Search results for the GEO ID: GSE20089  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM502016 | GPL570 |
|
PS fraction of U87 cell line replicate 1
|
U87 pseudopod fraction
|
cell line: U87
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502016
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502016/suppl/GSM502016.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502017 | GPL570 |
|
PS fraction of U87 cell line replicate 2
|
U87 pseudopod fraction
|
cell line: U87
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502017
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502017/suppl/GSM502017.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502018 | GPL570 |
|
PS fraction of U87 cell line replicate 3
|
U87 pseudopod fraction
|
cell line: U87
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502018
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502018/suppl/GSM502018.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502019 | GPL570 |
|
PS fraction of U251 cell line replicate 1
|
U251 pseudopod fraction
|
cell line: U251
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502019
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502019/suppl/GSM502019.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502020 | GPL570 |
|
PS fraction of U251 cell line replicate 2
|
U251 pseudopod fraction
|
cell line: U251
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502020
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502020/suppl/GSM502020.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502021 | GPL570 |
|
PS fraction of U251 cell line replicate 3
|
U251 pseudopod fraction
|
cell line: U251
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502021
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502021/suppl/GSM502021.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502022 | GPL570 |
|
PS fraction of HT1080 cell line replicate 1
|
HT1080 pseudopod fraction
|
cell line: HT1080
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502022
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502022/suppl/GSM502022.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502023 | GPL570 |
|
PS fraction of HT1080 cell line replicate 2
|
HT1080 pseudopod fraction
|
cell line: HT1080
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502023
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502023/suppl/GSM502023.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502024 | GPL570 |
|
PS fraction of HT1080 cell line replicate 3
|
HT1080 pseudopod fraction
|
cell line: HT1080
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502024
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502024/suppl/GSM502024.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502025 | GPL570 |
|
PS fraction of DU145 cell line replicate 1
|
DU145 pseudopod fraction
|
cell line: DU145
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502025
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502025/suppl/GSM502025.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502026 | GPL570 |
|
PS fraction of DU145 cell line replicate 2
|
DU145 pseudopod fraction
|
cell line: DU145
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502026
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502026/suppl/GSM502026.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502027 | GPL570 |
|
PS fraction of DU145 cell line replicate 3
|
DU145 pseudopod fraction
|
cell line: DU145
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502027
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502027/suppl/GSM502027.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502028 | GPL570 |
|
PS fraction of MDA231 cell line replicate 1
|
MDA231 pseudopod fraction
|
cell line: MDA231
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502028
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502028/suppl/GSM502028.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502029 | GPL570 |
|
PS fraction of MDA231 cell line replicate 2
|
MDA231 pseudopod fraction
|
cell line: MDA231
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502029
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502029/suppl/GSM502029.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502030 | GPL570 |
|
PS fraction of MDA231 cell line replicate 3
|
MDA231 pseudopod fraction
|
cell line: MDA231
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502030
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502030/suppl/GSM502030.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502031 | GPL570 |
|
PS fraction of MDA435 cell line replicate 1
|
MDA435 pseudopod fraction
|
cell line: MDA435
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502031
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502031/suppl/GSM502031.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502032 | GPL570 |
|
PS fraction of MDA435 cell line replicate 2
|
MDA435 pseudopod fraction
|
cell line: MDA435
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502032
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502032/suppl/GSM502032.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502033 | GPL570 |
|
PS fraction of MDA435 cell line replicate 3
|
MDA435 pseudopod fraction
|
cell line: MDA435
|
Gene expression from PS fraction
|
| Sample_geo_accession | GSM502033
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502033/suppl/GSM502033.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502034 | GPL570 |
|
CB fraction of U87 cell line replicate 1
|
U87 cell body fraction
|
cell line: U87
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502034
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502034/suppl/GSM502034.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502035 | GPL570 |
|
CB fraction of U87 cell line replicate 2
|
U87 cell body fraction
|
cell line: U87
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502035
