Search results for the GEO ID: GSE36643  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM914927 | GPL570 |
|
CD24high-1
|
HMLER
|
cell line: Ras-transformed human mammary epithelial cells (HMLER cells)
facs-sorted cell population: CD24_high
|
cd24h1
|
| Sample_geo_accession | GSM914927
| | Sample_status | Public on Apr 13 2012
| | Sample_submission_date | Apr 13 2012
| | Sample_last_update_date | Apr 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | The cells were culture in MEGM media mixed 1:1 with DMEM/F12. Se Mani et al, Cell 2008
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA easy kit was used for RNA isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | By using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, P/N 900431), 1ug of total RNA undergoes reverse transcription to synthesize first-strand cDNA by using a T7 Oligo (dT) promoter. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction (GeneChip® IVT Labeling Kit Affymetrix, P/N 900449) Synthesizes cRNA and incorporates a biotin-conjugated nucleotide. The cRNA is then purified (using GeneChip® Sample Cleanup Module Affymetrix, P/N 900371 for cDNA and cRNA purification) and fragmented before hybridization.
| | Sample_hyb_protocol | Then, a hybridization cocktail is prepared, including the fragmented target (cRNA) and probe array controls (GeneChip® Hybridization Control Kit (Affymetrix, P/N 900454). It is then hybridized to the probe array for 16-hours at 45oC in the hybridization oven 640 (Affymetrix, P/N 800138) and Rotate at 60 rpm.
| | Sample_scan_protocol | Once the probe array has been hybridized, washed, and stained, it is Scanned by the GeneChip® Scanner 3000
| | Sample_data_processing | The scanner is controlled by Affymetrix® GeneChip® Command Console® 3.0. The software defines the probe cells and computes intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kurt,,Evans
| | Sample_contact_email | kevans01@gmail.com
| | Sample_contact_institute | MDACC
| | 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/GSM914nnn/GSM914927/suppl/GSM914927_CD24_high_1.CEL.gz
| | Sample_series_id | GSE36643
| | Sample_data_row_count | 54675
| | |
|
GSM914928 | GPL570 |
|
CD24high-2
|
HMLER
|
cell line: Ras-transformed human mammary epithelial cells (HMLER cells)
facs-sorted cell population: CD24_high
|
cd24h2
|
| Sample_geo_accession | GSM914928
| | Sample_status | Public on Apr 13 2012
| | Sample_submission_date | Apr 13 2012
| | Sample_last_update_date | Apr 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | The cells were culture in MEGM media mixed 1:1 with DMEM/F12. Se Mani et al, Cell 2008
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA easy kit was used for RNA isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | By using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, P/N 900431), 1ug of total RNA undergoes reverse transcription to synthesize first-strand cDNA by using a T7 Oligo (dT) promoter. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction (GeneChip® IVT Labeling Kit Affymetrix, P/N 900449) Synthesizes cRNA and incorporates a biotin-conjugated nucleotide. The cRNA is then purified (using GeneChip® Sample Cleanup Module Affymetrix, P/N 900371 for cDNA and cRNA purification) and fragmented before hybridization.
| | Sample_hyb_protocol | Then, a hybridization cocktail is prepared, including the fragmented target (cRNA) and probe array controls (GeneChip® Hybridization Control Kit (Affymetrix, P/N 900454). It is then hybridized to the probe array for 16-hours at 45oC in the hybridization oven 640 (Affymetrix, P/N 800138) and Rotate at 60 rpm.
