Search results for the GEO ID: GSE12305  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM309429 | GPL570 |
|
Normal Human Astrocyte_Rep1
|
Normal Human Astrocytes from Lonza
|
Cell strain: Normal Human Astrocytes (NHA)
Passage: 4
Growth Medium: Astrocyte Basal Medium (ABM™) and the following growth supplements: rhEGF, 0.5 ml; Insulin, 1.25 ml; Ascorbic Acid, 0.5 ml; GA-1000, 0.5 ml, L-Glutamine, 5.0 ml; FBS, 15 ml.
Grown at 37C in 5%CO2, seeded at 5000 cells/cm2
Untreated
|
The control for hybridization and labeling were from Affymetrix.
|
| Sample_geo_accession | GSM309429
| | Sample_status | Public on Dec 31 2008
| | Sample_submission_date | Jul 31 2008
| | Sample_last_update_date | Aug 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Lonza (Basel, Switzerland)
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | Growth Medium: Astrocyte Basal Medium (ABM™) and the following growth supplements: rhEGF, 0.5 ml; Insulin, 1.25 ml; Ascorbic Acid, 0.5 ml; GA-1000, 0.5 ml, L-Glutamine, 5.0 ml; FBS, 15 ml.
| | Sample_growth_protocol_ch1 | Grown at 37C in 5%CO2, seeded at 5000 cells/cm2
| | Sample_growth_protocol_ch1 | Untreated
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. Typically 40,000 cells were used. 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 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 Human Genome HG-U133_Plus_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 2 out of 3 NHA samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition
| | Sample_platform_id | GPL570
| | 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/GSM309nnn/GSM309429/suppl/GSM309429.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM309nnn/GSM309429/suppl/GSM309429.CHP.gz
| | Sample_series_id | GSE12305
| | Sample_data_row_count | 54675
| | |
|
GSM309431 | GPL570 |
|
Normal Human Astrocyte_Rep2
|
Normal Human Astrocytes from Lonza
|
Cell strain: Normal Human Astrocytes (NHA)
Passage: 4
Growth Medium: Astrocyte Basal Medium (ABM™) and the following growth supplements: rhEGF, 0.5 ml; Insulin, 1.25 ml; Ascorbic Acid, 0.5 ml; GA-1000, 0.5 ml, L-Glutamine, 5.0 ml; FBS, 15 ml.
Grown at 37C in 5%CO2, seeded at 5000 cells/cm2
Untreated
|
The control for hybridization and labeling were from Affymetrix.
|
| Sample_geo_accession | GSM309431
| | Sample_status | Public on Dec 31 2008
| | Sample_submission_date | Jul 31 2008
| | Sample_last_update_date | Aug 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Lonza (Basel, Switzerland)
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | Growth Medium: Astrocyte Basal Medium (ABM™) and the following growth supplements: rhEGF, 0.5 ml; Insulin, 1.25 ml; Ascorbic Acid, 0.5 ml; GA-1000, 0.5 ml, L-Glutamine, 5.0 ml; FBS, 15 ml.
| | Sample_growth_protocol_ch1 | Grown at 37C in 5%CO2, seeded at 5000 cells/cm2
| | Sample_growth_protocol_ch1 | Untreated
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. Typically 40,000 cells were used. 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 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 Human Genome HG-U133_Plus_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 2 out of 3 NHA samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition
| | Sample_platform_id | GPL570
| | 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/GSM309nnn/GSM309431/suppl/GSM309431.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM309nnn/GSM309431/suppl/GSM309431.CHP.gz
| | Sample_series_id | GSE12305
| | Sample_data_row_count | 54675
| | |
|
GSM309432 | GPL570 |
|
Normal Human Astrocyte_Rep3
|
Normal Human Astrocytes from Lonza
|
Cell strain: Normal Human Astrocytes (NHA)
Passage: 4
Growth Medium: Astrocyte Basal Medium (ABM™) and the following growth supplements: rhEGF, 0.5 ml; Insulin, 1.25 ml; Ascorbic Acid, 0.5 ml; GA-1000, 0.5 ml, L-Glutamine, 5.0 ml; FBS, 15 ml.
Grown at 37C in 5%CO2, seeded at 5000 cells/cm2
Untreated
|
The control for hybridization and labeling were from Affymetrix.
|
| Sample_geo_accession | GSM309432
| | Sample_status | Public on Dec 31 2008
| | Sample_submission_date | Jul 31 2008
| | Sample_last_update_date | Aug 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Lonza (Basel, Switzerland)
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | Growth Medium: Astrocyte Basal Medium (ABM™) and the following growth supplements: rhEGF, 0.5 ml; Insulin, 1.25 ml; Ascorbic Acid, 0.5 ml; GA-1000, 0.5 ml, L-Glutamine, 5.0 ml; FBS, 15 ml.
| | Sample_growth_protocol_ch1 | Grown at 37C in 5%CO2, seeded at 5000 cells/cm2
| | Sample_growth_protocol_ch1 | Untreated
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. Typically 40,000 cells were used. 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 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 Human Genome HG-U133_Plus_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 2 out of 3 NHA samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition
| | Sample_platform_id | GPL570
| | 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/GSM309nnn/GSM309432/suppl/GSM309432.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM309nnn/GSM309432/suppl/GSM309432.CHP.gz
| | Sample_series_id | GSE12305
| | Sample_data_row_count | 54675
| | |
|
GSM309433 | GPL570 |
|
U251_Rep1
|
ATCC
|
Cell strain: Normal Human Astrocytes (NHA)
Passage: 50
Growth Medium: Dulbecco's Modified Eagle Medium and the following growth supplements: Penicillin/streptomycin, 5.0 ml; L-Glutamine, 5.0 ml; FBS, 15 ml.
