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Search results for the GEO ID: GSE31123

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Description

Characteristics

GSM770680

GPL1261

Metastatic (VEGF-D) LN EC, biological rep 1

endothelial cells from lymph nodes draining metastatic (VEGF-D-overexpressing) tumors

cell type: enriched endothelial cell fraction from tumor-draining lymph nodes strain: SCID/NOD gender: female age: 6-8 weeks sorting: Tumor cells and leukocytes depleted before culture and endothelial cell positive selection

Gene expression data from endothelial cells isolated from draining LNs of tumors

Sample_geo_accession	GSM770680
Sample_status	Public on Sep 23 2011
Sample_submission_date	Aug 02 2011
Sample_last_update_date	Sep 23 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	To create tumors, 2.5 x 10^7 293-VEGF-D (metastatic) or 293-Apex (non-metastatic) tumor cells were injected subcutaneously into the left flank of female SCID/NOD mice. The left axillary lymph node which drains this tumor site was harvested when the tumors reached 1600-2500 mm^3 (3-4 weeks). LNs were then digested enzymatically, after which tumor cells and leukocytes were depleted via immunomagnetic selection for class I HLA and CD16/CD32 respectively. The resulting LN stromal cells were cultured briefly in EGM-2 MV growth medium with supplements (Cambrex/Lonza). Podoplanin was then used as a positive immunomagnetic selection marker to enrich for lymphatic and other endothelial cells in the lymph node.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from lymph node endothelial cells using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Mouse total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the Nanochip protocol. A total of 3 ug was labelled using the Affymetrix One Cycle cDNA synthesis kit (Millennium Sciences cat no. 900431). The subsequent cDNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371). Upon cleaning of the cDNA the next step was to incorporate biotin into the resultant cRNA using the Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449). After the IVT process the labelled cRNA was cleaned using the above GeneChip Sample Cleanup kit. The quantity of product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol. A total of 20ug of labelled cRNA was then fragmented to the 50-200bp size range and quality control checked using the Bioanalyser 2100 using the NanoChip protocol.
Sample_hyb_protocol	Samples were prepared for hybridisation to the Mouse 430 version 2.0 GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO. A total hybridisation volume of 300 ul was prepared for each sample and 200 ul loaded into a Mouse 430 version 2.0 GeneChip. The chip was hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm. After hybridisation the chip was washed using the appropriate fluidics script in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	Chips were scanned using the Affymetrix GeneChip Scanner 3000. The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which was then used for generating subsequent CEL and CHP files for analysis.
Sample_data_processing	The raw signal intensity values were normalised using Robust Multiarray Analysis and linear modelling in AffylmGUI software (Wettenhall et al. 2006, Bioinformatics 22:897-9)
Sample_platform_id	GPL1261
Sample_contact_name	Rae,,Farnsworth
Sample_contact_email	rae.farnsworth@monash.edu
Sample_contact_institute	Monash University
Sample_contact_address	Wellington Rd
Sample_contact_city	Clayton
Sample_contact_state	VIC
Sample_contact_zip/postal_code	3800
Sample_contact_country	Australia
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM770nnn/GSM770680/suppl/GSM770680.CEL.gz
Sample_series_id	GSE31123
Sample_data_row_count	45101

GSM770681

GPL1261

Metastatic (VEGF-D) LN EC, biological rep 2

endothelial cells from lymph nodes draining metastatic (VEGF-D-overexpressing) tumors

