Search results for the GEO ID: GSE24879  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM611715 | GPL1355 |
|
A16 vs Tumor F111 cells 16 h adhesion, biological replicate 1, technical replicate 1 (PLIER)
|
F111 fibroblast cell lines, adherent for 16h
|
cell line: F111
cell type: A16
|
Expression profile of F111 fibroblast cell lines, 16 h after adhesion
|
| Sample_geo_accession | GSM611715
| | Sample_status | Public on Nov 14 2010
| | Sample_submission_date | Oct 21 2010
| | Sample_last_update_date | Oct 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A16 cells are F111 cell lines that were plated for growth on plastic for a period of 16 h. NA16 cells are F111 cell lines that were plated for growth on suspension for a period of 16h. Tumor cells are prepared from tumors that are arised due to injection of NA16 cells in nude mice. Colony cells were obtained after placing NA16 cells in soft agar for 7 days
| | Sample_growth_protocol_ch1 | A16 cells, NA16, cells, colony and tumor cells were cultured in Dulbeccos modified eagle medium with 10% Fetal calf serum at 37°C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 5 million F111 cells grown for 16h time period on adhesion and non-adhesion surfaces were used as starting material for the total RNA isolation using Rneasy mini kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)
| | Sample_hyb_protocol | The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rat 230_2 Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450
| | Sample_scan_protocol | The gene chips were scanned on an Affymetrix Scanner 3000
| | Sample_data_processing | The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to AvadisTM software version 4.3 (Strand Life Sciences, Bangalore, India) for further analysis. The PLIER and RMA algorithms were used for data normalization.Test samples (NA16, Colony and tumor samples) were analyzed (using Avadis) individually with the control A16.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Dr. Gopal,,Pande
| | Sample_contact_email | gpande@ccmb.res.in
| | Sample_contact_fax | +91 40 2716 0591
| | Sample_contact_institute | Centre for Cellular and Molecular Biology
| | Sample_contact_address | Uppal Road
| | Sample_contact_city | Hyderabad
| | Sample_contact_state | Andhra Pradesh
| | Sample_contact_zip/postal_code | 500 007
| | Sample_contact_country | India
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM611nnn/GSM611715/suppl/GSM611715.CEL.gz
| | Sample_series_id | GSE24879
| | Sample_series_id | GSE24893
| | Sample_data_row_count | 31099
| | |
|
GSM611716 | GPL1355 |
|
A16 vs Tumor F111 cells 16 h adhesion, biological replicate 1, technical replicate 1 (RMA)
|
F111 fibroblast cell lines, adherent for 16h
|
cell line: F111
cell type: A16
|
Expression profile of F111 fibroblast cell lines, 16 h after adhesion
|
| Sample_geo_accession | GSM611716
| | Sample_status | Public on Nov 14 2010
| | Sample_submission_date | Oct 21 2010
| | Sample_last_update_date | Oct 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A16 cells are F111 cell lines that were plated for growth on plastic for a period of 16 h. NA16 cells are F111 cell lines that were plated for growth on suspension for a period of 16h. Tumor cells are prepared from tumors that are arised due to injection of NA16 cells in nude mice. Colony cells were obtained after placing NA16 cells in soft agar for 7 days
| | Sample_growth_protocol_ch1 | A16 cells, NA16, cells, colony and tumor cells were cultured in Dulbeccos modified eagle medium with 10% Fetal calf serum at 37°C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 5 million F111 cells grown for 16h time period on adhesion and non-adhesion surfaces were used as starting material for the total RNA isolation using Rneasy mini kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)
| | Sample_hyb_protocol | The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rat 230_2 Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450
| | Sample_scan_protocol | The gene chips were scanned on an Affymetrix Scanner 3000
| | Sample_data_processing | The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to AvadisTM software version 4.3 (Strand Life Sciences, Bangalore, India) for further analysis. The PLIER and RMA algorithms were used for data normalization.Test samples (NA16, Colony and tumor samples) were analyzed (using Avadis) individually with the control A16.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Dr. Gopal,,Pande
