Search results for the GEO ID: GSE17073  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM427194 | GPL96 |
|
small airway epithelial cells (SAEC) replicate number 1
|
small airway epithelial cells in culture
|
cell line: SAEC
|
airway epithelial cells form the lung and purchased from Cambrex/Clonetics. Cells were used at the second passage.
The sample is one replicate of two small airway epithelial cells (SAEC) which are considered normal (non-malignant) lung epithelial cells from the small airways of the lung.
|
| Sample_geo_accession | GSM427194
| | Sample_status | Public on Jul 16 2009
| | Sample_submission_date | Jul 13 2009
| | Sample_last_update_date | Jul 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 extracted and purified using the RNeasy mini kit from Qiagen according to the manufacturer's instructions. RNA was treated with DNase provided by Qiagen to elilminate any genomic DNA. a total of 1 microgram of RNA was reverse-transcribed using the Quantitect Reverse Transcription kit from Qiagen for generation of first-strand cDNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following clean-up of double-stranded cDNA by phenol/chloroform extraction and ethanol precipitation, biotin-labeled cRNA were synthesized by in vitro transcription (IVT) reaction using the ENZO BioArray High Yield RNA transcript labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_label_protocol_ch1 | The following were added to a fresh 1.5-mL microcentrifuge tube: 1 µg double-stranded cDNA, RNase/Dnase free water, 4 µL of 10X HY reaction buffer, 4 µL of 10X Biotin-labeled ribonucleotides, 4 µL of 10X DTT, 4 µL of 10X RNase inhibitor mix and 2 µL of T7 RNA polymerase.
| | Sample_label_protocol_ch1 | The mixture was incubated at 37°C for 4 – 5 hours, mixing the tube every 30 – 45 minutes.
| | Sample_label_protocol_ch1 | cRNA were then cleaned with RNeasy spin columns from Qiagen with two rounds of elution for maximum recovery followed by ethanol precipitation and dilution in RNase free water.
| | Sample_hyb_protocol | One vial of the 20X eukaryotic hybridization controls and a vial of oligo B2 (included in the GeneChip Eukaryotic hybridization control kit) were thawed by heating the vials at 65°C for 5 minutes.
| | Sample_hyb_protocol | A hybridization cocktail consisting of 15 micrograms of the cRNA, 5 ul of the control oligo B2, 15 ul of eukaryotic hybridization controls, 3 ul of Herring sperm DNA, 3 ul of acetylated BSA, 150 ul of 2 x hybridization buffer and 300 ul of water.
| | Sample_hyb_protocol | Probe arrays were then equilibrated to room temperature.
| | Sample_hyb_protocol | The hybridization cocktail was heated to 99°C for 5 minutes, spun briefly and transfered to 45°C for 5 minutes.
| | Sample_hyb_protocol | Hybridization/cocktail was spun at maximum speed for 5 minutes to remove any insoluble material.
| | Sample_hyb_protocol | The probe array was wetted by filling it through one of the septa with 1X hybridization buffer and incubated at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | The buffer solution was then removed from the probe array which was then filled with the appropriate amount of the clarified hybridization cocktail. Hybridization was then performed overnight at 45°C with rotation.
| | Sample_scan_protocol | The array was scanned with a GeneChip® Scanner 3000 from Affymetrix and raw image file was converted to probe set data (*.CEL file), using the Affymetrix GeneChip® Operating Software.
| | Sample_data_processing | The raw data were analyzed by normalization using robust multichip average (RMA). Values were log (base 2) transformed.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Humam,,Kadara
| | Sample_contact_institute | University of Texas MD Anderson Cancer Center
| | Sample_contact_address | 1515 Holcombe Blvd
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM427nnn/GSM427194/suppl/GSM427194.CEL.gz
| | Sample_series_id | GSE17073
| | Sample_data_row_count | 22283
| | |
|
GSM427195 | GPL96 |
|
small airway epithelial cells (SAEC) replicate number 2
|
small airway epithelial cells in culture
|
cell line: SAEC
|
epithelial cells from the small airway of the lung purchased fromCambrex/Clonetics and used at the second passage
The sample is one replicate of two small airway epithelial cells (SAEC) which are considered normal (non-malignant) lung epithelial cells from the small airways of the lung.
|
| Sample_geo_accession | GSM427195
| | Sample_status | Public on Jul 16 2009
| | Sample_submission_date | Jul 13 2009
| | Sample_last_update_date | Jul 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 extracted and purified using the RNeasy mini kit from Qiagen according to the manufacturer's instructions. RNA was treated with DNase provided by Qiagen to elilminate any genomic DNA. a total of 1 microgram of RNA was reverse-transcribed using the Quantitect Reverse Transcription kit from Qiagen for generation of first-strand cDNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following clean-up of double-stranded cDNA by phenol/chloroform extraction and ethanol precipitation, biotin-labeled cRNA were synthesized by in vitro transcription (IVT) reaction using the ENZO BioArray High Yield RNA transcript labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_label_protocol_ch1 | The following were added to a fresh 1.5-mL microcentrifuge tube: 1 µg double-stranded cDNA, RNase/Dnase free water, 4 µL of 10X HY reaction buffer, 4 µL of 10X Biotin-labeled ribonucleotides, 4 µL of 10X DTT, 4 µL of 10X RNase inhibitor mix and 2 µL of T7 RNA polymerase.
| | Sample_label_protocol_ch1 | The mixture was incubated at 37°C for 4 – 5 hours, mixing the tube every 30 – 45 minutes.
| | Sample_label_protocol_ch1 | cRNA were then cleaned with RNeasy spin columns from Qiagen with two rounds of elution for maximum recovery followed by ethanol precipitation and dilution in RNase free water.
| | Sample_hyb_protocol | One vial of the 20X eukaryotic hybridization controls and a vial of oligo B2 (included in the GeneChip Eukaryotic hybridization control kit) were thawed by heating the vials at 65°C for 5 minutes.