Gene expression data from endothelial cells isolated from draining LNs of tumors

Sample_geo_accession	GSM770681
Sample_status	Public on Sep 23 2011
Sample_submission_date	Aug 02 2011
Sample_last_update_date	Sep 23 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	To create tumors, 2.5 x 10^7 293-VEGF-D (metastatic) or 293-Apex (non-metastatic) tumor cells were injected subcutaneously into the left flank of female SCID/NOD mice. The left axillary lymph node which drains this tumor site was harvested when the tumors reached 1600-2500 mm^3 (3-4 weeks). LNs were then digested enzymatically, after which tumor cells and leukocytes were depleted via immunomagnetic selection for class I HLA and CD16/CD32 respectively. The resulting LN stromal cells were cultured briefly in EGM-2 MV growth medium with supplements (Cambrex/Lonza). Podoplanin was then used as a positive immunomagnetic selection marker to enrich for lymphatic and other endothelial cells in the lymph node.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from lymph node endothelial cells using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Mouse total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the Nanochip protocol. A total of 3 ug was labelled using the Affymetrix One Cycle cDNA synthesis kit (Millennium Sciences cat no. 900431). The subsequent cDNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371). Upon cleaning of the cDNA the next step was to incorporate biotin into the resultant cRNA using the Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449). After the IVT process the labelled cRNA was cleaned using the above GeneChip Sample Cleanup kit. The quantity of product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol. A total of 20ug of labelled cRNA was then fragmented to the 50-200bp size range and quality control checked using the Bioanalyser 2100 using the NanoChip protocol.
Sample_hyb_protocol	Samples were prepared for hybridisation to the Mouse 430 version 2.0 GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO. A total hybridisation volume of 300 ul was prepared for each sample and 200 ul loaded into a Mouse 430 version 2.0 GeneChip. The chip was hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm. After hybridisation the chip was washed using the appropriate fluidics script in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	Chips were scanned using the Affymetrix GeneChip Scanner 3000. The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which was then used for generating subsequent CEL and CHP files for analysis.
Sample_data_processing	The raw signal intensity values were normalised using Robust Multiarray Analysis and linear modelling in AffylmGUI software (Wettenhall et al. 2006, Bioinformatics 22:897-9)
Sample_platform_id	GPL1261
Sample_contact_name	Rae,,Farnsworth
Sample_contact_email	rae.farnsworth@monash.edu
Sample_contact_institute	Monash University
Sample_contact_address	Wellington Rd
Sample_contact_city	Clayton
Sample_contact_state	VIC
Sample_contact_zip/postal_code	3800
Sample_contact_country	Australia
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM770nnn/GSM770681/suppl/GSM770681.CEL.gz
Sample_series_id	GSE31123
Sample_data_row_count	45101

GSM770682

GPL1261

Non-metastatic LN EC, biological rep 1

endothelial cells from lymph nodes draining non-metastatic (no VEGF-D) tumors

cell type: enriched endothelial cell fraction from tumor-draining lymph nodes strain: SCID/NOD gender: female age: 6-8 weeks sorting: No depletion prior to culture and endothelial cell positive selection

Gene expression data from endothelial cells isolated from draining LNs of tumors

Sample_geo_accession	GSM770682
Sample_status	Public on Sep 23 2011
Sample_submission_date	Aug 02 2011
Sample_last_update_date	Sep 23 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	To create tumors, 2.5 x 10^7 293-VEGF-D (metastatic) or 293-Apex (non-metastatic) tumor cells were injected subcutaneously into the left flank of female SCID/NOD mice. The left axillary lymph node which drains this tumor site was harvested when the tumors reached 1600-2500 mm^3 (3-4 weeks). LNs were then digested enzymatically, after which tumor cells and leukocytes were depleted via immunomagnetic selection for class I HLA and CD16/CD32 respectively. The resulting LN stromal cells were cultured briefly in EGM-2 MV growth medium with supplements (Cambrex/Lonza). Podoplanin was then used as a positive immunomagnetic selection marker to enrich for lymphatic and other endothelial cells in the lymph node.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from lymph node endothelial cells using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Mouse total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the Nanochip protocol. A total of 3 ug was labelled using the Affymetrix One Cycle cDNA synthesis kit (Millennium Sciences cat no. 900431). The subsequent cDNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371). Upon cleaning of the cDNA the next step was to incorporate biotin into the resultant cRNA using the Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449). After the IVT process the labelled cRNA was cleaned using the above GeneChip Sample Cleanup kit. The quantity of product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol. A total of 20ug of labelled cRNA was then fragmented to the 50-200bp size range and quality control checked using the Bioanalyser 2100 using the NanoChip protocol.
Sample_hyb_protocol	Samples were prepared for hybridisation to the Mouse 430 version 2.0 GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO. A total hybridisation volume of 300 ul was prepared for each sample and 200 ul loaded into a Mouse 430 version 2.0 GeneChip. The chip was hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm. After hybridisation the chip was washed using the appropriate fluidics script in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	Chips were scanned using the Affymetrix GeneChip Scanner 3000. The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which was then used for generating subsequent CEL and CHP files for analysis.
Sample_data_processing	The raw signal intensity values were normalised using Robust Multiarray Analysis and linear modelling in AffylmGUI software (Wettenhall et al. 2006, Bioinformatics 22:897-9)
Sample_platform_id	GPL1261
Sample_contact_name	Rae,,Farnsworth
Sample_contact_email	rae.farnsworth@monash.edu
Sample_contact_institute	Monash University
Sample_contact_address	Wellington Rd
Sample_contact_city	Clayton
Sample_contact_state	VIC
Sample_contact_zip/postal_code	3800
Sample_contact_country	Australia
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM770nnn/GSM770682/suppl/GSM770682.CEL.gz
Sample_series_id	GSE31123
Sample_data_row_count	45101