| | Sample_scan_protocol | Once the probe array has been hybridized, washed, and stained, it is Scanned by the GeneChip® Scanner 3000
| | Sample_data_processing | The scanner is controlled by Affymetrix® GeneChip® Command Console® 3.0. The software defines the probe cells and computes intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kurt,,Evans
| | Sample_contact_email | kevans01@gmail.com
| | Sample_contact_institute | MDACC
| | 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/GSM914nnn/GSM914928/suppl/GSM914928_CD24_high_2.CEL.gz
| | Sample_series_id | GSE36643
| | Sample_data_row_count | 54675
| | |
|
GSM914929 | GPL570 |
|
CD24high-3
|
HMLER
|
cell line: Ras-transformed human mammary epithelial cells (HMLER cells)
facs-sorted cell population: CD24_high
|
cd24h3
|
| Sample_geo_accession | GSM914929
| | Sample_status | Public on Apr 13 2012
| | Sample_submission_date | Apr 13 2012
| | Sample_last_update_date | Apr 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | The cells were culture in MEGM media mixed 1:1 with DMEM/F12. Se Mani et al, Cell 2008
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA easy kit was used for RNA isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | By using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, P/N 900431), 1ug of total RNA undergoes reverse transcription to synthesize first-strand cDNA by using a T7 Oligo (dT) promoter. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction (GeneChip® IVT Labeling Kit Affymetrix, P/N 900449) Synthesizes cRNA and incorporates a biotin-conjugated nucleotide. The cRNA is then purified (using GeneChip® Sample Cleanup Module Affymetrix, P/N 900371 for cDNA and cRNA purification) and fragmented before hybridization.
| | Sample_hyb_protocol | Then, a hybridization cocktail is prepared, including the fragmented target (cRNA) and probe array controls (GeneChip® Hybridization Control Kit (Affymetrix, P/N 900454). It is then hybridized to the probe array for 16-hours at 45oC in the hybridization oven 640 (Affymetrix, P/N 800138) and Rotate at 60 rpm.
| | Sample_scan_protocol | Once the probe array has been hybridized, washed, and stained, it is Scanned by the GeneChip® Scanner 3000
| | Sample_data_processing | The scanner is controlled by Affymetrix® GeneChip® Command Console® 3.0. The software defines the probe cells and computes intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kurt,,Evans
| | Sample_contact_email | kevans01@gmail.com
| | Sample_contact_institute | MDACC
| | 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/GSM914nnn/GSM914929/suppl/GSM914929_CD24_high_3.CEL.gz
| | Sample_series_id | GSE36643
| | Sample_data_row_count | 54675
| | |
|
GSM914930 | GPL570 |
|
CD44high-1
|
HMLER
|
cell line: Ras-transformed human mammary epithelial cells (HMLER cells)
facs-sorted cell population: CD44_high
|
cd44h1
|
| Sample_geo_accession | GSM914930
| | Sample_status | Public on Apr 13 2012
| | Sample_submission_date | Apr 13 2012
| | Sample_last_update_date | Apr 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | The cells were culture in MEGM media mixed 1:1 with DMEM/F12. Se Mani et al, Cell 2008
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA easy kit was used for RNA isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | By using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, P/N 900431), 1ug of total RNA undergoes reverse transcription to synthesize first-strand cDNA by using a T7 Oligo (dT) promoter. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction (GeneChip® IVT Labeling Kit Affymetrix, P/N 900449) Synthesizes cRNA and incorporates a biotin-conjugated nucleotide. The cRNA is then purified (using GeneChip® Sample Cleanup Module Affymetrix, P/N 900371 for cDNA and cRNA purification) and fragmented before hybridization.
| | Sample_hyb_protocol | Then, a hybridization cocktail is prepared, including the fragmented target (cRNA) and probe array controls (GeneChip® Hybridization Control Kit (Affymetrix, P/N 900454). It is then hybridized to the probe array for 16-hours at 45oC in the hybridization oven 640 (Affymetrix, P/N 800138) and Rotate at 60 rpm.