| | Sample_hyb_protocol | A hybridization cocktail consisting of 15 micrograms of the cRNA, 5 ul of the control oligo B2, 15 ul of eukaryotic hybridization controls, 3 ul of Herring sperm DNA, 3 ul of acetylated BSA, 150 ul of 2 x hybridization buffer and 300 ul of water.
| | Sample_hyb_protocol | Probe arrays were then equilibrated to room temperature.
| | Sample_hyb_protocol | The hybridization cocktail was heated to 99°C for 5 minutes, spun briefly and transfered to 45°C for 5 minutes.
| | Sample_hyb_protocol | Hybridization/cocktail was spun at maximum speed for 5 minutes to remove any insoluble material.
| | Sample_hyb_protocol | The probe array was wetted by filling it through one of the septa with 1X hybridization buffer and incubated at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | The buffer solution was then removed from the probe array which was then filled with the appropriate amount of the clarified hybridization cocktail. Hybridization was then performed overnight at 45°C with rotation.
| | Sample_scan_protocol | The array was scanned with a GeneChip® Scanner 3000 from Affymetrix and raw image file was converted to probe set data (*.CEL file), using the Affymetrix GeneChip® Operating Software.
| | Sample_data_processing | The raw data were analyzed by normalization using robust multichip average (RMA). Values were log (base 2) transformed.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Humam,,Kadara
| | Sample_contact_institute | University of Texas MD Anderson Cancer Center
| | Sample_contact_address | 1515 Holcombe Blvd
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM427nnn/GSM427195/suppl/GSM427195.CEL.gz
| | Sample_series_id | GSE17073
| | Sample_data_row_count | 22283
| | |
|
GSM427196 | GPL96 |
|
normal human bronchial epithelial cells (NHBE) replicate number 1
|
normal human bronchial epithelial cells in culture
|
cell line: NHBE
|
NHBE cells purchased from Cambrex/Clonetics and used at the second passage.
This sample is the first replicate of two samples of normal human bronchial epithelial cells.
|
| Sample_geo_accession | GSM427196
| | Sample_status | Public on Jul 16 2009
| | Sample_submission_date | Jul 13 2009
| | Sample_last_update_date | Jul 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 extracted and purified using the RNeasy mini kit from Qiagen according to the manufacturer's instructions. RNA was treated with DNase provided by Qiagen to remove any genomic DNA. a total of 1 microgram of RNA was reverse-transcribed using the Quantitect Reverse Transcription kit from Qiagen for generation of first-strand cDNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following clean-up of double-stranded cDNA by phenol/chloroform extraction and ethanol precipitation, biotin-labeled cRNA were synthesized by in vitro transcription (IVT) reaction using the ENZO BioArray High Yield RNA transcript labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_label_protocol_ch1 | The following were added to a fresh 1.5-mL microcentrifuge tube: 1 µg double-stranded cDNA, RNase/Dnase free water, 4 µL of 10X HY reaction buffer, 4 µL of 10X Biotin-labeled ribonucleotides, 4 µL of 10X DTT, 4 µL of 10X RNase inhibitor mix and 2 µL of T7 RNA polymerase.
| | Sample_label_protocol_ch1 | The mixture was incubated at 37°C for 4 – 5 hours, mixing the tube every 30 – 45 minutes.
| | Sample_label_protocol_ch1 | cRNA were then cleaned with RNeasy spin columns from Qiagen with two rounds of elution for maximum recovery followed by ethanol precipitation and dilution in RNase free water.
| | Sample_hyb_protocol | One vial of the 20X eukaryotic hybridization controls and a vial of oligo B2 (included in the GeneChip Eukaryotic hybridization control kit) were thawed by heating the vials at 65°C for 5 minutes.
| | Sample_hyb_protocol | A hybridization cocktail consisting of 15 micrograms of the cRNA, 5 ul of the control oligo B2, 15 ul of eukaryotic hybridization controls, 3 ul of Herring sperm DNA, 3 ul of acetylated BSA, 150 ul of 2 x hybridization buffer and 300 ul of water.
| | Sample_hyb_protocol | Probe arrays were then equilibrated to room temperature.
| | Sample_hyb_protocol | The hybridization cocktail was heated to 99°C for 5 minutes, spun briefly and transfered to 45°C for 5 minutes.
| | Sample_hyb_protocol | Hybridization/cocktail was spun at maximum speed for 5 minutes to remove any insoluble material.
| | Sample_hyb_protocol | The probe array was wetted by filling it through one of the septa with 1X hybridization buffer and incubated at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | The buffer solution was then removed from the probe array which was then filled with the appropriate amount of the clarified hybridization cocktail. Hybridization was then performed overnight at 45°C with rotation.
| | Sample_scan_protocol | The array was scanned with a GeneChip® Scanner 3000 from Affymetrix and raw image file was converted to probe set data (*.CEL file), using the Affymetrix GeneChip® Operating Software.
