Search results for the GEO ID: GSE12253 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM287147 | GPL570 |
|
Untreated-Rep1
|
airway epithelial cells, lot number, ethanol treated or vehicle untreated
|
human airway epithelial cells were obtained from commercial source.
|
Cells were grown on millicells inserts of a 24-well tissue dish. Cells were seeded with 10,000 per millicell initially and used at 24,000 to 46,000 cells.
|
Sample_geo_accession | GSM287147
| Sample_status | Public on Apr 05 2010
| Sample_submission_date | May 06 2008
| Sample_last_update_date | Apr 05 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_biomaterial_provider_ch1 | Lonza
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Sample was processed using the Trizol method.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 5 ug total RNA was used for first strand synthesis using T7-(dT)24 primer (Affymetrix) and SuperScript cDNA Synthesis Kit (Invitrogen). Synthesis of biotinylated-labeled cRNA was carried out using the RNA Transcript Labeling Kit (ENZO).
| Sample_hyb_protocol | After the prehybridization of the GeneChip, 15 ug of fragmented cDNA was pipetted into a GeneChip and hybridized overnight in the Hybridization Oven 640 at 60 rpm, washed, stained with streptavidin-phycoerythrin using a microfluidics station as described by the manufacture.
| Sample_scan_protocol | Chips were scanned with the High Resolution 3000 Scanner (G7) and signal and background intensities were quantitated by pixel intensity, and expression signals were analyzed using the GeneChip Operating Software (GCOS 1.4). Expresson signals were scaled to a target intensity of 500.
| Sample_data_processing | The CEL data file from each array was imported into Genespring GX 7.3 (Agilent Technologies) and preprocessed using the robust multichip average (RMA) method and per gene normalization was applied using the median values of the no EtOH control samples. The CHP files were also imported and the detection call metrics from the CHP files were used to filter out transcripts that were found absent in all nine samples. In addition, transcripts that were not within a standard deviation of 1.4 and exhibiting less than 1.5 fold change were also removed from further analysis. To identify up-regulated and down-regulated transcripts, genes were filtered using the volcano plot with the limit set at p<0.01 and 2.0 fold change. The parametric test, with variance not equal, was applied without multiple test correction.
| Sample_platform_id | GPL570
| Sample_contact_name | guoshon,,wang
| Sample_contact_email | gwang@lsuhsc.edu
| Sample_contact_fax | 504-568-8500
| Sample_contact_department | Gene Therapy
| Sample_contact_institute | LSUHSC
| Sample_contact_address | 533 Bolivar St.
| Sample_contact_city | New Orleans
| Sample_contact_state | LA
| Sample_contact_zip/postal_code | 70112
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287147/suppl/GSM287147.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287147/suppl/GSM287147.CHP.gz
| Sample_series_id | GSE12253
| Sample_data_row_count | 54675
| |
|
GSM287502 | GPL570 |
|
100mM Ethanol-Rep1
|
airway epithelial cells-lot number, ethanol treated or vehicle untreated
|
human airway epithelial cells were obtained from commercial source
|
Cells were grown on millicells inserts of a 24-well tissue dish. Cells were seeded with 10,000 per millicell initially and used at 24,000 to 46,000 cells.
|
Sample_geo_accession | GSM287502
| Sample_status | Public on Apr 05 2010
| Sample_submission_date | May 07 2008
| Sample_last_update_date | Apr 05 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | sample was processed using the Trizol method
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 5 ug total RNA was used for first strand synthesis using T7-(dT)24 primer (Affymetrix) and SuperScript cDNA Synthesis Kit (Invitrogen). Synthesis of biotinylated-labeled cRNA was carried out using the RNA Transcript Labeling Kit (ENZO).
