/postal_code	31 Biopolis Way
Sample_contact_country	Singapore
Sample_contact_web_link	www.ibn.a-star.edu.sg
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361568/suppl/GSM361568.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361568/suppl/GSM361568.CHP.gz
Sample_series_id	GSE14484
Sample_data_row_count	31099

GSM361860

GPL1355

Brain_BVi_2

Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of inactivated baculovirus vectors (5E7 viral particles)

strain: Wistar gender: Male weight: 250-300g age: NA tissue: Brain agent: Inactivated baculovirus vectors

GeneSpring processed/normalized data not provided by submitter

Sample_geo_accession	GSM361860
Sample_status	Public on Apr 17 2009
Sample_submission_date	Jan 21 2009
Sample_last_update_date	Apr 16 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_biomaterial_provider_ch1	Zhao Ying
Sample_treatment_protocol_ch1	Inactivated baculovirus vectors were obtained by placing 200 µl of purified baculovirus (at 107pfu/ µl) on ice at a distance of 5 cm and subjected to short wavelength UV radiation (254nm UV) for 1 hour using a HL-2000 Hybrilinker (UVP, LLC Upland, CA). The inactivation of infectivity was verified by infecting U87 glioma cells. The inactivated baculoviruses (5ul, 5E07 viral particles) were injected stereotaxically into the striatum at two injection sites (AP ±1.0mm, ML +2.5mm, and DV -5.0mm from bregma and dura) using a 10 μl Hamilton syringe connected with a 30-gauge needle, at a speed of 0.5 μl/min. The needle remained in place for another 5 min before being slowly retracted. Rats were sacrificed and the brain tissues were collected 48 hours later for analysis.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. RNA was further cleaned up using RNeasy mini kit (Qiagen). Total RNA was quantified using a Nanodrop spectrophotometer and its quality was further assessed using an RNA nanochip on a Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1 = One to 10 ug of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands)^SAMPLE	GSM361860
Sample_label_protocol_ch1	One to 10 ug of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands)
Sample_hyb_protocol	Hybridization mixes with 15 ug of fragmented cRNA previously checked on the bioanalyzer were prepared according to Affymetrix’s GeneChip® Hybridization, Wash, and Stain Kit’s instruction and used to hybridize the GeneChip Rat Genome 230 2.0 for 16 hours at 45ºC. The arrays were washed and stained with phycoerythrin according to the manufacturer’s instructions.
Sample_scan_protocol	Chips were scanned using GeneChip® Scanner 3000 and data acquired using the GCOS software
Sample_data_processing	Data obtained from GCOS was exported using the Data Transfer Tool and transferred to GeneSpring and Genedata software respectively. The GC-RMA preprocessor file was used to re-process imported CEL files and to normalize the data at the probe level. Replicates (at least 3 per experiment) were grouped and data normalized using the default setting of Genespring (Data transformation: values less than 0.01 to 0.001; Global normalization function: Per Chip normalization to median or a percentile; Gene normalization function: normalize to median was used. The Genedata’s Refiner function was used to assess the overall quality of the hybridization. To analyze the data, the genes were grouped according to the cells’ or brain’s treatment (Non- infected/infected) and the log of normalized values were taken for further analysis. Data was filtered according to their flags in such a way that at least 3 out of 4 brain samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition
Sample_data_processing
Sample_data_processing
Sample_platform_id	GPL1355
Sample_contact_name	Jerome,,Boulaire
Sample_contact_email	jboulaire@ibn.a-star.edu.sg
Sample_contact_phone	+65 6824 7172
Sample_contact_fax	+65 6478 9083
Sample_contact_department	Gene Delivery
Sample_contact_institute	Institute of Bioengineering and Nanotechnology
Sample_contact_address	31 Biopolis Way
Sample_contact_city	Singapore
Sample_contact_zip/postal_code	31 Biopolis Way
Sample_contact_country	Singapore
Sample_contact_web_link	www.ibn.a-star.edu.sg
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361860/suppl/GSM361860.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361860/suppl/GSM361860.CHP.gz
Sample_series_id	GSE14484
Sample_data_row_count	31099