| | Sample_data_processing | The raw data were analyzed by normalization using robust multichip average (RMA). Values were log (base 2) transformed.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Humam,,Kadara
| | Sample_contact_institute | University of Texas MD Anderson Cancer Center
| | Sample_contact_address | 1515 Holcombe Blvd
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM427nnn/GSM427196/suppl/GSM427196.CEL.gz
| | Sample_series_id | GSE17073
| | Sample_data_row_count | 22283
| | |
|
GSM427197 | GPL96 |
|
normal human bronchial epithelial cells (NHBE) replicate number 2
|
transcriptome of normal human bronchial epithelial cells
|
cell line: NHBE
|
NHBE cells purchased from Cambrex/Clonetics and used at the second passage
This sample is the second replicate of normal human bronchial epithelial cells
|
| Sample_geo_accession | GSM427197
| | Sample_status | Public on Jul 16 2009
| | Sample_submission_date | Jul 13 2009
| | Sample_last_update_date | Jul 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 extracted and purified using the RNeasy mini kit from Qiagen according to the manufacturer's instructions. RNA was treated with DNase provided by Qiagen to remove any genomic DNA. a total of 1 microgram of RNA was reverse-transcribed using the Quantitect Reverse Transcription kit from Qiagen for generation of first-strand cDNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following clean-up of double-stranded cDNA by phenol/chloroform extraction and ethanol precipitation, biotin-labeled cRNA were synthesized by in vitro transcription (IVT) reaction using the ENZO BioArray High Yield RNA transcript labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_label_protocol_ch1 | The following were added to a fresh 1.5-mL microcentrifuge tube: 1 µg double-stranded cDNA, RNase/Dnase free water, 4 µL of 10X HY reaction buffer, 4 µL of 10X Biotin-labeled ribonucleotides, 4 µL of 10X DTT, 4 µL of 10X RNase inhibitor mix and 2 µL of T7 RNA polymerase.
| | Sample_label_protocol_ch1 | The mixture was incubated at 37°C for 4 – 5 hours, mixing the tube every 30 – 45 minutes.
| | Sample_label_protocol_ch1 | cRNA were then cleaned with RNeasy spin columns from Qiagen with two rounds of elution for maximum recovery followed by ethanol precipitation and dilution in RNase free water.
| | Sample_hyb_protocol | One vial of the 20X eukaryotic hybridization controls and a vial of oligo B2 (included in the GeneChip Eukaryotic hybridization control kit) were thawed by heating the vials at 65°C for 5 minutes.
| | Sample_hyb_protocol | A hybridization cocktail consisting of 15 micrograms of the cRNA, 5 ul of the control oligo B2, 15 ul of eukaryotic hybridization controls, 3 ul of Herring sperm DNA, 3 ul of acetylated BSA, 150 ul of 2 x hybridization buffer and 300 ul of water.
| | Sample_hyb_protocol | Probe arrays were then equilibrated to room temperature.
| | Sample_hyb_protocol | The hybridization cocktail was heated to 99°C for 5 minutes, spun briefly and transfered to 45°C for 5 minutes.
| | Sample_hyb_protocol | Hybridization/cocktail was spun at maximum speed for 5 minutes to remove any insoluble material.
| | Sample_hyb_protocol | The probe array was wetted by filling it through one of the septa with 1X hybridization buffer and incubated at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | The buffer solution was then removed from the probe array which was then filled with the appropriate amount of the clarified hybridization cocktail. Hybridization was then performed overnight at 45°C with rotation.
| | Sample_scan_protocol | The array was scanned with a GeneChip® Scanner 3000 from Affymetrix and raw image file was converted to probe set data (*.CEL file), using the Affymetrix GeneChip® Operating Software.
| | Sample_data_processing | The raw data were analyzed by normalization using robust multichip average (RMA). Values were log (base 2) transformed.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Humam,,Kadara
| | Sample_contact_institute | University of Texas MD Anderson Cancer Center
| | Sample_contact_address | 1515 Holcombe Blvd
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM427nnn/GSM427197/suppl/GSM427197.CEL.gz
| | Sample_series_id | GSE17073
| | Sample_data_row_count | 22283
| | |
|
GSM427198 | GPL96 |
|
immortalized bronchial epithelial cells (BEAS-2B) replicate number 1
|
SV40 large T-immortalized bronchial epithelial cells
|
cell line: BEAS-2B
|
The BEAS-2B cells were generated by Klein-Szanto et al in 1992 by introduction of the SV40 large cell T-antigen into normal bronchial epithelial cells rendering them immortalized.
This sample is the first replicate of immortalized BEAS-2B cells.
|
| Sample_geo_accession | GSM427198
| | Sample_status | Public on Jul 16 2009
| | Sample_submission_date | Jul 13 2009
| | Sample_last_update_date | Jul 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 extracted and purified using the RNeasy mini kit from Qiagen according to the manufacturer's instructions. RNA was treated with DNase provided by Qiagen to remove any genomic DNA. a total of 1 microgram of RNA was reverse-transcribed using the Quantitect Reverse Transcription kit from Qiagen for generation of first-strand cDNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following clean-up of double-stranded cDNA by phenol/chloroform extraction and ethanol precipitation, biotin-labeled cRNA were synthesized by in vitro transcription (IVT) reaction using the ENZO BioArray High Yield RNA transcript labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_label_protocol_ch1 | The following were added to a fresh 1.5-mL microcentrifuge tube: 1 µg double-stranded cDNA, RNase/Dnase free water, 4 µL of 10X HY reaction buffer, 4 µL of 10X Biotin-labeled ribonucleotides, 4 µL of 10X DTT, 4 µL of 10X RNase inhibitor mix and 2 µL of T7 RNA polymerase.
| | Sample_label_protocol_ch1 | The mixture was incubated at 37°C for 4 – 5 hours, mixing the tube every 30 – 45 minutes.
| | Sample_label_protocol_ch1 | cRNA were then cleaned with RNeasy spin columns from Qiagen with two rounds of elution for maximum recovery followed by ethanol precipitation and dilution in RNase free water.
| | Sample_hyb_protocol | One vial of the 20X eukaryotic hybridization controls and a vial of oligo B2 (included in the GeneChip Eukaryotic hybridization control kit) were thawed by heating the vials at 65°C for 5 minutes.
| | Sample_hyb_protocol | A hybridization cocktail consisting of 15 micrograms of the cRNA, 5 ul of the control oligo B2, 15 ul of eukaryotic hybridization controls, 3 ul of Herring sperm DNA, 3 ul of acetylated BSA, 150 ul of 2 x hybridization buffer and 300 ul of water.
| | Sample_hyb_protocol | Probe arrays were then equilibrated to room temperature.
