Search results for the GEO ID: GSE18454  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM459743 | GPL570 |
|
normal human bronchial epithelial cell line treated with 5-AZA rep 1
|
NHBE AZA rep 1
|
tissue: Lung
cell line: NHBE
agent: 5-aza-dC and TSA
|
no additional information
|
| Sample_geo_accession | GSM459743
| | Sample_status | Public on Oct 07 2010
| | Sample_submission_date | Oct 07 2009
| | Sample_last_update_date | Oct 07 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis. Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY). IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer. 15ug cRNA is fragmented using 5X fragmentation buffer (made in-house).
| | Sample_hyb_protocol | Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA. 10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours. After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain.
| | Sample_scan_protocol | All arrays are scanned in the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,,Glazer
| | Sample_contact_institute | Johns Hopkins Medical Institutions
| | Sample_contact_address | 1550 Orleans St. CRB II-574
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM459nnn/GSM459743/suppl/GSM459743.CEL.gz
| | Sample_series_id | GSE18454
| | Sample_data_row_count | 54613
| | |
|
GSM459744 | GPL570 |
|
normal human bronchial epithelial cell line treated with 5-AZA rep 2
|
NHBE AZA rep 2
|
tissue: Lung
cell line: NHBE
agent: 5-aza-dC and TSA
|
no additional information
|
| Sample_geo_accession | GSM459744
| | Sample_status | Public on Oct 07 2010
| | Sample_submission_date | Oct 07 2009
| | Sample_last_update_date | Oct 07 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis. Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY). IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer. 15ug cRNA is fragmented using 5X fragmentation buffer (made in-house).
| | Sample_hyb_protocol | Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA. 10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours. After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain.
| | Sample_scan_protocol | All arrays are scanned in the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,,Glazer
| | Sample_contact_institute | Johns Hopkins Medical Institutions
| | Sample_contact_address | 1550 Orleans St. CRB II-574
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM459nnn/GSM459744/suppl/GSM459744.CEL.gz
| | Sample_series_id | GSE18454
| | Sample_data_row_count | 54613
| | |
|
GSM459745 | GPL570 |
|
normal human bronchial epithelial cell line treated with 5-AZA rep 3
|
NHBE AZA rep 3
|
tissue: Lung
cell line: NHBE
agent: 5-aza-dC and TSA
|
no additional information
|
| Sample_geo_accession | GSM459745
| | Sample_status | Public on Oct 07 2010
| | Sample_submission_date | Oct 07 2009
| | Sample_last_update_date | Oct 07 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis. Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY). IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer. 15ug cRNA is fragmented using 5X fragmentation buffer (made in-house).
| | Sample_hyb_protocol | Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA. 10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours. After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain.
| | Sample_scan_protocol | All arrays are scanned in the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,,Glazer
| | Sample_contact_institute | Johns Hopkins Medical Institutions
| | Sample_contact_address | 1550 Orleans St. CRB II-574
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM459nnn/GSM459745/suppl/GSM459745.CEL.gz
| | Sample_series_id | GSE18454
| | Sample_data_row_count | 54613
| | |
|
GSM459746 | GPL570 |
|
normal human bronchial epithelial cell line control rep 1
|
NHBE control rep 1
|
tissue: Lung
cell line: NHBE
agent: mock-treated
|
no additional information
|
| Sample_geo_accession | GSM459746
| | Sample_status | Public on Oct 07 2010
| | Sample_submission_date | Oct 07 2009
| | Sample_last_update_date | Oct 07 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis. Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY). IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer. 15ug cRNA is fragmented using 5X fragmentation buffer (made in-house).
| | Sample_hyb_protocol | Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA. 10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours. After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain.