GSM361861

GPL1355

Brain_BVi_3

Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of inactivated baculovirus vectors (5E7 viral particles)

strain: Wistar gender: Male weight: 250-300g age: NA tissue: Brain agent: Inactivated baculovirus vectors

GeneSpring processed/normalized data not provided by submitter

Sample_geo_accession	GSM361861
Sample_status	Public on Apr 17 2009
Sample_submission_date	Jan 21 2009
Sample_last_update_date	Apr 16 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_biomaterial_provider_ch1	Zhao Ying
Sample_treatment_protocol_ch1	Inactivated baculovirus vectors were obtained by placing 200 µl of purified baculovirus (at 107pfu/ µl) on ice at a distance of 5 cm and subjected to short wavelength UV radiation (254nm UV) for 1 hour using a HL-2000 Hybrilinker (UVP, LLC Upland, CA). The inactivation of infectivity was verified by infecting U87 glioma cells. The inactivated baculoviruses (5ul, 5E07 viral particles) were injected stereotaxically into the striatum at two injection sites (AP ±1.0mm, ML +2.5mm, and DV -5.0mm from bregma and dura) using a 10 μl Hamilton syringe connected with a 30-gauge needle, at a speed of 0.5 μl/min. The needle remained in place for another 5 min before being slowly retracted. Rats were sacrificed and the brain tissues were collected 48 hours later for analysis.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. RNA was further cleaned up using RNeasy mini kit (Qiagen). Total RNA was quantified using a Nanodrop spectrophotometer and its quality was further assessed using an RNA nanochip on a Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	One to 10 ug of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands)
Sample_hyb_protocol	Hybridization mixes with 15 ug of fragmented cRNA previously checked on the bioanalyzer were prepared according to Affymetrix’s GeneChip® Hybridization, Wash, and Stain Kit’s instruction and used to hybridize the GeneChip Rat Genome 230 2.0 for 16 hours at 45ºC. The arrays were washed and stained with phycoerythrin according to the manufacturer’s instructions.
Sample_scan_protocol	Chips were scanned using GeneChip® Scanner 3000 and data acquired using the GCOS software
Sample_data_processing	Data obtained from GCOS was exported using the Data Transfer Tool and transferred to GeneSpring and Genedata software respectively. The GC-RMA preprocessor file was used to re-process imported CEL files and to normalize the data at the probe level. Replicates (at least 3 per experiment) were grouped and data normalized using the default setting of Genespring (Data transformation: values less than 0.01 to 0.001; Global normalization function: Per Chip normalization to median or a percentile; Gene normalization function: normalize to median was used. The Genedata’s Refiner function was used to assess the overall quality of the hybridization. To analyze the data, the genes were grouped according to the cells’ or brain’s treatment (Non- infected/infected) and the log of normalized values were taken for further analysis. Data was filtered according to their flags in such a way that at least 3 out of 4 brain samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition
Sample_data_processing
Sample_data_processing
Sample_platform_id	GPL1355
Sample_contact_name	Jerome,,Boulaire
Sample_contact_email	jboulaire@ibn.a-star.edu.sg
Sample_contact_phone	+65 6824 7172
Sample_contact_fax	+65 6478 9083
Sample_contact_department	Gene Delivery
Sample_contact_institute	Institute of Bioengineering and Nanotechnology
Sample_contact_address	31 Biopolis Way
Sample_contact_city	Singapore
Sample_contact_zip/postal_code	31 Biopolis Way
Sample_contact_country	Singapore
Sample_contact_web_link	www.ibn.a-star.edu.sg
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361861/suppl/GSM361861.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361861/suppl/GSM361861.CHP.gz
Sample_series_id	GSE14484
Sample_data_row_count	31099

GSM361863

GPL1355

Brain_BVi_4

Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of inactivated baculovirus vectors (5E7 viral particles)

strain: Wistar gender: Male weight: 250-300g age: NA tissue: Brain agent: Inactivated baculovirus vectors

