Search results for the GEO ID: GSE26148  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM641895 | GPL96 |
|
MCF10A-2D-2days-1
|
cells cultured in 2D for 2 days
|
cell type: mammary epithelial cells
cell line: MCF10A cells
culture condition: traditional monolayer cell culture setting (2D)
time: 2 days
|
Gene expression data from cells cultured in 2D for 2 days
|
| Sample_geo_accession | GSM641895
| | Sample_status | Public on Jun 01 2011
| | Sample_submission_date | Dec 17 2010
| | Sample_last_update_date | Jun 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | MCF10A cells were grown in 2D and 3D cells as described previously (Xiang and Muthuswamy 2006, PMID:16472698).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The RNA was isolated using TriZol according to Invitrogen's protocols as directed by the Affymettrix GeneChip Expression Analysis Technical Manual.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg total RNA was reverse transcribed using a T7- Oligo(dT) promoter primer for first-strand cDNA synthesis. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45˚C for 16 hours in a rotation oven. The hybridized chips were subjected to washes and stained in a Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned with an Affymetrix Genechip Scanner 3000 and processed automatically into digital CEL files.
| | Sample_data_processing | The raw data (CEL files) were analyzed with Affymetrix Gene Expression Console. Background correction and normalization were conducted using the RMA algorithm implemented in the Affymetrix package (version 1.26.1) of the Bioconductor software.
| | Sample_platform_id | GPL96
| | Sample_contact_name | David,,Simpson
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | Suite 4140 Medical Research Building III
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37212
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM641nnn/GSM641895/suppl/GSM641895.cel.gz
| | Sample_series_id | GSE26148
| | Sample_data_row_count | 22283
| | |
|
GSM641896 | GPL96 |
|
MCF10A-2D-2days-2
|
cells cultured in 2D for 2 days
|
cell type: mammary epithelial cells
cell line: MCF10A cells
culture condition: traditional monolayer cell culture setting (2D)
time: 2 days
|
Gene expression data from cells cultured in 2D for 2 days
|
| Sample_geo_accession | GSM641896
| | Sample_status | Public on Jun 01 2011
| | Sample_submission_date | Dec 17 2010
| | Sample_last_update_date | Jun 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | MCF10A cells were grown in 2D and 3D cells as described previously (Xiang and Muthuswamy 2006, PMID:16472698).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The RNA was isolated using TriZol according to Invitrogen's protocols as directed by the Affymettrix GeneChip Expression Analysis Technical Manual.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg total RNA was reverse transcribed using a T7- Oligo(dT) promoter primer for first-strand cDNA synthesis. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45˚C for 16 hours in a rotation oven. The hybridized chips were subjected to washes and stained in a Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned with an Affymetrix Genechip Scanner 3000 and processed automatically into digital CEL files.
| | Sample_data_processing | The raw data (CEL files) were analyzed with Affymetrix Gene Expression Console. Background correction and normalization were conducted using the RMA algorithm implemented in the Affymetrix package (version 1.26.1) of the Bioconductor software.
| | Sample_platform_id | GPL96
| | Sample_contact_name | David,,Simpson
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | Suite 4140 Medical Research Building III
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37212
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM641nnn/GSM641896/suppl/GSM641896.cel.gz
| | Sample_series_id | GSE26148
| | Sample_data_row_count | 22283
| | |
|
GSM641897 | GPL96 |
|
MCF10A-2D-2days-3
|
cells cultured in 2D for 2 days
|
cell type: mammary epithelial cells
cell line: MCF10A cells
culture condition: traditional monolayer cell culture setting (2D)
time: 2 days
|
Gene expression data from cells cultured in 2D for 2 days
|
| Sample_geo_accession | GSM641897
| | Sample_status | Public on Jun 01 2011
| | Sample_submission_date | Dec 17 2010
| | Sample_last_update_date | Jun 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | MCF10A cells were grown in 2D and 3D cells as described previously (Xiang and Muthuswamy 2006, PMID:16472698).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The RNA was isolated using TriZol according to Invitrogen's protocols as directed by the Affymettrix GeneChip Expression Analysis Technical Manual.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg total RNA was reverse transcribed using a T7- Oligo(dT) promoter primer for first-strand cDNA synthesis. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45˚C for 16 hours in a rotation oven. The hybridized chips were subjected to washes and stained in a Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned with an Affymetrix Genechip Scanner 3000 and processed automatically into digital CEL files.