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | After the prehybridization of the GeneChip, 15 ug of fragmented cDNA was pipetted into a GeneChip and hybridized overnight in the Hybridization Oven 640 at 60 rpm, washed, stained with streptavidin-phycoerythrin using a microfluidics station as described by the manufacture.
| Sample_scan_protocol | Chips were scanned with the High Resolution 3000 Scanner (G7) and signal and background intensities were quantitated by pixel intensity, and expression signals were analyzed using the GeneChip Operating Software (GCOS 1.4). Expresson signals were scaled to a target intensity of 500.
| Sample_scan_protocol |
| Sample_scan_protocol |
| Sample_data_processing | The CEL data file from each array was imported into Genespring GX 7.3 (Agilent Technologies) and preprocessed using the robust multichip average (RMA) method and per gene normalization was applied using the median values of the no EtOH control samples. The CHP files were also imported and the detection call metrics from the CHP files were used to filter out transcripts that were found absent in all nine samples. In addition, transcripts that were not within a standard deviation of 1.4 and exhibiting less than 1.5 fold change were also removed from further analysis. To identify up-regulated and down-regulated transcripts, genes were filtered using the volcano plot with the limit set at p<0.01 and 2.0 fold change. The parametric test, with variance not equal, was applied without multiple test correction.
| Sample_data_processing |
| Sample_platform_id | GPL570
| Sample_contact_name | guoshon,,wang
| Sample_contact_email | gwang@lsuhsc.edu
| Sample_contact_fax | 504-568-8500
| Sample_contact_department | Gene Therapy
| Sample_contact_institute | LSUHSC
| Sample_contact_address | 533 Bolivar St.
| Sample_contact_city | New Orleans
| Sample_contact_state | LA
| Sample_contact_zip/postal_code | 70112
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287502/suppl/GSM287502.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287502/suppl/GSM287502.CHP.gz
| Sample_series_id | GSE12253
| Sample_data_row_count | 54675
| |
|
GSM287504 | GPL570 |
|
Untreated-Rep2
|
airway epithelial cells, lot number, ethanol treated or vehicle untreated
|
human airway epithelial cells were obtained from commercial source
|
Cells were grown on millicells inserts of a 24-well tissue dish. Cells were seeded with 10,000 per millicell initially and used at 24,000 to 46,000 cells.
|
Sample_geo_accession | GSM287504
| Sample_status | Public on Apr 05 2010
| Sample_submission_date | May 07 2008
| Sample_last_update_date | Apr 05 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | sample was processed using the Trizol method
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 5 ug total RNA was used for first strand synthesis using T7-(dT)24 primer (Affymetrix) and SuperScript cDNA Synthesis Kit (Invitrogen). Synthesis of biotinylated-labeled cRNA was carried out using the RNA Transcript Labeling Kit (ENZO).
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | After the prehybridization of the GeneChip, 15 ug of fragmented cDNA was pipetted into a GeneChip and hybridized overnight in the Hybridization Oven 640 at 60 rpm, washed, stained with streptavidin-phycoerythrin using a microfluidics station as described by the manufacture.
| Sample_scan_protocol | Chips were scanned with the High Resolution 3000 Scanner (G7) and signal and background intensities were quantitated by pixel intensity, and expression signals were analyzed using the GeneChip Operating Software (GCOS 1.4). Expresson signals were scaled to a target intensity of 500.
| Sample_scan_protocol |
| Sample_scan_protocol |
| Sample_data_processing | The CEL data file from each array was imported into Genespring GX 7.3 (Agilent Technologies) and preprocessed using the robust multichip average (RMA) method and per gene normalization was applied using the median values of the no EtOH control samples. The CHP files were also imported and the detection call metrics from the CHP files were used to filter out transcripts that were found absent in all nine samples. In addition, transcripts that were not within a standard deviation of 1.4 and exhibiting less than 1.5 fold change were also removed from further analysis. To identify up-regulated and down-regulated transcripts, genes were filtered using the volcano plot with the limit set at p<0.01 and 2.0 fold change. The parametric test, with variance not equal, was applied without multiple test correction.
| Sample_data_processing |
| Sample_platform_id | GPL570
| Sample_contact_name | guoshon,,wang
| Sample_contact_email | gwang@lsuhsc.edu
| Sample_contact_fax | 504-568-8500
| Sample_contact_department | Gene Therapy
| Sample_contact_institute | LSUHSC
| Sample_contact_address | 533 Bolivar St.