GSM770683

GPL1261

Non-metastatic LN EC, biological rep 2

endothelial cells from lymph nodes draining non-metastatic (no VEGF-D) tumors

Gene expression data from endothelial cells isolated from draining LNs of tumors

Sample_geo_accession	GSM770683
Sample_status	Public on Sep 23 2011
Sample_submission_date	Aug 02 2011
Sample_last_update_date	Sep 23 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	To create tumors, 2.5 x 10^7 293-VEGF-D (metastatic) or 293-Apex (non-metastatic) tumor cells were injected subcutaneously into the left flank of female SCID/NOD mice. The left axillary lymph node which drains this tumor site was harvested when the tumors reached 1600-2500 mm^3 (3-4 weeks). LNs were then digested enzymatically, after which tumor cells and leukocytes were depleted via immunomagnetic selection for class I HLA and CD16/CD32 respectively. The resulting LN stromal cells were cultured briefly in EGM-2 MV growth medium with supplements (Cambrex/Lonza). Podoplanin was then used as a positive immunomagnetic selection marker to enrich for lymphatic and other endothelial cells in the lymph node.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from lymph node endothelial cells using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Mouse total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the Nanochip protocol. A total of 3 ug was labelled using the Affymetrix One Cycle cDNA synthesis kit (Millennium Sciences cat no. 900431). The subsequent cDNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371). Upon cleaning of the cDNA the next step was to incorporate biotin into the resultant cRNA using the Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449). After the IVT process the labelled cRNA was cleaned using the above GeneChip Sample Cleanup kit. The quantity of product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol. A total of 20ug of labelled cRNA was then fragmented to the 50-200bp size range and quality control checked using the Bioanalyser 2100 using the NanoChip protocol.
Sample_hyb_protocol	Samples were prepared for hybridisation to the Mouse 430 version 2.0 GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO. A total hybridisation volume of 300 ul was prepared for each sample and 200 ul loaded into a Mouse 430 version 2.0 GeneChip. The chip was hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm. After hybridisation the chip was washed using the appropriate fluidics script in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	Chips were scanned using the Affymetrix GeneChip Scanner 3000. The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which was then used for generating subsequent CEL and CHP files for analysis.
Sample_data_processing	The raw signal intensity values were normalised using Robust Multiarray Analysis and linear modelling in AffylmGUI software (Wettenhall et al. 2006, Bioinformatics 22:897-9)
Sample_platform_id	GPL1261
Sample_contact_name	Rae,,Farnsworth
Sample_contact_email	rae.farnsworth@monash.edu
Sample_contact_institute	Monash University
Sample_contact_address	Wellington Rd
Sample_contact_city	Clayton
Sample_contact_state	VIC
Sample_contact_zip/postal_code	3800
Sample_contact_country	Australia
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM770nnn/GSM770683/suppl/GSM770683.CEL.gz
Sample_series_id	GSE31123
Sample_data_row_count	45101

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