| | Sample_data_processing | The raw data (CEL files) were analyzed with Affymetrix Gene Expression Console. Background correction and normalization were conducted using the RMA algorithm implemented in the Affymetrix package (version 1.26.1) of the Bioconductor software.
| | Sample_platform_id | GPL96
| | Sample_contact_name | David,,Simpson
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | Suite 4140 Medical Research Building III
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37212
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM641nnn/GSM641897/suppl/GSM641897.cel.gz
| | Sample_series_id | GSE26148
| | Sample_data_row_count | 22283
| | |
|
GSM641898 | GPL96 |
|
MCF10A-2D-5days-1
|
cells cultured in 2D for 5 days
|
cell type: mammary epithelial cells
cell line: MCF10A cells
culture condition: traditional monolayer cell culture setting (2D)
time: 5 days
|
Gene expression data from cells cultured in 2D for 5 days
|
| Sample_geo_accession | GSM641898
| | Sample_status | Public on Jun 01 2011
| | Sample_submission_date | Dec 17 2010
| | Sample_last_update_date | Jun 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | MCF10A cells were grown in 2D and 3D cells as described previously (Xiang and Muthuswamy 2006, PMID:16472698).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The RNA was isolated using TriZol according to Invitrogen's protocols as directed by the Affymettrix GeneChip Expression Analysis Technical Manual.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg total RNA was reverse transcribed using a T7- Oligo(dT) promoter primer for first-strand cDNA synthesis. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45˚C for 16 hours in a rotation oven. The hybridized chips were subjected to washes and stained in a Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned with an Affymetrix Genechip Scanner 3000 and processed automatically into digital CEL files.
| | Sample_data_processing | The raw data (CEL files) were analyzed with Affymetrix Gene Expression Console. Background correction and normalization were conducted using the RMA algorithm implemented in the Affymetrix package (version 1.26.1) of the Bioconductor software.
| | Sample_platform_id | GPL96
| | Sample_contact_name | David,,Simpson
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | Suite 4140 Medical Research Building III
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37212
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM641nnn/GSM641898/suppl/GSM641898.cel.gz
| | Sample_series_id | GSE26148
| | Sample_data_row_count | 22283
| | |
|
GSM641899 | GPL96 |
|
MCF10A-2D-5days-2
|
cells cultured in 2D for 5 days
|
cell type: mammary epithelial cells
cell line: MCF10A cells
culture condition: traditional monolayer cell culture setting (2D)
time: 5 days
|
Gene expression data from cells cultured in 2D for 5 days
|
| Sample_geo_accession | GSM641899
| | Sample_status | Public on Jun 01 2011
| | Sample_submission_date | Dec 17 2010
| | Sample_last_update_date | Jun 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | MCF10A cells were grown in 2D and 3D cells as described previously (Xiang and Muthuswamy 2006, PMID:16472698).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The RNA was isolated using TriZol according to Invitrogen's protocols as directed by the Affymettrix GeneChip Expression Analysis Technical Manual.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg total RNA was reverse transcribed using a T7- Oligo(dT) promoter primer for first-strand cDNA synthesis. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45˚C for 16 hours in a rotation oven. The hybridized chips were subjected to washes and stained in a Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned with an Affymetrix Genechip Scanner 3000 and processed automatically into digital CEL files.