| | Sample_contact_email | gpande@ccmb.res.in
| | Sample_contact_fax | +91 40 2716 0591
| | Sample_contact_institute | Centre for Cellular and Molecular Biology
| | Sample_contact_address | Uppal Road
| | Sample_contact_city | Hyderabad
| | Sample_contact_state | Andhra Pradesh
| | Sample_contact_zip/postal_code | 500 007
| | Sample_contact_country | India
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM611nnn/GSM611716/suppl/GSM611716.CEL.gz
| | Sample_series_id | GSE24879
| | Sample_series_id | GSE24893
| | Sample_data_row_count | 31099
| | |
|
GSM611717 | GPL1355 |
|
A16 vs Tumor F111 cells 16 h adhesion, biological replicate 2 (PLIER)
|
F111 fibroblast cell lines, adherent for 16h
|
cell line: F111
cell type: A16
|
Expression profile of F111 fibroblast cell lines, 16 h after adhesion
|
| Sample_geo_accession | GSM611717
| | Sample_status | Public on Nov 14 2010
| | Sample_submission_date | Oct 21 2010
| | Sample_last_update_date | Oct 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A16 cells are F111 cell lines that were plated for growth on plastic for a period of 16 h. NA16 cells are F111 cell lines that were plated for growth on suspension for a period of 16h. Tumor cells are prepared from tumors that are arised due to injection of NA16 cells in nude mice. Colony cells were obtained after placing NA16 cells in soft agar for 7 days
| | Sample_growth_protocol_ch1 | A16 cells, NA16, cells, colony and tumor cells were cultured in Dulbeccos modified eagle medium with 10% Fetal calf serum at 37°C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 5 million F111 cells grown for 16h time period on adhesion and non-adhesion surfaces were used as starting material for the total RNA isolation using Rneasy mini kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)
| | Sample_hyb_protocol | The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rat 230_2 Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450
| | Sample_scan_protocol | The gene chips were scanned on an Affymetrix Scanner 3000
| | Sample_data_processing | The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to AvadisTM software version 4.3 (Strand Life Sciences, Bangalore, India) for further analysis. The PLIER and RMA algorithms were used for data normalization.Test samples (NA16, Colony and tumor samples) were analyzed (using Avadis) individually with the control A16.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Dr. Gopal,,Pande
| | Sample_contact_email | gpande@ccmb.res.in
| | Sample_contact_fax | +91 40 2716 0591
| | Sample_contact_institute | Centre for Cellular and Molecular Biology
| | Sample_contact_address | Uppal Road
| | Sample_contact_city | Hyderabad
| | Sample_contact_state | Andhra Pradesh
| | Sample_contact_zip/postal_code | 500 007
| | Sample_contact_country | India
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM611nnn/GSM611717/suppl/GSM611717.CEL.gz
| | Sample_series_id | GSE24879
| | Sample_series_id | GSE24893
| | Sample_data_row_count | 31099
| | |
|
GSM611718 | GPL1355 |
|
A16 vs Tumor F111 cells 16 h adhesion, biological replicate 2 (RMA)
|
F111 fibroblast cell lines, adherent for 16h
|
cell line: F111
cell type: A16
|
Expression profile of F111 fibroblast cell lines, 16 h after adhesion
|
| Sample_geo_accession | GSM611718
| | Sample_status | Public on Nov 14 2010
| | Sample_submission_date | Oct 21 2010
| | Sample_last_update_date | Oct 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A16 cells are F111 cell lines that were plated for growth on plastic for a period of 16 h. NA16 cells are F111 cell lines that were plated for growth on suspension for a period of 16h. Tumor cells are prepared from tumors that are arised due to injection of NA16 cells in nude mice. Colony cells were obtained after placing NA16 cells in soft agar for 7 days
| | Sample_growth_protocol_ch1 | A16 cells, NA16, cells, colony and tumor cells were cultured in Dulbeccos modified eagle medium with 10% Fetal calf serum at 37°C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 5 million F111 cells grown for 16h time period on adhesion and non-adhesion surfaces were used as starting material for the total RNA isolation using Rneasy mini kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)