| | Sample_hyb_protocol | The hybridization cocktail was heated to 99°C for 5 minutes, spun briefly and transfered to 45°C for 5 minutes.
| | Sample_hyb_protocol | Hybridization/cocktail was spun at maximum speed for 5 minutes to remove any insoluble material.
| | Sample_hyb_protocol | The probe array was wetted by filling it through one of the septa with 1X hybridization buffer and incubated at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | The buffer solution was then removed from the probe array which was then filled with the appropriate amount of the clarified hybridization cocktail. Hybridization was then performed overnight at 45°C with rotation.
| | Sample_scan_protocol | The array was scanned with a GeneChip® Scanner 3000 from Affymetrix and raw image file was converted to probe set data (*.CEL file), using the Affymetrix GeneChip® Operating Software.
| | Sample_data_processing | The raw data were analyzed by normalization using robust multichip average (RMA). Values were log (base 2) transformed.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Humam,,Kadara
| | Sample_contact_institute | University of Texas MD Anderson Cancer Center
| | Sample_contact_address | 1515 Holcombe Blvd
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM427nnn/GSM427198/suppl/GSM427198.CEL.gz
| | Sample_series_id | GSE17073
| | Sample_data_row_count | 22283
| | |
|
GSM427199 | GPL96 |
|
immortalized bronchial epithelial cells (BEAS-2B) replicate number 2
|
SV40 large T-immortalized bronchial epithelial cells
|
cell line: BEAS-2B
|
The BEAS-2B cells were generated by Klein-Szanto et al in 1992 by introduction of the SV40 large cell T-antigen into normal bronchial epithelial cells rendering them immortalized.
This sample is the second replicate of immortalized BEAS-2B cells.
|
| Sample_geo_accession | GSM427199
| | Sample_status | Public on Jul 16 2009
| | Sample_submission_date | Jul 13 2009
| | Sample_last_update_date | Jul 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 extracted and purified using the RNeasy mini kit from Qiagen according to the manufacturer's instructions. RNA was treated with DNase provided by Qiagen to remove any genomic DNA. a total of 1 microgram of RNA was reverse-transcribed using the Quantitect Reverse Transcription kit from Qiagen for generation of first-strand cDNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following clean-up of double-stranded cDNA by phenol/chloroform extraction and ethanol precipitation, biotin-labeled cRNA were synthesized by in vitro transcription (IVT) reaction using the ENZO BioArray High Yield RNA transcript labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_label_protocol_ch1 | The following were added to a fresh 1.5-mL microcentrifuge tube: 1 µg double-stranded cDNA, RNase/Dnase free water, 4 µL of 10X HY reaction buffer, 4 µL of 10X Biotin-labeled ribonucleotides, 4 µL of 10X DTT, 4 µL of 10X RNase inhibitor mix and 2 µL of T7 RNA polymerase.
| | Sample_label_protocol_ch1 | The mixture was incubated at 37°C for 4 – 5 hours, mixing the tube every 30 – 45 minutes.
| | Sample_label_protocol_ch1 | cRNA were then cleaned with RNeasy spin columns from Qiagen with two rounds of elution for maximum recovery followed by ethanol precipitation and dilution in RNase free water.
| | Sample_hyb_protocol | One vial of the 20X eukaryotic hybridization controls and a vial of oligo B2 (included in the GeneChip Eukaryotic hybridization control kit) were thawed by heating the vials at 65°C for 5 minutes.
| | Sample_hyb_protocol | A hybridization cocktail consisting of 15 micrograms of the cRNA, 5 ul of the control oligo B2, 15 ul of eukaryotic hybridization controls, 3 ul of Herring sperm DNA, 3 ul of acetylated BSA, 150 ul of 2 x hybridization buffer and 300 ul of water.
| | Sample_hyb_protocol | Probe arrays were then equilibrated to room temperature.
| | Sample_hyb_protocol | The hybridization cocktail was heated to 99°C for 5 minutes, spun briefly and transfered to 45°C for 5 minutes.
| | Sample_hyb_protocol | Hybridization/cocktail was spun at maximum speed for 5 minutes to remove any insoluble material.
| | Sample_hyb_protocol | The probe array was wetted by filling it through one of the septa with 1X hybridization buffer and incubated at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | The buffer solution was then removed from the probe array which was then filled with the appropriate amount of the clarified hybridization cocktail. Hybridization was then performed overnight at 45°C with rotation.
| | Sample_scan_protocol | The array was scanned with a GeneChip® Scanner 3000 from Affymetrix and raw image file was converted to probe set data (*.CEL file), using the Affymetrix GeneChip® Operating Software.
| | Sample_data_processing | The raw data were analyzed by normalization using robust multichip average (RMA). Values were log (base 2) transformed.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Humam,,Kadara
| | Sample_contact_institute | University of Texas MD Anderson Cancer Center
| | Sample_contact_address | 1515 Holcombe Blvd
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM427nnn/GSM427199/suppl/GSM427199.CEL.gz
| | Sample_series_id | GSE17073
| | Sample_data_row_count | 22283
| | |
|
GSM427200 | GPL96 |
|
1799 immortalized lung epithelial cells replicate number 1
|
1799 immortalized lung epithelial cells in culture isolated from xenografts in mice
|
cell line: 1799
|
The 1799 immortalized lung epithelial cells were isolated and cultured from xenografts in mice (by Klein-Szanto et al, 1992) after introduction of de-epitheliazed tracheas containing the immortalized BEAS-2B cells and a beeswax pellet containing an organic solvent vehicle.