| | Sample_scan_protocol | Once the probe array has been hybridized, washed, and stained, it is Scanned by the GeneChip® Scanner 3000
| | Sample_data_processing | The scanner is controlled by Affymetrix® GeneChip® Command Console® 3.0. The software defines the probe cells and computes intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kurt,,Evans
| | Sample_contact_email | kevans01@gmail.com
| | Sample_contact_institute | MDACC
| | 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/GSM914nnn/GSM914930/suppl/GSM914930_CD44_HIGH-1.CEL.gz
| | Sample_series_id | GSE36643
| | Sample_data_row_count | 54675
| | |
|
GSM914931 | GPL570 |
|
CD44high-2
|
HMLER
|
cell line: Ras-transformed human mammary epithelial cells (HMLER cells)
facs-sorted cell population: CD44_high
|
cd44h2
|
| Sample_geo_accession | GSM914931
| | Sample_status | Public on Apr 13 2012
| | Sample_submission_date | Apr 13 2012
| | Sample_last_update_date | Apr 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | The cells were culture in MEGM media mixed 1:1 with DMEM/F12. Se Mani et al, Cell 2008
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA easy kit was used for RNA isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | By using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, P/N 900431), 1ug of total RNA undergoes reverse transcription to synthesize first-strand cDNA by using a T7 Oligo (dT) promoter. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction (GeneChip® IVT Labeling Kit Affymetrix, P/N 900449) Synthesizes cRNA and incorporates a biotin-conjugated nucleotide. The cRNA is then purified (using GeneChip® Sample Cleanup Module Affymetrix, P/N 900371 for cDNA and cRNA purification) and fragmented before hybridization.
| | Sample_hyb_protocol | Then, a hybridization cocktail is prepared, including the fragmented target (cRNA) and probe array controls (GeneChip® Hybridization Control Kit (Affymetrix, P/N 900454). It is then hybridized to the probe array for 16-hours at 45oC in the hybridization oven 640 (Affymetrix, P/N 800138) and Rotate at 60 rpm.
| | Sample_scan_protocol | Once the probe array has been hybridized, washed, and stained, it is Scanned by the GeneChip® Scanner 3000
| | Sample_data_processing | The scanner is controlled by Affymetrix® GeneChip® Command Console® 3.0. The software defines the probe cells and computes intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kurt,,Evans
| | Sample_contact_email | kevans01@gmail.com
| | Sample_contact_institute | MDACC
| | 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/GSM914nnn/GSM914931/suppl/GSM914931_CD44_HIGH-2.CEL.gz
| | Sample_series_id | GSE36643
| | Sample_data_row_count | 54675
| | |
|
GSM914932 | GPL570 |
|
CD44high-3
|
HMLER
|
cell line: Ras-transformed human mammary epithelial cells (HMLER cells)
facs-sorted cell population: CD44_high
|
cd44h3
|
| Sample_geo_accession | GSM914932
| | Sample_status | Public on Apr 13 2012
| | Sample_submission_date | Apr 13 2012
| | Sample_last_update_date | Apr 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | The cells were culture in MEGM media mixed 1:1 with DMEM/F12. Se Mani et al, Cell 2008
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA easy kit was used for RNA isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | By using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, P/N 900431), 1ug of total RNA undergoes reverse transcription to synthesize first-strand cDNA by using a T7 Oligo (dT) promoter. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction (GeneChip® IVT Labeling Kit Affymetrix, P/N 900449) Synthesizes cRNA and incorporates a biotin-conjugated nucleotide. The cRNA is then purified (using GeneChip® Sample Cleanup Module Affymetrix, P/N 900371 for cDNA and cRNA purification) and fragmented before hybridization.
| | Sample_hyb_protocol | Then, a hybridization cocktail is prepared, including the fragmented target (cRNA) and probe array controls (GeneChip® Hybridization Control Kit (Affymetrix, P/N 900454). It is then hybridized to the probe array for 16-hours at 45oC in the hybridization oven 640 (Affymetrix, P/N 800138) and Rotate at 60 rpm.
