Search results for the GEO ID: GSE16354  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM410666 | GPL570 |
|
LEC control, rep1
|
lymphatic endothelial cells
|
cell type: lymphatic endothelial cell
infection: none
|
Biological replicate 1 of 6.
|
| Sample_geo_accession | GSM410666
| | Sample_status | Public on Sep 30 2009
| | Sample_submission_date | May 31 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410666/suppl/GSM410666.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410667 | GPL570 |
|
LEC control, rep2
|
lymphatic endothelial cells
|
cell type: lymphatic endothelial cell
infection: none
|
Biological replicate 2 of 6.
|
| Sample_geo_accession | GSM410667
| | Sample_status | Public on Sep 30 2009
| | Sample_submission_date | May 31 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410667/suppl/GSM410667.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410668 | GPL570 |
|
LEC control, rep3
|
lymphatic endothelial cells
|
cell type: lymphatic endothelial cell
infection: none
|
Biological replicate 3 of 6.
|
| Sample_geo_accession | GSM410668
| | Sample_status | Public on Sep 30 2009
| | Sample_submission_date | May 31 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410668/suppl/GSM410668.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410669 | GPL570 |
|
LEC control, rep4
|
lymphatic endothelial cells
|
cell type: lymphatic endothelial cell
infection: none
|
Biological replicate 4 of 6.
|
| Sample_geo_accession | GSM410669
| | Sample_status | Public on Sep 30 2009
| | Sample_submission_date | May 31 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410669/suppl/GSM410669.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410670 | GPL570 |
|
LEC control, rep5
|
lymphatic endothelial cells
|
cell type: lymphatic endothelial cell
infection: none
|
Biological replicate 5 of 6.
|
| Sample_geo_accession | GSM410670
| | 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) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410670/suppl/GSM410670.CEL.gz
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410671 | GPL570 |
|
LEC control, rep6
|
lymphatic endothelial cells
|
cell type: lymphatic endothelial cell
infection: none
|
Biological replicate 6 of 6.
|
| Sample_geo_accession | GSM410671
| | 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) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410671/suppl/GSM410671.CEL.gz
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410672 | GPL570 |
|
LEC KSHV 72h, rep1
|
lymphatic endothelial cells, KSHV-infected, 72h
|
cell type: lymphatic endothelial cell
infection: KSHV
|
Biological replicate 1 of 6.
|
| Sample_geo_accession | GSM410672
| | Sample_status | Public on Sep 30 2009
| | Sample_submission_date | May 31 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410672/suppl/GSM410672.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410673 | GPL570 |
|
LEC KSHV 72h, rep2
|
lymphatic endothelial cells, KSHV-infected, 72h
|
cell type: lymphatic endothelial cell
infection: KSHV
|
Biological replicate 2 of 6.
|
| Sample_geo_accession | GSM410673
| | Sample_status | Public on Sep 30 2009
| | Sample_submission_date | May 31 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410673/suppl/GSM410673.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410674 | GPL570 |
|
LEC KSHV 72h, rep3
|
lymphatic endothelial cells, KSHV-infected, 72h
|
cell type: lymphatic endothelial cell
infection: KSHV
|
Biological replicate 3 of 6.
|
| Sample_geo_accession | GSM410674
| | Sample_status | Public on Sep 30 2009
| | Sample_submission_date | May 31 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410674/suppl/GSM410674.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410675 | GPL570 |
|
LEC KSHV 72h, rep4
|
lymphatic endothelial cells, KSHV-infected, 72h
|
cell type: lymphatic endothelial cell
infection: KSHV
|
Biological replicate 4 of 6.
|
| Sample_geo_accession | GSM410675
| | Sample_status | Public on Sep 30 2009
| | Sample_submission_date | May 31 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410675/suppl/GSM410675.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410676 | GPL570 |
|
LEC KSHV 72h, rep5
|
lymphatic endothelial cells, KSHV-infected, 72h
|
cell type: lymphatic endothelial cell
infection: KSHV
|
Biological replicate 5 of 6.
|
| Sample_geo_accession | GSM410676
| | 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) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410676/suppl/GSM410676.CEL.gz
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410677 | GPL570 |
|
LEC KSHV 72h, rep6
|
lymphatic endothelial cells, KSHV-infected, 72h
|
cell type: lymphatic endothelial cell
infection: KSHV
|
Biological replicate 6 of 6.
|
| Sample_geo_accession | GSM410677
| | 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) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410677/suppl/GSM410677.CEL.gz
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410678 | GPL570 |
|
BEC control, rep1
|
blood vessel endothelial cells
|
cell type: blood vessel endothelial cell
infection: none
|
Biological replicate 1 of 6.
