Search results for the GEO ID: GSE17540 |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM437354 | GPL570 |
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Control
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MCF7 cells transfected with CEACAM1-S double-A mutant T457A,S459A (DA)
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cell line: MCF7 (ATCC HTB-22)
cell type: epithelial
organ: mammary gland
disease: adenocarcinoma
metastatic site: pleural effusion
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MCF7 cells transfected with CEACAM1-S double-A mutant T457A,S459A (DA)
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Sample_geo_accession | GSM437354
| Sample_status | Public on Oct 01 2009
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | Aug 06 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | The three-dimensional Matrigel (BD Biosciences) sandwich assay has been previously described (12). Briefly, 10 ml culture dishes were coated with 1 ml of Matrigel and incubated at 37 °C for 30 min until the Matrigel solidified, cells (1x106) in 10 ml of mammary epithelial basal medium (MEBM) plus pituitary gland extract (PGE) (Lonza Group LTD, Switzerland) were added to each well. After 3 hr of incubation, the floating cells were removed and the bound cells were overlaid with 1ml of 50% Matrigel in MEBM plus PGE. At day 4 , the acini were recovered by adding 10 ml of dissolving solution into each dish and incubated at 4oC for 3 hrs by gentle rotation. The cells were harvested and RNA isolated for Gene chip analysis
| Sample_growth_protocol_ch1 | The human mammary adenocarcinoma cell line MCF7 was obtained from ATCC (HTB-22™). MCF7 cells were cultured in MEM medium supplemented with 10% Fetal Bovine Serum, 1% penicillin/streptomycin/Am, 1% sodium pyruvate, 2% sodium bicarbonate, and 1% non-essential amino acids
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted from cells using the Tri-Reagent (Molecular Research Center) according to the manufacturer’s instruction
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | One-Cycle target labeling was performed using 5ug of total RNA according to Affymetrix's Eukaryotic Target Labeling protocol
| Sample_hyb_protocol | The chips were hybridized by Affymetrix Hybridization Oven 640 and washed by Affymetrix Fluidics Station 450 according to manufacturer's protocols
| Sample_scan_protocol | The chips were scanned by Affymetrix scanner 3000 7G using manufacturer's default settings
| Sample_data_processing | Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Bioconductor package Affy.
| Sample_platform_id | GPL570
| Sample_contact_name | Xiwei,,Wu
| Sample_contact_email | xwu@coh.org
| Sample_contact_department | Biomedical Informatics
| Sample_contact_institute | City of Hope National Medical Center
| Sample_contact_address | 1500 E. Duarte Rd.
| Sample_contact_city | Duarte
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 91010
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437354/suppl/GSM437354.CEL.gz
| Sample_series_id | GSE17540
| Sample_data_row_count | 54675
| |
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GSM437355 | GPL570 |
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SW2
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MCF7 cells transfected with CEACAM1-S wild-type (SW)
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cell line: MCF7 (ATCC HTB-22)
cell type: epithelial
organ: mammary gland
disease: adenocarcinoma
metastatic site: pleural effusion
|
MCF7 cells transfected with CEACAM1-S wild-type (SW)
|
Sample_geo_accession | GSM437355
| Sample_status | Public on Oct 01 2009
| Sample_submission_date | Aug 06 2009
| Sample_last_update_date | Aug 06 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | The three-dimensional Matrigel (BD Biosciences) sandwich assay has been previously described (12). Briefly, 10 ml culture dishes were coated with 1 ml of Matrigel and incubated at 37 °C for 30 min until the Matrigel solidified, cells (1x106) in 10 ml of mammary epithelial basal medium (MEBM) plus pituitary gland extract (PGE) (Lonza Group LTD, Switzerland) were added to each well. After 3 hr of incubation, the floating cells were removed and the bound cells were overlaid with 1ml of 50% Matrigel in MEBM plus PGE. At day 4 , the acini were recovered by adding 10 ml of dissolving solution into each dish and incubated at 4oC for 3 hrs by gentle rotation. The cells were harvested and RNA isolated for Gene chip analysis
| Sample_growth_protocol_ch1 | The human mammary adenocarcinoma cell line MCF7 was obtained from ATCC (HTB-22™). MCF7 cells were cultured in MEM medium supplemented with 10% Fetal Bovine Serum, 1% penicillin/streptomycin/Am, 1% sodium pyruvate, 2% sodium bicarbonate, and 1% non-essential amino acids
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was extracted from cells using the Tri-Reagent (Molecular Research Center) according to the manufacturer’s instruction
| Sample_label_ch1 | Biotin
| Sample_label_protocol_ch1 | One-Cycle target labeling was performed using 5ug of total RNA according to Affymetrix's Eukaryotic Target Labeling protocol
| Sample_hyb_protocol | The chips were hybridized by Affymetrix Hybridization Oven 640 and washed by Affymetrix Fluidics Station 450 according to manufacturer's protocols
| Sample_scan_protocol | The chips were scanned by Affymetrix scanner 3000 7G using manufacturer's default settings
| Sample_data_processing | Raw Affymetrix intensity measurements of all probe sets were background-corrected, normalized, and summarized into gene level expression measurements using RMA method implemented in Bioconductor package Affy.
| Sample_platform_id | GPL570
| Sample_contact_name | Xiwei,,Wu
| Sample_contact_email | xwu@coh.org
| Sample_contact_department | Biomedical Informatics
| Sample_contact_institute | City of Hope National Medical Center
| Sample_contact_address | 1500 E. Duarte Rd.
| Sample_contact_city | Duarte
| Sample_contact_state | CA
| Sample_contact_zip/postal_code | 91010
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437355/suppl/GSM437355.CEL.gz
| Sample_series_id | GSE17540
| Sample_data_row_count | 54675
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