GeneSpring processed/normalized data not provided by submitter

Sample_geo_accession	GSM361863
Sample_status	Public on Apr 17 2009
Sample_submission_date	Jan 21 2009
Sample_last_update_date	Apr 16 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_biomaterial_provider_ch1	Zhao Ying
Sample_treatment_protocol_ch1	Inactivated baculovirus vectors were obtained by placing 200 µl of purified baculovirus (at 107pfu/ µl) on ice at a distance of 5 cm and subjected to short wavelength UV radiation (254nm UV) for 1 hour using a HL-2000 Hybrilinker (UVP, LLC Upland, CA). The inactivation of infectivity was verified by infecting U87 glioma cells. The inactivated baculoviruses (5ul, 5E07 viral particles) were injected stereotaxically into the striatum at two injection sites (AP ±1.0mm, ML +2.5mm, and DV -5.0mm from bregma and dura) using a 10 μl Hamilton syringe connected with a 30-gauge needle, at a speed of 0.5 μl/min. The needle remained in place for another 5 min before being slowly retracted. Rats were sacrificed and the brain tissues were collected 48 hours later for analysis.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. RNA was further cleaned up using RNeasy mini kit (Qiagen). Total RNA was quantified using a Nanodrop spectrophotometer and its quality was further assessed using an RNA nanochip on a Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	One to 10 ug of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands)
Sample_hyb_protocol	Hybridization mixes with 15 ug of fragmented cRNA previously checked on the bioanalyzer were prepared according to Affymetrix’s GeneChip® Hybridization, Wash, and Stain Kit’s instruction and used to hybridize the GeneChip Rat Genome 230 2.0 for 16 hours at 45ºC. The arrays were washed and stained with phycoerythrin according to the manufacturer’s instructions.
Sample_scan_protocol	Chips were scanned using GeneChip® Scanner 3000 and data acquired using the GCOS software
Sample_data_processing	Data obtained from GCOS was exported using the Data Transfer Tool and transferred to GeneSpring and Genedata software respectively. The GC-RMA preprocessor file was used to re-process imported CEL files and to normalize the data at the probe level. Replicates (at least 3 per experiment) were grouped and data normalized using the default setting of Genespring (Data transformation: values less than 0.01 to 0.001; Global normalization function: Per Chip normalization to median or a percentile; Gene normalization function: normalize to median was used. The Genedata’s Refiner function was used to assess the overall quality of the hybridization. To analyze the data, the genes were grouped according to the cells’ or brain’s treatment (Non- infected/infected) and the log of normalized values were taken for further analysis. Data was filtered according to their flags in such a way that at least 3 out of 4 brain samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition
Sample_data_processing
Sample_data_processing
Sample_platform_id	GPL1355
Sample_contact_name	Jerome,,Boulaire
Sample_contact_email	jboulaire@ibn.a-star.edu.sg
Sample_contact_phone	+65 6824 7172
Sample_contact_fax	+65 6478 9083
Sample_contact_department	Gene Delivery
Sample_contact_institute	Institute of Bioengineering and Nanotechnology
Sample_contact_address	31 Biopolis Way
Sample_contact_city	Singapore
Sample_contact_zip/postal_code	31 Biopolis Way
Sample_contact_country	Singapore
Sample_contact_web_link	www.ibn.a-star.edu.sg
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361863/suppl/GSM361863.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361863/suppl/GSM361863.CHP.gz
Sample_series_id	GSE14484
Sample_data_row_count	31099