| Sample_contact_city | New Orleans
| Sample_contact_state | LA
| Sample_contact_zip/postal_code | 70112
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287504/suppl/GSM287504.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287504/suppl/GSM287504.CHP.gz
| Sample_series_id | GSE12253
| Sample_data_row_count | 54675
| |
|
GSM287507 | GPL570 |
|
50mM Ethanol-Rep2
|
airway epithelial cells, lot number, ethanol treated or vehicle untreated
|
human airway epithelial cells were obtained from commercial source
|
Cells were grown on millicells inserts of a 24-well tissue dish. Cells were seeded with 10,000 per millicell initially and used at 24,000 to 46,000 cells.
|
Sample_geo_accession | GSM287507
| Sample_status | Public on Apr 05 2010
| Sample_submission_date | May 07 2008
| Sample_last_update_date | Apr 05 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | sample was processed using the Trizol method
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 5 ug total RNA was used for first strand synthesis using T7-(dT)24 primer (Affymetrix) and SuperScript cDNA Synthesis Kit (Invitrogen). Synthesis of biotinylated-labeled cRNA was carried out using the RNA Transcript Labeling Kit (ENZO).
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | After the prehybridization of the GeneChip, 15 ug of fragmented cDNA was pipetted into a GeneChip and hybridized overnight in the Hybridization Oven 640 at 60 rpm, washed, stained with streptavidin-phycoerythrin using a microfluidics station as described by the manufacture.
| Sample_scan_protocol | Chips were scanned with the High Resolution 3000 Scanner (G7) and signal and background intensities were quantitated by pixel intensity, and expression signals were analyzed using the GeneChip Operating Software (GCOS 1.4). Expresson signals were scaled to a target intensity of 500.
| Sample_scan_protocol |
| Sample_scan_protocol |
| Sample_data_processing | The CEL data file from each array was imported into Genespring GX 7.3 (Agilent Technologies) and preprocessed using the robust multichip average (RMA) method and per gene normalization was applied using the median values of the no EtOH control samples. The CHP files were also imported and the detection call metrics from the CHP files were used to filter out transcripts that were found absent in all nine samples. In addition, transcripts that were not within a standard deviation of 1.4 and exhibiting less than 1.5 fold change were also removed from further analysis. To identify up-regulated and down-regulated transcripts, genes were filtered using the volcano plot with the limit set at p<0.01 and 2.0 fold change. The parametric test, with variance not equal, was applied without multiple test correction.
| Sample_data_processing |
| Sample_platform_id | GPL570
| Sample_contact_name | guoshon,,wang
| Sample_contact_email | gwang@lsuhsc.edu
| Sample_contact_fax | 504-568-8500
| Sample_contact_department | Gene Therapy
| Sample_contact_institute | LSUHSC
| Sample_contact_address | 533 Bolivar St.
| Sample_contact_city | New Orleans
| Sample_contact_state | LA
| Sample_contact_zip/postal_code | 70112
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287507/suppl/GSM287507.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287507/suppl/GSM287507.CHP.gz
| Sample_series_id | GSE12253
| Sample_data_row_count | 54675
| |
|
GSM287508 | GPL570 |
|
100mM Ethanol-Rep2
|
airway epithelial cells, lot number, ethanol treated or vehicle untreated
|
human airway epithelial cells were obtained from commercial source
|
Cells were grown on millicells inserts of a 24-well tissue dish. Cells were seeded with 10,000 per millicell initially and used at 24,000 to 46,000 cells.
|
Sample_geo_accession | GSM287508
| Sample_status | Public on Apr 05 2010
| Sample_submission_date | May 07 2008
| Sample_last_update_date | Apr 05 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | sample was processed using the Trizol method
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 5 ug total RNA was used for first strand synthesis using T7-(dT)24 primer (Affymetrix) and SuperScript cDNA Synthesis Kit (Invitrogen). Synthesis of biotinylated-labeled cRNA was carried out using the RNA Transcript Labeling Kit (ENZO).