| | Sample_scan_protocol | Once the probe array has been hybridized, washed, and stained, it is Scanned by the GeneChip® Scanner 3000
| | Sample_data_processing | The scanner is controlled by Affymetrix® GeneChip® Command Console® 3.0. The software defines the probe cells and computes intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kurt,,Evans
| | Sample_contact_email | kevans01@gmail.com
| | Sample_contact_institute | MDACC
| | 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/GSM914nnn/GSM914932/suppl/GSM914932_CD44_HIGH-3.CEL.gz
| | Sample_series_id | GSE36643
| | Sample_data_row_count | 54675
| | |
|
GSM914933 | GPL570 |
|
GD2+HMLER_1
|
HMLER
|
cell line: Ras-transformed human mammary epithelial cells (HMLER cells)
facs-sorted cell population: GD2+
|
GD2.m.1
|
| Sample_geo_accession | GSM914933
| | Sample_status | Public on Apr 13 2012
| | Sample_submission_date | Apr 13 2012
| | Sample_last_update_date | Apr 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | The cells were culture in MEGM media mixed 1:1 with DMEM/F12. Se Mani et al, Cell 2008
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA easy kit was used for RNA isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | By using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, P/N 900431), 1ug of total RNA undergoes reverse transcription to synthesize first-strand cDNA by using a T7 Oligo (dT) promoter. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction (GeneChip® IVT Labeling Kit Affymetrix, P/N 900449) Synthesizes cRNA and incorporates a biotin-conjugated nucleotide. The cRNA is then purified (using GeneChip® Sample Cleanup Module Affymetrix, P/N 900371 for cDNA and cRNA purification) and fragmented before hybridization.
| | Sample_hyb_protocol | Then, a hybridization cocktail is prepared, including the fragmented target (cRNA) and probe array controls (GeneChip® Hybridization Control Kit (Affymetrix, P/N 900454). It is then hybridized to the probe array for 16-hours at 45oC in the hybridization oven 640 (Affymetrix, P/N 800138) and Rotate at 60 rpm.
| | Sample_scan_protocol | Once the probe array has been hybridized, washed, and stained, it is Scanned by the GeneChip® Scanner 3000
| | Sample_data_processing | The scanner is controlled by Affymetrix® GeneChip® Command Console® 3.0. The software defines the probe cells and computes intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kurt,,Evans
| | Sample_contact_email | kevans01@gmail.com
| | Sample_contact_institute | MDACC
| | 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/GSM914nnn/GSM914933/suppl/GSM914933_GD2+HMLER_1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE36643
| | Sample_data_row_count | 54675
| | |
|
GSM914934 | GPL570 |
|
GD2+HMLER_2
|
HMLER
|
cell line: Ras-transformed human mammary epithelial cells (HMLER cells)
facs-sorted cell population: GD2+
|
GD2.m.2
|
| Sample_geo_accession | GSM914934
| | Sample_status | Public on Apr 13 2012
| | Sample_submission_date | Apr 13 2012
| | Sample_last_update_date | Apr 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | The cells were culture in MEGM media mixed 1:1 with DMEM/F12. Se Mani et al, Cell 2008
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA easy kit was used for RNA isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | By using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, P/N 900431), 1ug of total RNA undergoes reverse transcription to synthesize first-strand cDNA by using a T7 Oligo (dT) promoter. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction (GeneChip® IVT Labeling Kit Affymetrix, P/N 900449) Synthesizes cRNA and incorporates a biotin-conjugated nucleotide. The cRNA is then purified (using GeneChip® Sample Cleanup Module Affymetrix, P/N 900371 for cDNA and cRNA purification) and fragmented before hybridization.
| | Sample_hyb_protocol | Then, a hybridization cocktail is prepared, including the fragmented target (cRNA) and probe array controls (GeneChip® Hybridization Control Kit (Affymetrix, P/N 900454). It is then hybridized to the probe array for 16-hours at 45oC in the hybridization oven 640 (Affymetrix, P/N 800138) and Rotate at 60 rpm.