| | Sample_data_processing | The raw data (CEL files) were analyzed with Affymetrix Gene Expression Console. Background correction and normalization were conducted using the RMA algorithm implemented in the Affymetrix package (version 1.26.1) of the Bioconductor software.
| | Sample_platform_id | GPL96
| | Sample_contact_name | David,,Simpson
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | Suite 4140 Medical Research Building III
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37212
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM641nnn/GSM641899/suppl/GSM641899.cel.gz
| | Sample_series_id | GSE26148
| | Sample_data_row_count | 22283
| | |
|
GSM641900 | GPL96 |
|
MCF10A-2D-5days-3
|
cells cultured in 2D for 5 days
|
cell type: mammary epithelial cells
cell line: MCF10A cells
culture condition: traditional monolayer cell culture setting (2D)
time: 5 days
|
Gene expression data from cells cultured in 2D for 5 days
|
| Sample_geo_accession | GSM641900
| | Sample_status | Public on Jun 01 2011
| | Sample_submission_date | Dec 17 2010
| | Sample_last_update_date | Jun 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | MCF10A cells were grown in 2D and 3D cells as described previously (Xiang and Muthuswamy 2006, PMID:16472698).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The RNA was isolated using TriZol according to Invitrogen's protocols as directed by the Affymettrix GeneChip Expression Analysis Technical Manual.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg total RNA was reverse transcribed using a T7- Oligo(dT) promoter primer for first-strand cDNA synthesis. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45˚C for 16 hours in a rotation oven. The hybridized chips were subjected to washes and stained in a Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned with an Affymetrix Genechip Scanner 3000 and processed automatically into digital CEL files.
| | Sample_data_processing | The raw data (CEL files) were analyzed with Affymetrix Gene Expression Console. Background correction and normalization were conducted using the RMA algorithm implemented in the Affymetrix package (version 1.26.1) of the Bioconductor software.
| | Sample_platform_id | GPL96
| | Sample_contact_name | David,,Simpson
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | Suite 4140 Medical Research Building III
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37212
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM641nnn/GSM641900/suppl/GSM641900.cel.gz
| | Sample_series_id | GSE26148
| | Sample_data_row_count | 22283
| | |
|
GSM641901 | GPL96 |
|
MCF10A-3D-8days-1
|
cells cultured in 3D for 8 days
|
cell type: mammary epithelial cells
cell line: MCF10A cells
culture condition: Matrigel (3D)
time: 8 days
|
Gene expression data from cells cultured in 3D for 8 days
|
| Sample_geo_accession | GSM641901
| | Sample_status | Public on Jun 01 2011
| | Sample_submission_date | Dec 17 2010
| | Sample_last_update_date | Jun 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | MCF10A cells were grown in 2D and 3D cells as described previously (Xiang and Muthuswamy 2006, PMID:16472698).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The RNA was isolated using TriZol according to Invitrogen's protocols as directed by the Affymettrix GeneChip Expression Analysis Technical Manual.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg total RNA was reverse transcribed using a T7- Oligo(dT) promoter primer for first-strand cDNA synthesis. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45˚C for 16 hours in a rotation oven. The hybridized chips were subjected to washes and stained in a Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned with an Affymetrix Genechip Scanner 3000 and processed automatically into digital CEL files.
| | Sample_data_processing | The raw data (CEL files) were analyzed with Affymetrix Gene Expression Console. Background correction and normalization were conducted using the RMA algorithm implemented in the Affymetrix package (version 1.26.1) of the Bioconductor software.