|
| Sample_geo_accession | GSM410678
| | Sample_status | Public on Sep 30 2009
| | Sample_submission_date | May 31 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410678/suppl/GSM410678.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410679 | GPL570 |
|
BEC control, rep2
|
blood vessel endothelial cells
|
cell type: blood vessel endothelial cell
infection: none
|
Biological replicate 2 of 6.
|
| Sample_geo_accession | GSM410679
| | Sample_status | Public on Sep 30 2009
| | Sample_submission_date | May 31 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410679/suppl/GSM410679.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410680 | GPL570 |
|
BEC control, rep3
|
blood vessel endothelial cells
|
cell type: blood vessel endothelial cell
infection: none
|
Biological replicate 3 of 6.
|
| Sample_geo_accession | GSM410680
| | Sample_status | Public on Sep 30 2009
| | Sample_submission_date | May 31 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410680/suppl/GSM410680.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410681 | GPL570 |
|
BEC control, rep4
|
blood vessel endothelial cells
|
cell type: blood vessel endothelial cell
infection: none
|
Biological replicate 4 of 6.
|
| Sample_geo_accession | GSM410681
| | Sample_status | Public on Sep 30 2009
| | Sample_submission_date | May 31 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410681/suppl/GSM410681.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410682 | GPL570 |
|
BEC control, rep5
|
blood vessel endothelial cells
|
cell type: blood vessel endothelial cell
infection: none
|
Biological replicate 5 of 6.
|
| Sample_geo_accession | GSM410682
| | 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) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410682/suppl/GSM410682.CEL.gz
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410683 | GPL570 |
|
BEC control, rep6
|
blood vessel endothelial cells
|
cell type: blood vessel endothelial cell
infection: none
|
Biological replicate 6 of 6.
|
| Sample_geo_accession | GSM410683
| | 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) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410683/suppl/GSM410683.CEL.gz
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410684 | GPL570 |
|
BEC KSHV 72h, rep1
|
blood vessel endothelial cells, KSHV-infected, 72h
|
cell type: blood vessel endothelial cell
infection: KSHV
|
Biological replicate 1 of 6.
|
| Sample_geo_accession | GSM410684
| | Sample_status | Public on Sep 30 2009
| | Sample_submission_date | May 31 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410684/suppl/GSM410684.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410685 | GPL570 |
|
BEC KSHV 72h, rep2
|
blood vessel endothelial cells, KSHV-infected, 72h
|
cell type: blood vessel endothelial cell
infection: KSHV
|
Biological replicate 2 of 6.
|
| Sample_geo_accession | GSM410685
| | Sample_status | Public on Sep 30 2009
| | Sample_submission_date | May 31 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410685/suppl/GSM410685.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410686 | GPL570 |
|
BEC KSHV 72h, rep3
|
blood vessel endothelial cells, KSHV-infected, 72h
|
cell type: blood vessel endothelial cell
infection: KSHV
|
Biological replicate 3 of 6.
|
| Sample_geo_accession | GSM410686
| | Sample_status | Public on Sep 30 2009
| | Sample_submission_date | May 31 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410686/suppl/GSM410686.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410687 | GPL570 |
|
BEC KSHV 72h, rep4
|
blood vessel endothelial cells, KSHV-infected, 72h
|
cell type: blood vessel endothelial cell
infection: KSHV
|
Biological replicate 4 of 6.
|
| Sample_geo_accession | GSM410687
| | Sample_status | Public on Sep 30 2009
| | Sample_submission_date | May 31 2009
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lymphatic endothelial cells (LECs) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410687/suppl/GSM410687.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410688 | GPL570 |
|
BEC KSHV 72h, rep5
|
blood vessel endothelial cells, KSHV-infected, 72h
|
cell type: blood vessel endothelial cell
infection: KSHV
|
Biological replicate 5 of 6.
|
| Sample_geo_accession | GSM410688
| | 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) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410688/suppl/GSM410688.CEL.gz
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
GSM410689 | GPL570 |
|
BEC KSHV 72h, rep6
|
blood vessel endothelial cells, KSHV-infected, 72h
|
cell type: blood vessel endothelial cell
infection: KSHV
|
Biological replicate 6 of 6.
|
| Sample_geo_accession | GSM410689
| | 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) and KSHV-infected LECs are cultured in 10-cm petri dishes till confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection cultures comprising of at least 45-50% GFP expressing LECs were used for RNA extraction.
| | Sample_growth_protocol_ch1 | Human lymphatic endothelial cells (LECs) and blood vessel endothelial cells (BEC) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker. Six batches of MVEC cells were isolated from 6 different donors 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-infected LEC and BEC 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/GSM410689/suppl/GSM410689.CEL.gz
| | Sample_series_id | GSE16354
| | Sample_series_id | GSE16357
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
