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Search results for the GEO ID: GSE22034

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GSM547760

GPL1261

Mouse_colon_BEC_rep1

Mouse, colon, normal, blood endothelial cells

strain: C57BL/6J gender: female age: 8 weeks tissue: colon cell type: blood vascular endothelial cells condition: normal, healthy cell isolation method: FACS

Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single-stranded cDNA. BEC_1

Sample_geo_accession	GSM547760
Sample_status	Public on Jun 16 2012
Sample_submission_date	May 27 2010
Sample_last_update_date	Jun 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Longitudinally opened mouse colons were washed in cold PBS and the mucus was gently scraped off in 1 mM DTT for 3 min. Colon pieces were incubated at 370C in 8 mg/ml collagenase IV (Invitrogen), 0.5 mg/ml DnaseI (Roche), and 5 mM CaCl2 in PBS for 15 min while rotating. Tissue suspensions were passed through a 70 µm cell strainer (BD Biosciences) while flushing with 2% FBS in PBS. Cell suspensions were centrifuged at 500 g for 10 min at RT and resuspended in PBS containing 2% FBS and 1 mM EDTA. The following antibodies were used for FACS: APC-conjugated rat anti-mouse CD31; FITC-conjugated rat anti-mouse CD45.2 (BD Biosciences); hamster anti-mouse podoplanin (clone 8.1.1) followed by anti-hamster PE-conjugated secondary antibody (Invitrogen); and isotype control antibodies (BD Biosciences). FACS was performed using a FACSAria and the FACSDiva software (BD Biosciences).
Sample_growth_protocol_ch1	Mice were maintained under conventional conditions.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells from mouse colon tissue were FACS sorted directly into RLT Plus lysis buffer (Qiagen) supplemented with β-mercaptoethanol at 4C, for immediate cell lysis and RNA preservation. Cells were lysed by vortexing for 1 min. RNeasy Micro Plus Kit (Qiagen) was used to extract total RNA according to manufacturer’s instructions. Note: gDNA eliminator column was used to eliminate genomic DNA. Extracted RNA was amplified using the Whole Transcriptome-Ovation Pico RNA Amplification System (NuGEN Technologies) according to the manufacturer’s instructions. Briefly, the primers had a DNA portion that hybridizes either to the 5’ portion of the poly (A) sequence or randomly across the transcript. SPIA amplification, a linear isothermal DNA amplification process, was used to prepare single-stranded cDNA in the antisense direction of the mRNA starting material. The quantity and quality of amplified cDNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies) and a Bioanalyzer 2100 (Agilent).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Single-stranded cDNA (4 μg) was fragmented and biotin-labeled using FL-Ovation cDNA Biotin Module V2 kit (NuGEN Technologies) according to the manufacturer’s instructions.
Sample_hyb_protocol	Biotin-labeled cDNA targets were mixed in 220 μl of Hybridization Mix (Affymetrix Inc.) containing hybridization controls and control oligonucleotide B2 (Affymetrix Inc.). Samples were hybridized to GeneChip Mouse Genome 430 2.0 arrays for 18h at 45°C. Arrays were washed using an Affymetrix Fluidics Station 450 FS450 0004 protocol.
Sample_scan_protocol	An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescence intensity emitted by the labeled target.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) as implemented in the BioConductor simpleaffy package using default parameters, in particular the trimmed mean target intensity of each array was set to 100. The data values in the Sample data table are Signal Log2 Values, as described in the Affymetrix Statistical Algorithms Description Document. They are calculated as Tukey bi-weight values from logged probe values. The chip description file used for summarization was the standard Affymetrix Mouse430_2 CDF file.
Sample_platform_id	GPL1261
Sample_contact_name	Giorgia,,Jurisic
Sample_contact_department	Institute of Pharmaceutical Sciences
Sample_contact_institute	ETH Zurich
Sample_contact_address	Wolfgang-Pauli Strasse 10
Sample_contact_city	Zurich
Sample_contact_zip/postal_code	8093
Sample_contact_country	Switzerland
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547760/suppl/GSM547760.CEL.gz
Sample_series_id	GSE22034
Sample_data_row_count	45101

