Search results for the GEO ID: GSE16355 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM410690 | GPL570 |
|
LEC KSHV_Cluster, rep1
|
lymphatic endothelial cells, KSHV microRNA cluster
|
cell type: lymphatic endothelial cells
vector: pSIN-MCS-KSCluster
|
Biological replicate 1 of 3.
|
Sample_geo_accession | GSM410690
| Sample_status | Public on Sep 30 2009
| Sample_submission_date | May 31 2009
| Sample_last_update_date | Aug 24 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) were plated in six well plates (10^5cells/well) and were transduced with lentiviruses encoding the KSHV microRNA cluster or empty vector (pSIN-MCS). Three days after infection, cultures were used for RNA extraction. Typically six wells of a 6-well plate were used per Affymetrix chip.
| Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker, and were cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) plus 10 ng/ml of VEGF-C, in fibronectin-coated plates. KSHV microRNA Cluster-transfected LEC were grown under the same conditions. All cells were mycoplasma free.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | TRIzol solution (Invitrogen) extraction followed by RNeasy Mini kit (Qiagen) purification. Assessed RNA integrity and quantity using RNA 6000 Nano chips (Agilent).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 1 ug of total RNA was used to generate cDNA using T7-linked oligo(dT)primer and the custom SuperScript dscDNA synthesis kit (Invitrogen). After second-strand syntheis, in vitro transcription was carried with biotinylated UTP and CTP using GeneChip® IVT Labeling Kit (http://www.affymetrix.com/support/technical/technotes/ivt_technote.pdf)
| Sample_hyb_protocol | Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix hgu133plus2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Affymetrix hgu133plus2 chips were scanned using the Affymetrix Scanner 3000 7G and the MAS 5.1 software as per the manufacturer's protocol http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf
| Sample_data_processing | Data was preprocessed and normalised using the Bioconductor 'affy' package, specifically the robust multiarray algorithm ('RMA').
| Sample_platform_id | GPL570
| Sample_contact_name | Stephen,,Henderson
| Sample_contact_email | s.henderson@ucl.ac.uk
| Sample_contact_phone | 02076796827
| Sample_contact_fax | 02076796851
| Sample_contact_laboratory | Viral Oncology
| Sample_contact_department | Cancer Institute
| Sample_contact_institute | UCL
| Sample_contact_address | Paul O'Gorman Building, Huntley Street
| Sample_contact_city | London
| Sample_contact_zip/postal_code | WC1E 6BT
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM410nnn/GSM410690/suppl/GSM410690.CEL.gz
| Sample_series_id | GSE16355
| Sample_series_id | GSE16357
| Sample_data_row_count | 54675
| |
|
GSM410691 | GPL570 |
|
LEC KSHV_Cluster, rep2
|
lymphatic endothelial cells, KSHV microRNA cluster
|
cell type: lymphatic endothelial cells
vector: pSIN-MCS-KSCluster
|
Biological replicate 2 of 3.
|
Sample_geo_accession | GSM410691
| Sample_status | Public on Sep 30 2009
| Sample_submission_date | May 31 2009
| Sample_last_update_date | Aug 24 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) were plated in six well plates (10^5cells/well) and were transduced with lentiviruses encoding the KSHV microRNA cluster or empty vector (pSIN-MCS). Three days after infection, cultures were used for RNA extraction. Typically six wells of a 6-well plate were used per Affymetrix chip.
| Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker, and were cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) plus 10 ng/ml of VEGF-C, in fibronectin-coated plates. KSHV microRNA Cluster-transfected LEC were grown under the same conditions. All cells were mycoplasma free.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | TRIzol solution (Invitrogen) extraction followed by RNeasy Mini kit (Qiagen) purification. Assessed RNA integrity and quantity using RNA 6000 Nano chips (Agilent).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 1 ug of total RNA was used to generate cDNA using T7-linked oligo(dT)primer and the custom SuperScript dscDNA synthesis kit (Invitrogen). After second-strand syntheis, in vitro transcription was carried with biotinylated UTP and CTP using GeneChip® IVT Labeling Kit (http://www.affymetrix.com/support/technical/technotes/ivt_technote.pdf)
| Sample_hyb_protocol | Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix hgu133plus2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Affymetrix hgu133plus2 chips were scanned using the Affymetrix Scanner 3000 7G and the MAS 5.1 software as per the manufacturer's protocol http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf
| Sample_data_processing | Data was preprocessed and normalised using the Bioconductor 'affy' package, specifically the robust multiarray algorithm ('RMA').
| Sample_platform_id | GPL570
| Sample_contact_name | Stephen,,Henderson
| Sample_contact_email | s.henderson@ucl.ac.uk
| Sample_contact_phone | 02076796827
| Sample_contact_fax | 02076796851
| Sample_contact_laboratory | Viral Oncology
| Sample_contact_department | Cancer Institute
| Sample_contact_institute | UCL
| Sample_contact_address | Paul O'Gorman Building, Huntley Street
| Sample_contact_city | London
| Sample_contact_zip/postal_code | WC1E 6BT
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM410nnn/GSM410691/suppl/GSM410691.CEL.gz
| Sample_series_id | GSE16355
| Sample_series_id | GSE16357
| Sample_data_row_count | 54675
| |
|
GSM410692 | GPL570 |
|
LEC KSHV_Cluster, rep3
|
lymphatic endothelial cells, KSHV microRNA cluster
|
cell type: lymphatic endothelial cells
vector: pSIN-MCS-KSCluster
|
Biological replicate 3 of 3.
|
Sample_geo_accession | GSM410692
| Sample_status | Public on Sep 30 2009
| Sample_submission_date | May 31 2009
| Sample_last_update_date | Aug 24 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) were plated in six well plates (10^5cells/well) and were transduced with lentiviruses encoding the KSHV microRNA cluster or empty vector (pSIN-MCS). Three days after infection, cultures were used for RNA extraction. Typically six wells of a 6-well plate were used per Affymetrix chip.
| Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker, and were cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) plus 10 ng/ml of VEGF-C, in fibronectin-coated plates. KSHV microRNA Cluster-transfected LEC were grown under the same conditions. All cells were mycoplasma free.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | TRIzol solution (Invitrogen) extraction followed by RNeasy Mini kit (Qiagen) purification. Assessed RNA integrity and quantity using RNA 6000 Nano chips (Agilent).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 1 ug of total RNA was used to generate cDNA using T7-linked oligo(dT)primer and the custom SuperScript dscDNA synthesis kit (Invitrogen). After second-strand syntheis, in vitro transcription was carried with biotinylated UTP and CTP using GeneChip® IVT Labeling Kit (http://www.affymetrix.com/support/technical/technotes/ivt_technote.pdf)
| Sample_hyb_protocol | Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix hgu133plus2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Affymetrix hgu133plus2 chips were scanned using the Affymetrix Scanner 3000 7G and the MAS 5.1 software as per the manufacturer's protocol http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf
| Sample_data_processing | Data was preprocessed and normalised using the Bioconductor 'affy' package, specifically the robust multiarray algorithm ('RMA').
| Sample_platform_id | GPL570
| Sample_contact_name | Stephen,,Henderson
| Sample_contact_email | s.henderson@ucl.ac.uk
| Sample_contact_phone | 02076796827
| Sample_contact_fax | 02076796851
| Sample_contact_laboratory | Viral Oncology
| Sample_contact_department | Cancer Institute
| Sample_contact_institute | UCL
| Sample_contact_address | Paul O'Gorman Building, Huntley Street
| Sample_contact_city | London
| Sample_contact_zip/postal_code | WC1E 6BT
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM410nnn/GSM410692/suppl/GSM410692.CEL.gz
| Sample_series_id | GSE16355
| Sample_series_id | GSE16357
| Sample_data_row_count | 54675
| |
|
GSM410693 | GPL570 |
|
LEC pSIN-MCS, rep1
|
lymphatic endothelial cells
|
cell type: lymphatic endothelial cells
vector: pSIN-MCS
|
Biological replicate 1 of 3.