GSM361865

GPL1355

Brain_PBSi_1

Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of PBS

strain: Wistar gender: Male weight: 250-300g age: NA tissue: Brain agent: PBS

GeneSpring processed/normalized data not provided by submitter

Sample_geo_accession	GSM361865
Sample_status	Public on Apr 17 2009
Sample_submission_date	Jan 21 2009
Sample_last_update_date	Apr 16 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_biomaterial_provider_ch1	Zhao Ying
Sample_treatment_protocol_ch1	5 ul of Phosphate buffered saline (PBS) were injected stereotaxically into the striatum at two injection sites (AP ±1.0mm, ML +2.5mm, and DV -5.0mm from bregma and dura) using a 10 μl Hamilton syringe connected with a 30-gauge needle, at a speed of 0.5 μl/min. The needle remained in place for another 5 min before being slowly retracted. Rats were sacrificed and the brain tissues were collected 48 hours later for analysis.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. RNA was further cleaned up using RNeasy mini kit (Qiagen). Total RNA was quantified using a Nanodrop spectrophotometer and its quality was further assessed using an RNA nanochip on a Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	One to 10 ug of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands)
Sample_hyb_protocol	Hybridization mixes with 15 ug of fragmented cRNA previously checked on the bioanalyzer were prepared according to Affymetrix’s GeneChip® Hybridization, Wash, and Stain Kit’s instruction and used to hybridize the GeneChip Rat Genome 230 2.0 for 16 hours at 45ºC. The arrays were washed and stained with phycoerythrin according to the manufacturer’s instructions.
Sample_scan_protocol	Chips were scanned using GeneChip® Scanner 3000 and data acquired using the GCOS software
Sample_data_processing	Data obtained from GCOS was exported using the Data Transfer Tool and transferred to GeneSpring and Genedata software respectively. The GC-RMA preprocessor file was used to re-process imported CEL files and to normalize the data at the probe level. Replicates (at least 3 per experiment) were grouped and data normalized using the default setting of Genespring (Data transformation: values less than 0.01 to 0.001; Global normalization function: Per Chip normalization to median or a percentile; Gene normalization function: normalize to median was used. The Genedata’s Refiner function was used to assess the overall quality of the hybridization. To analyze the data, the genes were grouped according to the cells’ or brain’s treatment (Non- infected/infected) and the log of normalized values were taken for further analysis. Data was filtered according to their flags in such a way that at least 3 out of 4 brain samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition
Sample_data_processing
Sample_data_processing
Sample_platform_id	GPL1355
Sample_contact_name	Jerome,,Boulaire
Sample_contact_email	jboulaire@ibn.a-star.edu.sg
Sample_contact_phone	+65 6824 7172
Sample_contact_fax	+65 6478 9083
Sample_contact_department	Gene Delivery
Sample_contact_institute	Institute of Bioengineering and Nanotechnology
Sample_contact_address	31 Biopolis Way
Sample_contact_city	Singapore
Sample_contact_zip/postal_code	31 Biopolis Way
Sample_contact_country	Singapore
Sample_contact_web_link	www.ibn.a-star.edu.sg
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361865/suppl/GSM361865.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361865/suppl/GSM361865.CHP.gz
Sample_series_id	GSE14484
Sample_data_row_count	31099

