Search results for the GEO ID: GSE34135  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM842274 | GPL1261 |
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Collecting lymphatic duct from Apex xenograft, biological rep1
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Murine collecting lymphatic endothelial cells with 293 Apex xenograft
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xenograft: 293EBNA cells transfected with empty APEX vector
cell type: collecting lymphatic endothelial cells
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af1c909-31-clec1-290107.CHP
af1c909-31-clec1-290107.CEL
Murine collecting lymphatic endothelial cells with 293 Apex xenograft
Collecting_Lymphatic_Endothelial_Cell_Apex_1
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| Sample_geo_accession | GSM842274
| | Sample_status | Public on Jan 15 2012
| | Sample_submission_date | Dec 05 2011
| | Sample_last_update_date | Jan 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Patent Blue V was injected into the tumor to visualize the draining collecting lymphatics which were subsequently microdissected. Single cell suspensions were prepared and endothelial cell populations isolated by MAC sorting.
| | Sample_growth_protocol_ch1 | 293EBNA tumor cells were injected into the flank of mice. The tumors were grown until they reached a volume of 2000 mm3.
| | 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 | Raw intensity data was analysed using GeneChip Operating Software (Affymetrix Inc) and profiles compared using AffylmGUI software (Wettenhall et al. 2006, Bioinformatics 22:897-9).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | tara,,karnezis
| | Sample_contact_email | tara.karnezis@petermac.org
| | Sample_contact_laboratory | angiogenesis
| | Sample_contact_institute | Peter macallum cancer center
| | Sample_contact_address | St.Andrews place
| | Sample_contact_city | Melbourne
| | Sample_contact_zip/postal_code | 3002
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842274/suppl/GSM842274.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842274/suppl/GSM842274.CHP.gz
| | Sample_series_id | GSE34135
| | Sample_data_row_count | 45101
| | |
|
GSM842275 | GPL1261 |
|
Collecting lymphatic duct from Apex xenograft, biological rep2
|
Murine collecting lymphatic endothelial cells with 293 Apex xenograft
|
xenograft: 293EBNA cells transfected with empty APEX vector
cell type: collecting lymphatic endothelial cells
|
af1c909-32-clec2-290107.CHP
af1c909-32-clec2-290107.CEL
Murine collecting lymphatic endothelial cells with 293 Apex xenograft
Collecting_Lymphatic_Endothelial_Cell_Apex_2
|
| Sample_geo_accession | GSM842275
| | Sample_status | Public on Jan 15 2012
| | Sample_submission_date | Dec 05 2011
| | Sample_last_update_date | Jan 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Patent Blue V was injected into the tumor to visualize the draining collecting lymphatics which were subsequently microdissected. Single cell suspensions were prepared and endothelial cell populations isolated by MAC sorting.
| | Sample_growth_protocol_ch1 | 293EBNA tumor cells were injected into the flank of mice. The tumors were grown until they reached a volume of 2000 mm3.
| | 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 | Raw intensity data was analysed using GeneChip Operating Software (Affymetrix Inc) and profiles compared using AffylmGUI software (Wettenhall et al. 2006, Bioinformatics 22:897-9).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | tara,,karnezis
| | Sample_contact_email | tara.karnezis@petermac.org
| | Sample_contact_laboratory | angiogenesis
| | Sample_contact_institute | Peter macallum cancer center
| | Sample_contact_address | St.Andrews place
| | Sample_contact_city | Melbourne
| | Sample_contact_zip/postal_code | 3002
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842275/suppl/GSM842275.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842275/suppl/GSM842275.CHP.gz
| | Sample_series_id | GSE34135
| | Sample_data_row_count | 45101
| | |
|
GSM842276 | GPL1261 |
|
Collecting lymphatic duct from Apex-VEGFD xenograft, biological rep1
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Murine collecting lymphatic endothelial cells with 293 Apex-VEGFD xenograft
|
xenograft: 293EBNA cells transfected with vector containing VEGFD
cell type: collecting lymphatic endothelial cells
|
af1c909-34-clec4-290107.CHP
af1c909-34-clec4-290107.CEL
Murine collecting lymphatic endothelial cells with 293 Apex-VEGFD xenograft
Collecting_Lymphatic_Endothelial_Cell_VEGFD_1
|
| Sample_geo_accession | GSM842276
| | Sample_status | Public on Jan 15 2012
| | Sample_submission_date | Dec 05 2011
| | Sample_last_update_date | Jan 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Patent Blue V was injected into the tumor to visualize the draining collecting lymphatics which were subsequently microdissected. Single cell suspensions were prepared and endothelial cell populations isolated by MAC sorting.
| | Sample_growth_protocol_ch1 | 293EBNA tumor cells were injected into the flank of mice. The tumors were grown until they reached a volume of 2000 mm3.
| | 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 | Raw intensity data was analysed using GeneChip Operating Software (Affymetrix Inc) and profiles compared using AffylmGUI software (Wettenhall et al. 2006, Bioinformatics 22:897-9).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | tara,,karnezis
| | Sample_contact_email | tara.karnezis@petermac.org
| | Sample_contact_laboratory | angiogenesis
| | Sample_contact_institute | Peter macallum cancer center
| | Sample_contact_address | St.Andrews place
| | Sample_contact_city | Melbourne
| | Sample_contact_zip/postal_code | 3002
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842276/suppl/GSM842276.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842276/suppl/GSM842276.CHP.gz
| | Sample_series_id | GSE34135
| | Sample_data_row_count | 45101
| | |
|
GSM842277 | GPL1261 |
|
Collecting lymphatic duct from Apex-VEGFD xenograft, biological rep2
|
Murine collecting lymphatic endothelial cells with 293 Apex-VEGFD xenograft
|
xenograft: 293EBNA cells transfected with vector containing VEGFD
cell type: collecting lymphatic endothelial cells
|
af1c909-35-clec5-290107.CHP
af1c909-35-clec5-290107.CEL
Murine collecting lymphatic endothelial cells with 293 Apex-VEGFD xenograft
Collecting_Lymphatic_Endothelial_Cell_VEGFD_2
|
| Sample_geo_accession | GSM842277
| | Sample_status | Public on Jan 15 2012
| | Sample_submission_date | Dec 05 2011
| | Sample_last_update_date | Jan 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Patent Blue V was injected into the tumor to visualize the draining collecting lymphatics which were subsequently microdissected. Single cell suspensions were prepared and endothelial cell populations isolated by MAC sorting.
| | Sample_growth_protocol_ch1 | 293EBNA tumor cells were injected into the flank of mice. The tumors were grown until they reached a volume of 2000 mm3.
| | 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 | Raw intensity data was analysed using GeneChip Operating Software (Affymetrix Inc) and profiles compared using AffylmGUI software (Wettenhall et al. 2006, Bioinformatics 22:897-9).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | tara,,karnezis
| | Sample_contact_email | tara.karnezis@petermac.org
| | Sample_contact_laboratory | angiogenesis
| | Sample_contact_institute | Peter macallum cancer center
| | Sample_contact_address | St.Andrews place
| | Sample_contact_city | Melbourne
| | Sample_contact_zip/postal_code | 3002
| | Sample_contact_country | Australia
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842277/suppl/GSM842277.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM842nnn/GSM842277/suppl/GSM842277.CHP.gz
| | Sample_series_id | GSE34135
| | Sample_data_row_count | 45101
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