Search results for the GEO ID: GSE9833  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM246377 | GPL1355 |
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RatBrain_BV_IBN_Rep1
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Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of baculovirus vectors (5E7 viral particles)
|
Strain: Wistar
Gender: Male
Weight: 250-300g
Age: NA
Tissue: Brain
Treatment: Baculovirus vectors (5ul, 5E07 viral particles) injected stereotaxically into the striatum at tw0injection sitesAP ±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.
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NIL
|
| Sample_geo_accession | GSM246377
| | Sample_status | Public on Dec 13 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Doreen Leung
| | 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 | phycoerythrin
| | Sample_label_protocol_ch1 | One to 10 u 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 5 out of 7 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/GSM246nnn/GSM246377/suppl/GSM246377.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246377/suppl/GSM246377.CHP.gz
| | Sample_series_id | GSE9833
| | Sample_data_row_count | 31099
| | |
|
GSM246381 | GPL1355 |
|
RatBrain_BV_IBN_Rep2
|
Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of baculovirus vectors (5E7 viral particles)
|
Strain: Wistar
Gender: Male
Weight: 250-300g
Age: NA
Tissue: Brain
Treatment: Baculovirus vectors (5ul, 5E07 viral particles) injected stereotaxically into the striatum at tw0injection sitesAP ±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.
|
NIL
|
| Sample_geo_accession | GSM246381
| | Sample_status | Public on Dec 13 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Doreen Leung
| | 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 | phycoerythrin
| | Sample_label_protocol_ch1 | One to 10 u 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 5 out of 7 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/GSM246nnn/GSM246381/suppl/GSM246381.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246381/suppl/GSM246381.CHP.gz
| | Sample_series_id | GSE9833
| | Sample_data_row_count | 31099
| | |
|
GSM246382 | GPL1355 |
|
RatBrain_BV_IBN_Rep3
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Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of baculovirus vectors (5E7 viral particles)
|
Strain: Wistar
Gender: Male
Weight: 250-300g
Age: NA
Tissue: Brain
Treatment: Baculovirus vectors (5ul, 5E07 viral particles) injected stereotaxically into the striatum at tw0injection sitesAP ±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.
|
NIL
|
| Sample_geo_accession | GSM246382
| | Sample_status | Public on Dec 13 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Doreen Leung
| | 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 | phycoerythrin
| | Sample_label_protocol_ch1 | One to 10 u 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 5 out of 7 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/GSM246nnn/GSM246382/suppl/GSM246382.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246382/suppl/GSM246382.CHP.gz
| | Sample_series_id | GSE9833
| | Sample_data_row_count | 31099
| | |
|
GSM246383 | GPL1355 |
|
RatBrain_BV_IBN_Rep4
|
Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of baculovirus vectors (5E7 viral particles)
|
Strain: Wistar
Gender: Male
Weight: 250-300g
Age: NA
Tissue: Brain
Treatment: Baculovirus vectors (5ul, 5E07 viral particles) injected stereotaxically into the striatum at tw0injection sitesAP ±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.
|
NIL
|
| Sample_geo_accession | GSM246383
| | Sample_status | Public on Dec 13 2007
| | Sample_submission_date | Dec 04 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Doreen Leung
| | 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 | phycoerythrin
| | Sample_label_protocol_ch1 | One to 10 u 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 5 out of 7 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/GSM246nnn/GSM246383/suppl/GSM246383.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM246nnn/GSM246383/suppl/GSM246383.CHP.gz
| | Sample_series_id | GSE9833
| | Sample_data_row_count | 31099
| | |
|
GSM247418 | GPL1355 |
|
RatBrain_BV_IBN_Rep5
|
Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of baculovirus vectors (5E7 viral particles)
|
Strain: Wistar
Gender: Male
Weight: 250-300g
Age: NA
Tissue: Brain
Treatment: Baculovirus vectors (5ul, 5E07 viral particles) injected stereotaxically into the striatum at tw0injection sitesAP ±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.