This sample is the firstreplicate of immortalized 1799 cells.
|
| Sample_geo_accession | GSM427200
| | Sample_status | Public on Jul 16 2009
| | Sample_submission_date | Jul 13 2009
| | Sample_last_update_date | Jul 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 extracted and purified using the RNeasy mini kit from Qiagen according to the manufacturer's instructions. RNA was treated with DNase provided by Qiagen to remove any genomic DNA. a total of 1 microgram of RNA was reverse-transcribed using the Quantitect Reverse Transcription kit from Qiagen for generation of first-strand cDNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following clean-up of double-stranded cDNA by phenol/chloroform extraction and ethanol precipitation, biotin-labeled cRNA were synthesized by in vitro transcription (IVT) reaction using the ENZO BioArray High Yield RNA transcript labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_label_protocol_ch1 | The following were added to a fresh 1.5-mL microcentrifuge tube: 1 µg double-stranded cDNA, RNase/Dnase free water, 4 µL of 10X HY reaction buffer, 4 µL of 10X Biotin-labeled ribonucleotides, 4 µL of 10X DTT, 4 µL of 10X RNase inhibitor mix and 2 µL of T7 RNA polymerase.
| | Sample_label_protocol_ch1 | The mixture was incubated at 37°C for 4 – 5 hours, mixing the tube every 30 – 45 minutes.
| | Sample_label_protocol_ch1 | cRNA were then cleaned with RNeasy spin columns from Qiagen with two rounds of elution for maximum recovery followed by ethanol precipitation and dilution in RNase free water.
| | Sample_hyb_protocol | One vial of the 20X eukaryotic hybridization controls and a vial of oligo B2 (included in the GeneChip Eukaryotic hybridization control kit) were thawed by heating the vials at 65°C for 5 minutes.
| | Sample_hyb_protocol | A hybridization cocktail consisting of 15 micrograms of the cRNA, 5 ul of the control oligo B2, 15 ul of eukaryotic hybridization controls, 3 ul of Herring sperm DNA, 3 ul of acetylated BSA, 150 ul of 2 x hybridization buffer and 300 ul of water.
| | Sample_hyb_protocol | Probe arrays were then equilibrated to room temperature.
| | Sample_hyb_protocol | The hybridization cocktail was heated to 99°C for 5 minutes, spun briefly and transfered to 45°C for 5 minutes.
| | Sample_hyb_protocol | Hybridization/cocktail was spun at maximum speed for 5 minutes to remove any insoluble material.
| | Sample_hyb_protocol | The probe array was wetted by filling it through one of the septa with 1X hybridization buffer and incubated at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | The buffer solution was then removed from the probe array which was then filled with the appropriate amount of the clarified hybridization cocktail. Hybridization was then performed overnight at 45°C with rotation.
| | Sample_scan_protocol | The array was scanned with a GeneChip® Scanner 3000 from Affymetrix and raw image file was converted to probe set data (*.CEL file), using the Affymetrix GeneChip® Operating Software.
| | Sample_data_processing | The raw data were analyzed by normalization using robust multichip average (RMA). Values were log (base 2) transformed.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Humam,,Kadara
| | Sample_contact_institute | University of Texas MD Anderson Cancer Center
| | Sample_contact_address | 1515 Holcombe Blvd
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM427nnn/GSM427200/suppl/GSM427200.CEL.gz
| | Sample_series_id | GSE17073
| | Sample_data_row_count | 22283
| | |
|
GSM427201 | GPL96 |
|
1799 immortalized lung epithelial cells replicate number 2
|
1799 immortalized lung epithelial cells in culture isolated from xenografts in mice
|
cell line: 1799
|
The 1799 immortalized lung epithelial cells were isolated and cultured from xenografts in mice (by Klein-Szanto et al, 1992) after introduction of de-epitheliazed tracheas containing the immortalized BEAS-2B cells and a beeswax pellet containing an organic solvent vehicle.
This sample is the second replicate of immortalized 1799 cells.
|
| Sample_geo_accession | GSM427201
| | Sample_status | Public on Jul 16 2009
| | Sample_submission_date | Jul 13 2009
| | Sample_last_update_date | Jul 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 extracted and purified using the RNeasy mini kit from Qiagen according to the manufacturer's instructions. RNA was treated with DNase provided by Qiagen to remove any genomic DNA. a total of 1 microgram of RNA was reverse-transcribed using the Quantitect Reverse Transcription kit from Qiagen for generation of first-strand cDNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following clean-up of double-stranded cDNA by phenol/chloroform extraction and ethanol precipitation, biotin-labeled cRNA were synthesized by in vitro transcription (IVT) reaction using the ENZO BioArray High Yield RNA transcript labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_label_protocol_ch1 | The following were added to a fresh 1.5-mL microcentrifuge tube: 1 µg double-stranded cDNA, RNase/Dnase free water, 4 µL of 10X HY reaction buffer, 4 µL of 10X Biotin-labeled ribonucleotides, 4 µL of 10X DTT, 4 µL of 10X RNase inhibitor mix and 2 µL of T7 RNA polymerase.
| | Sample_label_protocol_ch1 | The mixture was incubated at 37°C for 4 – 5 hours, mixing the tube every 30 – 45 minutes.
| | Sample_label_protocol_ch1 | cRNA were then cleaned with RNeasy spin columns from Qiagen with two rounds of elution for maximum recovery followed by ethanol precipitation and dilution in RNase free water.
| | Sample_hyb_protocol | One vial of the 20X eukaryotic hybridization controls and a vial of oligo B2 (included in the GeneChip Eukaryotic hybridization control kit) were thawed by heating the vials at 65°C for 5 minutes.
| | Sample_hyb_protocol | A hybridization cocktail consisting of 15 micrograms of the cRNA, 5 ul of the control oligo B2, 15 ul of eukaryotic hybridization controls, 3 ul of Herring sperm DNA, 3 ul of acetylated BSA, 150 ul of 2 x hybridization buffer and 300 ul of water.
| | Sample_hyb_protocol | Probe arrays were then equilibrated to room temperature.