| | Sample_scan_protocol | Once the probe array has been hybridized, washed, and stained, it is Scanned by the GeneChip® Scanner 3000
| | Sample_data_processing | The scanner is controlled by Affymetrix® GeneChip® Command Console® 3.0. The software defines the probe cells and computes intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kurt,,Evans
| | Sample_contact_email | kevans01@gmail.com
| | Sample_contact_institute | MDACC
| | 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/GSM914nnn/GSM914934/suppl/GSM914934_GD2+HMLER_2_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE36643
| | Sample_data_row_count | 54675
| | |
|
GSM914935 | GPL570 |
|
GD2+HMLER_3
|
HMLER
|
cell line: Ras-transformed human mammary epithelial cells (HMLER cells)
facs-sorted cell population: GD2+
|
GD2.m.3
|
| Sample_geo_accession | GSM914935
| | Sample_status | Public on Apr 13 2012
| | Sample_submission_date | Apr 13 2012
| | Sample_last_update_date | Apr 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | The cells were culture in MEGM media mixed 1:1 with DMEM/F12. Se Mani et al, Cell 2008
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA easy kit was used for RNA isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | By using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, P/N 900431), 1ug of total RNA undergoes reverse transcription to synthesize first-strand cDNA by using a T7 Oligo (dT) promoter. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction (GeneChip® IVT Labeling Kit Affymetrix, P/N 900449) Synthesizes cRNA and incorporates a biotin-conjugated nucleotide. The cRNA is then purified (using GeneChip® Sample Cleanup Module Affymetrix, P/N 900371 for cDNA and cRNA purification) and fragmented before hybridization.
| | Sample_hyb_protocol | Then, a hybridization cocktail is prepared, including the fragmented target (cRNA) and probe array controls (GeneChip® Hybridization Control Kit (Affymetrix, P/N 900454). It is then hybridized to the probe array for 16-hours at 45oC in the hybridization oven 640 (Affymetrix, P/N 800138) and Rotate at 60 rpm.
| | Sample_scan_protocol | Once the probe array has been hybridized, washed, and stained, it is Scanned by the GeneChip® Scanner 3000
| | Sample_data_processing | The scanner is controlled by Affymetrix® GeneChip® Command Console® 3.0. The software defines the probe cells and computes intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kurt,,Evans
| | Sample_contact_email | kevans01@gmail.com
| | Sample_contact_institute | MDACC
| | 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/GSM914nnn/GSM914935/suppl/GSM914935_GD2+HMLER_3_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE36643
| | Sample_data_row_count | 54675
| | |
|
GSM914936 | GPL570 |
|
GD2-HMLER_1
|
HMLER
|
cell line: Ras-transformed human mammary epithelial cells (HMLER cells)
facs-sorted cell population: GD2-
|
GD2.p.1
|
| Sample_geo_accession | GSM914936
| | Sample_status | Public on Apr 13 2012
| | Sample_submission_date | Apr 13 2012
| | Sample_last_update_date | Apr 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | The cells were culture in MEGM media mixed 1:1 with DMEM/F12. Se Mani et al, Cell 2008
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA easy kit was used for RNA isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | By using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, P/N 900431), 1ug of total RNA undergoes reverse transcription to synthesize first-strand cDNA by using a T7 Oligo (dT) promoter. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction (GeneChip® IVT Labeling Kit Affymetrix, P/N 900449) Synthesizes cRNA and incorporates a biotin-conjugated nucleotide. The cRNA is then purified (using GeneChip® Sample Cleanup Module Affymetrix, P/N 900371 for cDNA and cRNA purification) and fragmented before hybridization.
| | Sample_hyb_protocol | Then, a hybridization cocktail is prepared, including the fragmented target (cRNA) and probe array controls (GeneChip® Hybridization Control Kit (Affymetrix, P/N 900454). It is then hybridized to the probe array for 16-hours at 45oC in the hybridization oven 640 (Affymetrix, P/N 800138) and Rotate at 60 rpm.
