Search results for the GEO ID: GSE11259  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM284329 | GPL1261 |
|
67NR_I
|
primary mammary gland tumor (67NR cells)
|
Strain: BALB/c
Age: 7-9 weeks old
Gender: female
Tissue: primary mammary gland tumor formed 15 days after injection of 1x10^6 viable 67NR/CMVLUC cells
|
DMB0212_79PT.CEL
|
| Sample_geo_accession | GSM284329
| | Sample_status | Public on Aug 01 2008
| | Sample_submission_date | Apr 24 2008
| | Sample_last_update_date | Apr 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was extracted from each population of microdissected tissues using a commercially available system (RNAeasy micro kit, Qiagen, Mississauga, ON). Subsequently, samples were re-extracted as described above and re-suspended in 10 µl diethylpyrocarbonate-treated water. RNA was quantified and qualified using Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).
| | Sample_label_ch1 | Cy3
| | Sample_label_protocol_ch1 | RNA probes were labeled accordng to the supplier's instructions using 2 µg of total RNA (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips were carried out according to the supplier's instructions.
| | Sample_scan_protocol | A Genechip scanner 3000 7G with autoloader (Affymetrix) was used for reading out the microarray.
| | Sample_data_processing | Data were processed using CARMAweb, a web front end to the Bioconductor package. Following R commands were automatically executed to generate rma normalized values:
| | Sample_data_processing | > library(affy)
| | Sample_data_processing | > library(maDB)
| | Sample_data_processing | > Filenames <- c("DMB0212_79PT.CEL", "DMB0222_90PT.CEL", "DMB0232_102PT.CEL",
| | Sample_data_processing | + "DMB0103_17PT.CEL", "DMB0171_18PT.CEL", "DMB0192_76PT.CEL",
| | Sample_data_processing | + "DMB0132_8PT.CEL", "DMB0152_10PT.CEL", "DMB0073_11PT.CEL")
| | Sample_data_processing = > Chips.raw <- read.affybatch(filenames | Filenames)
| | Sample_data_processing | > Chips.norm <- rma(Chips.raw)
| | Sample_data_processing | Background correcting
| | Sample_data_processing | Normalizing
| | Sample_data_processing | Calculating Expression
| | Sample_data_processing | > Chips.norm <- newMadbSet(Chips.norm)
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shoukat,,Dedhar
| | Sample_contact_institute | BC Cancer Research Centre
| | Sample_contact_address | 675 West 10th Avenue
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V5Z 1L3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284329/suppl/GSM284329.CEL.gz
| | Sample_series_id | GSE11259
| | Sample_data_row_count | 45101
| | |
|
GSM284330 | GPL1261 |
|
67NR_II
|
primary mammary gland tumor (67NR cells)
|
Strain: BALB/c
Age: 7-9 weeks
Gender: female
|
DMB0222_90PT.CEL
|
| Sample_geo_accession | GSM284330
| | Sample_status | Public on Aug 01 2008
| | Sample_submission_date | Apr 24 2008
| | Sample_last_update_date | Apr 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was extracted from each population of microdissected tissues using a commercially available system (RNAeasy micro kit, Qiagen, Mississauga, ON). Subsequently, samples were re-extracted as described above and re-suspended in 10 µl diethylpyrocarbonate-treated water. RNA was quantified and qualified using Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).
| | Sample_label_ch1 | Cy3
| | Sample_label_protocol_ch1 | RNA probes were labeled accordng to the supplier's instructions using 2 µg of total RNA (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips were carried out according to the supplier's instructions.
| | Sample_scan_protocol | A Genechip scanner 3000 7G with autoloader (Affymetrix) was used for reading out the microarray.
