Search results for the GEO ID: GSE22841  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM564567 | GPL1261 |
|
SMP_sarcoma_01
|
GFP-positive fraction of sarcoma, SMP
|
strain: mixed B6.129 background
tissue: sarcoma
sarcoma cell-of-origin: skeletal muscle precursor cells (SMPs)
oncogenes: KRAS(G12V), p16p19null
gfp status: positive
|
Gene expression data from sarcomas of SMP origin.
|
| Sample_geo_accession | GSM564567
| | Sample_status | Public on Nov 10 2011
| | Sample_submission_date | Jul 08 2010
| | Sample_last_update_date | Nov 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Tumors were harvested, digested in DMEM + 0.2% collagenase type II (Invitrogen) + 0.05% dispase (Invitrogen) for 90 minutes at 37°C. Cells were suspended in HBSS with 2% FBS and 2mM EDTA containing 1μg/ml propidium iodide and 10μM calcein blue (Invitrogen) to identify the viable fraction of cells from which GFP-positive cells were isolated by FACS sorting. Cells were sorted twice to maximize purity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Mouse Genome 430 2.0 array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were imported into D-chip (version 1.0.0.1) and normalized in batch against an invariant set. Filtered probe sets were identified based on variation across samples being 1< standard deviation/Mean < 1000 with 50% of probes being present in array comparisons. Expression level cut offs were made at >600, >400 and >200, and expression being found in ≥ 50% of microarray samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amy,J,Wagers
| | Sample_contact_laboratory | Wagers lab
| | Sample_contact_department | Islet Cell and Regenerative Biology
| | Sample_contact_institute | Joslin Diabetes Center
| | Sample_contact_address | 1 Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564567/suppl/GSM564567.CEL.gz
| | Sample_series_id | GSE22841
| | Sample_data_row_count | 45037
| | |
|
GSM564568 | GPL1261 |
|
SMP_sarcoma_02
|
GFP-positive fraction of sarcoma, SMP
|
strain: mixed B6.129 background
tissue: sarcoma
sarcoma cell-of-origin: skeletal muscle precursor cells (SMPs)
oncogenes: KRAS(G12V), p16p19null
gfp status: positive
|
Gene expression data from sarcomas of SMP origin.
|
| Sample_geo_accession | GSM564568
| | Sample_status | Public on Nov 10 2011
| | Sample_submission_date | Jul 08 2010
| | Sample_last_update_date | Nov 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Tumors were harvested, digested in DMEM + 0.2% collagenase type II (Invitrogen) + 0.05% dispase (Invitrogen) for 90 minutes at 37°C. Cells were suspended in HBSS with 2% FBS and 2mM EDTA containing 1μg/ml propidium iodide and 10μM calcein blue (Invitrogen) to identify the viable fraction of cells from which GFP-positive cells were isolated by FACS sorting. Cells were sorted twice to maximize purity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Mouse Genome 430 2.0 array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were imported into D-chip (version 1.0.0.1) and normalized in batch against an invariant set. Filtered probe sets were identified based on variation across samples being 1< standard deviation/Mean < 1000 with 50% of probes being present in array comparisons. Expression level cut offs were made at >600, >400 and >200, and expression being found in ≥ 50% of microarray samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amy,J,Wagers
| | Sample_contact_laboratory | Wagers lab
| | Sample_contact_department | Islet Cell and Regenerative Biology
| | Sample_contact_institute | Joslin Diabetes Center
| | Sample_contact_address | 1 Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564568/suppl/GSM564568.CEL.gz
| | Sample_series_id | GSE22841
| | Sample_data_row_count | 45037
| | |
|
GSM564569 | GPL1261 |
|
SMP_sarcoma_03
|
GFP-positive fraction of sarcoma, SMP
|
strain: mixed B6.129 background
tissue: sarcoma
sarcoma cell-of-origin: skeletal muscle precursor cells (SMPs)
oncogenes: KRAS(G12V), p16p19null
gfp status: positive
|
Gene expression data from sarcomas of SMP origin.