| | Sample_scan_protocol | All arrays are scanned in the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,,Glazer
| | Sample_contact_institute | Johns Hopkins Medical Institutions
| | Sample_contact_address | 1550 Orleans St. CRB II-574
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM459nnn/GSM459746/suppl/GSM459746.CEL.gz
| | Sample_series_id | GSE18454
| | Sample_data_row_count | 54613
| | |
|
GSM459747 | GPL570 |
|
normal human bronchial epithelial cell line control rep 2
|
NHBE control rep 2
|
tissue: Lung
cell line: NHBE
agent: mock-treated
|
no additional information
|
| Sample_geo_accession | GSM459747
| | Sample_status | Public on Oct 07 2010
| | Sample_submission_date | Oct 07 2009
| | Sample_last_update_date | Oct 07 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis. Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY). IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer. 15ug cRNA is fragmented using 5X fragmentation buffer (made in-house).
| | Sample_hyb_protocol | Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA. 10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours. After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain.
| | Sample_scan_protocol | All arrays are scanned in the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,,Glazer
| | Sample_contact_institute | Johns Hopkins Medical Institutions
| | Sample_contact_address | 1550 Orleans St. CRB II-574
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM459nnn/GSM459747/suppl/GSM459747.CEL.gz
| | Sample_series_id | GSE18454
| | Sample_data_row_count | 54613
| | |
|
GSM459748 | GPL570 |
|
normal human bronchial epithelial cell line control rep 3
|
NHBE control rep 3
|
tissue: Lung
cell line: NHBE
agent: mock-treated
|
no additional information
|
| Sample_geo_accession | GSM459748
| | Sample_status | Public on Oct 07 2010
| | Sample_submission_date | Oct 07 2009
| | Sample_last_update_date | Oct 07 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis. Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY). IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer. 15ug cRNA is fragmented using 5X fragmentation buffer (made in-house).
| | Sample_hyb_protocol | Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA. 10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours. After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain.
| | Sample_scan_protocol | All arrays are scanned in the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,,Glazer
| | Sample_contact_institute | Johns Hopkins Medical Institutions
| | Sample_contact_address | 1550 Orleans St. CRB II-574
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM459nnn/GSM459748/suppl/GSM459748.CEL.gz
| | Sample_series_id | GSE18454
| | Sample_data_row_count | 54613
| | |
|
GSM459749 | GPL570 |
|
normal human small airway epithelial cell line treated with 5-AZA rep 1
|
SAEC AZA rep 1
|
tissue: Lung
cell line: SAEC
agent: 5-aza-dC and TSA
|
no additional information
|
| Sample_geo_accession | GSM459749
| | Sample_status | Public on Oct 07 2010
| | Sample_submission_date | Oct 07 2009
| | Sample_last_update_date | Oct 07 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis. Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY). IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer. 15ug cRNA is fragmented using 5X fragmentation buffer (made in-house).
| | Sample_hyb_protocol | Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA. 10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours. After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain.
| | Sample_scan_protocol | All arrays are scanned in the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,,Glazer
| | Sample_contact_institute | Johns Hopkins Medical Institutions
| | Sample_contact_address | 1550 Orleans St. CRB II-574
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM459nnn/GSM459749/suppl/GSM459749.CEL.gz
| | Sample_series_id | GSE18454
| | Sample_data_row_count | 54613
| | |
|
GSM459750 | GPL570 |
|
normal human small airway epithelial cell line treated with 5-AZA rep 2
|
SAEC AZA rep 2
|
tissue: Lung
cell line: SAEC
agent: 5-aza-dC and TSA
|
no additional information
|
| Sample_geo_accession | GSM459750
| | Sample_status | Public on Oct 07 2010
| | Sample_submission_date | Oct 07 2009
| | Sample_last_update_date | Oct 07 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis. Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY). IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer. 15ug cRNA is fragmented using 5X fragmentation buffer (made in-house).
| | Sample_hyb_protocol | Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA. 10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours. After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain.
