Result

Search results for the GEO ID: GSE16547

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Title

Source name

Description

Characteristics

GSM415804

GPL570

pSin_1

lymphatic endothelial cells (pSin co-culture)

co-culture: lymphatic endothelial cells co-culture vector: pSin

VE2.CEL

Sample_geo_accession	GSM415804
Sample_status	Public on Dec 01 2009
Sample_submission_date	Jun 10 2009
Sample_last_update_date	Jun 11 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Lymphatic endothelial cells (LEC) were plated in six well plates (1x10^5cells/well) overnight. The cells were infected with lentivirus expressing empty vector (pSIN), Dll4, or JAG1 to equivalent levels. After 72 hours, cells were trypsinized, counted and plated in triplicate in 10cm dishes with uninfected LEC stained with CellTracker™ Green CMFDA (Invitrogen) at a ratio of 1:3. Cells were co-cultured for 60hrs before being trypsinised and sorted. Green cells were sorted directly into Qiazol reagent (Qiagen) for RNA extraction. One 10cm dish was 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 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	Qiazol 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 synthesis, in vitro transcription was carried out 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 according to the manufacturers' protocol (http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf).
Sample_data_processing	Data was preprocessed and normalized using the Bioconductor 'affy' package, specifically the robust multiarray ('rma') algorithm was used.
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/GSM415nnn/GSM415804/suppl/GSM415804.CEL.gz
Sample_series_id	GSE16547
Sample_data_row_count	54675

GSM415805

GPL570

pSin_2

lymphatic endothelial cells (pSin co-culture)

co-culture: lymphatic endothelial cells co-culture vector: pSin

VE3.CEL

Sample_geo_accession	GSM415805
Sample_status	Public on Dec 01 2009
Sample_submission_date	Jun 10 2009
Sample_last_update_date	Jun 11 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Lymphatic endothelial cells (LEC) were plated in six well plates (1x10^5cells/well) overnight. The cells were infected with lentivirus expressing empty vector (pSIN), Dll4, or JAG1 to equivalent levels. After 72 hours, cells were trypsinized, counted and plated in triplicate in 10cm dishes with uninfected LEC stained with CellTracker™ Green CMFDA (Invitrogen) at a ratio of 1:3. Cells were co-cultured for 60hrs before being trypsinised and sorted. Green cells were sorted directly into Qiazol reagent (Qiagen) for RNA extraction. One 10cm dish was 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 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	Qiazol 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 synthesis, in vitro transcription was carried out 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 according to the manufacturers' protocol (http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf).
Sample_data_processing	Data was preprocessed and normalized using the Bioconductor 'affy' package, specifically the robust multiarray ('rma') algorithm was used.
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/GSM415nnn/GSM415805/suppl/GSM415805.CEL.gz
Sample_series_id	GSE16547
Sample_data_row_count	54675

GSM415806

GPL570

DLL4_1

lymphatic endothelial cells (pSin-DLL4 co-culture)

co-culture: lymphatic endothelial cells co-culture vector: pSin-DLL4

VE4.CEL

Sample_geo_accession	GSM415806
Sample_status	Public on Dec 01 2009
Sample_submission_date	Jun 10 2009
Sample_last_update_date	Jun 11 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Lymphatic endothelial cells (LEC) were plated in six well plates (1x10^5cells/well) overnight. The cells were infected with lentivirus expressing empty vector (pSIN), Dll4, or JAG1 to equivalent levels. After 72 hours, cells were trypsinized, counted and plated in triplicate in 10cm dishes with uninfected LEC stained with CellTracker™ Green CMFDA (Invitrogen) at a ratio of 1:3. Cells were co-cultured for 60hrs before being trypsinised and sorted. Green cells were sorted directly into Qiazol reagent (Qiagen) for RNA extraction. One 10cm dish was 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 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	Qiazol 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 synthesis, in vitro transcription was carried out 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 according to the manufacturers' protocol (http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf).
Sample_data_processing	Data was preprocessed and normalized using the Bioconductor 'affy' package, specifically the robust multiarray ('rma') algorithm was used.
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/GSM415nnn/GSM415806/suppl/GSM415806.CEL.gz
Sample_series_id	GSE16547
Sample_data_row_count	54675

GSM415807

GPL570

DLL4_2

lymphatic endothelial cells (pSin-DLL4 co-culture)

co-culture: lymphatic endothelial cells co-culture vector: pSin-DLL4

VE5.CEL

Sample_geo_accession	GSM415807
Sample_status	Public on Dec 01 2009
Sample_submission_date	Jun 10 2009
Sample_last_update_date	Jun 11 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Lymphatic endothelial cells (LEC) were plated in six well plates (1x10^5cells/well) overnight. The cells were infected with lentivirus expressing empty vector (pSIN), Dll4, or JAG1 to equivalent levels. After 72 hours, cells were trypsinized, counted and plated in triplicate in 10cm dishes with uninfected LEC stained with CellTracker™ Green CMFDA (Invitrogen) at a ratio of 1:3. Cells were co-cultured for 60hrs before being trypsinised and sorted. Green cells were sorted directly into Qiazol reagent (Qiagen) for RNA extraction. One 10cm dish was 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 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	Qiazol 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 synthesis, in vitro transcription was carried out 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 according to the manufacturers' protocol (http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf).
Sample_data_processing	Data was preprocessed and normalized using the Bioconductor 'affy' package, specifically the robust multiarray ('rma') algorithm was used.
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/GSM415nnn/GSM415807/suppl/GSM415807.CEL.gz
Sample_series_id	GSE16547
Sample_data_row_count	54675

