Search results for the GEO ID: GSE13979  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM351283 | GPL339 |
|
bFGF-monolayer, rep1
|
bFGF-treated monolayer JB6 cells
|
naïve JB6 cells
|
bFGF_Mono_A
|
| Sample_geo_accession | GSM351283
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Dec 15 2008
| | Sample_last_update_date | Mar 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were seeded over soft agar in 10 cm dishes (5 x 104 cells/dish) to induce colony formation. RT101 cells (tumor variant) received no treatment and parental JB6 clone 41-5A cells were treated with 10 ng/ml bFGF. Colonies were harvested on day 7 to minimize selection of large colonies with necrotic centers.
| | Sample_growth_protocol_ch1 | JB6 cells were cultured in Eagle’s minimal essential medium (EMEM; BioWhittaker, Walkersville, MD) supplemented with 4% fetal bovine serum (FBS), 2 mM L-glutamine and 25 mg/mL gentamicin (Life Technologies/Gibco, Gaithersburg, MD)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized from 5ug of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA using Affymetrix reagents.
| | Sample_hyb_protocol | Biotin-labeled cRNA (15ug) was fragmented to a size range between 50-200 bases and used for array hybridization with Affymetrix reagents. After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were processed with RMA background correction and quantile normalization using Bioconductor packages
| | Sample_platform_id | GPL339
| | Sample_contact_name | Katrina,M,Waters
| | Sample_contact_email | katrina.waters@pnl.gov
| | Sample_contact_department | Computational Biology & Bioinformatics
| | Sample_contact_institute | Pacific Northwest National Laboratory
| | Sample_contact_address | 902 Battelle Blvd; MSIN K7-90
| | Sample_contact_city | Richland
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 99352
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351283/suppl/GSM351283.CEL.gz
| | Sample_series_id | GSE13979
| | Sample_data_row_count | 22690
| | |
|
GSM351284 | GPL339 |
|
bFGF-monolayer, rep2
|
bFGF-treated monolayer JB6 cells
|
naïve JB6 cells
|
bFGF_Mono_B
|
| Sample_geo_accession | GSM351284
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Dec 15 2008
| | Sample_last_update_date | Mar 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were seeded over soft agar in 10 cm dishes (5 x 104 cells/dish) to induce colony formation. RT101 cells (tumor variant) received no treatment and parental JB6 clone 41-5A cells were treated with 10 ng/ml bFGF. Colonies were harvested on day 7 to minimize selection of large colonies with necrotic centers.
| | Sample_growth_protocol_ch1 | JB6 cells were cultured in Eagle’s minimal essential medium (EMEM; BioWhittaker, Walkersville, MD) supplemented with 4% fetal bovine serum (FBS), 2 mM L-glutamine and 25 mg/mL gentamicin (Life Technologies/Gibco, Gaithersburg, MD)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized from 5ug of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA using Affymetrix reagents.
| | Sample_hyb_protocol | Biotin-labeled cRNA (15ug) was fragmented to a size range between 50-200 bases and used for array hybridization with Affymetrix reagents. After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were processed with RMA background correction and quantile normalization using Bioconductor packages
| | Sample_platform_id | GPL339
| | Sample_contact_name | Katrina,M,Waters
| | Sample_contact_email | katrina.waters@pnl.gov
| | Sample_contact_department | Computational Biology & Bioinformatics
| | Sample_contact_institute | Pacific Northwest National Laboratory
| | Sample_contact_address | 902 Battelle Blvd; MSIN K7-90
| | Sample_contact_city | Richland
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 99352
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351284/suppl/GSM351284.CEL.gz
| | Sample_series_id | GSE13979
| | Sample_data_row_count | 22690
| | |
|
GSM351285 | GPL339 |
|
bFGF-monolayer, rep3
|
bFGF-treated monolayer JB6 cells
|
naïve JB6 cells
|
bFGF_Mono_C
|
| Sample_geo_accession | GSM351285
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Dec 15 2008
| | Sample_last_update_date | Mar 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were seeded over soft agar in 10 cm dishes (5 x 104 cells/dish) to induce colony formation. RT101 cells (tumor variant) received no treatment and parental JB6 clone 41-5A cells were treated with 10 ng/ml bFGF. Colonies were harvested on day 7 to minimize selection of large colonies with necrotic centers.