| | Sample_scan_protocol | All arrays are scanned in the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,,Glazer
| | Sample_contact_institute | Johns Hopkins Medical Institutions
| | Sample_contact_address | 1550 Orleans St. CRB II-574
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM459nnn/GSM459750/suppl/GSM459750.CEL.gz
| | Sample_series_id | GSE18454
| | Sample_data_row_count | 54613
| | |
|
GSM459751 | GPL570 |
|
normal human small airway epithelial cell line treated with 5-AZA rep 3
|
SAEC AZA rep 3
|
tissue: Lung
cell line: SAEC
agent: 5-aza-dC and TSA
|
no additional information
|
| Sample_geo_accession | GSM459751
| | Sample_status | Public on Oct 07 2010
| | Sample_submission_date | Oct 07 2009
| | Sample_last_update_date | Oct 07 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis. Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY). IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer. 15ug cRNA is fragmented using 5X fragmentation buffer (made in-house).
| | Sample_hyb_protocol | Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA. 10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours. After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain.
| | Sample_scan_protocol | All arrays are scanned in the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,,Glazer
| | Sample_contact_institute | Johns Hopkins Medical Institutions
| | Sample_contact_address | 1550 Orleans St. CRB II-574
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM459nnn/GSM459751/suppl/GSM459751.CEL.gz
| | Sample_series_id | GSE18454
| | Sample_data_row_count | 54613
| | |
|
GSM459752 | GPL570 |
|
normal human small airway epithelial cell line control rep 1
|
SAEC control rep 1
|
tissue: Lung
cell line: SAEC
agent: mock-treated
|
no additional information
|
| Sample_geo_accession | GSM459752
| | Sample_status | Public on Oct 07 2010
| | Sample_submission_date | Oct 07 2009
| | Sample_last_update_date | Oct 07 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis. Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY). IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer. 15ug cRNA is fragmented using 5X fragmentation buffer (made in-house).
| | Sample_hyb_protocol | Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA. 10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours. After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain.
| | Sample_scan_protocol | All arrays are scanned in the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,,Glazer
| | Sample_contact_institute | Johns Hopkins Medical Institutions
| | Sample_contact_address | 1550 Orleans St. CRB II-574
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM459nnn/GSM459752/suppl/GSM459752.CEL.gz
| | Sample_series_id | GSE18454
| | Sample_data_row_count | 54613
| | |
|
GSM459753 | GPL570 |
|
normal human small airway epithelial cell line control rep 2
|
SAEC control rep 2
|
tissue: Lung
cell line: SAEC
agent: mock-treated
|
no additional information
|
| Sample_geo_accession | GSM459753
| | Sample_status | Public on Oct 07 2010
| | Sample_submission_date | Oct 07 2009
| | Sample_last_update_date | Oct 07 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis. Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY). IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer. 15ug cRNA is fragmented using 5X fragmentation buffer (made in-house).
| | Sample_hyb_protocol | Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA. 10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours. After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain.
| | Sample_scan_protocol | All arrays are scanned in the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,,Glazer
| | Sample_contact_institute | Johns Hopkins Medical Institutions
| | Sample_contact_address | 1550 Orleans St. CRB II-574
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM459nnn/GSM459753/suppl/GSM459753.CEL.gz
| | Sample_series_id | GSE18454
| | Sample_data_row_count | 54613
| | |
|
GSM459754 | GPL570 |
|
normal human small airway epithelial cell line control rep 3
|
SAEC control rep 3
|
tissue: Lung
cell line: SAEC
agent: mock-treated
|
no additional information
|
| Sample_geo_accession | GSM459754
| | Sample_status | Public on Oct 07 2010
| | Sample_submission_date | Oct 07 2009
| | Sample_last_update_date | Oct 07 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis. Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY). IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer. 15ug cRNA is fragmented using 5X fragmentation buffer (made in-house).
| | Sample_hyb_protocol | Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA. 10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours. After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain.
| | Sample_scan_protocol | All arrays are scanned in the Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4
| | Sample_platform_id | GPL570
| | Sample_contact_name | Chad,,Glazer
| | Sample_contact_institute | Johns Hopkins Medical Institutions
| | Sample_contact_address | 1550 Orleans St. CRB II-574
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21231
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM459nnn/GSM459754/suppl/GSM459754.CEL.gz
| | Sample_series_id | GSE18454
| | Sample_data_row_count | 54613
| | |
|
| |
| |
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