| | Sample_platform_id | GPL96
| | Sample_contact_name | David,,Simpson
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | Suite 4140 Medical Research Building III
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37212
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM641nnn/GSM641901/suppl/GSM641901.cel.gz
| | Sample_series_id | GSE26148
| | Sample_data_row_count | 22283
| | |
|
GSM641902 | GPL96 |
|
MCF10A-3D-8days-2
|
cells cultured in 3D for 8 days
|
cell type: mammary epithelial cells
cell line: MCF10A cells
culture condition: Matrigel (3D)
time: 8 days
|
Gene expression data from cells cultured in 3D for 8 days
|
| Sample_geo_accession | GSM641902
| | Sample_status | Public on Jun 01 2011
| | Sample_submission_date | Dec 17 2010
| | Sample_last_update_date | Jun 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | MCF10A cells were grown in 2D and 3D cells as described previously (Xiang and Muthuswamy 2006, PMID:16472698).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The RNA was isolated using TriZol according to Invitrogen's protocols as directed by the Affymettrix GeneChip Expression Analysis Technical Manual.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg total RNA was reverse transcribed using a T7- Oligo(dT) promoter primer for first-strand cDNA synthesis. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45˚C for 16 hours in a rotation oven. The hybridized chips were subjected to washes and stained in a Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned with an Affymetrix Genechip Scanner 3000 and processed automatically into digital CEL files.
| | Sample_data_processing | The raw data (CEL files) were analyzed with Affymetrix Gene Expression Console. Background correction and normalization were conducted using the RMA algorithm implemented in the Affymetrix package (version 1.26.1) of the Bioconductor software.
| | Sample_platform_id | GPL96
| | Sample_contact_name | David,,Simpson
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | Suite 4140 Medical Research Building III
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37212
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM641nnn/GSM641902/suppl/GSM641902.cel.gz
| | Sample_series_id | GSE26148
| | Sample_data_row_count | 22283
| | |
|
GSM641903 | GPL96 |
|
MCF10A-3D-8days-3
|
cells cultured in 3D for 8 days
|
cell type: mammary epithelial cells
cell line: MCF10A cells
culture condition: Matrigel (3D)
time: 8 days
|
Gene expression data from cells cultured in 3D for 8 days
|
| Sample_geo_accession | GSM641903
| | Sample_status | Public on Jun 01 2011
| | Sample_submission_date | Dec 17 2010
| | Sample_last_update_date | Jun 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | MCF10A cells were grown in 2D and 3D cells as described previously (Xiang and Muthuswamy 2006, PMID:16472698).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The RNA was isolated using TriZol according to Invitrogen's protocols as directed by the Affymettrix GeneChip Expression Analysis Technical Manual.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg total RNA was reverse transcribed using a T7- Oligo(dT) promoter primer for first-strand cDNA synthesis. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45˚C for 16 hours in a rotation oven. The hybridized chips were subjected to washes and stained in a Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned with an Affymetrix Genechip Scanner 3000 and processed automatically into digital CEL files.
| | Sample_data_processing | The raw data (CEL files) were analyzed with Affymetrix Gene Expression Console. Background correction and normalization were conducted using the RMA algorithm implemented in the Affymetrix package (version 1.26.1) of the Bioconductor software.
| | Sample_platform_id | GPL96
| | Sample_contact_name | David,,Simpson
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | Suite 4140 Medical Research Building III
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37212
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM641nnn/GSM641903/suppl/GSM641903.cel.gz
| | Sample_series_id | GSE26148
| | Sample_data_row_count | 22283
| | |
|
GSM641904 | GPL96 |
|
MCF10A-3D-16days-1
|
cells cultured in 3D for 16 days
|
cell type: mammary epithelial cells
cell line: MCF10A cells
culture condition: Matrigel (3D)
time: 16 days
|
Gene expression data from cells cultured in 3D for 16 days
|
| Sample_geo_accession | GSM641904
| | Sample_status | Public on Jun 01 2011
| | Sample_submission_date | Dec 17 2010
| | Sample_last_update_date | Jun 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | MCF10A cells were grown in 2D and 3D cells as described previously (Xiang and Muthuswamy 2006, PMID:16472698).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The RNA was isolated using TriZol according to Invitrogen's protocols as directed by the Affymettrix GeneChip Expression Analysis Technical Manual.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg total RNA was reverse transcribed using a T7- Oligo(dT) promoter primer for first-strand cDNA synthesis. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45˚C for 16 hours in a rotation oven. The hybridized chips were subjected to washes and stained in a Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned with an Affymetrix Genechip Scanner 3000 and processed automatically into digital CEL files.