GSM361866

GPL1355

Brain_PBSi_2

Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of PBS

gender: Male weight: 250-300g age: NA tissue: Brain agent: PBS

GeneSpring processed/normalized data not provided by submitter

Sample_geo_accession	GSM361866
Sample_status	Public on Apr 17 2009
Sample_submission_date	Jan 21 2009
Sample_last_update_date	Apr 16 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_biomaterial_provider_ch1	Zhao Ying
Sample_treatment_protocol_ch1	5 ul of Phosphate buffered saline (PBS) were injected stereotaxically into the striatum at two injection sites (AP ±1.0mm, ML +2.5mm, and DV -5.0mm from bregma and dura) using a 10 μl Hamilton syringe connected with a 30-gauge needle, at a speed of 0.5 μl/min. The needle remained in place for another 5 min before being slowly retracted. Rats were sacrificed and the brain tissues were collected 48 hours later for analysis.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. RNA was further cleaned up using RNeasy mini kit (Qiagen). Total RNA was quantified using a Nanodrop spectrophotometer and its quality was further assessed using an RNA nanochip on a Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	One to 10 ug of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands)
Sample_hyb_protocol	Hybridization mixes with 15 ug of fragmented cRNA previously checked on the bioanalyzer were prepared according to Affymetrix’s GeneChip® Hybridization, Wash, and Stain Kit’s instruction and used to hybridize the GeneChip Rat Genome 230 2.0 for 16 hours at 45ºC. The arrays were washed and stained with phycoerythrin according to the manufacturer’s instructions.
Sample_scan_protocol	Chips were scanned using GeneChip® Scanner 3000 and data acquired using the GCOS software
Sample_data_processing	Data obtained from GCOS was exported using the Data Transfer Tool and transferred to GeneSpring and Genedata software respectively. The GC-RMA preprocessor file was used to re-process imported CEL files and to normalize the data at the probe level. Replicates (at least 3 per experiment) were grouped and data normalized using the default setting of Genespring (Data transformation: values less than 0.01 to 0.001; Global normalization function: Per Chip normalization to median or a percentile; Gene normalization function: normalize to median was used. The Genedata’s Refiner function was used to assess the overall quality of the hybridization. To analyze the data, the genes were grouped according to the cells’ or brain’s treatment (Non- infected/infected) and the log of normalized values were taken for further analysis. Data was filtered according to their flags in such a way that at least 3 out of 4 brain samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition
Sample_data_processing
Sample_data_processing
Sample_platform_id	GPL1355
Sample_contact_name	Jerome,,Boulaire
Sample_contact_email	jboulaire@ibn.a-star.edu.sg
Sample_contact_phone	+65 6824 7172
Sample_contact_fax	+65 6478 9083
Sample_contact_department	Gene Delivery
Sample_contact_institute	Institute of Bioengineering and Nanotechnology
Sample_contact_address	31 Biopolis Way
Sample_contact_city	Singapore
Sample_contact_zip/postal_code	31 Biopolis Way
Sample_contact_country	Singapore
Sample_contact_web_link	www.ibn.a-star.edu.sg
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361866/suppl/GSM361866.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361866/suppl/GSM361866.CHP.gz
Sample_series_id	GSE14484
Sample_data_row_count	31099

GSM361867

GPL1355

Brain_PBSi_3

Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of PBS

strain: Wistar gender: Male weight: 250-300g age: NA tissue: Brain agent: PBS

GeneSpring processed/normalized data not provided by submitter

Sample_geo_accession	GSM361867
Sample_status	Public on Apr 17 2009
Sample_submission_date	Jan 21 2009
Sample_last_update_date	Apr 16 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_biomaterial_provider_ch1	Zhao Ying
Sample_treatment_protocol_ch1	5 ul of Phosphate buffered saline (PBS) were injected stereotaxically into the striatum at two injection sites (AP ±1.0mm, ML +2.5mm, and DV -5.0mm from bregma and dura) using a 10 μl Hamilton syringe connected with a 30-gauge needle, at a speed of 0.5 μl/min. The needle remained in place for another 5 min before being slowly retracted. Rats were sacrificed and the brain tissues were collected 48 hours later for analysis.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. RNA was further cleaned up using RNeasy mini kit (Qiagen). Total RNA was quantified using a Nanodrop spectrophotometer and its quality was further assessed using an RNA nanochip on a Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	One to 10 ug of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands)
Sample_hyb_protocol	Hybridization mixes with 15 ug of fragmented cRNA previously checked on the bioanalyzer were prepared according to Affymetrix’s GeneChip® Hybridization, Wash, and Stain Kit’s instruction and used to hybridize the GeneChip Rat Genome 230 2.0 for 16 hours at 45ºC. The arrays were washed and stained with phycoerythrin according to the manufacturer’s instructions.
Sample_scan_protocol	Chips were scanned using GeneChip® Scanner 3000 and data acquired using the GCOS software
Sample_data_processing	Data obtained from GCOS was exported using the Data Transfer Tool and transferred to GeneSpring and Genedata software respectively. The GC-RMA preprocessor file was used to re-process imported CEL files and to normalize the data at the probe level. Replicates (at least 3 per experiment) were grouped and data normalized using the default setting of Genespring (Data transformation: values less than 0.01 to 0.001; Global normalization function: Per Chip normalization to median or a percentile; Gene normalization function: normalize to median was used. The Genedata’s Refiner function was used to assess the overall quality of the hybridization. To analyze the data, the genes were grouped according to the cells’ or brain’s treatment (Non- infected/infected) and the log of normalized values were taken for further analysis. Data was filtered according to their flags in such a way that at least 3 out of 4 brain samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition
Sample_data_processing
Sample_data_processing
Sample_platform_id	GPL1355
Sample_contact_name	Jerome,,Boulaire
Sample_contact_email	jboulaire@ibn.a-star.edu.sg
Sample_contact_phone	+65 6824 7172
Sample_contact_fax	+65 6478 9083
Sample_contact_department	Gene Delivery
Sample_contact_institute	Institute of Bioengineering and Nanotechnology
Sample_contact_address	31 Biopolis Way
Sample_contact_city	Singapore
Sample_contact_zip/postal_code	31 Biopolis Way
Sample_contact_country	Singapore
Sample_contact_web_link	www.ibn.a-star.edu.sg
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361867/suppl/GSM361867.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361867/suppl/GSM361867.CHP.gz
Sample_series_id	GSE14484
Sample_data_row_count	31099