| | Sample_hyb_protocol | The hybridization cocktail was heated to 99°C for 5 minutes, spun briefly and transfered to 45°C for 5 minutes.
| | Sample_hyb_protocol | Hybridization/cocktail was spun at maximum speed for 5 minutes to remove any insoluble material.
| | Sample_hyb_protocol | The probe array was wetted by filling it through one of the septa with 1X hybridization buffer and incubated at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | The buffer solution was then removed from the probe array which was then filled with the appropriate amount of the clarified hybridization cocktail. Hybridization was then performed overnight at 45°C with rotation.
| | Sample_scan_protocol | The array was scanned with a GeneChip® Scanner 3000 from Affymetrix and raw image file was converted to probe set data (*.CEL file), using the Affymetrix GeneChip® Operating Software.
| | Sample_data_processing | The raw data were analyzed by normalization using robust multichip average (RMA). Values were log (base 2) transformed.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Humam,,Kadara
| | Sample_contact_institute | University of Texas MD Anderson Cancer Center
| | Sample_contact_address | 1515 Holcombe Blvd
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM427nnn/GSM427201/suppl/GSM427201.CEL.gz
| | Sample_series_id | GSE17073
| | Sample_data_row_count | 22283
| | |
|
GSM427202 | GPL96 |
|
1198 transformed lung epithelial cells replicate number 1
|
1198 transformed lung epithelial cells isolated from xenografts in mice
|
cell line: 1198
|
The 1198 transformed lung epithelial cells were isolated and cultured from xenografts in mice (by Klein-Szanto et al, 1992) after introduction of de-epitheliazed tracheas containing the immortalized BEAS-2B cells and a beeswax pellet containing tobacco-specific carcinogen. The 1198 therefore developed in vivo rather than by in vitro manipulations. The 1198 exhibit transformed properties as they are able to grow in soft agar.
This sample is the first replicate of immortalized 1198 cells.
|
| Sample_geo_accession | GSM427202
| | Sample_status | Public on Jul 16 2009
| | Sample_submission_date | Jul 13 2009
| | Sample_last_update_date | Jul 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 extracted and purified using the RNeasy mini kit from Qiagen according to the manufacturer's instructions. RNA was treated with DNase provided by Qiagen to remove any genomic DNA. a total of 1 microgram of RNA was reverse-transcribed using the Quantitect Reverse Transcription kit from Qiagen for generation of first-strand cDNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following clean-up of double-stranded cDNA by phenol/chloroform extraction and ethanol precipitation, biotin-labeled cRNA were synthesized by in vitro transcription (IVT) reaction using the ENZO BioArray High Yield RNA transcript labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_label_protocol_ch1 | The following were added to a fresh 1.5-mL microcentrifuge tube: 1 µg double-stranded cDNA, RNase/Dnase free water, 4 µL of 10X HY reaction buffer, 4 µL of 10X Biotin-labeled ribonucleotides, 4 µL of 10X DTT, 4 µL of 10X RNase inhibitor mix and 2 µL of T7 RNA polymerase.
| | Sample_label_protocol_ch1 | The mixture was incubated at 37°C for 4 – 5 hours, mixing the tube every 30 – 45 minutes.
| | Sample_label_protocol_ch1 | cRNA were then cleaned with RNeasy spin columns from Qiagen with two rounds of elution for maximum recovery followed by ethanol precipitation and dilution in RNase free water.
| | Sample_hyb_protocol | One vial of the 20X eukaryotic hybridization controls and a vial of oligo B2 (included in the GeneChip Eukaryotic hybridization control kit) were thawed by heating the vials at 65°C for 5 minutes.
| | Sample_hyb_protocol | A hybridization cocktail consisting of 15 micrograms of the cRNA, 5 ul of the control oligo B2, 15 ul of eukaryotic hybridization controls, 3 ul of Herring sperm DNA, 3 ul of acetylated BSA, 150 ul of 2 x hybridization buffer and 300 ul of water.
| | Sample_hyb_protocol | Probe arrays were then equilibrated to room temperature.
| | Sample_hyb_protocol | The hybridization cocktail was heated to 99°C for 5 minutes, spun briefly and transfered to 45°C for 5 minutes.
| | Sample_hyb_protocol | Hybridization/cocktail was spun at maximum speed for 5 minutes to remove any insoluble material.
| | Sample_hyb_protocol | The probe array was wetted by filling it through one of the septa with 1X hybridization buffer and incubated at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | The buffer solution was then removed from the probe array which was then filled with the appropriate amount of the clarified hybridization cocktail. Hybridization was then performed overnight at 45°C with rotation.
| | Sample_scan_protocol | The array was scanned with a GeneChip® Scanner 3000 from Affymetrix and raw image file was converted to probe set data (*.CEL file), using the Affymetrix GeneChip® Operating Software.
| | Sample_data_processing | The raw data were analyzed by normalization using robust multichip average (RMA). Values were log (base 2) transformed.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Humam,,Kadara
| | Sample_contact_institute | University of Texas MD Anderson Cancer Center
| | Sample_contact_address | 1515 Holcombe Blvd
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM427nnn/GSM427202/suppl/GSM427202.CEL.gz
| | Sample_series_id | GSE17073
| | Sample_data_row_count | 22283
| | |
|
GSM427203 | GPL96 |
|
1198 transformed lung epithelial cells replicate number 2
|
1198 transformed lung epithelial cells isolated and cultured from xenografts in mice
|
cell line: 1198
|
The 1198 transformed lung epithelial cells were isolated and cultured from xenografts in mice (by Klein-Szanto et al, 1992) after introduction of de-epitheliazed tracheas containing the immortalized BEAS-2B cells and a beeswax pellet containing tobacco-specific carcinogen. The 1198 developed in vivo rather than with in vitro manipulations. The 1198 lung epithelial cells exhibited transformed properties as they were able to grow on soft agar.