| | Sample_data_processing | The raw data (CEL files) were analyzed with Affymetrix Gene Expression Console. Background correction and normalization were conducted using the RMA algorithm implemented in the Affymetrix package (version 1.26.1) of the Bioconductor software.
| | Sample_platform_id | GPL96
| | Sample_contact_name | David,,Simpson
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | Suite 4140 Medical Research Building III
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37212
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM641nnn/GSM641904/suppl/GSM641904.cel.gz
| | Sample_series_id | GSE26148
| | Sample_data_row_count | 22283
| | |
|
GSM641905 | GPL96 |
|
MCF10A-3D-16days-2
|
cells cultured in 3D for 16 days
|
cell type: mammary epithelial cells
cell line: MCF10A cells
culture condition: Matrigel (3D)
time: 16 days
|
Gene expression data from cells cultured in 3D for 16 days
|
| Sample_geo_accession | GSM641905
| | Sample_status | Public on Jun 01 2011
| | Sample_submission_date | Dec 17 2010
| | Sample_last_update_date | Jun 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | MCF10A cells were grown in 2D and 3D cells as described previously (Xiang and Muthuswamy 2006, PMID:16472698).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The RNA was isolated using TriZol according to Invitrogen's protocols as directed by the Affymettrix GeneChip Expression Analysis Technical Manual.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg total RNA was reverse transcribed using a T7- Oligo(dT) promoter primer for first-strand cDNA synthesis. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45˚C for 16 hours in a rotation oven. The hybridized chips were subjected to washes and stained in a Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned with an Affymetrix Genechip Scanner 3000 and processed automatically into digital CEL files.
| | Sample_data_processing | The raw data (CEL files) were analyzed with Affymetrix Gene Expression Console. Background correction and normalization were conducted using the RMA algorithm implemented in the Affymetrix package (version 1.26.1) of the Bioconductor software.
| | Sample_platform_id | GPL96
| | Sample_contact_name | David,,Simpson
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | Suite 4140 Medical Research Building III
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37212
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM641nnn/GSM641905/suppl/GSM641905.cel.gz
| | Sample_series_id | GSE26148
| | Sample_data_row_count | 22283
| | |
|
GSM641906 | GPL96 |
|
MCF10A-3D-16days-3
|
cells cultured in 3D for 16 days
|
cell type: mammary epithelial cells
cell line: MCF10A cells
culture condition: Matrigel (3D)
time: 16 days
|
Gene expression data from cells cultured in 3D for 16 days
|
| Sample_geo_accession | GSM641906
| | Sample_status | Public on Jun 01 2011
| | Sample_submission_date | Dec 17 2010
| | Sample_last_update_date | Jun 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | MCF10A cells were grown in 2D and 3D cells as described previously (Xiang and Muthuswamy 2006, PMID:16472698).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The RNA was isolated using TriZol according to Invitrogen's protocols as directed by the Affymettrix GeneChip Expression Analysis Technical Manual.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg total RNA was reverse transcribed using a T7- Oligo(dT) promoter primer for first-strand cDNA synthesis. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45˚C for 16 hours in a rotation oven. The hybridized chips were subjected to washes and stained in a Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned with an Affymetrix Genechip Scanner 3000 and processed automatically into digital CEL files.
| | Sample_data_processing | The raw data (CEL files) were analyzed with Affymetrix Gene Expression Console. Background correction and normalization were conducted using the RMA algorithm implemented in the Affymetrix package (version 1.26.1) of the Bioconductor software.