| | Sample_data_processing | Data were processed using CARMAweb, a web front end to the Bioconductor package. Following R commands were automatically executed to generate rma normalized values:
| | Sample_data_processing | > library(affy)
| | Sample_data_processing | > library(maDB)
| | Sample_data_processing | > Filenames <- c("DMB0212_79PT.CEL", "DMB0222_90PT.CEL", "DMB0232_102PT.CEL",
| | Sample_data_processing | + "DMB0103_17PT.CEL", "DMB0171_18PT.CEL", "DMB0192_76PT.CEL",
| | Sample_data_processing | + "DMB0132_8PT.CEL", "DMB0152_10PT.CEL", "DMB0073_11PT.CEL")
| | Sample_data_processing = > Chips.raw <- read.affybatch(filenames | Filenames)
| | Sample_data_processing | > Chips.norm <- rma(Chips.raw)
| | Sample_data_processing | Background correcting
| | Sample_data_processing | Normalizing
| | Sample_data_processing | Calculating Expression
| | Sample_data_processing | > Chips.norm <- newMadbSet(Chips.norm)
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shoukat,,Dedhar
| | Sample_contact_institute | BC Cancer Research Centre
| | Sample_contact_address | 675 West 10th Avenue
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V5Z 1L3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284330/suppl/GSM284330.CEL.gz
| | Sample_series_id | GSE11259
| | Sample_data_row_count | 45101
| | |
|
GSM284331 | GPL1261 |
|
67NR_III
|
primary mammary gland tumor (67NR cells)
|
Strain: BALB/c
Age: 7-9 weeks
Gender: female
|
DMB0232_102PT.CEL
|
| Sample_geo_accession | GSM284331
| | Sample_status | Public on Aug 01 2008
| | Sample_submission_date | Apr 24 2008
| | Sample_last_update_date | Apr 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was extracted from each population of microdissected tissues using a commercially available system (RNAeasy micro kit, Qiagen, Mississauga, ON). Subsequently, samples were re-extracted as described above and re-suspended in 10 µl diethylpyrocarbonate-treated water. RNA was quantified and qualified using Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).
| | Sample_label_ch1 | Cy3
| | Sample_label_protocol_ch1 | RNA probes were labeled accordng to the supplier's instructions using 2 µg of total RNA (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips were carried out according to the supplier's instructions.
| | Sample_scan_protocol | A Genechip scanner 3000 7G with autoloader (Affymetrix) was used for reading out the microarray.
| | Sample_data_processing | Data were processed using CARMAweb, a web front end to the Bioconductor package. Following R commands were automatically executed to generate rma normalized values:
| | Sample_data_processing | library(affy)
| | Sample_data_processing | library(maDB)
| | Sample_data_processing | Filenames <- c("DMB0212_79PT.CEL", "DMB0222_90PT.CEL", "DMB0232_102PT.CEL",
| | Sample_data_processing | + "DMB0103_17PT.CEL", "DMB0171_18PT.CEL", "DMB0192_76PT.CEL",
| | Sample_data_processing | + "DMB0132_8PT.CEL", "DMB0152_10PT.CEL", "DMB0073_11PT.CEL")
| | Sample_data_processing = Chips.raw <- read.affybatch(filenames | Filenames)
| | Sample_data_processing | Chips.norm <- rma(Chips.raw)
| | Sample_data_processing | Background correcting
| | Sample_data_processing | Normalizing
| | Sample_data_processing | Calculating Expression
| | Sample_data_processing | Chips.norm <- newMadbSet(Chips.norm)
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shoukat,,Dedhar
| | Sample_contact_institute | BC Cancer Research Centre
| | Sample_contact_address | 675 West 10th Avenue
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V5Z 1L3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284331/suppl/GSM284331.CEL.gz
| | Sample_series_id | GSE11259
| | Sample_data_row_count | 45101
| | |
|
GSM284332 | GPL1261 |
|
66cl4_I
|
primary mammary gland tumor (66cl4 cells)
|
Strain: BALB/c
Age: 7-9 weeks old
Gender: female
Tissue: primary mammary gland tumor formed 15 days after injection of 1x10^6 viable 66cl4/CMVLUC cells
|
DMB0103_17PT.CEL
|
| Sample_geo_accession | GSM284332
| | Sample_status | Public on Aug 01 2008
| | Sample_submission_date | Apr 24 2008
| | Sample_last_update_date | Apr 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was extracted from each population of microdissected tissues using a commercially available system (RNAeasy micro kit, Qiagen, Mississauga, ON). Subsequently, samples were re-extracted as described above and re-suspended in 10 µl diethylpyrocarbonate-treated water. RNA was quantified and qualified using Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).
| | Sample_label_ch1 | Cy3
| | Sample_label_protocol_ch1 | RNA probes were labeled accordng to the supplier's instructions using 2 µg of total RNA (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips were carried out according to the supplier's instructions.
| | Sample_scan_protocol | A Genechip scanner 3000 7G with autoloader (Affymetrix) was used for reading out the microarray.