| | Sample_growth_protocol_ch1 | JB6 cells were cultured in Eagle’s minimal essential medium (EMEM; BioWhittaker, Walkersville, MD) supplemented with 4% fetal bovine serum (FBS), 2 mM L-glutamine and 25 mg/mL gentamicin (Life Technologies/Gibco, Gaithersburg, MD)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized from 5ug of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA using Affymetrix reagents.
| | Sample_hyb_protocol | Biotin-labeled cRNA (15ug) was fragmented to a size range between 50-200 bases and used for array hybridization with Affymetrix reagents. After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were processed with RMA background correction and quantile normalization using Bioconductor packages
| | Sample_platform_id | GPL339
| | Sample_contact_name | Katrina,M,Waters
| | Sample_contact_email | katrina.waters@pnl.gov
| | Sample_contact_department | Computational Biology & Bioinformatics
| | Sample_contact_institute | Pacific Northwest National Laboratory
| | Sample_contact_address | 902 Battelle Blvd; MSIN K7-90
| | Sample_contact_city | Richland
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 99352
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351285/suppl/GSM351285.CEL.gz
| | Sample_series_id | GSE13979
| | Sample_data_row_count | 22690
| | |
|
GSM351286 | GPL339 |
|
bFGF-colonies, rep1
|
bFGF-treated colonies, JB6 cells
|
naïve JB6 cells
|
bFGF_AIG_A
|
| Sample_geo_accession | GSM351286
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Dec 15 2008
| | Sample_last_update_date | Mar 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were seeded over soft agar in 10 cm dishes (5 x 104 cells/dish) to induce colony formation. RT101 cells (tumor variant) received no treatment and parental JB6 clone 41-5A cells were treated with 10 ng/ml bFGF. Colonies were harvested on day 7 to minimize selection of large colonies with necrotic centers.
| | Sample_growth_protocol_ch1 | JB6 cells were cultured in Eagle’s minimal essential medium (EMEM; BioWhittaker, Walkersville, MD) supplemented with 4% fetal bovine serum (FBS), 2 mM L-glutamine and 25 mg/mL gentamicin (Life Technologies/Gibco, Gaithersburg, MD)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized from 5ug of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA using Affymetrix reagents.
| | Sample_hyb_protocol | Biotin-labeled cRNA (15ug) was fragmented to a size range between 50-200 bases and used for array hybridization with Affymetrix reagents. After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were processed with RMA background correction and quantile normalization using Bioconductor packages
| | Sample_platform_id | GPL339
| | Sample_contact_name | Katrina,M,Waters
| | Sample_contact_email | katrina.waters@pnl.gov
| | Sample_contact_department | Computational Biology & Bioinformatics
| | Sample_contact_institute | Pacific Northwest National Laboratory
| | Sample_contact_address | 902 Battelle Blvd; MSIN K7-90
| | Sample_contact_city | Richland
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 99352
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351286/suppl/GSM351286.CEL.gz
| | Sample_series_id | GSE13979
| | Sample_data_row_count | 22690
| | |
|
GSM351287 | GPL339 |
|
bFGF-colonies, rep2
|
bFGF-treated colonies, JB6 cells
|
naïve JB6 cells
|
bFGF_AIG_B
|
| Sample_geo_accession | GSM351287
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Dec 15 2008
| | Sample_last_update_date | Mar 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were seeded over soft agar in 10 cm dishes (5 x 104 cells/dish) to induce colony formation. RT101 cells (tumor variant) received no treatment and parental JB6 clone 41-5A cells were treated with 10 ng/ml bFGF. Colonies were harvested on day 7 to minimize selection of large colonies with necrotic centers.