| | Sample_hyb_protocol | The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rat 230_2 Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450
| | Sample_scan_protocol | The gene chips were scanned on an Affymetrix Scanner 3000
| | Sample_data_processing | The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to AvadisTM software version 4.3 (Strand Life Sciences, Bangalore, India) for further analysis. The PLIER and RMA algorithms were used for data normalization.Test samples (NA16, Colony and tumor samples) were analyzed (using Avadis) individually with the control A16.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Dr. Gopal,,Pande
| | Sample_contact_email | gpande@ccmb.res.in
| | Sample_contact_fax | +91 40 2716 0591
| | Sample_contact_institute | Centre for Cellular and Molecular Biology
| | Sample_contact_address | Uppal Road
| | Sample_contact_city | Hyderabad
| | Sample_contact_state | Andhra Pradesh
| | Sample_contact_zip/postal_code | 500 007
| | Sample_contact_country | India
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM611nnn/GSM611718/suppl/GSM611718.CEL.gz
| | Sample_series_id | GSE24879
| | Sample_series_id | GSE24893
| | Sample_data_row_count | 31099
| | |
|
GSM611719 | GPL1355 |
|
A16 vs Tumor F111 cells 16 h adhesion, technical replicate 2 (PLIER)
|
F111 fibroblast cell lines, adherent for 16h
|
cell line: F111
cell type: A16
|
Expression profile of F111 fibroblast cell lines, 16 h after adhesion
|
| Sample_geo_accession | GSM611719
| | Sample_status | Public on Nov 14 2010
| | Sample_submission_date | Oct 21 2010
| | Sample_last_update_date | Oct 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A16 cells are F111 cell lines that were plated for growth on plastic for a period of 16 h. NA16 cells are F111 cell lines that were plated for growth on suspension for a period of 16h. Tumor cells are prepared from tumors that are arised due to injection of NA16 cells in nude mice. Colony cells were obtained after placing NA16 cells in soft agar for 7 days
| | Sample_growth_protocol_ch1 | A16 cells, NA16, cells, colony and tumor cells were cultured in Dulbeccos modified eagle medium with 10% Fetal calf serum at 37°C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 5 million F111 cells grown for 16h time period on adhesion and non-adhesion surfaces were used as starting material for the total RNA isolation using Rneasy mini kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)
| | Sample_hyb_protocol | The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rat 230_2 Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450
| | Sample_scan_protocol | The gene chips were scanned on an Affymetrix Scanner 3000
| | Sample_data_processing | The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to AvadisTM software version 4.3 (Strand Life Sciences, Bangalore, India) for further analysis. The PLIER and RMA algorithms were used for data normalization.Test samples (NA16, Colony and tumor samples) were analyzed (using Avadis) individually with the control A16.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Dr. Gopal,,Pande
| | Sample_contact_email | gpande@ccmb.res.in
| | Sample_contact_fax | +91 40 2716 0591
| | Sample_contact_institute | Centre for Cellular and Molecular Biology
| | Sample_contact_address | Uppal Road
| | Sample_contact_city | Hyderabad
| | Sample_contact_state | Andhra Pradesh
| | Sample_contact_zip/postal_code | 500 007
| | Sample_contact_country | India
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM611nnn/GSM611719/suppl/GSM611719.CEL.gz
| | Sample_series_id | GSE24879
| | Sample_series_id | GSE24893
| | Sample_data_row_count | 31099
| | |
|
GSM611720 | GPL1355 |
|
A16 vs Tumor F111 cells 16 h adhesion, technical replicate 2 (RMA)
|
F111 fibroblast cell lines, adherent for 16h
|
cell line: F111
cell type: A16
|
Expression profile of F111 fibroblast cell lines, 16 h after adhesion
|
| Sample_geo_accession | GSM611720
| | Sample_status | Public on Nov 14 2010
| | Sample_submission_date | Oct 21 2010
| | Sample_last_update_date | Oct 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A16 cells are F111 cell lines that were plated for growth on plastic for a period of 16 h. NA16 cells are F111 cell lines that were plated for growth on suspension for a period of 16h. Tumor cells are prepared from tumors that are arised due to injection of NA16 cells in nude mice. Colony cells were obtained after placing NA16 cells in soft agar for 7 days