|
NIL
|
| Sample_geo_accession | GSM247418
| | Sample_status | Public on Dec 13 2007
| | Sample_submission_date | Dec 06 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Doreen Leung
| | 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 | phycoerythrin
| | Sample_label_protocol_ch1 | One to 10 u 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 5 out of 7 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/GSM247nnn/GSM247418/suppl/GSM247418.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM247nnn/GSM247418/suppl/GSM247418.CHP.gz
| | Sample_series_id | GSE9833
| | Sample_data_row_count | 31099
| | |
|
GSM247420 | GPL1355 |
|
RatBrain_BV_IBN_Rep6
|
Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of baculovirus vectors (5E7 viral particles)
|
Strain: Wistar
Gender: Male
Weight: 250-300g
Age: NA
Tissue: Brain
Treatment: Baculovirus vectors (5ul, 5E07 viral particles) injected stereotaxically into the striatum at tw0injection sitesAP ±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.
|
NIL
|
| Sample_geo_accession | GSM247420
| | Sample_status | Public on Dec 13 2007
| | Sample_submission_date | Dec 06 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Doreen Leung
| | 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 | phycoerythrin
| | Sample_label_protocol_ch1 | One to 10 u 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 5 out of 7 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/GSM247nnn/GSM247420/suppl/GSM247420.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM247nnn/GSM247420/suppl/GSM247420.CHP.gz
| | Sample_series_id | GSE9833
| | Sample_data_row_count | 31099
| | |
|
GSM247421 | GPL1355 |
|
RatBrain_BV_IBN_Rep7
|
Adult male Wistar Rat Brain injected stereotaxically into the striatum with 5ul of baculovirus vectors (5E7 viral particles)
|
Strain: Wistar
Gender: Male
Weight: 250-300g
Age: NA
Tissue: Brain
Treatment: Baculovirus vectors (5ul, 5E07 viral particles) injected stereotaxically into the striatum at tw0injection sitesAP ±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.
|
NIL
|
| Sample_geo_accession | GSM247421
| | Sample_status | Public on Dec 13 2007
| | Sample_submission_date | Dec 06 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Doreen Leung
| | 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 | phycoerythrin
| | Sample_label_protocol_ch1 | One to 10 u 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 5 out of 7 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/GSM247nnn/GSM247421/suppl/GSM247421.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM247nnn/GSM247421/suppl/GSM247421.CHP.gz
| | Sample_series_id | GSE9833
| | Sample_data_row_count | 31099
| | |
|
GSM247423 | GPL1355 |
|
RatBrain_CTL_IBN_Rep1
|
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
Treatment: PBS (5ul) injected stereotaxically into the striatum at tw0injection sitesAP ±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.
|
NIL
|
| Sample_geo_accession | GSM247423
| | Sample_status | Public on Dec 13 2007
| | Sample_submission_date | Dec 06 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Doreen Leung
| | 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 | phycoerythrin
| | Sample_label_protocol_ch1 | One to 10 u 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 5 out of 7 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/GSM247nnn/GSM247423/suppl/GSM247423.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM247nnn/GSM247423/suppl/GSM247423.CHP.gz
| | Sample_series_id | GSE9833
| | Sample_data_row_count | 31099
| | |
|
GSM247425 | GPL1355 |
|
RatBrain_CTL_IBN_Rep2
|
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
Treatment: PBS (5ul) injected stereotaxically into the striatum at tw0injection sitesAP ±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.
|
NIL
|
| Sample_geo_accession | GSM247425
| | Sample_status | Public on Dec 13 2007
| | Sample_submission_date | Dec 06 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Doreen Leung
| | 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 | phycoerythrin
| | Sample_label_protocol_ch1 | One to 10 u 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 5 out of 7 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/GSM247nnn/GSM247425/suppl/GSM247425.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM247nnn/GSM247425/suppl/GSM247425.CHP.gz
| | Sample_series_id | GSE9833
| | Sample_data_row_count | 31099
| | |
|
GSM247426 | GPL1355 |
|
RatBrain_CTL_IBN_Rep3
|
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
Treatment: PBS (5ul) injected stereotaxically into the striatum at tw0injection sitesAP ±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.