GSM547761

GPL1261

Mouse_colon_LEC_rep1

Mouse, colon, normal, lymphatic endothelial cells

strain: C57BL/6J gender: female age: 8 weeks tissue: colon cell type: lymphatic endothelial cells condition: normal, healthy cell isolation method: FACS

Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single-stranded cDNA. LEC_1

Sample_geo_accession	GSM547761
Sample_status	Public on Jun 16 2012
Sample_submission_date	May 27 2010
Sample_last_update_date	Jun 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Longitudinally opened mouse colons were washed in cold PBS and the mucus was gently scraped off in 1 mM DTT for 3 min. Colon pieces were incubated at 370C in 8 mg/ml collagenase IV (Invitrogen), 0.5 mg/ml DnaseI (Roche), and 5 mM CaCl2 in PBS for 15 min while rotating. Tissue suspensions were passed through a 70 µm cell strainer (BD Biosciences) while flushing with 2% FBS in PBS. Cell suspensions were centrifuged at 500 g for 10 min at RT and resuspended in PBS containing 2% FBS and 1 mM EDTA. The following antibodies were used for FACS: APC-conjugated rat anti-mouse CD31; FITC-conjugated rat anti-mouse CD45.2 (BD Biosciences); hamster anti-mouse podoplanin (clone 8.1.1) followed by anti-hamster PE-conjugated secondary antibody (Invitrogen); and isotype control antibodies (BD Biosciences). FACS was performed using a FACSAria and the FACSDiva software (BD Biosciences).
Sample_growth_protocol_ch1	Mice were maintained under conventional conditions.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells from mouse colon tissue were FACS sorted directly into RLT Plus lysis buffer (Qiagen) supplemented with β-mercaptoethanol at 4C, for immediate cell lysis and RNA preservation. Cells were lysed by vortexing for 1 min. RNeasy Micro Plus Kit (Qiagen) was used to extract total RNA according to manufacturer’s instructions. Note: gDNA eliminator column was used to eliminate genomic DNA. Extracted RNA was amplified using the Whole Transcriptome-Ovation Pico RNA Amplification System (NuGEN Technologies) according to the manufacturer’s instructions. Briefly, the primers had a DNA portion that hybridizes either to the 5’ portion of the poly (A) sequence or randomly across the transcript. SPIA amplification, a linear isothermal DNA amplification process, was used to prepare single-stranded cDNA in the antisense direction of the mRNA starting material. The quantity and quality of amplified cDNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies) and a Bioanalyzer 2100 (Agilent).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Single-stranded cDNA (4 μg) was fragmented and biotin-labeled using FL-Ovation cDNA Biotin Module V2 kit (NuGEN Technologies) according to the manufacturer’s instructions.
Sample_hyb_protocol	Biotin-labeled cDNA targets were mixed in 220 μl of Hybridization Mix (Affymetrix Inc.) containing hybridization controls and control oligonucleotide B2 (Affymetrix Inc.). Samples were hybridized to GeneChip Mouse Genome 430 2.0 arrays for 18h at 45°C. Arrays were washed using an Affymetrix Fluidics Station 450 FS450 0004 protocol.
Sample_scan_protocol	An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescence intensity emitted by the labeled target.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) as implemented in the BioConductor simpleaffy package using default parameters, in particular the trimmed mean target intensity of each array was set to 100. The data values in the Sample data table are Signal Log2 Values, as described in the Affymetrix Statistical Algorithms Description Document. They are calculated as Tukey bi-weight values from logged probe values. The chip description file used for summarization was the standard Affymetrix Mouse430_2 CDF file.
Sample_platform_id	GPL1261
Sample_contact_name	Giorgia,,Jurisic
Sample_contact_department	Institute of Pharmaceutical Sciences
Sample_contact_institute	ETH Zurich
Sample_contact_address	Wolfgang-Pauli Strasse 10
Sample_contact_city	Zurich
Sample_contact_zip/postal_code	8093
Sample_contact_country	Switzerland
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547761/suppl/GSM547761.CEL.gz
Sample_series_id	GSE22034
Sample_data_row_count	45101