| | Sample_growth_protocol_ch1 | A16 cells, NA16, cells, colony and tumor cells were cultured in Dulbeccos modified eagle medium with 10% Fetal calf serum at 37°C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 5 million F111 cells grown for 16h time period on adhesion and non-adhesion surfaces were used as starting material for the total RNA isolation using Rneasy mini kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)
| | Sample_hyb_protocol | The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rat 230_2 Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450
| | Sample_scan_protocol | The gene chips were scanned on an Affymetrix Scanner 3000
| | Sample_data_processing | The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to AvadisTM software version 4.3 (Strand Life Sciences, Bangalore, India) for further analysis. The PLIER and RMA algorithms were used for data normalization.Test samples (NA16, Colony and tumor samples) were analyzed (using Avadis) individually with the control A16.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Dr. Gopal,,Pande
| | Sample_contact_email | gpande@ccmb.res.in
| | Sample_contact_fax | +91 40 2716 0591
| | Sample_contact_institute | Centre for Cellular and Molecular Biology
| | Sample_contact_address | Uppal Road
| | Sample_contact_city | Hyderabad
| | Sample_contact_state | Andhra Pradesh
| | Sample_contact_zip/postal_code | 500 007
| | Sample_contact_country | India
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM611nnn/GSM611720/suppl/GSM611720.CEL.gz
| | Sample_series_id | GSE24879
| | Sample_series_id | GSE24893
| | Sample_data_row_count | 31099
| | |
|
GSM611721 | GPL1355 |
|
NA16 cells injected subcutaneously for tumor formation, biological replicate 1, technical replicate 1 (PLIER)
|
F111 fibroblast cell lines, tumor formation after subcutaneous injection of NA16 cells
|
cell line: F111
cell type: tumor
|
Expression profile of F111 fibroblast cell lines, 3 months after subcutaneous injection of NA16 cells
|
| Sample_geo_accession | GSM611721
| | Sample_status | Public on Nov 14 2010
| | Sample_submission_date | Oct 21 2010
| | Sample_last_update_date | Oct 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A16 cells are F111 cell lines that were plated for growth on plastic for a period of 16 h. NA16 cells are F111 cell lines that were plated for growth on suspension for a period of 16h. Tumor cells are prepared from tumors that are arised due to injection of NA16 cells in nude mice. Colony cells were obtained after placing NA16 cells in soft agar for 7 days
| | Sample_growth_protocol_ch1 | A16 cells, NA16, cells, colony and tumor cells were cultured in Dulbeccos modified eagle medium with 10% Fetal calf serum at 37°C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 5 million F111 cells grown for 16h time period on adhesion and non-adhesion surfaces were used as starting material for the total RNA isolation using Rneasy mini kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)
| | Sample_hyb_protocol | The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rat 230_2 Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450
| | Sample_scan_protocol | The gene chips were scanned on an Affymetrix Scanner 3000
| | Sample_data_processing | The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to AvadisTM software version 4.3 (Strand Life Sciences, Bangalore, India) for further analysis. The PLIER and RMA algorithms were used for data normalization.Test samples (NA16, Colony and tumor samples) were analyzed (using Avadis) individually with the control A16.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Dr. Gopal,,Pande
| | Sample_contact_email | gpande@ccmb.res.in
| | Sample_contact_fax | +91 40 2716 0591
| | Sample_contact_institute | Centre for Cellular and Molecular Biology
| | Sample_contact_address | Uppal Road
| | Sample_contact_city | Hyderabad
| | Sample_contact_state | Andhra Pradesh
| | Sample_contact_zip/postal_code | 500 007
| | Sample_contact_country | India
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM611nnn/GSM611721/suppl/GSM611721.CEL.gz
| | Sample_series_id | GSE24879
| | Sample_series_id | GSE24893
| | Sample_data_row_count | 31099
| | |
|
GSM611722 | GPL1355 |
|