GSM361869

GPL1355

Brain_PBSi_4

Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of PBS

strain: Wistar gender: Male weight: 250-300g age: NA tissue: Brain agent: PBS

GeneSpring processed/normalized data not provided by submitter

Sample_geo_accession	GSM361869
Sample_status	Public on Apr 17 2009
Sample_submission_date	Jan 21 2009
Sample_last_update_date	Apr 16 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	5 ul of Phosphate buffered saline (PBS) were injected stereotaxically into the striatum at two injection sites (AP ±1.0mm, ML +2.5mm, and DV -5.0mm from bregma and dura) using a 10 μl Hamilton syringe connected with a 30-gauge needle, at a speed of 0.5 μl/min. The needle remained in place for another 5 min before being slowly retracted. Rats were sacrificed and the brain tissues were collected 48 hours later for analysis.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. RNA was further cleaned up using RNeasy mini kit (Qiagen). Total RNA was quantified using a Nanodrop spectrophotometer and its quality was further assessed using an RNA nanochip on a Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	One to 10 ug of good quality RNA (i.e. A260/A280 > 2.0 and A230/A260 > 2.1) was used to prepare labeled cRNA using either Affymetrix’s One-Cycle Target Labeling and Control Reagents or Kreatech’s RNA ampULSe amplification and labeling kit (Kreatech, Amsterdam, The Netherlands)
Sample_hyb_protocol	Hybridization mixes with 15 ug of fragmented cRNA previously checked on the bioanalyzer were prepared according to Affymetrix’s GeneChip® Hybridization, Wash, and Stain Kit’s instruction and used to hybridize the GeneChip Rat Genome 230 2.0 for 16 hours at 45ºC. The arrays were washed and stained with phycoerythrin according to the manufacturer’s instructions.
Sample_scan_protocol	Chips were scanned using GeneChip® Scanner 3000 and data acquired using the GCOS software
Sample_data_processing	Data obtained from GCOS was exported using the Data Transfer Tool and transferred to GeneSpring and Genedata software respectively. The GC-RMA preprocessor file was used to re-process imported CEL files and to normalize the data at the probe level. Replicates (at least 3 per experiment) were grouped and data normalized using the default setting of Genespring (Data transformation: values less than 0.01 to 0.001; Global normalization function: Per Chip normalization to median or a percentile; Gene normalization function: normalize to median was used. The Genedata’s Refiner function was used to assess the overall quality of the hybridization. To analyze the data, the genes were grouped according to the cells’ or brain’s treatment (Non- infected/infected) and the log of normalized values were taken for further analysis. Data was filtered according to their flags in such a way that at least 3 out of 4 brain samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition
Sample_platform_id	GPL1355
Sample_contact_name	Jerome,,Boulaire
Sample_contact_email	jboulaire@ibn.a-star.edu.sg
Sample_contact_phone	+65 6824 7172
Sample_contact_fax	+65 6478 9083
Sample_contact_department	Gene Delivery
Sample_contact_institute	Institute of Bioengineering and Nanotechnology
Sample_contact_address	31 Biopolis Way
Sample_contact_city	Singapore
Sample_contact_zip/postal_code	31 Biopolis Way
Sample_contact_country	Singapore
Sample_contact_web_link	www.ibn.a-star.edu.sg
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361869/suppl/GSM361869.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361869/suppl/GSM361869.CHP.gz
Sample_series_id	GSE14484
Sample_data_row_count	31099

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