GSM547762

GPL1261

Mouse_colon_BEC_rep2

Mouse, colon, normal, blood endothelial cells

strain: C57BL/6J gender: female age: 8 weeks tissue: colon cell type: blood vascular endothelial cells condition: normal, healthy cell isolation method: FACS

Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single-stranded cDNA. BEC_2

Sample_geo_accession	GSM547762
Sample_status	Public on Jun 16 2012
Sample_submission_date	May 27 2010
Sample_last_update_date	Jun 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Longitudinally opened mouse colons were washed in cold PBS and the mucus was gently scraped off in 1 mM DTT for 3 min. Colon pieces were incubated at 370C in 8 mg/ml collagenase IV (Invitrogen), 0.5 mg/ml DnaseI (Roche), and 5 mM CaCl2 in PBS for 15 min while rotating. Tissue suspensions were passed through a 70 µm cell strainer (BD Biosciences) while flushing with 2% FBS in PBS. Cell suspensions were centrifuged at 500 g for 10 min at RT and resuspended in PBS containing 2% FBS and 1 mM EDTA. The following antibodies were used for FACS: APC-conjugated rat anti-mouse CD31; FITC-conjugated rat anti-mouse CD45.2 (BD Biosciences); hamster anti-mouse podoplanin (clone 8.1.1) followed by anti-hamster PE-conjugated secondary antibody (Invitrogen); and isotype control antibodies (BD Biosciences). FACS was performed using a FACSAria and the FACSDiva software (BD Biosciences).
Sample_growth_protocol_ch1	Mice were maintained under conventional conditions.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells from mouse colon tissue were FACS sorted directly into RLT Plus lysis buffer (Qiagen) supplemented with β-mercaptoethanol at 4C, for immediate cell lysis and RNA preservation. Cells were lysed by vortexing for 1 min. RNeasy Micro Plus Kit (Qiagen) was used to extract total RNA according to manufacturer’s instructions. Note: gDNA eliminator column was used to eliminate genomic DNA. Extracted RNA was amplified using the Whole Transcriptome-Ovation Pico RNA Amplification System (NuGEN Technologies) according to the manufacturer’s instructions. Briefly, the primers had a DNA portion that hybridizes either to the 5’ portion of the poly (A) sequence or randomly across the transcript. SPIA amplification, a linear isothermal DNA amplification process, was used to prepare single-stranded cDNA in the antisense direction of the mRNA starting material. The quantity and quality of amplified cDNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies) and a Bioanalyzer 2100 (Agilent).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Single-stranded cDNA (4 μg) was fragmented and biotin-labeled using FL-Ovation cDNA Biotin Module V2 kit (NuGEN Technologies) according to the manufacturer’s instructions.
Sample_hyb_protocol	Biotin-labeled cDNA targets were mixed in 220 μl of Hybridization Mix (Affymetrix Inc.) containing hybridization controls and control oligonucleotide B2 (Affymetrix Inc.). Samples were hybridized to GeneChip Mouse Genome 430 2.0 arrays for 18h at 45°C. Arrays were washed using an Affymetrix Fluidics Station 450 FS450 0004 protocol.
Sample_scan_protocol	An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescence intensity emitted by the labeled target.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) as implemented in the BioConductor simpleaffy package using default parameters, in particular the trimmed mean target intensity of each array was set to 100. The data values in the Sample data table are Signal Log2 Values, as described in the Affymetrix Statistical Algorithms Description Document. They are calculated as Tukey bi-weight values from logged probe values. The chip description file used for summarization was the standard Affymetrix Mouse430_2 CDF file.
Sample_platform_id	GPL1261
Sample_contact_name	Giorgia,,Jurisic
Sample_contact_department	Institute of Pharmaceutical Sciences
Sample_contact_institute	ETH Zurich
Sample_contact_address	Wolfgang-Pauli Strasse 10
Sample_contact_city	Zurich
Sample_contact_zip/postal_code	8093
Sample_contact_country	Switzerland
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547762/suppl/GSM547762.CEL.gz
Sample_series_id	GSE22034
Sample_data_row_count	45101