| | Sample_data_processing | Data were processed using CARMAweb, a web front end to the Bioconductor package. Following R commands were automatically executed to generate rma normalized values:
| | Sample_data_processing | library(affy)
| | Sample_data_processing | library(maDB)
| | Sample_data_processing | Filenames <- c("DMB0212_79PT.CEL", "DMB0222_90PT.CEL", "DMB0232_102PT.CEL",
| | Sample_data_processing | + "DMB0103_17PT.CEL", "DMB0171_18PT.CEL", "DMB0192_76PT.CEL",
| | Sample_data_processing | + "DMB0132_8PT.CEL", "DMB0152_10PT.CEL", "DMB0073_11PT.CEL")
| | Sample_data_processing = Chips.raw <- read.affybatch(filenames | Filenames)
| | Sample_data_processing | Chips.norm <- rma(Chips.raw)
| | Sample_data_processing | Background correcting
| | Sample_data_processing | Normalizing
| | Sample_data_processing | Calculating Expression
| | Sample_data_processing | Chips.norm <- newMadbSet(Chips.norm)
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shoukat,,Dedhar
| | Sample_contact_institute | BC Cancer Research Centre
| | Sample_contact_address | 675 West 10th Avenue
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V5Z 1L3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284332/suppl/GSM284332.CEL.gz
| | Sample_series_id | GSE11259
| | Sample_data_row_count | 45101
| | |
|
GSM284333 | GPL1261 |
|
66cl4_II
|
primary mammary gland tumor (66cl4 cells)
|
Strain: BALB/c
Age: 7-9 weeks old
Gender: female
Tissue: primary mammary gland tumor formed 15 days after injection of 1x10^6 viable 66cl4/CMVLUC cells
|
DMB0171_18PT.CEL
|
| Sample_geo_accession | GSM284333
| | Sample_status | Public on Aug 01 2008
| | Sample_submission_date | Apr 24 2008
| | Sample_last_update_date | Apr 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was extracted from each population of microdissected tissues using a commercially available system (RNAeasy micro kit, Qiagen, Mississauga, ON). Subsequently, samples were re-extracted as described above and re-suspended in 10 µl diethylpyrocarbonate-treated water. RNA was quantified and qualified using Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).
| | Sample_label_ch1 | Cy3
| | Sample_label_protocol_ch1 | RNA probes were labeled accordng to the supplier's instructions using 2 µg of total RNA (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips were carried out according to the supplier's instructions.
| | Sample_scan_protocol | A Genechip scanner 3000 7G with autoloader (Affymetrix) was used for reading out the microarray.
| | Sample_data_processing | Data were processed using CARMAweb, a web front end to the Bioconductor package. Following R commands were automatically executed to generate rma normalized values:
| | Sample_data_processing | library(affy)
| | Sample_data_processing | library(maDB)
| | Sample_data_processing | Filenames <- c("DMB0212_79PT.CEL", "DMB0222_90PT.CEL", "DMB0232_102PT.CEL",
| | Sample_data_processing | + "DMB0103_17PT.CEL", "DMB0171_18PT.CEL", "DMB0192_76PT.CEL",
| | Sample_data_processing | + "DMB0132_8PT.CEL", "DMB0152_10PT.CEL", "DMB0073_11PT.CEL")
| | Sample_data_processing = Chips.raw <- read.affybatch(filenames | Filenames)
| | Sample_data_processing | Chips.norm <- rma(Chips.raw)
| | Sample_data_processing | Background correcting
| | Sample_data_processing | Normalizing
| | Sample_data_processing | Calculating Expression
| | Sample_data_processing | Chips.norm <- newMadbSet(Chips.norm)
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shoukat,,Dedhar
| | Sample_contact_institute | BC Cancer Research Centre
| | Sample_contact_address | 675 West 10th Avenue
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V5Z 1L3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284333/suppl/GSM284333.CEL.gz
| | Sample_series_id | GSE11259
| | Sample_data_row_count | 45101
| | |
|
GSM284334 | GPL1261 |
|
66cl4_III
|
primary mammary gland tumor (66cl4 cells)
|
Strain: BALB/c
Age: 7-9 weeks old
Gender: female
Tissue: primary mammary gland tumor formed 15 days after injection of 1x10^6 viable 66cl4/CMVLUC cells
|
DMB0192_76PT.CEL
|
| Sample_geo_accession | GSM284334
| | Sample_status | Public on Aug 01 2008
| | Sample_submission_date | Apr 24 2008
| | Sample_last_update_date | Apr 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was extracted from each population of microdissected tissues using a commercially available system (RNAeasy micro kit, Qiagen, Mississauga, ON). Subsequently, samples were re-extracted as described above and re-suspended in 10 µl diethylpyrocarbonate-treated water. RNA was quantified and qualified using Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).
| | Sample_label_ch1 | Cy3
| | Sample_label_protocol_ch1 | RNA probes were labeled accordng to the supplier's instructions using 2 µg of total RNA (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips were carried out according to the supplier's instructions.
| | Sample_scan_protocol | A Genechip scanner 3000 7G with autoloader (Affymetrix) was used for reading out the microarray.