Grown at 37C in 5%CO2, seeded at 5000 cells/cm2
Untreated
|
The control for hybridization and labeling were from Affymetrix.
|
| Sample_geo_accession | GSM309433
| | Sample_status | Public on Dec 31 2008
| | Sample_submission_date | Jul 31 2008
| | Sample_last_update_date | Aug 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Lonza (Basel, Switzerland)
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | Growth Medium: Dulbecco's Modified Eagle Medium and the following growth supplements: Penicillin/streptomycin, 5.0 ml; L-Glutamine, 5.0 ml; FBS, 15 ml.
| | Sample_growth_protocol_ch1 | Grown at 37C in 5%CO2, seeded at 5000 cells/cm2
| | Sample_growth_protocol_ch1 | Untreated
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. Typically 40,000 cells were used. 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 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 Human Genome HG-U133_Plus_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 2 out of 3 NHA samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition
| | Sample_platform_id | GPL570
| | 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/GSM309nnn/GSM309433/suppl/GSM309433.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM309nnn/GSM309433/suppl/GSM309433.CHP.gz
| | Sample_series_id | GSE12305
| | Sample_data_row_count | 54675
| | |
|
GSM309435 | GPL570 |
|
U251_Rep2
|
ATCC
|
Cell strain: Normal Human Astrocytes (NHA)
Passage: 50
Growth Medium: Dulbecco's Modified Eagle Medium and the following growth supplements: Penicillin/streptomycin, 5.0 ml; L-Glutamine, 5.0 ml; FBS, 15 ml.
Grown at 37C in 5%CO2, seeded at 5000 cells/cm2
Untreated
|
The control for hybridization and labeling were from Affymetrix.
|
| Sample_geo_accession | GSM309435
| | Sample_status | Public on Dec 31 2008
| | Sample_submission_date | Jul 31 2008
| | Sample_last_update_date | Aug 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | Growth Medium: Dulbecco's Modified Eagle Medium and the following growth supplements: Penicillin/streptomycin, 5.0 ml; L-Glutamine, 5.0 ml; FBS, 15 ml.
| | Sample_growth_protocol_ch1 | Grown at 37C in 5%CO2, seeded at 5000 cells/cm2
| | Sample_growth_protocol_ch1 | Untreated
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. Typically 40,000 cells were used. 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 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 Human Genome HG-U133_Plus_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 2 out of 3 NHA samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition
| | Sample_platform_id | GPL570
| | 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/GSM309nnn/GSM309435/suppl/GSM309435.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM309nnn/GSM309435/suppl/GSM309435.CHP.gz
| | Sample_series_id | GSE12305
| | Sample_data_row_count | 54675
| | |
|
GSM309437 | GPL570 |
|
U251_Rep3
|
ATCC
|
Cell strain: Normal Human Astrocytes (NHA)
Passage: 50
Growth Medium: Dulbecco's Modified Eagle Medium and the following growth supplements: Penicillin/streptomycin, 5.0 ml; L-Glutamine, 5.0 ml; FBS, 15 ml.
Grown at 37C in 5%CO2, seeded at 5000 cells/cm2
Untreated
|
The control for hybridization and labeling were from Affymetrix.
|
| Sample_geo_accession | GSM309437
| | Sample_status | Public on Dec 31 2008
| | Sample_submission_date | Jul 31 2008
| | Sample_last_update_date | Aug 04 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | ATCC
| | Sample_treatment_protocol_ch1 | None
| | Sample_growth_protocol_ch1 | Growth Medium: Dulbecco's Modified Eagle Medium and the following growth supplements: Penicillin/streptomycin, 5.0 ml; L-Glutamine, 5.0 ml; FBS, 15 ml.
| | Sample_growth_protocol_ch1 | Grown at 37C in 5%CO2, seeded at 5000 cells/cm2
| | Sample_growth_protocol_ch1 | Untreated
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol® (Invitrogen, Carlsbad,CA) according to the manufacturer’s instruction. Typically 40,000 cells were used. 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 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 Human Genome HG-U133_Plus_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 2 out of 3 NHA samples had a present call and that at least one of the groups of replicates (non-infected/infected) fulfilled this condition
| | Sample_platform_id | GPL570
| | 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/GSM309nnn/GSM309437/suppl/GSM309437.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM309nnn/GSM309437/suppl/GSM309437.CHP.gz
| | Sample_series_id | GSE12305
| | Sample_data_row_count | 54675
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