|
NIL
|
| Sample_geo_accession | GSM247426
| | Sample_status | Public on Dec 13 2007
| | Sample_submission_date | Dec 06 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Doreen Leung
| | 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 | phycoerythrin
| | Sample_label_protocol_ch1 | One to 10 u 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 5 out of 7 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/GSM247nnn/GSM247426/suppl/GSM247426.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM247nnn/GSM247426/suppl/GSM247426.CHP.gz
| | Sample_series_id | GSE9833
| | Sample_data_row_count | 31099
| | |
|
GSM247428 | GPL1355 |
|
RatBrain_CTL_IBN_Rep4
|
RatBrain_CTL_IBN_Rep1
|
Strain: Wistar
Gender: Male
Weight: 250-300g
Age: NA
Tissue: Brain
Treatment: PBS (5ul) injected stereotaxically into the striatum at tw0injection sitesAP ±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.
|
NIL
|
| Sample_geo_accession | GSM247428
| | Sample_status | Public on Dec 13 2007
| | Sample_submission_date | Dec 06 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Doreen Leung
| | 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 | phycoerythrin
| | Sample_label_protocol_ch1 | One to 10 u 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 5 out of 7 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/GSM247nnn/GSM247428/suppl/GSM247428.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM247nnn/GSM247428/suppl/GSM247428.CHP.gz
| | Sample_series_id | GSE9833
| | Sample_data_row_count | 31099
| | |
|
GSM247429 | GPL1355 |
|
RatBrain_CTL_IBN_Rep5
|
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
Treatment: PBS (5ul) injected stereotaxically into the striatum at tw0injection sitesAP ±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.
|
NIL
|
| Sample_geo_accession | GSM247429
| | Sample_status | Public on Dec 13 2007
| | Sample_submission_date | Dec 06 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Doreen Leung
| | 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 | phycoerythrin
| | Sample_label_protocol_ch1 | One to 10 u 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 5 out of 7 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/GSM247nnn/GSM247429/suppl/GSM247429.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM247nnn/GSM247429/suppl/GSM247429.CHP.gz
| | Sample_series_id | GSE9833
| | Sample_data_row_count | 31099
| | |
|
GSM247431 | GPL1355 |
|
RatBrain_CTL_IBN_Rep6
|
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
Treatment: PBS (5ul) injected stereotaxically into the striatum at two injection sitesAP ±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.
|
NIL
|
| Sample_geo_accession | GSM247431
| | Sample_status | Public on Dec 13 2007
| | Sample_submission_date | Dec 06 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Doreen Leung
| | 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 | phycoerythrin
| | Sample_label_protocol_ch1 | One to 10 u 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 5 out of 7 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/GSM247nnn/GSM247431/suppl/GSM247431.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM247nnn/GSM247431/suppl/GSM247431.CHP.gz
| | Sample_series_id | GSE9833
| | Sample_data_row_count | 31099
| | |
|
GSM247432 | GPL1355 |
|
RatBrain_CTL_IBN_Rep7
|
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
Treatment: PBS (5ul) injected stereotaxically into the striatum at tw0injection sitesAP ±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.
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NIL
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| Sample_geo_accession | GSM247432
| | Sample_status | Public on Dec 13 2007
| | Sample_submission_date | Dec 06 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_biomaterial_provider_ch1 | Doreen Leung
| | 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 | phycoerythrin
| | Sample_label_protocol_ch1 | One to 10 u 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 5 out of 7 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/GSM247nnn/GSM247432/suppl/GSM247432.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM247nnn/GSM247432/suppl/GSM247432.CHP.gz
| | Sample_series_id | GSE9833
| | Sample_data_row_count | 31099
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