|
| Sample_geo_accession | GSM564569
| | Sample_status | Public on Nov 10 2011
| | Sample_submission_date | Jul 08 2010
| | Sample_last_update_date | Nov 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Tumors were harvested, digested in DMEM + 0.2% collagenase type II (Invitrogen) + 0.05% dispase (Invitrogen) for 90 minutes at 37°C. Cells were suspended in HBSS with 2% FBS and 2mM EDTA containing 1μg/ml propidium iodide and 10μM calcein blue (Invitrogen) to identify the viable fraction of cells from which GFP-positive cells were isolated by FACS sorting. Cells were sorted twice to maximize purity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Mouse Genome 430 2.0 array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were imported into D-chip (version 1.0.0.1) and normalized in batch against an invariant set. Filtered probe sets were identified based on variation across samples being 1< standard deviation/Mean < 1000 with 50% of probes being present in array comparisons. Expression level cut offs were made at >600, >400 and >200, and expression being found in ≥ 50% of microarray samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amy,J,Wagers
| | Sample_contact_laboratory | Wagers lab
| | Sample_contact_department | Islet Cell and Regenerative Biology
| | Sample_contact_institute | Joslin Diabetes Center
| | Sample_contact_address | 1 Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564569/suppl/GSM564569.CEL.gz
| | Sample_series_id | GSE22841
| | Sample_data_row_count | 45037
| | |
|
GSM564570 | GPL1261 |
|
SMP_sarcoma_04
|
GFP-positive fraction of sarcoma, SMP
|
strain: mixed B6.129 background
tissue: sarcoma
sarcoma cell-of-origin: skeletal muscle precursor cells (SMPs)
oncogenes: KRAS(G12V), p16p19null
gfp status: positive
|
Gene expression data from sarcomas of SMP origin.
|
| Sample_geo_accession | GSM564570
| | Sample_status | Public on Nov 10 2011
| | Sample_submission_date | Jul 08 2010
| | Sample_last_update_date | Nov 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Tumors were harvested, digested in DMEM + 0.2% collagenase type II (Invitrogen) + 0.05% dispase (Invitrogen) for 90 minutes at 37°C. Cells were suspended in HBSS with 2% FBS and 2mM EDTA containing 1μg/ml propidium iodide and 10μM calcein blue (Invitrogen) to identify the viable fraction of cells from which GFP-positive cells were isolated by FACS sorting. Cells were sorted twice to maximize purity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Mouse Genome 430 2.0 array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were imported into D-chip (version 1.0.0.1) and normalized in batch against an invariant set. Filtered probe sets were identified based on variation across samples being 1< standard deviation/Mean < 1000 with 50% of probes being present in array comparisons. Expression level cut offs were made at >600, >400 and >200, and expression being found in ≥ 50% of microarray samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amy,J,Wagers
| | Sample_contact_laboratory | Wagers lab
| | Sample_contact_department | Islet Cell and Regenerative Biology
| | Sample_contact_institute | Joslin Diabetes Center
| | Sample_contact_address | 1 Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564570/suppl/GSM564570.CEL.gz
| | Sample_series_id | GSE22841
| | Sample_data_row_count | 45037
| | |
|
GSM564571 | GPL1261 |
|
CXCR4neg_sarcoma_01
|
GFP-positive fraction of sarcoma, CXCR4-
|
strain: mixed B6.129 background
tissue: sarcoma
sarcoma cell-of-origin: CD45-MAC1-TER119-Sca1-CXCR4- cells
oncogenes: KRAS(G12V), p16p19null
gfp status: positive
|
Gene expression data from sarcomas of CD45-MAC1-TER119-Sca1-CXCR4- cellular origin.
|
| Sample_geo_accession | GSM564571
| | Sample_status | Public on Nov 10 2011
| | Sample_submission_date | Jul 08 2010
| | Sample_last_update_date | Nov 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Tumors were harvested, digested in DMEM + 0.2% collagenase type II (Invitrogen) + 0.05% dispase (Invitrogen) for 90 minutes at 37°C. Cells were suspended in HBSS with 2% FBS and 2mM EDTA containing 1μg/ml propidium iodide and 10μM calcein blue (Invitrogen) to identify the viable fraction of cells from which GFP-positive cells were isolated by FACS sorting. Cells were sorted twice to maximize purity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Mouse Genome 430 2.0 array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were imported into D-chip (version 1.0.0.1) and normalized in batch against an invariant set. Filtered probe sets were identified based on variation across samples being 1< standard deviation/Mean < 1000 with 50% of probes being present in array comparisons. Expression level cut offs were made at >600, >400 and >200, and expression being found in ≥ 50% of microarray samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amy,J,Wagers
| | Sample_contact_laboratory | Wagers lab
| | Sample_contact_department | Islet Cell and Regenerative Biology
| | Sample_contact_institute | Joslin Diabetes Center
| | Sample_contact_address | 1 Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564571/suppl/GSM564571.CEL.gz
| | Sample_series_id | GSE22841
| | Sample_data_row_count | 45037
| | |
|
GSM564572 | GPL1261 |
|
CXCR4neg_sarcoma_02
|
GFP-positive fraction of sarcoma, CXCR4-
|
strain: mixed B6.129 background
tissue: sarcoma
sarcoma cell-of-origin: CD45-MAC1-TER119-Sca1-CXCR4- cells
oncogenes: KRAS(G12V), p16p19null
gfp status: positive
|
Gene expression data from sarcomas of CD45-MAC1-TER119-Sca1-CXCR4- cellular origin.