| | Sample_data_processing | Data were processed using CARMAweb, a web front end to the Bioconductor package. Following R commands were automatically executed to generate rma normalized values:
| | Sample_data_processing | library(affy)
| | Sample_data_processing | library(maDB)
| | Sample_data_processing | Filenames <- c("DMB0212_79PT.CEL", "DMB0222_90PT.CEL", "DMB0232_102PT.CEL",
| | Sample_data_processing | + "DMB0103_17PT.CEL", "DMB0171_18PT.CEL", "DMB0192_76PT.CEL",
| | Sample_data_processing | + "DMB0132_8PT.CEL", "DMB0152_10PT.CEL", "DMB0073_11PT.CEL")
| | Sample_data_processing = Chips.raw <- read.affybatch(filenames | Filenames)
| | Sample_data_processing | Chips.norm <- rma(Chips.raw)
| | Sample_data_processing | Background correcting
| | Sample_data_processing | Normalizing
| | Sample_data_processing | Calculating Expression
| | Sample_data_processing | Chips.norm <- newMadbSet(Chips.norm)
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shoukat,,Dedhar
| | Sample_contact_institute | BC Cancer Research Centre
| | Sample_contact_address | 675 West 10th Avenue
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V5Z 1L3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284334/suppl/GSM284334.CEL.gz
| | Sample_series_id | GSE11259
| | Sample_data_row_count | 45101
| | |
|
GSM284335 | GPL1261 |
|
4T1_I
|
primary mammary gland tumor (4T1 cells)
|
Strain: BALB/c
Age: 7-9 weeks old
Gender: female
Tissue: primary mammary gland tumor formed 15 days after injection of 1x10^6 viable 4T1/CMVLUC cells
|
DMB0132_8PT.CEL
|
| Sample_geo_accession | GSM284335
| | Sample_status | Public on Aug 01 2008
| | Sample_submission_date | Apr 24 2008
| | Sample_last_update_date | Apr 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was extracted from each population of microdissected tissues using a commercially available system (RNAeasy micro kit, Qiagen, Mississauga, ON). Subsequently, samples were re-extracted as described above and re-suspended in 10 µl diethylpyrocarbonate-treated water. RNA was quantified and qualified using Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).
| | Sample_label_ch1 | Cy3
| | Sample_label_protocol_ch1 | RNA probes were labeled accordng to the supplier's instructions using 2 µg of total RNA (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips were carried out according to the supplier's instructions.
| | Sample_scan_protocol | A Genechip scanner 3000 7G with autoloader (Affymetrix) was used for reading out the microarray.
| | Sample_data_processing | Data were processed using CARMAweb, a web front end to the Bioconductor package. Following R commands were automatically executed to generate rma normalized values:
| | Sample_data_processing | library(affy)
| | Sample_data_processing | library(maDB)
| | Sample_data_processing | Filenames <- c("DMB0212_79PT.CEL", "DMB0222_90PT.CEL", "DMB0232_102PT.CEL",
| | Sample_data_processing | + "DMB0103_17PT.CEL", "DMB0171_18PT.CEL", "DMB0192_76PT.CEL",
| | Sample_data_processing | + "DMB0132_8PT.CEL", "DMB0152_10PT.CEL", "DMB0073_11PT.CEL")
| | Sample_data_processing = Chips.raw <- read.affybatch(filenames | Filenames)
| | Sample_data_processing | Chips.norm <- rma(Chips.raw)
| | Sample_data_processing | Background correcting
| | Sample_data_processing | Normalizing
| | Sample_data_processing | Calculating Expression
| | Sample_data_processing | Chips.norm <- newMadbSet(Chips.norm)
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shoukat,,Dedhar
| | Sample_contact_institute | BC Cancer Research Centre
| | Sample_contact_address | 675 West 10th Avenue
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V5Z 1L3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284335/suppl/GSM284335.CEL.gz
| | Sample_series_id | GSE11259
| | Sample_data_row_count | 45101
| | |
|
GSM284336 | GPL1261 |
|
4T1_II
|
primary mammary gland tumor (4T1 cells)
|
Strain: BALB/c
Age: 7-9 weeks old
Gender: female
Tissue: primary mammary gland tumor formed 15 days after injection of 1x10^6 viable 4T1/CMVLUC cells
|
DMB0152_10PT.CEL
|
| Sample_geo_accession | GSM284336
| | Sample_status | Public on Aug 01 2008
| | Sample_submission_date | Apr 24 2008
| | Sample_last_update_date | Apr 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was extracted from each population of microdissected tissues using a commercially available system (RNAeasy micro kit, Qiagen, Mississauga, ON). Subsequently, samples were re-extracted as described above and re-suspended in 10 µl diethylpyrocarbonate-treated water. RNA was quantified and qualified using Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).