GSM415808

GPL570

DLL4_3

lymphatic endothelial cells (pSin-DLL4 co-culture)

co-culture: lymphatic endothelial cells co-culture vector: pSin-DLL4

VE6.CEL

Sample_geo_accession	GSM415808
Sample_status	Public on Dec 01 2009
Sample_submission_date	Jun 10 2009
Sample_last_update_date	Jun 11 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Lymphatic endothelial cells (LEC) were plated in six well plates (1x10^5cells/well) overnight. The cells were infected with lentivirus expressing empty vector (pSIN), Dll4, or JAG1 to equivalent levels. After 72 hours, cells were trypsinized, counted and plated in triplicate in 10cm dishes with uninfected LEC stained with CellTracker™ Green CMFDA (Invitrogen) at a ratio of 1:3. Cells were co-cultured for 60hrs before being trypsinised and sorted. Green cells were sorted directly into Qiazol reagent (Qiagen) for RNA extraction. One 10cm dish was 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 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	Qiazol 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 synthesis, in vitro transcription was carried out 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 according to the manufacturers' protocol (http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf).
Sample_data_processing	Data was preprocessed and normalized using the Bioconductor 'affy' package, specifically the robust multiarray ('rma') algorithm was used.
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/GSM415nnn/GSM415808/suppl/GSM415808.CEL.gz
Sample_series_id	GSE16547
Sample_data_row_count	54675

GSM415809

GPL570

JAG1_1

lymphatic endothelial cells (pSin-JAG1 co-culture)

co-culture: lymphatic endothelial cells co-culture vector: pSin-JAG1

VE7.CEL

Sample_geo_accession	GSM415809
Sample_status	Public on Dec 01 2009
Sample_submission_date	Jun 10 2009
Sample_last_update_date	Jun 11 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Lymphatic endothelial cells (LEC) were plated in six well plates (1x10^5cells/well) overnight. The cells were infected with lentivirus expressing empty vector (pSIN), Dll4, or JAG1 to equivalent levels. After 72 hours, cells were trypsinized, counted and plated in triplicate in 10cm dishes with uninfected LEC stained with CellTracker™ Green CMFDA (Invitrogen) at a ratio of 1:3. Cells were co-cultured for 60hrs before being trypsinised and sorted. Green cells were sorted directly into Qiazol reagent (Qiagen) for RNA extraction. One 10cm dish was 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 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	Qiazol 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 synthesis, in vitro transcription was carried out 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 according to the manufacturers' protocol (http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf).
Sample_data_processing	Data was preprocessed and normalized using the Bioconductor 'affy' package, specifically the robust multiarray ('rma') algorithm was used.
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/GSM415nnn/GSM415809/suppl/GSM415809.CEL.gz
Sample_series_id	GSE16547
Sample_data_row_count	54675

GSM415810

GPL570

JAG1_2

lymphatic endothelial cells (pSin-JAG1 co-culture)

co-culture: lymphatic endothelial cells co-culture vector: pSin-JAG1

VE8.CEL

Sample_geo_accession	GSM415810
Sample_status	Public on Dec 01 2009
Sample_submission_date	Jun 10 2009
Sample_last_update_date	Jun 11 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Lymphatic endothelial cells (LEC) were plated in six well plates (1x10^5cells/well) overnight. The cells were infected with lentivirus expressing empty vector (pSIN), Dll4, or JAG1 to equivalent levels. After 72 hours, cells were trypsinized, counted and plated in triplicate in 10cm dishes with uninfected LEC stained with CellTracker™ Green CMFDA (Invitrogen) at a ratio of 1:3. Cells were co-cultured for 60hrs before being trypsinised and sorted. Green cells were sorted directly into Qiazol reagent (Qiagen) for RNA extraction. One 10cm dish was 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 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	Qiazol 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 synthesis, in vitro transcription was carried out 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 according to the manufacturers' protocol (http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf).
Sample_data_processing	Data was preprocessed and normalized using the Bioconductor 'affy' package, specifically the robust multiarray ('rma') algorithm was used.
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/GSM415nnn/GSM415810/suppl/GSM415810.CEL.gz
Sample_series_id	GSE16547
Sample_data_row_count	54675

GSM415811

GPL570

JAG1_3

lymphatic endothelial cells (pSin-JAG1 co-culture)

co-culture: lymphatic endothelial cells co-culture vector: pSin-JAG1

VE9.CEL

Sample_geo_accession	GSM415811
Sample_status	Public on Dec 01 2009
Sample_submission_date	Jun 10 2009
Sample_last_update_date	Jun 11 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Lymphatic endothelial cells (LEC) were plated in six well plates (1x10^5cells/well) overnight. The cells were infected with lentivirus expressing empty vector (pSIN), Dll4, or JAG1 to equivalent levels. After 72 hours, cells were trypsinized, counted and plated in triplicate in 10cm dishes with uninfected LEC stained with CellTracker™ Green CMFDA (Invitrogen) at a ratio of 1:3. Cells were co-cultured for 60hrs before being trypsinised and sorted. Green cells were sorted directly into Qiazol reagent (Qiagen) for RNA extraction. One 10cm dish was 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 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	Qiazol 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 synthesis, in vitro transcription was carried out 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 according to the manufacturers' protocol (http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf).
Sample_data_processing	Data was preprocessed and normalized using the Bioconductor 'affy' package, specifically the robust multiarray ('rma') algorithm was used.
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/GSM415nnn/GSM415811/suppl/GSM415811.CEL.gz
Sample_series_id	GSE16547
Sample_data_row_count	54675

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