|
| Sample_geo_accession | GSM564572
| | Sample_status | Public on Nov 10 2011
| | Sample_submission_date | Jul 08 2010
| | Sample_last_update_date | Nov 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Tumors were harvested, digested in DMEM + 0.2% collagenase type II (Invitrogen) + 0.05% dispase (Invitrogen) for 90 minutes at 37°C. Cells were suspended in HBSS with 2% FBS and 2mM EDTA containing 1μg/ml propidium iodide and 10μM calcein blue (Invitrogen) to identify the viable fraction of cells from which GFP-positive cells were isolated by FACS sorting. Cells were sorted twice to maximize purity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Mouse Genome 430 2.0 array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were imported into D-chip (version 1.0.0.1) and normalized in batch against an invariant set. Filtered probe sets were identified based on variation across samples being 1< standard deviation/Mean < 1000 with 50% of probes being present in array comparisons. Expression level cut offs were made at >600, >400 and >200, and expression being found in ≥ 50% of microarray samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amy,J,Wagers
| | Sample_contact_laboratory | Wagers lab
| | Sample_contact_department | Islet Cell and Regenerative Biology
| | Sample_contact_institute | Joslin Diabetes Center
| | Sample_contact_address | 1 Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564572/suppl/GSM564572.CEL.gz
| | Sample_series_id | GSE22841
| | Sample_data_row_count | 45037
| | |
|
GSM564573 | GPL1261 |
|
CXCR4neg_sarcoma_03
|
GFP-positive fraction of sarcoma, CXCR4-
|
strain: mixed B6.129 background
tissue: sarcoma
sarcoma cell-of-origin: CD45-MAC1-TER119-Sca1-CXCR4- cells
oncogenes: KRAS(G12V), p16p19null
gfp status: positive
|
Gene expression data from sarcomas of CD45-MAC1-TER119-Sca1-CXCR4- cellular origin.
|
| Sample_geo_accession | GSM564573
| | Sample_status | Public on Nov 10 2011
| | Sample_submission_date | Jul 08 2010
| | Sample_last_update_date | Nov 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Tumors were harvested, digested in DMEM + 0.2% collagenase type II (Invitrogen) + 0.05% dispase (Invitrogen) for 90 minutes at 37°C. Cells were suspended in HBSS with 2% FBS and 2mM EDTA containing 1μg/ml propidium iodide and 10μM calcein blue (Invitrogen) to identify the viable fraction of cells from which GFP-positive cells were isolated by FACS sorting. Cells were sorted twice to maximize purity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Mouse Genome 430 2.0 array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were imported into D-chip (version 1.0.0.1) and normalized in batch against an invariant set. Filtered probe sets were identified based on variation across samples being 1< standard deviation/Mean < 1000 with 50% of probes being present in array comparisons. Expression level cut offs were made at >600, >400 and >200, and expression being found in ≥ 50% of microarray samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amy,J,Wagers
| | Sample_contact_laboratory | Wagers lab
| | Sample_contact_department | Islet Cell and Regenerative Biology
| | Sample_contact_institute | Joslin Diabetes Center
| | Sample_contact_address | 1 Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564573/suppl/GSM564573.CEL.gz
| | Sample_series_id | GSE22841
| | Sample_data_row_count | 45037
| | |
|
GSM564574 | GPL1261 |
|
CXCR4neg_sarcoma_04
|
GFP-positive fraction of sarcoma, CXCR4-
|
strain: mixed B6.129 background
tissue: sarcoma
sarcoma cell-of-origin: CD45-MAC1-TER119-Sca1-CXCR4- cells
oncogenes: KRAS(G12V), p16p19null
gfp status: positive
|
Gene expression data from sarcomas of CD45-MAC1-TER119-Sca1-CXCR4- cellular origin.