| | Sample_platform_id | GPL96
| | Sample_contact_name | David,,Simpson
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | Suite 4140 Medical Research Building III
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37212
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM641nnn/GSM641906/suppl/GSM641906.cel.gz
| | Sample_series_id | GSE26148
| | Sample_data_row_count | 22283
| | |
|
GSM641907 | GPL96 |
|
MCF10A-3D-16days-4
|
cells cultured in 3D for 16 days
|
cell type: mammary epithelial cells
cell line: MCF10A cells
culture condition: Matrigel (3D)
time: 16 days
|
Gene expression data from cells cultured in 3D for 16 days
|
| Sample_geo_accession | GSM641907
| | Sample_status | Public on Jun 01 2011
| | Sample_submission_date | Dec 17 2010
| | Sample_last_update_date | Jun 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | MCF10A cells were grown in 2D and 3D cells as described previously (Xiang and Muthuswamy 2006, PMID:16472698).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The RNA was isolated using TriZol according to Invitrogen's protocols as directed by the Affymettrix GeneChip Expression Analysis Technical Manual.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg total RNA was reverse transcribed using a T7- Oligo(dT) promoter primer for first-strand cDNA synthesis. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45˚C for 16 hours in a rotation oven. The hybridized chips were subjected to washes and stained in a Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned with an Affymetrix Genechip Scanner 3000 and processed automatically into digital CEL files.
| | Sample_data_processing | The raw data (CEL files) were analyzed with Affymetrix Gene Expression Console. Background correction and normalization were conducted using the RMA algorithm implemented in the Affymetrix package (version 1.26.1) of the Bioconductor software.
| | Sample_platform_id | GPL96
| | Sample_contact_name | David,,Simpson
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | Suite 4140 Medical Research Building III
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37212
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM641nnn/GSM641907/suppl/GSM641907.cel.gz
| | Sample_series_id | GSE26148
| | Sample_data_row_count | 22283
| | |
|
GSM641908 | GPL96 |
|
MCF10A-3D-16days-5
|
cells cultured in 3D for 16 days
|
cell type: mammary epithelial cells
cell line: MCF10A cells
culture condition: Matrigel (3D)
time: 16 days
|
Gene expression data from cells cultured in 3D for 16 days
|
| Sample_geo_accession | GSM641908
| | Sample_status | Public on Jun 01 2011
| | Sample_submission_date | Dec 17 2010
| | Sample_last_update_date | Jun 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | MCF10A cells were grown in 2D and 3D cells as described previously (Xiang and Muthuswamy 2006, PMID:16472698).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The RNA was isolated using TriZol according to Invitrogen's protocols as directed by the Affymettrix GeneChip Expression Analysis Technical Manual.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 5μg total RNA was reverse transcribed using a T7- Oligo(dT) promoter primer for first-strand cDNA synthesis. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA was purified and served as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
| | Sample_hyb_protocol | The biotinylated cRNA targets were cleaned up, fragmented, and hybridized to GeneChip expression arrays at 45˚C for 16 hours in a rotation oven. The hybridized chips were subjected to washes and stained in a Fluidics Station 450.
| | Sample_scan_protocol | The arrays were scanned with an Affymetrix Genechip Scanner 3000 and processed automatically into digital CEL files.
| | Sample_data_processing | The raw data (CEL files) were analyzed with Affymetrix Gene Expression Console. Background correction and normalization were conducted using the RMA algorithm implemented in the Affymetrix package (version 1.26.1) of the Bioconductor software.
| | Sample_platform_id | GPL96
| | Sample_contact_name | David,,Simpson
| | Sample_contact_institute | Vanderbilt University Medical Center
| | Sample_contact_address | Suite 4140 Medical Research Building III
| | Sample_contact_city | Nashville
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 37212
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM641nnn/GSM641908/suppl/GSM641908.cel.gz
| | Sample_series_id | GSE26148
| | Sample_data_row_count | 22283
| | |
|
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