| | Sample_scan_protocol | Once the probe array has been hybridized, washed, and stained, it is Scanned by the GeneChip® Scanner 3000
| | Sample_data_processing | The scanner is controlled by Affymetrix® GeneChip® Command Console® 3.0. The software defines the probe cells and computes intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kurt,,Evans
| | Sample_contact_email | kevans01@gmail.com
| | Sample_contact_institute | MDACC
| | 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/GSM914nnn/GSM914936/suppl/GSM914936_GD2-HMLER_1_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE36643
| | Sample_data_row_count | 54675
| | |
|
GSM914937 | GPL570 |
|
GD2-HMLER_2
|
HMLER
|
cell line: Ras-transformed human mammary epithelial cells (HMLER cells)
facs-sorted cell population: GD2-
|
GD2.p.2
|
| Sample_geo_accession | GSM914937
| | Sample_status | Public on Apr 13 2012
| | Sample_submission_date | Apr 13 2012
| | Sample_last_update_date | Apr 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | The cells were culture in MEGM media mixed 1:1 with DMEM/F12. Se Mani et al, Cell 2008
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA easy kit was used for RNA isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | By using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, P/N 900431), 1ug of total RNA undergoes reverse transcription to synthesize first-strand cDNA by using a T7 Oligo (dT) promoter. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction (GeneChip® IVT Labeling Kit Affymetrix, P/N 900449) Synthesizes cRNA and incorporates a biotin-conjugated nucleotide. The cRNA is then purified (using GeneChip® Sample Cleanup Module Affymetrix, P/N 900371 for cDNA and cRNA purification) and fragmented before hybridization.
| | Sample_hyb_protocol | Then, a hybridization cocktail is prepared, including the fragmented target (cRNA) and probe array controls (GeneChip® Hybridization Control Kit (Affymetrix, P/N 900454). It is then hybridized to the probe array for 16-hours at 45oC in the hybridization oven 640 (Affymetrix, P/N 800138) and Rotate at 60 rpm.
| | Sample_scan_protocol | Once the probe array has been hybridized, washed, and stained, it is Scanned by the GeneChip® Scanner 3000
| | Sample_data_processing | The scanner is controlled by Affymetrix® GeneChip® Command Console® 3.0. The software defines the probe cells and computes intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kurt,,Evans
| | Sample_contact_email | kevans01@gmail.com
| | Sample_contact_institute | MDACC
| | 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/GSM914nnn/GSM914937/suppl/GSM914937_GD2-HMLER_2_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE36643
| | Sample_data_row_count | 54675
| | |
|
GSM914938 | GPL570 |
|
GD2-HMLER_3
|
HMLER
|
cell line: Ras-transformed human mammary epithelial cells (HMLER cells)
facs-sorted cell population: GD2-
|
GD2.p.3
|
| Sample_geo_accession | GSM914938
| | Sample_status | Public on Apr 13 2012
| | Sample_submission_date | Apr 13 2012
| | Sample_last_update_date | Apr 13 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment
| | Sample_growth_protocol_ch1 | The cells were culture in MEGM media mixed 1:1 with DMEM/F12. Se Mani et al, Cell 2008
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA easy kit was used for RNA isolation
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | By using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, P/N 900431), 1ug of total RNA undergoes reverse transcription to synthesize first-strand cDNA by using a T7 Oligo (dT) promoter. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction (GeneChip® IVT Labeling Kit Affymetrix, P/N 900449) Synthesizes cRNA and incorporates a biotin-conjugated nucleotide. The cRNA is then purified (using GeneChip® Sample Cleanup Module Affymetrix, P/N 900371 for cDNA and cRNA purification) and fragmented before hybridization.
| | Sample_hyb_protocol | Then, a hybridization cocktail is prepared, including the fragmented target (cRNA) and probe array controls (GeneChip® Hybridization Control Kit (Affymetrix, P/N 900454). It is then hybridized to the probe array for 16-hours at 45oC in the hybridization oven 640 (Affymetrix, P/N 800138) and Rotate at 60 rpm.
| | Sample_scan_protocol | Once the probe array has been hybridized, washed, and stained, it is Scanned by the GeneChip® Scanner 3000
| | Sample_data_processing | The scanner is controlled by Affymetrix® GeneChip® Command Console® 3.0. The software defines the probe cells and computes intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kurt,,Evans
| | Sample_contact_email | kevans01@gmail.com
| | Sample_contact_institute | MDACC
| | 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/GSM914nnn/GSM914938/suppl/GSM914938_GD2-HMLER_3_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE36643
| | Sample_data_row_count | 54675
| | |
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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