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | After the prehybridization of the GeneChip, 15 ug of fragmented cDNA was pipetted into a GeneChip and hybridized overnight in the Hybridization Oven 640 at 60 rpm, washed, stained with streptavidin-phycoerythrin using a microfluidics station as described by the manufacture.
| Sample_scan_protocol | Chips were scanned with the High Resolution 3000 Scanner (G7) and signal and background intensities were quantitated by pixel intensity, and expression signals were analyzed using the GeneChip Operating Software (GCOS 1.4). Expresson signals were scaled to a target intensity of 500.
| Sample_scan_protocol |
| Sample_scan_protocol |
| Sample_data_processing | The CEL data file from each array was imported into Genespring GX 7.3 (Agilent Technologies) and preprocessed using the robust multichip average (RMA) method and per gene normalization was applied using the median values of the no EtOH control samples. The CHP files were also imported and the detection call metrics from the CHP files were used to filter out transcripts that were found absent in all nine samples. In addition, transcripts that were not within a standard deviation of 1.4 and exhibiting less than 1.5 fold change were also removed from further analysis. To identify up-regulated and down-regulated transcripts, genes were filtered using the volcano plot with the limit set at p<0.01 and 2.0 fold change. The parametric test, with variance not equal, was applied without multiple test correction.
| Sample_data_processing |
| Sample_platform_id | GPL570
| Sample_contact_name | guoshon,,wang
| Sample_contact_email | gwang@lsuhsc.edu
| Sample_contact_fax | 504-568-8500
| Sample_contact_department | Gene Therapy
| Sample_contact_institute | LSUHSC
| Sample_contact_address | 533 Bolivar St.
| Sample_contact_city | New Orleans
| Sample_contact_state | LA
| Sample_contact_zip/postal_code | 70112
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287508/suppl/GSM287508.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287508/suppl/GSM287508.CHP.gz
| Sample_series_id | GSE12253
| Sample_data_row_count | 54675
| |
|
GSM287509 | GPL570 |
|
Untreated-Rep3
|
airway epithelial cells, lot number, ethanol treated or vehicle untreated
|
human airway epithelial cells were obtained from commercial source
|
Cells were grown on millicells inserts of a 24-well tissue dish. Cells were seeded with 10,000 per millicell initially and used at 24,000 to 46,000 cells.
|
Sample_geo_accession | GSM287509
| Sample_status | Public on Apr 05 2010
| Sample_submission_date | May 07 2008
| Sample_last_update_date | Apr 05 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | sample was processed using the Trizol method
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 5 ug total RNA was used for first strand synthesis using T7-(dT)24 primer (Affymetrix) and SuperScript cDNA Synthesis Kit (Invitrogen). Synthesis of biotinylated-labeled cRNA was carried out using the RNA Transcript Labeling Kit (ENZO).
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | After the prehybridization of the GeneChip, 15 ug of fragmented cDNA was pipetted into a GeneChip and hybridized overnight in the Hybridization Oven 640 at 60 rpm, washed, stained with streptavidin-phycoerythrin using a microfluidics station as described by the manufacture.
| Sample_scan_protocol | Chips were scanned with the High Resolution 3000 Scanner (G7) and signal and background intensities were quantitated by pixel intensity, and expression signals were analyzed using the GeneChip Operating Software (GCOS 1.4). Expresson signals were scaled to a target intensity of 500.
| Sample_scan_protocol |
| Sample_scan_protocol |
| Sample_data_processing | The CEL data file from each array was imported into Genespring GX 7.3 (Agilent Technologies) and preprocessed using the robust multichip average (RMA) method and per gene normalization was applied using the median values of the no EtOH control samples. The CHP files were also imported and the detection call metrics from the CHP files were used to filter out transcripts that were found absent in all nine samples. In addition, transcripts that were not within a standard deviation of 1.4 and exhibiting less than 1.5 fold change were also removed from further analysis. To identify up-regulated and down-regulated transcripts, genes were filtered using the volcano plot with the limit set at p<0.01 and 2.0 fold change. The parametric test, with variance not equal, was applied without multiple test correction.
| Sample_data_processing |
| Sample_platform_id | GPL570
| Sample_contact_name | guoshon,,wang
| Sample_contact_email | gwang@lsuhsc.edu
| Sample_contact_fax | 504-568-8500
| Sample_contact_department | Gene Therapy
| Sample_contact_institute | LSUHSC
| Sample_contact_address | 533 Bolivar St.