NA16 cells injected subcutaneously for tumor formation, biological replicate 1, technical replicate 1 (RMA)
|
F111 fibroblast cell lines, tumor formation after subcutaneous injection of NA16 cells
|
cell line: F111
cell type: tumor
|
Expression profile of F111 fibroblast cell lines, 3 months after subcutaneous injection of NA16 cells
|
| Sample_geo_accession | GSM611722
| | Sample_status | Public on Nov 14 2010
| | Sample_submission_date | Oct 21 2010
| | Sample_last_update_date | Oct 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A16 cells are F111 cell lines that were plated for growth on plastic for a period of 16 h. NA16 cells are F111 cell lines that were plated for growth on suspension for a period of 16h. Tumor cells are prepared from tumors that are arised due to injection of NA16 cells in nude mice. Colony cells were obtained after placing NA16 cells in soft agar for 7 days
| | Sample_growth_protocol_ch1 | A16 cells, NA16, cells, colony and tumor cells were cultured in Dulbeccos modified eagle medium with 10% Fetal calf serum at 37°C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 5 million F111 cells grown for 16h time period on adhesion and non-adhesion surfaces were used as starting material for the total RNA isolation using Rneasy mini kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)
| | Sample_hyb_protocol | The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rat 230_2 Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450
| | Sample_scan_protocol | The gene chips were scanned on an Affymetrix Scanner 3000
| | Sample_data_processing | The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to AvadisTM software version 4.3 (Strand Life Sciences, Bangalore, India) for further analysis. The PLIER and RMA algorithms were used for data normalization.Test samples (NA16, Colony and tumor samples) were analyzed (using Avadis) individually with the control A16.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Dr. Gopal,,Pande
| | Sample_contact_email | gpande@ccmb.res.in
| | Sample_contact_fax | +91 40 2716 0591
| | Sample_contact_institute | Centre for Cellular and Molecular Biology
| | Sample_contact_address | Uppal Road
| | Sample_contact_city | Hyderabad
| | Sample_contact_state | Andhra Pradesh
| | Sample_contact_zip/postal_code | 500 007
| | Sample_contact_country | India
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM611nnn/GSM611722/suppl/GSM611722.CEL.gz
| | Sample_series_id | GSE24879
| | Sample_series_id | GSE24893
| | Sample_data_row_count | 31099
| | |
|
GSM611723 | GPL1355 |
|
NA16 cells injected subcutaneously for tumor formation, technical replicate 2 (PLIER)
|
F111 fibroblast cell lines, tumor formation after subcutaneous injection of NA16 cells
|
cell line: F111
cell type: tumor
|
Expression profile of F111 fibroblast cell lines, 3 months after subcutaneous injection of NA16 cells
|
| Sample_geo_accession | GSM611723
| | Sample_status | Public on Nov 14 2010
| | Sample_submission_date | Oct 21 2010
| | Sample_last_update_date | Oct 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A16 cells are F111 cell lines that were plated for growth on plastic for a period of 16 h. NA16 cells are F111 cell lines that were plated for growth on suspension for a period of 16h. Tumor cells are prepared from tumors that are arised due to injection of NA16 cells in nude mice. Colony cells were obtained after placing NA16 cells in soft agar for 7 days
| | Sample_growth_protocol_ch1 | A16 cells, NA16, cells, colony and tumor cells were cultured in Dulbeccos modified eagle medium with 10% Fetal calf serum at 37°C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 5 million F111 cells grown for 16h time period on adhesion and non-adhesion surfaces were used as starting material for the total RNA isolation using Rneasy mini kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)
| | Sample_hyb_protocol | The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rat 230_2 Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450
| | Sample_scan_protocol | The gene chips were scanned on an Affymetrix Scanner 3000
| | Sample_data_processing | The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to AvadisTM software version 4.3 (Strand Life Sciences, Bangalore, India) for further analysis. The PLIER and RMA algorithms were used for data normalization.Test samples (NA16, Colony and tumor samples) were analyzed (using Avadis) individually with the control A16.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Dr. Gopal,,Pande