|
| Sample_geo_accession | GSM564574
| | Sample_status | Public on Nov 10 2011
| | Sample_submission_date | Jul 08 2010
| | Sample_last_update_date | Nov 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Tumors were harvested, digested in DMEM + 0.2% collagenase type II (Invitrogen) + 0.05% dispase (Invitrogen) for 90 minutes at 37°C. Cells were suspended in HBSS with 2% FBS and 2mM EDTA containing 1μg/ml propidium iodide and 10μM calcein blue (Invitrogen) to identify the viable fraction of cells from which GFP-positive cells were isolated by FACS sorting. Cells were sorted twice to maximize purity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Mouse Genome 430 2.0 array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were imported into D-chip (version 1.0.0.1) and normalized in batch against an invariant set. Filtered probe sets were identified based on variation across samples being 1< standard deviation/Mean < 1000 with 50% of probes being present in array comparisons. Expression level cut offs were made at >600, >400 and >200, and expression being found in ≥ 50% of microarray samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amy,J,Wagers
| | Sample_contact_laboratory | Wagers lab
| | Sample_contact_department | Islet Cell and Regenerative Biology
| | Sample_contact_institute | Joslin Diabetes Center
| | Sample_contact_address | 1 Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564574/suppl/GSM564574.CEL.gz
| | Sample_series_id | GSE22841
| | Sample_data_row_count | 45037
| | |
|
GSM564575 | GPL1261 |
|
ScaPC_sarcoma_01
|
GFP-positive fraction of sarcoma, ScaPC
|
strain: mixed B6.129 background
tissue: sarcoma
sarcoma cell-of-origin: non-myogenic progenitors (ScaPCs)
oncogenes: KRAS(G12V), p16p19null
gfp status: positive
|
Gene expression data from sarcomas of ScaPC origin.
|
| Sample_geo_accession | GSM564575
| | Sample_status | Public on Nov 10 2011
| | Sample_submission_date | Jul 08 2010
| | Sample_last_update_date | Nov 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Tumors were harvested, digested in DMEM + 0.2% collagenase type II (Invitrogen) + 0.05% dispase (Invitrogen) for 90 minutes at 37°C. Cells were suspended in HBSS with 2% FBS and 2mM EDTA containing 1μg/ml propidium iodide and 10μM calcein blue (Invitrogen) to identify the viable fraction of cells from which GFP-positive cells were isolated by FACS sorting. Cells were sorted twice to maximize purity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Mouse Genome 430 2.0 array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were imported into D-chip (version 1.0.0.1) and normalized in batch against an invariant set. Filtered probe sets were identified based on variation across samples being 1< standard deviation/Mean < 1000 with 50% of probes being present in array comparisons. Expression level cut offs were made at >600, >400 and >200, and expression being found in ≥ 50% of microarray samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amy,J,Wagers
| | Sample_contact_laboratory | Wagers lab
| | Sample_contact_department | Islet Cell and Regenerative Biology
| | Sample_contact_institute | Joslin Diabetes Center
| | Sample_contact_address | 1 Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564575/suppl/GSM564575.CEL.gz
| | Sample_series_id | GSE22841
| | Sample_data_row_count | 45037
| | |
|
GSM564576 | GPL1261 |
|
ScaPC_sarcoma_02
|
GFP-positive fraction of sarcoma, ScaPC
|
strain: mixed B6.129 background
tissue: sarcoma
sarcoma cell-of-origin: non-myogenic progenitors (ScaPCs)
oncogenes: KRAS(G12V), p16p19null
gfp status: positive
|
Gene expression data from sarcomas of ScaPC origin.