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502035/suppl/GSM502035.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502036 | GPL570 |
|
CB fraction of U87 cell line replicate 3
|
U87 cell body fraction
|
cell line: U87
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502036
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502036/suppl/GSM502036.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502037 | GPL570 |
|
CB fraction of U251 cell line replicate 1
|
U251 cell body fraction
|
cell line: U251
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502037
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502037/suppl/GSM502037.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502038 | GPL570 |
|
CB fraction of U251 cell line replicate 2
|
U251 cell body fraction
|
cell line: U251
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502038
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502038/suppl/GSM502038.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502039 | GPL570 |
|
CB fraction of U251 cell line replicate 3
|
U251 cell body fraction
|
cell line: U251
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502039
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502039/suppl/GSM502039.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502040 | GPL570 |
|
CB fraction of HT1080 cell line replicate 1
|
HT1080 cell body fraction
|
cell line: HT1080
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502040
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502040/suppl/GSM502040.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502041 | GPL570 |
|
CB fraction of HT1080 cell line replicate 2
|
HT1080 cell body fraction
|
cell line: HT1080
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502041
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502041/suppl/GSM502041.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502042 | GPL570 |
|
CB fraction of HT1080 cell line replicate 3
|
HT1080 cell body fraction
|
cell line: HT1080
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502042
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502042/suppl/GSM502042.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502043 | GPL570 |
|
CB fraction of DU145 cell line replicate 1
|
DU145 cell body fraction
|
cell line: DU145
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502043
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502043/suppl/GSM502043.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502044 | GPL570 |
|
CB fraction of DU145 cell line replicate 2
|
DU145 cell body fraction
|
cell line: DU145
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502044
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502044/suppl/GSM502044.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502045 | GPL570 |
|
CB fraction of DU145 cell line replicate 3
|
DU145 cell body fraction
|
cell line: DU145
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502045
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502045/suppl/GSM502045.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502046 | GPL570 |
|
CB fraction of MDA231 cell line replicate 1
|
MDA231 cell body fraction
|
cell line: MDA231
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502046
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502046/suppl/GSM502046.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502047 | GPL570 |
|
CB fraction of MDA231 cell line replicate 2
|
MDA231 cell body fraction
|
cell line: MDA231
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502047
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502047/suppl/GSM502047.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502048 | GPL570 |
|
CB fraction of MDA231 cell line replicate 3
|
MDA231 cell body fraction
|
cell line: MDA231
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502048
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502048/suppl/GSM502048.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502049 | GPL570 |
|
CB fraction of MDA435 cell line replicate 1
|
MDA435 cell body fraction
|
cell line: MDA435
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502049
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502049/suppl/GSM502049.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502050 | GPL570 |
|
CB fraction of MDA435 cell line replicate 2
|
MDA435 cell body fraction
|
cell line: MDA435
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502050
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502050/suppl/GSM502050.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
GSM502051 | GPL570 |
|
CB fraction of MDA435 cell line replicate 3
|
MDA435 cell body fraction
|
cell line: MDA435
|
Gene expression from CB fraction
|
| Sample_geo_accession | GSM502051
| | Sample_status | Public on Mar 30 2010
| | Sample_submission_date | Jan 28 2010
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_growth_protocol_ch1 | U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium and MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)
| | Sample_hyb_protocol | 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400
| | Sample_scan_protocol | GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)
| | Sample_data_processing | RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Ivan,Robert,Nabi
| | Sample_contact_email | irnabi@interchange.ubc.ca
| | Sample_contact_phone | 604-822-7000
| | Sample_contact_laboratory | Lab No: 3.420
| | Sample_contact_department | CPS
| | Sample_contact_institute | University of British Columbia
| | Sample_contact_address | LSI, 2350 health sciences Mall
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British columbia
| | Sample_contact_zip/postal_code | V6T1Z3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM502nnn/GSM502051/suppl/GSM502051.CEL.gz
| | Sample_series_id | GSE20089
| | Sample_data_row_count | 54593
| | |
|
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