| | Sample_contact_email | gpande@ccmb.res.in
| | Sample_contact_fax | +91 40 2716 0591
| | Sample_contact_institute | Centre for Cellular and Molecular Biology
| | Sample_contact_address | Uppal Road
| | Sample_contact_city | Hyderabad
| | Sample_contact_state | Andhra Pradesh
| | Sample_contact_zip/postal_code | 500 007
| | Sample_contact_country | India
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM611nnn/GSM611723/suppl/GSM611723.CEL.gz
| | Sample_series_id | GSE24879
| | Sample_series_id | GSE24893
| | Sample_data_row_count | 31099
| | |
|
GSM611724 | GPL1355 |
|
NA16 cells injected subcutaneously for tumor formation, technical replicate 2 (RMA)
|
F111 fibroblast cell lines, tumor formation after subcutaneous injection of NA16 cells
|
cell line: F111
cell type: tumor
|
Expression profile of F111 fibroblast cell lines, 3 months after subcutaneous injection of NA16 cells
|
| Sample_geo_accession | GSM611724
| | Sample_status | Public on Nov 14 2010
| | Sample_submission_date | Oct 21 2010
| | Sample_last_update_date | Oct 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A16 cells are F111 cell lines that were plated for growth on plastic for a period of 16 h. NA16 cells are F111 cell lines that were plated for growth on suspension for a period of 16h. Tumor cells are prepared from tumors that are arised due to injection of NA16 cells in nude mice. Colony cells were obtained after placing NA16 cells in soft agar for 7 days
| | Sample_growth_protocol_ch1 | A16 cells, NA16, cells, colony and tumor cells were cultured in Dulbeccos modified eagle medium with 10% Fetal calf serum at 37°C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 5 million F111 cells grown for 16h time period on adhesion and non-adhesion surfaces were used as starting material for the total RNA isolation using Rneasy mini kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)
| | Sample_hyb_protocol | The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rat 230_2 Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450
| | Sample_scan_protocol | The gene chips were scanned on an Affymetrix Scanner 3000
| | Sample_data_processing | The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to AvadisTM software version 4.3 (Strand Life Sciences, Bangalore, India) for further analysis. The PLIER and RMA algorithms were used for data normalization.Test samples (NA16, Colony and tumor samples) were analyzed (using Avadis) individually with the control A16.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Dr. Gopal,,Pande
| | Sample_contact_email | gpande@ccmb.res.in
| | Sample_contact_fax | +91 40 2716 0591
| | Sample_contact_institute | Centre for Cellular and Molecular Biology
| | Sample_contact_address | Uppal Road
| | Sample_contact_city | Hyderabad
| | Sample_contact_state | Andhra Pradesh
| | Sample_contact_zip/postal_code | 500 007
| | Sample_contact_country | India
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM611nnn/GSM611724/suppl/GSM611724.CEL.gz
| | Sample_series_id | GSE24879
| | Sample_series_id | GSE24893
| | Sample_data_row_count | 31099
| | |
|
GSM611725 | GPL1355 |
|
NA16 cells injected subcutaneously for tumor formation, biological replicate 2 (PLIER)
|
F111 fibroblast cell lines, tumor formation after subcutaneous injection of NA16 cells
|
cell line: F111
cell type: tumor
|
Expression profile of F111 fibroblast cell lines, 3 months after subcutaneous injection of NA16 cells
|
| Sample_geo_accession | GSM611725
| | Sample_status | Public on Nov 14 2010
| | Sample_submission_date | Oct 21 2010
| | Sample_last_update_date | Oct 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A16 cells are F111 cell lines that were plated for growth on plastic for a period of 16 h. NA16 cells are F111 cell lines that were plated for growth on suspension for a period of 16h. Tumor cells are prepared from tumors that are arised due to injection of NA16 cells in nude mice. Colony cells were obtained after placing NA16 cells in soft agar for 7 days
| | Sample_growth_protocol_ch1 | A16 cells, NA16, cells, colony and tumor cells were cultured in Dulbeccos modified eagle medium with 10% Fetal calf serum at 37°C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 5 million F111 cells grown for 16h time period on adhesion and non-adhesion surfaces were used as starting material for the total RNA isolation using Rneasy mini kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)