GSM547763

GPL1261

Mouse_colon_LEC_rep2

Mouse, colon, normal, lymphatic endothelial cells

strain: C57BL/6J gender: female age: 8 weeks tissue: colon cell type: lymphatic endothelial cells condition: normal, healthy cell isolation method: FACS

Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single-stranded cDNA. LEC_2

Sample_geo_accession	GSM547763
Sample_status	Public on Jun 16 2012
Sample_submission_date	May 27 2010
Sample_last_update_date	Jun 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Longitudinally opened mouse colons were washed in cold PBS and the mucus was gently scraped off in 1 mM DTT for 3 min. Colon pieces were incubated at 370C in 8 mg/ml collagenase IV (Invitrogen), 0.5 mg/ml DnaseI (Roche), and 5 mM CaCl2 in PBS for 15 min while rotating. Tissue suspensions were passed through a 70 µm cell strainer (BD Biosciences) while flushing with 2% FBS in PBS. Cell suspensions were centrifuged at 500 g for 10 min at RT and resuspended in PBS containing 2% FBS and 1 mM EDTA. The following antibodies were used for FACS: APC-conjugated rat anti-mouse CD31; FITC-conjugated rat anti-mouse CD45.2 (BD Biosciences); hamster anti-mouse podoplanin (clone 8.1.1) followed by anti-hamster PE-conjugated secondary antibody (Invitrogen); and isotype control antibodies (BD Biosciences). FACS was performed using a FACSAria and the FACSDiva software (BD Biosciences).
Sample_growth_protocol_ch1	Mice were maintained under conventional conditions.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells from mouse colon tissue were FACS sorted directly into RLT Plus lysis buffer (Qiagen) supplemented with β-mercaptoethanol at 4C, for immediate cell lysis and RNA preservation. Cells were lysed by vortexing for 1 min. RNeasy Micro Plus Kit (Qiagen) was used to extract total RNA according to manufacturer’s instructions. Note: gDNA eliminator column was used to eliminate genomic DNA. Extracted RNA was amplified using the Whole Transcriptome-Ovation Pico RNA Amplification System (NuGEN Technologies) according to the manufacturer’s instructions. Briefly, the primers had a DNA portion that hybridizes either to the 5’ portion of the poly (A) sequence or randomly across the transcript. SPIA amplification, a linear isothermal DNA amplification process, was used to prepare single-stranded cDNA in the antisense direction of the mRNA starting material. The quantity and quality of amplified cDNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies) and a Bioanalyzer 2100 (Agilent).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Single-stranded cDNA (4 μg) was fragmented and biotin-labeled using FL-Ovation cDNA Biotin Module V2 kit (NuGEN Technologies) according to the manufacturer’s instructions.
Sample_hyb_protocol	Biotin-labeled cDNA targets were mixed in 220 μl of Hybridization Mix (Affymetrix Inc.) containing hybridization controls and control oligonucleotide B2 (Affymetrix Inc.). Samples were hybridized to GeneChip Mouse Genome 430 2.0 arrays for 18h at 45°C. Arrays were washed using an Affymetrix Fluidics Station 450 FS450 0004 protocol.
Sample_scan_protocol	An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescence intensity emitted by the labeled target.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) as implemented in the BioConductor simpleaffy package using default parameters, in particular the trimmed mean target intensity of each array was set to 100. The data values in the Sample data table are Signal Log2 Values, as described in the Affymetrix Statistical Algorithms Description Document. They are calculated as Tukey bi-weight values from logged probe values. The chip description file used for summarization was the standard Affymetrix Mouse430_2 CDF file.
Sample_platform_id	GPL1261
Sample_contact_name	Giorgia,,Jurisic
Sample_contact_department	Institute of Pharmaceutical Sciences
Sample_contact_institute	ETH Zurich
Sample_contact_address	Wolfgang-Pauli Strasse 10
Sample_contact_city	Zurich
Sample_contact_zip/postal_code	8093
Sample_contact_country	Switzerland
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547763/suppl/GSM547763.CEL.gz
Sample_series_id	GSE22034
Sample_data_row_count	45101