| | Sample_label_ch1 | Cy3
| | Sample_label_protocol_ch1 | RNA probes were labeled accordng to the supplier's instructions using 2 µg of total RNA (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips were carried out according to the supplier's instructions.
| | Sample_scan_protocol | A Genechip scanner 3000 7G with autoloader (Affymetrix) was used for reading out the microarray.
| | Sample_data_processing | Data were processed using CARMAweb, a web front end to the Bioconductor package. Following R commands were automatically executed to generate rma normalized values:
| | Sample_data_processing | library(affy)
| | Sample_data_processing | library(maDB)
| | Sample_data_processing | Filenames <- c("DMB0212_79PT.CEL", "DMB0222_90PT.CEL", "DMB0232_102PT.CEL",
| | Sample_data_processing | + "DMB0103_17PT.CEL", "DMB0171_18PT.CEL", "DMB0192_76PT.CEL",
| | Sample_data_processing | + "DMB0132_8PT.CEL", "DMB0152_10PT.CEL", "DMB0073_11PT.CEL")
| | Sample_data_processing = Chips.raw <- read.affybatch(filenames | Filenames)
| | Sample_data_processing | Chips.norm <- rma(Chips.raw)
| | Sample_data_processing | Background correcting
| | Sample_data_processing | Normalizing
| | Sample_data_processing | Calculating Expression
| | Sample_data_processing | Chips.norm <- newMadbSet(Chips.norm)
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shoukat,,Dedhar
| | Sample_contact_institute | BC Cancer Research Centre
| | Sample_contact_address | 675 West 10th Avenue
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V5Z 1L3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284336/suppl/GSM284336.CEL.gz
| | Sample_series_id | GSE11259
| | Sample_data_row_count | 45101
| | |
|
GSM284347 | GPL1261 |
|
4T1_III
|
primary mammary gland tumor (4T1 cells)
|
Strain: BALB/c
Age: 7-9 weeks old
Gender: female
Tissue: primary mammary gland tumor formed 15 days after injection of 1x10^6 viable 4T1/CMVLUC cells
|
DMB0073_11PT.CEL
|
| Sample_geo_accession | GSM284347
| | Sample_status | Public on Aug 01 2008
| | Sample_submission_date | Apr 24 2008
| | Sample_last_update_date | Apr 28 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total cellular RNA was extracted from each population of microdissected tissues using a commercially available system (RNAeasy micro kit, Qiagen, Mississauga, ON). Subsequently, samples were re-extracted as described above and re-suspended in 10 µl diethylpyrocarbonate-treated water. RNA was quantified and qualified using Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).
| | Sample_label_ch1 | Cy3
| | Sample_label_protocol_ch1 | RNA probes were labeled accordng to the supplier's instructions using 2 µg of total RNA (Affymetrix, Santa Clara, CA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips were carried out according to the supplier's instructions.
| | Sample_scan_protocol | A Genechip scanner 3000 7G with autoloader (Affymetrix) was used for reading out the microarray.
| | Sample_data_processing | Data were processed using CARMAweb, a web front end to the Bioconductor package. Following R commands were automatically executed to generate rma normalized values:
| | Sample_data_processing | library(affy)
| | Sample_data_processing | library(maDB)
| | Sample_data_processing | Filenames <- c("DMB0212_79PT.CEL", "DMB0222_90PT.CEL", "DMB0232_102PT.CEL",
| | Sample_data_processing | + "DMB0103_17PT.CEL", "DMB0171_18PT.CEL", "DMB0192_76PT.CEL",
| | Sample_data_processing | + "DMB0132_8PT.CEL", "DMB0152_10PT.CEL", "DMB0073_11PT.CEL")
| | Sample_data_processing = Chips.raw <- read.affybatch(filenames | Filenames)
| | Sample_data_processing | Chips.norm <- rma(Chips.raw)
| | Sample_data_processing | Background correcting
| | Sample_data_processing | Normalizing
| | Sample_data_processing | Calculating Expression
| | Sample_data_processing | Chips.norm <- newMadbSet(Chips.norm)
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shoukat,,Dedhar
| | Sample_contact_institute | BC Cancer Research Centre
| | Sample_contact_address | 675 West 10th Avenue
| | Sample_contact_city | Vancouver
| | Sample_contact_state | British Columbia
| | Sample_contact_zip/postal_code | V5Z 1L3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM284nnn/GSM284347/suppl/GSM284347.CEL.gz
| | Sample_series_id | GSE11259
| | Sample_data_row_count | 45101
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