| | Sample_hyb_protocol | The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rat 230_2 Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450
| | Sample_scan_protocol | The gene chips were scanned on an Affymetrix Scanner 3000
| | Sample_data_processing | The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to AvadisTM software version 4.3 (Strand Life Sciences, Bangalore, India) for further analysis. The PLIER and RMA algorithms were used for data normalization.Test samples (NA16, Colony and tumor samples) were analyzed (using Avadis) individually with the control A16.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Dr. Gopal,,Pande
| | Sample_contact_email | gpande@ccmb.res.in
| | Sample_contact_fax | +91 40 2716 0591
| | Sample_contact_institute | Centre for Cellular and Molecular Biology
| | Sample_contact_address | Uppal Road
| | Sample_contact_city | Hyderabad
| | Sample_contact_state | Andhra Pradesh
| | Sample_contact_zip/postal_code | 500 007
| | Sample_contact_country | India
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM611nnn/GSM611725/suppl/GSM611725.CEL.gz
| | Sample_series_id | GSE24879
| | Sample_series_id | GSE24893
| | Sample_data_row_count | 31099
| | |
|
GSM611726 | GPL1355 |
|
NA16 cells injected subcutaneously for tumor formation, biological replicate 2 (RMA)
|
F111 fibroblast cell lines, tumor formation after subcutaneous injection of NA16 cells
|
cell line: F111
cell type: tumor
|
Expression profile of F111 fibroblast cell lines, 3 months after subcutaneous injection of NA16 cells
|
| Sample_geo_accession | GSM611726
| | Sample_status | Public on Nov 14 2010
| | Sample_submission_date | Oct 21 2010
| | Sample_last_update_date | Oct 22 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | A16 cells are F111 cell lines that were plated for growth on plastic for a period of 16 h. NA16 cells are F111 cell lines that were plated for growth on suspension for a period of 16h. Tumor cells are prepared from tumors that are arised due to injection of NA16 cells in nude mice. Colony cells were obtained after placing NA16 cells in soft agar for 7 days
| | Sample_growth_protocol_ch1 | A16 cells, NA16, cells, colony and tumor cells were cultured in Dulbeccos modified eagle medium with 10% Fetal calf serum at 37°C, 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 5 million F111 cells grown for 16h time period on adhesion and non-adhesion surfaces were used as starting material for the total RNA isolation using Rneasy mini kit (Qiagen)
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 8µg of total RNA were converted into biotinylated cRNA using Affymetrix one cycle labeling kit as per instructions of the manufacturer (Expression analysis technical manual, 2001, Affymetrix)
| | Sample_hyb_protocol | The biotinylated cRNAs were fragmented and 15µg of this sample was hybridized to Gene Chip Rat 230_2 Genome Array for 16h at 450C and 60rpm. The hybridized gene chips were subjected to washing and staining protocol using an Affymetrix fluidics station 450
| | Sample_scan_protocol | The gene chips were scanned on an Affymetrix Scanner 3000
| | Sample_data_processing | The CEL files generated by the Gene Chip Operating System (Affymetrix) were subjected to AvadisTM software version 4.3 (Strand Life Sciences, Bangalore, India) for further analysis. The PLIER and RMA algorithms were used for data normalization.Test samples (NA16, Colony and tumor samples) were analyzed (using Avadis) individually with the control A16.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Dr. Gopal,,Pande
| | Sample_contact_email | gpande@ccmb.res.in
| | Sample_contact_fax | +91 40 2716 0591
| | Sample_contact_institute | Centre for Cellular and Molecular Biology
| | Sample_contact_address | Uppal Road
| | Sample_contact_city | Hyderabad
| | Sample_contact_state | Andhra Pradesh
| | Sample_contact_zip/postal_code | 500 007
| | Sample_contact_country | India
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM611nnn/GSM611726/suppl/GSM611726.CEL.gz
| | Sample_series_id | GSE24879
| | Sample_series_id | GSE24893
| | Sample_data_row_count | 31099
| | |
|
| |
| |
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