GSM547764

GPL1261

Mouse_colon_BEC_rep3

Mouse, colon, normal, blood endothelial cells

strain: C57BL/6J gender: female age: 8 weeks tissue: colon cell type: blood vascular endothelial cells condition: normal, healthy cell isolation method: FACS

Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single-stranded cDNA. BEC_3

Sample_geo_accession	GSM547764
Sample_status	Public on Jun 16 2012
Sample_submission_date	May 27 2010
Sample_last_update_date	Jun 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Longitudinally opened mouse colons were washed in cold PBS and the mucus was gently scraped off in 1 mM DTT for 3 min. Colon pieces were incubated at 370C in 8 mg/ml collagenase IV (Invitrogen), 0.5 mg/ml DnaseI (Roche), and 5 mM CaCl2 in PBS for 15 min while rotating. Tissue suspensions were passed through a 70 µm cell strainer (BD Biosciences) while flushing with 2% FBS in PBS. Cell suspensions were centrifuged at 500 g for 10 min at RT and resuspended in PBS containing 2% FBS and 1 mM EDTA. The following antibodies were used for FACS: APC-conjugated rat anti-mouse CD31; FITC-conjugated rat anti-mouse CD45.2 (BD Biosciences); hamster anti-mouse podoplanin (clone 8.1.1) followed by anti-hamster PE-conjugated secondary antibody (Invitrogen); and isotype control antibodies (BD Biosciences). FACS was performed using a FACSAria and the FACSDiva software (BD Biosciences).
Sample_growth_protocol_ch1	Mice were maintained under conventional conditions.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells from mouse colon tissue were FACS sorted directly into RLT Plus lysis buffer (Qiagen) supplemented with β-mercaptoethanol at 4C, for immediate cell lysis and RNA preservation. Cells were lysed by vortexing for 1 min. RNeasy Micro Plus Kit (Qiagen) was used to extract total RNA according to manufacturer’s instructions. Note: gDNA eliminator column was used to eliminate genomic DNA. Extracted RNA was amplified using the Whole Transcriptome-Ovation Pico RNA Amplification System (NuGEN Technologies) according to the manufacturer’s instructions. Briefly, the primers had a DNA portion that hybridizes either to the 5’ portion of the poly (A) sequence or randomly across the transcript. SPIA amplification, a linear isothermal DNA amplification process, was used to prepare single-stranded cDNA in the antisense direction of the mRNA starting material. The quantity and quality of amplified cDNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies) and a Bioanalyzer 2100 (Agilent).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Single-stranded cDNA (4 μg) was fragmented and biotin-labeled using FL-Ovation cDNA Biotin Module V2 kit (NuGEN Technologies) according to the manufacturer’s instructions.
Sample_hyb_protocol	Biotin-labeled cDNA targets were mixed in 220 μl of Hybridization Mix (Affymetrix Inc.) containing hybridization controls and control oligonucleotide B2 (Affymetrix Inc.). Samples were hybridized to GeneChip Mouse Genome 430 2.0 arrays for 18h at 45°C. Arrays were washed using an Affymetrix Fluidics Station 450 FS450 0004 protocol.
Sample_scan_protocol	An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescence intensity emitted by the labeled target.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) as implemented in the BioConductor simpleaffy package using default parameters, in particular the trimmed mean target intensity of each array was set to 100. The data values in the Sample data table are Signal Log2 Values, as described in the Affymetrix Statistical Algorithms Description Document. They are calculated as Tukey bi-weight values from logged probe values. The chip description file used for summarization was the standard Affymetrix Mouse430_2 CDF file.
Sample_platform_id	GPL1261
Sample_contact_name	Giorgia,,Jurisic
Sample_contact_department	Institute of Pharmaceutical Sciences
Sample_contact_institute	ETH Zurich
Sample_contact_address	Wolfgang-Pauli Strasse 10
Sample_contact_city	Zurich
Sample_contact_zip/postal_code	8093
Sample_contact_country	Switzerland
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547764/suppl/GSM547764.CEL.gz
Sample_series_id	GSE22034
Sample_data_row_count	45101