| Sample_contact_city | New Orleans
| Sample_contact_state | LA
| Sample_contact_zip/postal_code | 70112
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287509/suppl/GSM287509.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287509/suppl/GSM287509.CHP.gz
| Sample_series_id | GSE12253
| Sample_data_row_count | 54675
| |
|
GSM287510 | GPL570 |
|
50mM Ethanol-Rep3
|
airway epithelial cells, lot number, ethanol treated or vehicle untreated
|
human airway epithelial cells were obtained from commercial source
|
Cells were grown on millicells inserts of a 24-well tissue dish. Cells were seeded with 10,000 per millicell initially and used at 24,000 to 46,000 cells.
|
Sample_geo_accession | GSM287510
| Sample_status | Public on Apr 05 2010
| Sample_submission_date | May 07 2008
| Sample_last_update_date | Apr 05 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | sample was processed using the Trizol method
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 5 ug total RNA was used for first strand synthesis using T7-(dT)24 primer (Affymetrix) and SuperScript cDNA Synthesis Kit (Invitrogen). Synthesis of biotinylated-labeled cRNA was carried out using the RNA Transcript Labeling Kit (ENZO).
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | After the prehybridization of the GeneChip, 15 ug of fragmented cDNA was pipetted into a GeneChip and hybridized overnight in the Hybridization Oven 640 at 60 rpm, washed, stained with streptavidin-phycoerythrin using a microfluidics station as described by the manufacture.
| Sample_scan_protocol | Chips were scanned with the High Resolution 3000 Scanner (G7) and signal and background intensities were quantitated by pixel intensity, and expression signals were analyzed using the GeneChip Operating Software (GCOS 1.4). Expresson signals were scaled to a target intensity of 500.
| Sample_scan_protocol |
| Sample_scan_protocol |
| Sample_data_processing | The CEL data file from each array was imported into Genespring GX 7.3 (Agilent Technologies) and preprocessed using the robust multichip average (RMA) method and per gene normalization was applied using the median values of the no EtOH control samples. The CHP files were also imported and the detection call metrics from the CHP files were used to filter out transcripts that were found absent in all nine samples. In addition, transcripts that were not within a standard deviation of 1.4 and exhibiting less than 1.5 fold change were also removed from further analysis. To identify up-regulated and down-regulated transcripts, genes were filtered using the volcano plot with the limit set at p<0.01 and 2.0 fold change. The parametric test, with variance not equal, was applied without multiple test correction.
| Sample_data_processing |
| Sample_platform_id | GPL570
| Sample_contact_name | guoshon,,wang
| Sample_contact_email | gwang@lsuhsc.edu
| Sample_contact_fax | 504-568-8500
| Sample_contact_department | Gene Therapy
| Sample_contact_institute | LSUHSC
| Sample_contact_address | 533 Bolivar St.
| Sample_contact_city | New Orleans
| Sample_contact_state | LA
| Sample_contact_zip/postal_code | 70112
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287510/suppl/GSM287510.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287510/suppl/GSM287510.CHP.gz
| Sample_series_id | GSE12253
| Sample_data_row_count | 54675
| |
|
GSM287514 | GPL570 |
|
100mM Ethanol-Rep3
|
airway epithelial cells, lot number, ethanol treated or vehicle untreated
|
human airway epithelial cells were obtained from commercial source
|
Cells were grown on millicells inserts of a 24-well tissue dish. Cells were seeded with 10,000 per millicell initially and used at 24,000 to 46,000 cells.
|
Sample_geo_accession | GSM287514
| Sample_status | Public on Apr 05 2010
| Sample_submission_date | May 07 2008
| Sample_last_update_date | Apr 05 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | sample was processed using the Trizol method
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 5 ug total RNA was used for first strand synthesis using T7-(dT)24 primer (Affymetrix) and SuperScript cDNA Synthesis Kit (Invitrogen). Synthesis of biotinylated-labeled cRNA was carried out using the RNA Transcript Labeling Kit (ENZO).