| | Sample_growth_protocol_ch1 | JB6 cells were cultured in Eagle’s minimal essential medium (EMEM; BioWhittaker, Walkersville, MD) supplemented with 4% fetal bovine serum (FBS), 2 mM L-glutamine and 25 mg/mL gentamicin (Life Technologies/Gibco, Gaithersburg, MD)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized from 5ug of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA using Affymetrix reagents.
| | Sample_hyb_protocol | Biotin-labeled cRNA (15ug) was fragmented to a size range between 50-200 bases and used for array hybridization with Affymetrix reagents. After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were processed with RMA background correction and quantile normalization using Bioconductor packages
| | Sample_platform_id | GPL339
| | Sample_contact_name | Katrina,M,Waters
| | Sample_contact_email | katrina.waters@pnl.gov
| | Sample_contact_department | Computational Biology & Bioinformatics
| | Sample_contact_institute | Pacific Northwest National Laboratory
| | Sample_contact_address | 902 Battelle Blvd; MSIN K7-90
| | Sample_contact_city | Richland
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 99352
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351287/suppl/GSM351287.CEL.gz
| | Sample_series_id | GSE13979
| | Sample_data_row_count | 22690
| | |
|
GSM351288 | GPL339 |
|
bFGF-colonies, rep3
|
bFGF-treated colonies, JB6 cells
|
naïve JB6 cells
|
bFGF_AIG_C
|
| Sample_geo_accession | GSM351288
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Dec 15 2008
| | Sample_last_update_date | Mar 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were seeded over soft agar in 10 cm dishes (5 x 104 cells/dish) to induce colony formation. RT101 cells (tumor variant) received no treatment and parental JB6 clone 41-5A cells were treated with 10 ng/ml bFGF. Colonies were harvested on day 7 to minimize selection of large colonies with necrotic centers.
| | Sample_growth_protocol_ch1 | JB6 cells were cultured in Eagle’s minimal essential medium (EMEM; BioWhittaker, Walkersville, MD) supplemented with 4% fetal bovine serum (FBS), 2 mM L-glutamine and 25 mg/mL gentamicin (Life Technologies/Gibco, Gaithersburg, MD)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized from 5ug of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA using Affymetrix reagents.
| | Sample_hyb_protocol | Biotin-labeled cRNA (15ug) was fragmented to a size range between 50-200 bases and used for array hybridization with Affymetrix reagents. After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were processed with RMA background correction and quantile normalization using Bioconductor packages
| | Sample_platform_id | GPL339
| | Sample_contact_name | Katrina,M,Waters
| | Sample_contact_email | katrina.waters@pnl.gov
| | Sample_contact_department | Computational Biology & Bioinformatics
| | Sample_contact_institute | Pacific Northwest National Laboratory
| | Sample_contact_address | 902 Battelle Blvd; MSIN K7-90
| | Sample_contact_city | Richland
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 99352
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351288/suppl/GSM351288.CEL.gz
| | Sample_series_id | GSE13979
| | Sample_data_row_count | 22690
| | |
|
GSM351289 | GPL339 |
|
RT101-monolayer, rep1
|
RT101 monolayer cells
|
RT101 cells
|
RT101_Mono_B
|
| Sample_geo_accession | GSM351289
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Dec 15 2008
| | Sample_last_update_date | Mar 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were seeded over soft agar in 10 cm dishes (5 x 104 cells/dish) to induce colony formation. RT101 cells (tumor variant) received no treatment and parental JB6 clone 41-5A cells were treated with 10 ng/ml bFGF. Colonies were harvested on day 7 to minimize selection of large colonies with necrotic centers.
| | Sample_growth_protocol_ch1 | JB6 cells were cultured in Eagle’s minimal essential medium (EMEM; BioWhittaker, Walkersville, MD) supplemented with 4% fetal bovine serum (FBS), 2 mM L-glutamine and 25 mg/mL gentamicin (Life Technologies/Gibco, Gaithersburg, MD)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized from 5ug of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA using Affymetrix reagents.