This sample is the second replicate of transformed 1198 cells.
|
| Sample_geo_accession | GSM427203
| | Sample_status | Public on Jul 16 2009
| | Sample_submission_date | Jul 13 2009
| | Sample_last_update_date | Jul 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 extracted and purified using the RNeasy mini kit from Qiagen according to the manufacturer's instructions. RNA was treated with DNase provided by Qiagen to remove any genomic DNA. a total of 1 microgram of RNA was reverse-transcribed using the Quantitect Reverse Transcription kit from Qiagen for generation of first-strand cDNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following clean-up of double-stranded cDNA by phenol/chloroform extraction and ethanol precipitation, biotin-labeled cRNA were synthesized by in vitro transcription (IVT) reaction using the ENZO BioArray High Yield RNA transcript labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_label_protocol_ch1 | The following were added to a fresh 1.5-mL microcentrifuge tube: 1 µg double-stranded cDNA, RNase/Dnase free water, 4 µL of 10X HY reaction buffer, 4 µL of 10X Biotin-labeled ribonucleotides, 4 µL of 10X DTT, 4 µL of 10X RNase inhibitor mix and 2 µL of T7 RNA polymerase.
| | Sample_label_protocol_ch1 | The mixture was incubated at 37°C for 4 – 5 hours, mixing the tube every 30 – 45 minutes.
| | Sample_label_protocol_ch1 | cRNA were then cleaned with RNeasy spin columns from Qiagen with two rounds of elution for maximum recovery followed by ethanol precipitation and dilution in RNase free water.
| | Sample_hyb_protocol | One vial of the 20X eukaryotic hybridization controls and a vial of oligo B2 (included in the GeneChip Eukaryotic hybridization control kit) were thawed by heating the vials at 65°C for 5 minutes.
| | Sample_hyb_protocol | A hybridization cocktail consisting of 15 micrograms of the cRNA, 5 ul of the control oligo B2, 15 ul of eukaryotic hybridization controls, 3 ul of Herring sperm DNA, 3 ul of acetylated BSA, 150 ul of 2 x hybridization buffer and 300 ul of water.
| | Sample_hyb_protocol | Probe arrays were then equilibrated to room temperature.
| | Sample_hyb_protocol | The hybridization cocktail was heated to 99°C for 5 minutes, spun briefly and transfered to 45°C for 5 minutes.
| | Sample_hyb_protocol | Hybridization/cocktail was spun at maximum speed for 5 minutes to remove any insoluble material.
| | Sample_hyb_protocol | The probe array was wetted by filling it through one of the septa with 1X hybridization buffer and incubated at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | The buffer solution was then removed from the probe array which was then filled with the appropriate amount of the clarified hybridization cocktail. Hybridization was then performed overnight at 45°C with rotation.
| | Sample_scan_protocol | The array was scanned with a GeneChip® Scanner 3000 from Affymetrix and raw image file was converted to probe set data (*.CEL file), using the Affymetrix GeneChip® Operating Software.
| | Sample_data_processing | The raw data were analyzed by normalization using robust multichip average (RMA). Values were log (base 2) transformed.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Humam,,Kadara
| | Sample_contact_institute | University of Texas MD Anderson Cancer Center
| | Sample_contact_address | 1515 Holcombe Blvd
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM427nnn/GSM427203/suppl/GSM427203.CEL.gz
| | Sample_series_id | GSE17073
| | Sample_data_row_count | 22283
| | |
|
GSM427204 | GPL96 |
|
1170-I tumorigenic lung epithelial cells replicate number 1
|
1170-I tumorigenic lung epithelial cells isolated and cultured from xenografts in mice
|
cell line: 1170-I
|
The 1170-I tumorigenic lung epithelial cells were isolated and cultured from xenografts in mice (by Klein-Szanto et al, 1992) after introduction of de-epitheliazed tracheas containing the immortalized BEAS-2B cells and a beeswax pellet containing a tobacco-specific carcinogen. The tumorigenic 1170-I cells developed in vivo rather than in vitro and were tumorigenic as they formed invasive lung adenocarcinomas when injected into nude mice.
This sample is the first replicate of tumorigenic 1170-I cells.
|
| Sample_geo_accession | GSM427204
| | Sample_status | Public on Jul 16 2009
| | Sample_submission_date | Jul 13 2009
| | Sample_last_update_date | Jul 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 extracted and purified using the RNeasy mini kit from Qiagen according to the manufacturer's instructions. RNA was treated with DNase provided by Qiagen to remove any genomic DNA. a total of 1 microgram of RNA was reverse-transcribed using the Quantitect Reverse Transcription kit from Qiagen for generation of first-strand cDNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following clean-up of double-stranded cDNA by phenol/chloroform extraction and ethanol precipitation, biotin-labeled cRNA were synthesized by in vitro transcription (IVT) reaction using the ENZO BioArray High Yield RNA transcript labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_label_protocol_ch1 | The following were added to a fresh 1.5-mL microcentrifuge tube: 1 µg double-stranded cDNA, RNase/Dnase free water, 4 µL of 10X HY reaction buffer, 4 µL of 10X Biotin-labeled ribonucleotides, 4 µL of 10X DTT, 4 µL of 10X RNase inhibitor mix and 2 µL of T7 RNA polymerase.
| | Sample_label_protocol_ch1 | The mixture was incubated at 37°C for 4 – 5 hours, mixing the tube every 30 – 45 minutes.
| | Sample_label_protocol_ch1 | cRNA were then cleaned with RNeasy spin columns from Qiagen with two rounds of elution for maximum recovery followed by ethanol precipitation and dilution in RNase free water.
| | Sample_hyb_protocol | One vial of the 20X eukaryotic hybridization controls and a vial of oligo B2 (included in the GeneChip Eukaryotic hybridization control kit) were thawed by heating the vials at 65°C for 5 minutes.