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | After the prehybridization of the GeneChip, 15 ug of fragmented cDNA was pipetted into a GeneChip and hybridized overnight in the Hybridization Oven 640 at 60 rpm, washed, stained with streptavidin-phycoerythrin using a microfluidics station as described by the manufacture.
| Sample_scan_protocol | Chips were scanned with the High Resolution 3000 Scanner (G7) and signal and background intensities were quantitated by pixel intensity, and expression signals were analyzed using the GeneChip Operating Software (GCOS 1.4). Expresson signals were scaled to a target intensity of 500.
| Sample_scan_protocol |
| Sample_scan_protocol |
| Sample_data_processing | The CEL data file from each array was imported into Genespring GX 7.3 (Agilent Technologies) and preprocessed using the robust multichip average (RMA) method and per gene normalization was applied using the median values of the no EtOH control samples. The CHP files were also imported and the detection call metrics from the CHP files were used to filter out transcripts that were found absent in all nine samples. In addition, transcripts that were not within a standard deviation of 1.4 and exhibiting less than 1.5 fold change were also removed from further analysis. To identify up-regulated and down-regulated transcripts, genes were filtered using the volcano plot with the limit set at p<0.01 and 2.0 fold change. The parametric test, with variance not equal, was applied without multiple test correction.
| Sample_data_processing |
| Sample_platform_id | GPL570
| Sample_contact_name | guoshon,,wang
| Sample_contact_email | gwang@lsuhsc.edu
| Sample_contact_fax | 504-568-8500
| Sample_contact_department | Gene Therapy
| Sample_contact_institute | LSUHSC
| Sample_contact_address | 533 Bolivar St.
| Sample_contact_city | New Orleans
| Sample_contact_state | LA
| Sample_contact_zip/postal_code | 70112
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287514/suppl/GSM287514.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287514/suppl/GSM287514.CHP.gz
| Sample_series_id | GSE12253
| Sample_data_row_count | 54675
| |
|
GSM287515 | GPL570 |
|
50mM Ethanol-Rep1
|
airway epithelial cells, lot number, ethanol treated or vehicle untreated
|
human airway epithelial cells were obtained from commercial source
|
Cells were grown on millicells inserts of a 24-well tissue dish. Cells were seeded with 10,000 per millicell initially and used at 24,000 to 46,000 cells.
|
Sample_geo_accession | GSM287515
| Sample_status | Public on Apr 05 2010
| Sample_submission_date | May 07 2008
| Sample_last_update_date | Apr 05 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | sample was processed using the Trizol method
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 5 ug total RNA was used for first strand synthesis using T7-(dT)24 primer (Affymetrix) and SuperScript cDNA Synthesis Kit (Invitrogen). Synthesis of biotinylated-labeled cRNA was carried out using the RNA Transcript Labeling Kit (ENZO).
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | After the prehybridization of the GeneChip, 15 ug of fragmented cDNA was pipetted into a GeneChip and hybridized overnight in the Hybridization Oven 640 at 60 rpm, washed, stained with streptavidin-phycoerythrin using a microfluidics station as described by the manufacture.
| Sample_scan_protocol | Chips were scanned with the High Resolution 3000 Scanner (G7) and signal and background intensities were quantitated by pixel intensity, and expression signals were analyzed using the GeneChip Operating Software (GCOS 1.4). Expresson signals were scaled to a target intensity of 500.
| Sample_scan_protocol |
| Sample_scan_protocol |
| Sample_data_processing | The CEL data file from each array was imported into Genespring GX 7.3 (Agilent Technologies) and preprocessed using the robust multichip average (RMA) method and per gene normalization was applied using the median values of the no EtOH control samples. The CHP files were also imported and the detection call metrics from the CHP files were used to filter out transcripts that were found absent in all nine samples. In addition, transcripts that were not within a standard deviation of 1.4 and exhibiting less than 1.5 fold change were also removed from further analysis. To identify up-regulated and down-regulated transcripts, genes were filtered using the volcano plot with the limit set at p<0.01 and 2.0 fold change. The parametric test, with variance not equal, was applied without multiple test correction.
| Sample_data_processing |
| Sample_platform_id | GPL570
| Sample_contact_name | guoshon,,wang
| Sample_contact_email | gwang@lsuhsc.edu
| Sample_contact_fax | 504-568-8500
| Sample_contact_department | Gene Therapy
| Sample_contact_institute | LSUHSC
| Sample_contact_address | 533 Bolivar St.
| Sample_contact_city | New Orleans
| Sample_contact_state | LA
| Sample_contact_zip/postal_code | 70112
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287515/suppl/GSM287515.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287515/suppl/GSM287515.CHP.gz
| Sample_series_id | GSE12253
| Sample_data_row_count | 54675
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