GSM547765

GPL1261

Mouse_colon_LEC_rep3

Mouse, colon, normal, lymphatic endothelial cells

strain: C57BL/6J gender: female age: 8 weeks tissue: colon cell type: lymphatic endothelial cells condition: normal, healthy cell isolation method: FACS

Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single-stranded cDNA. LEC_3

Sample_geo_accession	GSM547765
Sample_status	Public on Jun 16 2012
Sample_submission_date	May 27 2010
Sample_last_update_date	Jun 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Longitudinally opened mouse colons were washed in cold PBS and the mucus was gently scraped off in 1 mM DTT for 3 min. Colon pieces were incubated at 370C in 8 mg/ml collagenase IV (Invitrogen), 0.5 mg/ml DnaseI (Roche), and 5 mM CaCl2 in PBS for 15 min while rotating. Tissue suspensions were passed through a 70 µm cell strainer (BD Biosciences) while flushing with 2% FBS in PBS. Cell suspensions were centrifuged at 500 g for 10 min at RT and resuspended in PBS containing 2% FBS and 1 mM EDTA. The following antibodies were used for FACS: APC-conjugated rat anti-mouse CD31; FITC-conjugated rat anti-mouse CD45.2 (BD Biosciences); hamster anti-mouse podoplanin (clone 8.1.1) followed by anti-hamster PE-conjugated secondary antibody (Invitrogen); and isotype control antibodies (BD Biosciences). FACS was performed using a FACSAria and the FACSDiva software (BD Biosciences).
Sample_growth_protocol_ch1	Mice were maintained under conventional conditions.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells from mouse colon tissue were FACS sorted directly into RLT Plus lysis buffer (Qiagen) supplemented with β-mercaptoethanol at 4C, for immediate cell lysis and RNA preservation. Cells were lysed by vortexing for 1 min. RNeasy Micro Plus Kit (Qiagen) was used to extract total RNA according to manufacturer’s instructions. Note: gDNA eliminator column was used to eliminate genomic DNA. Extracted RNA was amplified using the Whole Transcriptome-Ovation Pico RNA Amplification System (NuGEN Technologies) according to the manufacturer’s instructions. Briefly, the primers had a DNA portion that hybridizes either to the 5’ portion of the poly (A) sequence or randomly across the transcript. SPIA amplification, a linear isothermal DNA amplification process, was used to prepare single-stranded cDNA in the antisense direction of the mRNA starting material. The quantity and quality of amplified cDNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies) and a Bioanalyzer 2100 (Agilent).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Single-stranded cDNA (4 μg) was fragmented and biotin-labeled using FL-Ovation cDNA Biotin Module V2 kit (NuGEN Technologies) according to the manufacturer’s instructions.
Sample_hyb_protocol	Biotin-labeled cDNA targets were mixed in 220 μl of Hybridization Mix (Affymetrix Inc.) containing hybridization controls and control oligonucleotide B2 (Affymetrix Inc.). Samples were hybridized to GeneChip Mouse Genome 430 2.0 arrays for 18h at 45°C. Arrays were washed using an Affymetrix Fluidics Station 450 FS450 0004 protocol.
Sample_scan_protocol	An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescence intensity emitted by the labeled target.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) as implemented in the BioConductor simpleaffy package using default parameters, in particular the trimmed mean target intensity of each array was set to 100. The data values in the Sample data table are Signal Log2 Values, as described in the Affymetrix Statistical Algorithms Description Document. They are calculated as Tukey bi-weight values from logged probe values. The chip description file used for summarization was the standard Affymetrix Mouse430_2 CDF file.
Sample_platform_id	GPL1261
Sample_contact_name	Giorgia,,Jurisic
Sample_contact_department	Institute of Pharmaceutical Sciences
Sample_contact_institute	ETH Zurich
Sample_contact_address	Wolfgang-Pauli Strasse 10
Sample_contact_city	Zurich
Sample_contact_zip/postal_code	8093
Sample_contact_country	Switzerland
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547765/suppl/GSM547765.CEL.gz
Sample_series_id	GSE22034
Sample_data_row_count	45101