|
| Sample_geo_accession | GSM564576
| | Sample_status | Public on Nov 10 2011
| | Sample_submission_date | Jul 08 2010
| | Sample_last_update_date | Nov 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Tumors were harvested, digested in DMEM + 0.2% collagenase type II (Invitrogen) + 0.05% dispase (Invitrogen) for 90 minutes at 37°C. Cells were suspended in HBSS with 2% FBS and 2mM EDTA containing 1μg/ml propidium iodide and 10μM calcein blue (Invitrogen) to identify the viable fraction of cells from which GFP-positive cells were isolated by FACS sorting. Cells were sorted twice to maximize purity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Mouse Genome 430 2.0 array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were imported into D-chip (version 1.0.0.1) and normalized in batch against an invariant set. Filtered probe sets were identified based on variation across samples being 1< standard deviation/Mean < 1000 with 50% of probes being present in array comparisons. Expression level cut offs were made at >600, >400 and >200, and expression being found in ≥ 50% of microarray samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amy,J,Wagers
| | Sample_contact_laboratory | Wagers lab
| | Sample_contact_department | Islet Cell and Regenerative Biology
| | Sample_contact_institute | Joslin Diabetes Center
| | Sample_contact_address | 1 Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564576/suppl/GSM564576.CEL.gz
| | Sample_series_id | GSE22841
| | Sample_data_row_count | 45037
| | |
|
GSM564577 | GPL1261 |
|
ScaPC_sarcoma_03
|
GFP-positive fraction of sarcoma, ScaPC
|
strain: mixed B6.129 background
tissue: sarcoma
sarcoma cell-of-origin: non-myogenic progenitors (ScaPCs)
oncogenes: KRAS(G12V), p16p19null
gfp status: positive
|
Gene expression data from sarcomas of ScaPC origin.
|
| Sample_geo_accession | GSM564577
| | Sample_status | Public on Nov 10 2011
| | Sample_submission_date | Jul 08 2010
| | Sample_last_update_date | Nov 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Tumors were harvested, digested in DMEM + 0.2% collagenase type II (Invitrogen) + 0.05% dispase (Invitrogen) for 90 minutes at 37°C. Cells were suspended in HBSS with 2% FBS and 2mM EDTA containing 1μg/ml propidium iodide and 10μM calcein blue (Invitrogen) to identify the viable fraction of cells from which GFP-positive cells were isolated by FACS sorting. Cells were sorted twice to maximize purity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Mouse Genome 430 2.0 array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were imported into D-chip (version 1.0.0.1) and normalized in batch against an invariant set. Filtered probe sets were identified based on variation across samples being 1< standard deviation/Mean < 1000 with 50% of probes being present in array comparisons. Expression level cut offs were made at >600, >400 and >200, and expression being found in ≥ 50% of microarray samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amy,J,Wagers
| | Sample_contact_laboratory | Wagers lab
| | Sample_contact_department | Islet Cell and Regenerative Biology
| | Sample_contact_institute | Joslin Diabetes Center
| | Sample_contact_address | 1 Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564577/suppl/GSM564577.CEL.gz
| | Sample_series_id | GSE22841
| | Sample_data_row_count | 45037
| | |
|
GSM564578 | GPL1261 |
|
ScaPC_sarcoma_04
|
GFP-positive fraction of sarcoma, ScaPC
|
strain: mixed B6.129 background
tissue: sarcoma
sarcoma cell-of-origin: non-myogenic progenitors (ScaPCs)
oncogenes: KRAS(G12V), p16p19null
gfp status: positive
|
Gene expression data from sarcomas of ScaPC origin.
|
| Sample_geo_accession | GSM564578
| | Sample_status | Public on Nov 10 2011
| | Sample_submission_date | Jul 08 2010
| | Sample_last_update_date | Nov 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Tumors were harvested, digested in DMEM + 0.2% collagenase type II (Invitrogen) + 0.05% dispase (Invitrogen) for 90 minutes at 37°C. Cells were suspended in HBSS with 2% FBS and 2mM EDTA containing 1μg/ml propidium iodide and 10μM calcein blue (Invitrogen) to identify the viable fraction of cells from which GFP-positive cells were isolated by FACS sorting. Cells were sorted twice to maximize purity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol.
| | Sample_hyb_protocol | 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Mouse Genome 430 2.0 array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were imported into D-chip (version 1.0.0.1) and normalized in batch against an invariant set. Filtered probe sets were identified based on variation across samples being 1< standard deviation/Mean < 1000 with 50% of probes being present in array comparisons. Expression level cut offs were made at >600, >400 and >200, and expression being found in ≥ 50% of microarray samples.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amy,J,Wagers
| | Sample_contact_laboratory | Wagers lab
| | Sample_contact_department | Islet Cell and Regenerative Biology
| | Sample_contact_institute | Joslin Diabetes Center
| | Sample_contact_address | 1 Joslin Place
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564578/suppl/GSM564578.CEL.gz
| | Sample_series_id | GSE22841
| | Sample_data_row_count | 45037
| | |
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