Search results for the GEO ID: GSE19500  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM486380 | GPL96 |
|
Control 0h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 2
|
Normal human bronchial epithelial cells Control 0h
|
| Sample_geo_accession | GSM486380
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486380/suppl/GSM486380.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
|
GSM486381 | GPL96 |
|
Control 1h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 2
|
Normal human bronchial epithelial cells Control 1h
|
| Sample_geo_accession | GSM486381
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486381/suppl/GSM486381.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
|
GSM486382 | GPL96 |
|
Control 3h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 1
|
Normal human bronchial epithelial cells Control 3h
|
| Sample_geo_accession | GSM486382
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486382/suppl/GSM486382.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
|
GSM486383 | GPL96 |
|
Control 8h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 1
|
Normal human bronchial epithelial cells Control 8h
|
| Sample_geo_accession | GSM486383
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486383/suppl/GSM486383.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
|
GSM486384 | GPL96 |
|
Pressure 1h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 2
|
Normal human bronchial epithelial cells Pressure 1h
|
| Sample_geo_accession | GSM486384
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486384/suppl/GSM486384.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
|
GSM486385 | GPL96 |
|
Pressure 3h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 1
|
Normal human bronchial epithelial cells Pressure 3h
|
| Sample_geo_accession | GSM486385
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486385/suppl/GSM486385.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
|
GSM486386 | GPL96 |
|
Pressure 8h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 1
|
Normal human bronchial epithelial cells Pressure 8h
|
| Sample_geo_accession | GSM486386
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486386/suppl/GSM486386.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
|
GSM486387 | GPL96 |
|
AG1478 0h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 1
|
Normal human bronchial epithelial cells AG1478 0h
|
| Sample_geo_accession | GSM486387
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486387/suppl/GSM486387.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
|
GSM486388 | GPL96 |
|
AG1478 1h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 1
|
Normal human bronchial epithelial cells AG1478 1h
|
| Sample_geo_accession | GSM486388
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486388/suppl/GSM486388.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
|
GSM486389 | GPL96 |
|
AG1478 3h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 1
|
Normal human bronchial epithelial cells AG1478 3h
|
| Sample_geo_accession | GSM486389
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486389/suppl/GSM486389.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
|
GSM486390 | GPL96 |
|
AG1478 8h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 1
|
Normal human bronchial epithelial cells AG1478 8h
|
| Sample_geo_accession | GSM486390
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486390/suppl/GSM486390.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
|
GSM486391 | GPL96 |
|
Pressure + AG1478 1h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 1
|
Normal human bronchial epithelial cells Pressure + AG1478 1h
|
| Sample_geo_accession | GSM486391
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486391/suppl/GSM486391.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
|
GSM486392 | GPL96 |
|
Pressure + AG1478 3h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 1
|
Normal human bronchial epithelial cells Pressure + AG1478 3h
|
| Sample_geo_accession | GSM486392
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486392/suppl/GSM486392.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
|
GSM486393 | GPL96 |
|
Pressure + AG1478 8h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 2
|
Normal human bronchial epithelial cells Pressure + AG1478 8h
|
| Sample_geo_accession | GSM486393
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486393/suppl/GSM486393.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
|
GSM486394 | GPL96 |
|
HBEGF 1h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 1
|
Normal human bronchial epithelial cells HBEGF 1h
|
| Sample_geo_accession | GSM486394
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486394/suppl/GSM486394.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
|
GSM486395 | GPL96 |
|
HBEGF 3h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 1
|
Normal human bronchial epithelial cells HBEGF 3h
|
| Sample_geo_accession | GSM486395
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486395/suppl/GSM486395.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
|
GSM486396 | GPL96 |
|
HBEGF 8h
|
Normal human bronchial epithelial cells
|
cell type: bronchial epithelial cells
hybridization batch: 1
|
Normal human bronchial epithelial cells HBEGF 8h
|
| Sample_geo_accession | GSM486396
| | Sample_status | Public on Dec 16 2009
| | Sample_submission_date | Dec 15 2009
| | Sample_last_update_date | Dec 15 2009
| | 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 | Total RNA was purified from cell lysates (Rneasy; Qiagen). Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
| | Sample_hyb_protocol | Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
| | Sample_scan_protocol | Scanning is carried out on a GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
| | Sample_data_processing | All 17 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Alvin,T.,Kho
| | Sample_contact_email | alvin_kho@hms.harvard.edu
| | Sample_contact_phone | 617-355-6393
| | Sample_contact_department | Informatics Program
| | Sample_contact_institute | Boston Children's Hospital
| | Sample_contact_address | 320 Longwood Avenue
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM486nnn/GSM486396/suppl/GSM486396.CEL.gz
| | Sample_series_id | GSE19500
| | Sample_data_row_count | 22283
| | |
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