GSM547766

GPL1261

Mouse_colon_BEC_rep4

Mouse, colon, normal, blood endothelial cells

strain: C57BL/6J gender: male age: 8 weeks tissue: colon cell type: blood vascular endothelial cells condition: normal, healthy cell isolation method: FACS

Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single-stranded cDNA. BEC_4

Sample_geo_accession	GSM547766
Sample_status	Public on Jun 16 2012
Sample_submission_date	May 27 2010
Sample_last_update_date	Jun 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Longitudinally opened mouse colons were washed in cold PBS and the mucus was gently scraped off in 1 mM DTT for 3 min. Colon pieces were incubated at 370C in 8 mg/ml collagenase IV (Invitrogen), 0.5 mg/ml DnaseI (Roche), and 5 mM CaCl2 in PBS for 15 min while rotating. Tissue suspensions were passed through a 70 µm cell strainer (BD Biosciences) while flushing with 2% FBS in PBS. Cell suspensions were centrifuged at 500 g for 10 min at RT and resuspended in PBS containing 2% FBS and 1 mM EDTA. The following antibodies were used for FACS: APC-conjugated rat anti-mouse CD31; FITC-conjugated rat anti-mouse CD45.2 (BD Biosciences); hamster anti-mouse podoplanin (clone 8.1.1) followed by anti-hamster PE-conjugated secondary antibody (Invitrogen); and isotype control antibodies (BD Biosciences). FACS was performed using a FACSAria and the FACSDiva software (BD Biosciences).
Sample_growth_protocol_ch1	Mice were maintained under conventional conditions.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells from mouse colon tissue were FACS sorted directly into RLT Plus lysis buffer (Qiagen) supplemented with β-mercaptoethanol at 4C, for immediate cell lysis and RNA preservation. Cells were lysed by vortexing for 1 min. RNeasy Micro Plus Kit (Qiagen) was used to extract total RNA according to manufacturer’s instructions. Note: gDNA eliminator column was used to eliminate genomic DNA. Extracted RNA was amplified using the Whole Transcriptome-Ovation Pico RNA Amplification System (NuGEN Technologies) according to the manufacturer’s instructions. Briefly, the primers had a DNA portion that hybridizes either to the 5’ portion of the poly (A) sequence or randomly across the transcript. SPIA amplification, a linear isothermal DNA amplification process, was used to prepare single-stranded cDNA in the antisense direction of the mRNA starting material. The quantity and quality of amplified cDNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies) and a Bioanalyzer 2100 (Agilent).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Single-stranded cDNA (4 μg) was fragmented and biotin-labeled using FL-Ovation cDNA Biotin Module V2 kit (NuGEN Technologies) according to the manufacturer’s instructions.
Sample_hyb_protocol	Biotin-labeled cDNA targets were mixed in 220 μl of Hybridization Mix (Affymetrix Inc.) containing hybridization controls and control oligonucleotide B2 (Affymetrix Inc.). Samples were hybridized to GeneChip Mouse Genome 430 2.0 arrays for 18h at 45°C. Arrays were washed using an Affymetrix Fluidics Station 450 FS450 0004 protocol.
Sample_scan_protocol	An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescence intensity emitted by the labeled target.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) as implemented in the BioConductor simpleaffy package using default parameters, in particular the trimmed mean target intensity of each array was set to 100. The data values in the Sample data table are Signal Log2 Values, as described in the Affymetrix Statistical Algorithms Description Document. They are calculated as Tukey bi-weight values from logged probe values. The chip description file used for summarization was the standard Affymetrix Mouse430_2 CDF file.
Sample_platform_id	GPL1261
Sample_contact_name	Giorgia,,Jurisic
Sample_contact_department	Institute of Pharmaceutical Sciences
Sample_contact_institute	ETH Zurich
Sample_contact_address	Wolfgang-Pauli Strasse 10
Sample_contact_city	Zurich
Sample_contact_zip/postal_code	8093
Sample_contact_country	Switzerland
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547766/suppl/GSM547766.CEL.gz
Sample_series_id	GSE22034
Sample_data_row_count	45101