| | Sample_hyb_protocol | Biotin-labeled cRNA (15ug) was fragmented to a size range between 50-200 bases and used for array hybridization with Affymetrix reagents. After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were processed with RMA background correction and quantile normalization using Bioconductor packages
| | Sample_platform_id | GPL339
| | Sample_contact_name | Katrina,M,Waters
| | Sample_contact_email | katrina.waters@pnl.gov
| | Sample_contact_department | Computational Biology & Bioinformatics
| | Sample_contact_institute | Pacific Northwest National Laboratory
| | Sample_contact_address | 902 Battelle Blvd; MSIN K7-90
| | Sample_contact_city | Richland
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 99352
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351289/suppl/GSM351289.CEL.gz
| | Sample_series_id | GSE13979
| | Sample_data_row_count | 22690
| | |
|
GSM351290 | GPL339 |
|
RT101-monolayer, rep2
|
RT101 monolayer cells
|
RT101 cells
|
RT101_Mono_C
|
| Sample_geo_accession | GSM351290
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Dec 15 2008
| | Sample_last_update_date | Mar 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were seeded over soft agar in 10 cm dishes (5 x 104 cells/dish) to induce colony formation. RT101 cells (tumor variant) received no treatment and parental JB6 clone 41-5A cells were treated with 10 ng/ml bFGF. Colonies were harvested on day 7 to minimize selection of large colonies with necrotic centers.
| | Sample_growth_protocol_ch1 | JB6 cells were cultured in Eagle’s minimal essential medium (EMEM; BioWhittaker, Walkersville, MD) supplemented with 4% fetal bovine serum (FBS), 2 mM L-glutamine and 25 mg/mL gentamicin (Life Technologies/Gibco, Gaithersburg, MD)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized from 5ug of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA using Affymetrix reagents.
| | Sample_hyb_protocol | Biotin-labeled cRNA (15ug) was fragmented to a size range between 50-200 bases and used for array hybridization with Affymetrix reagents. After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were processed with RMA background correction and quantile normalization using Bioconductor packages
| | Sample_platform_id | GPL339
| | Sample_contact_name | Katrina,M,Waters
| | Sample_contact_email | katrina.waters@pnl.gov
| | Sample_contact_department | Computational Biology & Bioinformatics
| | Sample_contact_institute | Pacific Northwest National Laboratory
| | Sample_contact_address | 902 Battelle Blvd; MSIN K7-90
| | Sample_contact_city | Richland
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 99352
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351290/suppl/GSM351290.CEL.gz
| | Sample_series_id | GSE13979
| | Sample_data_row_count | 22690
| | |
|
GSM351291 | GPL339 |
|
RT101-colonies, rep1
|
RT101 colonies
|
RT101 cells
|
RT101_AIG_A
|
| Sample_geo_accession | GSM351291
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Dec 15 2008
| | Sample_last_update_date | Mar 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were seeded over soft agar in 10 cm dishes (5 x 104 cells/dish) to induce colony formation. RT101 cells (tumor variant) received no treatment and parental JB6 clone 41-5A cells were treated with 10 ng/ml bFGF. Colonies were harvested on day 7 to minimize selection of large colonies with necrotic centers.
| | Sample_growth_protocol_ch1 | JB6 cells were cultured in Eagle’s minimal essential medium (EMEM; BioWhittaker, Walkersville, MD) supplemented with 4% fetal bovine serum (FBS), 2 mM L-glutamine and 25 mg/mL gentamicin (Life Technologies/Gibco, Gaithersburg, MD)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized from 5ug of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA using Affymetrix reagents.