|
Sample_geo_accession | GSM410693
| Sample_status | Public on Sep 30 2009
| Sample_submission_date | May 31 2009
| Sample_last_update_date | Aug 24 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) were plated in six well plates (10^5cells/well) and were transduced with lentiviruses encoding the KSHV microRNA cluster or empty vector (pSIN-MCS). Three days after infection, cultures were used for RNA extraction. Typically six wells of a 6-well plate were used per Affymetrix chip.
| Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker, and were cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) plus 10 ng/ml of VEGF-C, in fibronectin-coated plates. KSHV microRNA Cluster-transfected LEC were grown under the same conditions. All cells were mycoplasma free.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | TRIzol solution (Invitrogen) extraction followed by RNeasy Mini kit (Qiagen) purification. Assessed RNA integrity and quantity using RNA 6000 Nano chips (Agilent).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 1 ug of total RNA was used to generate cDNA using T7-linked oligo(dT)primer and the custom SuperScript dscDNA synthesis kit (Invitrogen). After second-strand syntheis, in vitro transcription was carried with biotinylated UTP and CTP using GeneChip® IVT Labeling Kit (http://www.affymetrix.com/support/technical/technotes/ivt_technote.pdf)
| Sample_hyb_protocol | Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix hgu133plus2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Affymetrix hgu133plus2 chips were scanned using the Affymetrix Scanner 3000 7G and the MAS 5.1 software as per the manufacturer's protocol http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf
| Sample_data_processing | Data was preprocessed and normalised using the Bioconductor 'affy' package, specifically the robust multiarray algorithm ('RMA').
| Sample_platform_id | GPL570
| Sample_contact_name | Stephen,,Henderson
| Sample_contact_email | s.henderson@ucl.ac.uk
| Sample_contact_phone | 02076796827
| Sample_contact_fax | 02076796851
| Sample_contact_laboratory | Viral Oncology
| Sample_contact_department | Cancer Institute
| Sample_contact_institute | UCL
| Sample_contact_address | Paul O'Gorman Building, Huntley Street
| Sample_contact_city | London
| Sample_contact_zip/postal_code | WC1E 6BT
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM410nnn/GSM410693/suppl/GSM410693.CEL.gz
| Sample_series_id | GSE16355
| Sample_series_id | GSE16357
| Sample_data_row_count | 54675
| |
|
GSM410694 | GPL570 |
|
LEC pSIN-MCS, rep2
|
lymphatic endothelial cells
|
cell type: lymphatic endothelial cells
vector: pSIN-MCS
|
Biological replicate 2 of 3.
|
Sample_geo_accession | GSM410694
| Sample_status | Public on Sep 30 2009
| Sample_submission_date | May 31 2009
| Sample_last_update_date | Aug 24 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) were plated in six well plates (10^5cells/well) and were transduced with lentiviruses encoding the KSHV microRNA cluster or empty vector (pSIN-MCS). Three days after infection, cultures were used for RNA extraction. Typically six wells of a 6-well plate were used per Affymetrix chip.
| Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker, and were cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) plus 10 ng/ml of VEGF-C, in fibronectin-coated plates. KSHV microRNA Cluster-transfected LEC were grown under the same conditions. All cells were mycoplasma free.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | TRIzol solution (Invitrogen) extraction followed by RNeasy Mini kit (Qiagen) purification. Assessed RNA integrity and quantity using RNA 6000 Nano chips (Agilent).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 1 ug of total RNA was used to generate cDNA using T7-linked oligo(dT)primer and the custom SuperScript dscDNA synthesis kit (Invitrogen). After second-strand syntheis, in vitro transcription was carried with biotinylated UTP and CTP using GeneChip® IVT Labeling Kit (http://www.affymetrix.com/support/technical/technotes/ivt_technote.pdf)
| Sample_hyb_protocol | Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix hgu133plus2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Affymetrix hgu133plus2 chips were scanned using the Affymetrix Scanner 3000 7G and the MAS 5.1 software as per the manufacturer's protocol http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf
| Sample_data_processing | Data was preprocessed and normalised using the Bioconductor 'affy' package, specifically the robust multiarray algorithm ('RMA').