| | Sample_hyb_protocol | A hybridization cocktail consisting of 15 micrograms of the cRNA, 5 ul of the control oligo B2, 15 ul of eukaryotic hybridization controls, 3 ul of Herring sperm DNA, 3 ul of acetylated BSA, 150 ul of 2 x hybridization buffer and 300 ul of water.
| | Sample_hyb_protocol | Probe arrays were then equilibrated to room temperature.
| | Sample_hyb_protocol | The hybridization cocktail was heated to 99°C for 5 minutes, spun briefly and transfered to 45°C for 5 minutes.
| | Sample_hyb_protocol | Hybridization/cocktail was spun at maximum speed for 5 minutes to remove any insoluble material.
| | Sample_hyb_protocol | The probe array was wetted by filling it through one of the septa with 1X hybridization buffer and incubated at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | The buffer solution was then removed from the probe array which was then filled with the appropriate amount of the clarified hybridization cocktail. Hybridization was then performed overnight at 45°C with rotation.
| | Sample_scan_protocol | The array was scanned with a GeneChip® Scanner 3000 from Affymetrix and raw image file was converted to probe set data (*.CEL file), using the Affymetrix GeneChip® Operating Software.
| | Sample_data_processing | The raw data were analyzed by normalization using robust multichip average (RMA). Values were log (base 2) transformed.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Humam,,Kadara
| | Sample_contact_institute | University of Texas MD Anderson Cancer Center
| | Sample_contact_address | 1515 Holcombe Blvd
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM427nnn/GSM427204/suppl/GSM427204.CEL.gz
| | Sample_series_id | GSE17073
| | Sample_data_row_count | 22283
| | |
|
GSM427205 | GPL96 |
|
1170-I tumorigenic lung epithelial cells replicate number 2
|
1170-I tumorigenic lung epithelial cells isolated and cultured from xenografts in mice
|
cell line: 1170-I
|
The 1170-I tumorigenic lung epithelial cells were isolated and cultured from xenografts in mice (by Klein-Szanto et al, 1992) after introduction of de-epitheliazed tracheas containing the immortalized human BEAS-2B cells and a beeswax pellet containing a tobacco-specific carcinogen. The tumorigenic 1170-I cells developed in vivo rather than in vitro and were tumorigenic as they formed invasive lung adenocarcinomas when injected into nude mice.
This sample is the second replicate of tumorigenic 1170-I cells.
|
| Sample_geo_accession | GSM427205
| | Sample_status | Public on Jul 16 2009
| | Sample_submission_date | Jul 13 2009
| | Sample_last_update_date | Jul 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 extracted and purified using the RNeasy mini kit from Qiagen according to the manufacturer's instructions. RNA was treated with DNase provided by Qiagen to remove any genomic DNA. a total of 1 microgram of RNA was reverse-transcribed using the Quantitect Reverse Transcription kit from Qiagen for generation of first-strand cDNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Following clean-up of double-stranded cDNA by phenol/chloroform extraction and ethanol precipitation, biotin-labeled cRNA were synthesized by in vitro transcription (IVT) reaction using the ENZO BioArray High Yield RNA transcript labeling kit (Affymetrix, Santa Clara, CA).
| | Sample_label_protocol_ch1 | The following were added to a fresh 1.5-mL microcentrifuge tube: 1 µg double-stranded cDNA, RNase/Dnase free water, 4 µL of 10X HY reaction buffer, 4 µL of 10X Biotin-labeled ribonucleotides, 4 µL of 10X DTT, 4 µL of 10X RNase inhibitor mix and 2 µL of T7 RNA polymerase.
| | Sample_label_protocol_ch1 | The mixture was incubated at 37°C for 4 – 5 hours, mixing the tube every 30 – 45 minutes.
| | Sample_label_protocol_ch1 | cRNA were then cleaned with RNeasy spin columns from Qiagen with two rounds of elution for maximum recovery followed by ethanol precipitation and dilution in RNase free water.
| | Sample_hyb_protocol | One vial of the 20X eukaryotic hybridization controls and a vial of oligo B2 (included in the GeneChip Eukaryotic hybridization control kit) were thawed by heating the vials at 65°C for 5 minutes.
| | Sample_hyb_protocol | A hybridization cocktail consisting of 15 micrograms of the cRNA, 5 ul of the control oligo B2, 15 ul of eukaryotic hybridization controls, 3 ul of Herring sperm DNA, 3 ul of acetylated BSA, 150 ul of 2 x hybridization buffer and 300 ul of water.
| | Sample_hyb_protocol | Probe arrays were then equilibrated to room temperature.
| | Sample_hyb_protocol | The hybridization cocktail was heated to 99°C for 5 minutes, spun briefly and transfered to 45°C for 5 minutes.
| | Sample_hyb_protocol | Hybridization/cocktail was spun at maximum speed for 5 minutes to remove any insoluble material.
| | Sample_hyb_protocol | The probe array was wetted by filling it through one of the septa with 1X hybridization buffer and incubated at 45°C for 10 minutes with rotation.
| | Sample_hyb_protocol | The buffer solution was then removed from the probe array which was then filled with the appropriate amount of the clarified hybridization cocktail. Hybridization was then performed overnight at 45°C with rotation.
| | Sample_scan_protocol | The array was scanned with a GeneChip® Scanner 3000 from Affymetrix and raw image file was converted to probe set data (*.CEL file), using the Affymetrix GeneChip® Operating Software.
| | Sample_data_processing | The raw data were analyzed by normalization using robust multichip average (RMA). Values were log (base 2) transformed.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Humam,,Kadara
| | Sample_contact_institute | University of Texas MD Anderson Cancer Center
| | Sample_contact_address | 1515 Holcombe Blvd
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM427nnn/GSM427205/suppl/GSM427205.CEL.gz
| | Sample_series_id | GSE17073
| | Sample_data_row_count | 22283
| | |
|
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