| | Sample_hyb_protocol | Biotin-labeled cRNA (15ug) was fragmented to a size range between 50-200 bases and used for array hybridization with Affymetrix reagents. After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were processed with RMA background correction and quantile normalization using Bioconductor packages
| | Sample_platform_id | GPL339
| | Sample_contact_name | Katrina,M,Waters
| | Sample_contact_email | katrina.waters@pnl.gov
| | Sample_contact_department | Computational Biology & Bioinformatics
| | Sample_contact_institute | Pacific Northwest National Laboratory
| | Sample_contact_address | 902 Battelle Blvd; MSIN K7-90
| | Sample_contact_city | Richland
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 99352
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351291/suppl/GSM351291.CEL.gz
| | Sample_series_id | GSE13979
| | Sample_data_row_count | 22690
| | |
|
GSM351292 | GPL339 |
|
RT101-colonies, rep2
|
RT101 colonies
|
RT101 cells
|
RT101_AIG_B
|
| Sample_geo_accession | GSM351292
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Dec 15 2008
| | Sample_last_update_date | Mar 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were seeded over soft agar in 10 cm dishes (5 x 104 cells/dish) to induce colony formation. RT101 cells (tumor variant) received no treatment and parental JB6 clone 41-5A cells were treated with 10 ng/ml bFGF. Colonies were harvested on day 7 to minimize selection of large colonies with necrotic centers.
| | Sample_growth_protocol_ch1 | JB6 cells were cultured in Eagle’s minimal essential medium (EMEM; BioWhittaker, Walkersville, MD) supplemented with 4% fetal bovine serum (FBS), 2 mM L-glutamine and 25 mg/mL gentamicin (Life Technologies/Gibco, Gaithersburg, MD)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized from 5ug of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA using Affymetrix reagents.
| | Sample_hyb_protocol | Biotin-labeled cRNA (15ug) was fragmented to a size range between 50-200 bases and used for array hybridization with Affymetrix reagents. After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were processed with RMA background correction and quantile normalization using Bioconductor packages
| | Sample_platform_id | GPL339
| | Sample_contact_name | Katrina,M,Waters
| | Sample_contact_email | katrina.waters@pnl.gov
| | Sample_contact_department | Computational Biology & Bioinformatics
| | Sample_contact_institute | Pacific Northwest National Laboratory
| | Sample_contact_address | 902 Battelle Blvd; MSIN K7-90
| | Sample_contact_city | Richland
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 99352
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351292/suppl/GSM351292.CEL.gz
| | Sample_series_id | GSE13979
| | Sample_data_row_count | 22690
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GSM351293 | GPL339 |
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RT101-colonies, rep3
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RT101 colonies
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RT101 cells
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RT101_AIG_C
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| Sample_geo_accession | GSM351293
| | Sample_status | Public on Jun 01 2009
| | Sample_submission_date | Dec 15 2008
| | Sample_last_update_date | Mar 12 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Cells were seeded over soft agar in 10 cm dishes (5 x 104 cells/dish) to induce colony formation. RT101 cells (tumor variant) received no treatment and parental JB6 clone 41-5A cells were treated with 10 ng/ml bFGF. Colonies were harvested on day 7 to minimize selection of large colonies with necrotic centers.
| | Sample_growth_protocol_ch1 | JB6 cells were cultured in Eagle’s minimal essential medium (EMEM; BioWhittaker, Walkersville, MD) supplemented with 4% fetal bovine serum (FBS), 2 mM L-glutamine and 25 mg/mL gentamicin (Life Technologies/Gibco, Gaithersburg, MD)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cDNA was synthesized from 5ug of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA using Affymetrix reagents.
| | Sample_hyb_protocol | Biotin-labeled cRNA (15ug) was fragmented to a size range between 50-200 bases and used for array hybridization with Affymetrix reagents. After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Data were processed with RMA background correction and quantile normalization using Bioconductor packages
| | Sample_platform_id | GPL339
| | Sample_contact_name | Katrina,M,Waters
| | Sample_contact_email | katrina.waters@pnl.gov
| | Sample_contact_department | Computational Biology & Bioinformatics
| | Sample_contact_institute | Pacific Northwest National Laboratory
| | Sample_contact_address | 902 Battelle Blvd; MSIN K7-90
| | Sample_contact_city | Richland
| | Sample_contact_state | WA
| | Sample_contact_zip/postal_code | 99352
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM351nnn/GSM351293/suppl/GSM351293.CEL.gz
| | Sample_series_id | GSE13979
| | Sample_data_row_count | 22690
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