GSM547767

GPL1261

Mouse_colon_LEC_rep4

Mouse, colon, normal, lymphatic endothelial cells

strain: C57BL/6J gender: male age: 8 weeks tissue: colon cell type: lymphatic endothelial cells condition: normal, healthy cell isolation method: FACS

Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single-stranded cDNA. LEC_4

Sample_geo_accession	GSM547767
Sample_status	Public on Jun 16 2012
Sample_submission_date	May 27 2010
Sample_last_update_date	Jun 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Longitudinally opened mouse colons were washed in cold PBS and the mucus was gently scraped off in 1 mM DTT for 3 min. Colon pieces were incubated at 370C in 8 mg/ml collagenase IV (Invitrogen), 0.5 mg/ml DnaseI (Roche), and 5 mM CaCl2 in PBS for 15 min while rotating. Tissue suspensions were passed through a 70 µm cell strainer (BD Biosciences) while flushing with 2% FBS in PBS. Cell suspensions were centrifuged at 500 g for 10 min at RT and resuspended in PBS containing 2% FBS and 1 mM EDTA. The following antibodies were used for FACS: APC-conjugated rat anti-mouse CD31; FITC-conjugated rat anti-mouse CD45.2 (BD Biosciences); hamster anti-mouse podoplanin (clone 8.1.1) followed by anti-hamster PE-conjugated secondary antibody (Invitrogen); and isotype control antibodies (BD Biosciences). FACS was performed using a FACSAria and the FACSDiva software (BD Biosciences).
Sample_growth_protocol_ch1	Mice were maintained under conventional conditions.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cells from mouse colon tissue were FACS sorted directly into RLT Plus lysis buffer (Qiagen) supplemented with β-mercaptoethanol at 4C, for immediate cell lysis and RNA preservation. Cells were lysed by vortexing for 1 min. RNeasy Micro Plus Kit (Qiagen) was used to extract total RNA according to manufacturer’s instructions. Note: gDNA eliminator column was used to eliminate genomic DNA. Extracted RNA was amplified using the Whole Transcriptome-Ovation Pico RNA Amplification System (NuGEN Technologies) according to the manufacturer’s instructions. Briefly, the primers had a DNA portion that hybridizes either to the 5’ portion of the poly (A) sequence or randomly across the transcript. SPIA amplification, a linear isothermal DNA amplification process, was used to prepare single-stranded cDNA in the antisense direction of the mRNA starting material. The quantity and quality of amplified cDNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies) and a Bioanalyzer 2100 (Agilent).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Single-stranded cDNA (4 μg) was fragmented and biotin-labeled using FL-Ovation cDNA Biotin Module V2 kit (NuGEN Technologies) according to the manufacturer’s instructions.
Sample_hyb_protocol	Biotin-labeled cDNA targets were mixed in 220 μl of Hybridization Mix (Affymetrix Inc.) containing hybridization controls and control oligonucleotide B2 (Affymetrix Inc.). Samples were hybridized to GeneChip Mouse Genome 430 2.0 arrays for 18h at 45°C. Arrays were washed using an Affymetrix Fluidics Station 450 FS450 0004 protocol.
Sample_scan_protocol	An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescence intensity emitted by the labeled target.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) as implemented in the BioConductor simpleaffy package using default parameters, in particular the trimmed mean target intensity of each array was set to 100. The data values in the Sample data table are Signal Log2 Values, as described in the Affymetrix Statistical Algorithms Description Document. They are calculated as Tukey bi-weight values from logged probe values. The chip description file used for summarization was the standard Affymetrix Mouse430_2 CDF file.
Sample_platform_id	GPL1261
Sample_contact_name	Giorgia,,Jurisic
Sample_contact_department	Institute of Pharmaceutical Sciences
Sample_contact_institute	ETH Zurich
Sample_contact_address	Wolfgang-Pauli Strasse 10
Sample_contact_city	Zurich
Sample_contact_zip/postal_code	8093
Sample_contact_country	Switzerland
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM547nnn/GSM547767/suppl/GSM547767.CEL.gz
Sample_series_id	GSE22034
Sample_data_row_count	45101

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