| Sample_platform_id | GPL570
| Sample_contact_name | Stephen,,Henderson
| Sample_contact_email | s.henderson@ucl.ac.uk
| Sample_contact_phone | 02076796827
| Sample_contact_fax | 02076796851
| Sample_contact_laboratory | Viral Oncology
| Sample_contact_department | Cancer Institute
| Sample_contact_institute | UCL
| Sample_contact_address | Paul O'Gorman Building, Huntley Street
| Sample_contact_city | London
| Sample_contact_zip/postal_code | WC1E 6BT
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM410nnn/GSM410694/suppl/GSM410694.CEL.gz
| Sample_series_id | GSE16355
| Sample_series_id | GSE16357
| Sample_data_row_count | 54675
| |
|
GSM410695 | GPL570 |
|
LEC pSIN-MCS, rep3
|
lymphatic endothelial cells
|
cell type: lymphatic endothelial cells
vector: pSIN-MCS
|
Biological replicate 3 of 3.
|
Sample_geo_accession | GSM410695
| Sample_status | Public on Sep 30 2009
| Sample_submission_date | May 31 2009
| Sample_last_update_date | Aug 24 2009
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) were plated in six well plates (10^5cells/well) and were transduced with lentiviruses encoding the KSHV microRNA cluster or empty vector (pSIN-MCS). Three days after infection, cultures were used for RNA extraction. Typically six wells of a 6-well plate were used per Affymetrix chip.
| Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker, and were cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) plus 10 ng/ml of VEGF-C, in fibronectin-coated plates. KSHV microRNA Cluster-transfected LEC were grown under the same conditions. All cells were mycoplasma free.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | TRIzol solution (Invitrogen) extraction followed by RNeasy Mini kit (Qiagen) purification. Assessed RNA integrity and quantity using RNA 6000 Nano chips (Agilent).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 1 ug of total RNA was used to generate cDNA using T7-linked oligo(dT)primer and the custom SuperScript dscDNA synthesis kit (Invitrogen). After second-strand syntheis, in vitro transcription was carried with biotinylated UTP and CTP using GeneChip® IVT Labeling Kit (http://www.affymetrix.com/support/technical/technotes/ivt_technote.pdf)
| Sample_hyb_protocol | Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix hgu133plus2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Affymetrix hgu133plus2 chips were scanned using the Affymetrix Scanner 3000 7G and the MAS 5.1 software as per the manufacturer's protocol http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf
| Sample_data_processing | Data was preprocessed and normalised using the Bioconductor 'affy' package, specifically the robust multiarray algorithm ('RMA').
| Sample_platform_id | GPL570
| Sample_contact_name | Stephen,,Henderson
| Sample_contact_email | s.henderson@ucl.ac.uk
| Sample_contact_phone | 02076796827
| Sample_contact_fax | 02076796851
| Sample_contact_laboratory | Viral Oncology
| Sample_contact_department | Cancer Institute
| Sample_contact_institute | UCL
| Sample_contact_address | Paul O'Gorman Building, Huntley Street
| Sample_contact_city | London
| Sample_contact_zip/postal_code | WC1E 6BT
| Sample_contact_country | United Kingdom
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM410nnn/GSM410695/suppl/GSM410695.CEL.gz
| Sample_series_id | GSE16355
| Sample_series_id | GSE16357
| Sample_data_row_count | 54675
| |
|
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