Result

Search results for the GEO ID: GSE48444

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM1178818

GPL570

BPLER3_R3NX2

Primary tumor explants

tumorigenic cell type: BPLER host strain: NOD/SCID mice

R3NX2

Sample_geo_accession	GSM1178818
Sample_status	Public on Jul 02 2013
Sample_submission_date	Jul 01 2013
Sample_last_update_date	Jul 02 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	No treatment
Sample_growth_protocol_ch1	Cells injected in matrigel in immunocompromised mice
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The standard protocols followed were per Affymetrix’s instructions (Genechip Expression Analysis Technical Manual 701021 Rev 4). Briefly, total RNA was isolated from tumors using Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s instructions. The RNA pellet was resuspended in 100 ul of RNAse free water. The RNeasy Clean-up kit (Qiagen, Valencia, CA) was utilized per manufacturer’s instructions resulting in 30 ul total RNA sample. The total RNA concentration and 260/280 ratio was evaluated on a NanoDrop ND- 1000 UV-Vis Spectrophotomter (NanoDrop Technologies, Rockland, DE). Only samples with a 260/280 ratio greater than 1.9 were further processed. An aliquot of 1 ul from each of the samples was diluted to be within the dynamic range of the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto, CA), with a target of 100 ng. The Nano Labchip protocol was followed as per manufacturer’s instructions and was placed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for evaluation. Samples with the highest concentration, only 2 distinct 18 S and 28 S peaks, and no evidence of degradation were further processed. Six hundred units of SuperScript II reverse transcriptase were used for the first strand cDNA synthesis reaction. The second strand DNA synthesis, the clean-up of the double-stranded cDNA, the synthesis of the biotin-labeled cRNA, and the clean-up of the biotin-labeled cRNA were per Affymetrix instructions. The Genechip Sample Cleanup module was used for the clean-up steps of the double stranded cDNA and the biotin-labeled cRNA. Quantification of the cRNA was evaluated on the NanoDrop.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	As per Affymetrix instructions
Sample_hyb_protocol	Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
Sample_scan_protocol	The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
Sample_data_processing	MAS5, R (v.2.15.2)/Bioconductor (v.2.11)
Sample_platform_id	GPL570
Sample_contact_name	Tan,A,Ince
Sample_contact_email	TInce@med.miami.edu
Sample_contact_department	Department of Pathology
Sample_contact_institute	Interdisciplinary Stem Cell Institute and Braman Family Breast Cancer Institute, Miller School of Medicine, University of Miami
Sample_contact_address	1501 NW 10th Avenue, Suite 913
Sample_contact_city	Miami
Sample_contact_state	FL
Sample_contact_zip/postal_code	33136
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178818/suppl/GSM1178818_AR2006011301.CEL.gz
Sample_series_id	GSE48444
Sample_data_row_count	54675

GSM1178819

GPL570

BPLER3_R3NX3

Primary tumor explants

tumorigenic cell type: BPLER host strain: NOD/SCID mice

R3NX3

Sample_geo_accession	GSM1178819
Sample_status	Public on Jul 02 2013
Sample_submission_date	Jul 01 2013
Sample_last_update_date	Jul 02 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	No treatment
Sample_growth_protocol_ch1	Cells injected in matrigel in immunocompromised mice
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The standard protocols followed were per Affymetrix’s instructions (Genechip Expression Analysis Technical Manual 701021 Rev 4). Briefly, total RNA was isolated from tumors using Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s instructions. The RNA pellet was resuspended in 100 ul of RNAse free water. The RNeasy Clean-up kit (Qiagen, Valencia, CA) was utilized per manufacturer’s instructions resulting in 30 ul total RNA sample. The total RNA concentration and 260/280 ratio was evaluated on a NanoDrop ND- 1000 UV-Vis Spectrophotomter (NanoDrop Technologies, Rockland, DE). Only samples with a 260/280 ratio greater than 1.9 were further processed. An aliquot of 1 ul from each of the samples was diluted to be within the dynamic range of the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto, CA), with a target of 100 ng. The Nano Labchip protocol was followed as per manufacturer’s instructions and was placed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for evaluation. Samples with the highest concentration, only 2 distinct 18 S and 28 S peaks, and no evidence of degradation were further processed. Six hundred units of SuperScript II reverse transcriptase were used for the first strand cDNA synthesis reaction. The second strand DNA synthesis, the clean-up of the double-stranded cDNA, the synthesis of the biotin-labeled cRNA, and the clean-up of the biotin-labeled cRNA were per Affymetrix instructions. The Genechip Sample Cleanup module was used for the clean-up steps of the double stranded cDNA and the biotin-labeled cRNA. Quantification of the cRNA was evaluated on the NanoDrop.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	As per Affymetrix instructions
Sample_hyb_protocol	Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
Sample_scan_protocol	The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
Sample_data_processing	MAS5, R (v.2.15.2)/Bioconductor (v.2.11)
Sample_platform_id	GPL570
Sample_contact_name	Tan,A,Ince
Sample_contact_email	TInce@med.miami.edu
Sample_contact_department	Department of Pathology
Sample_contact_institute	Interdisciplinary Stem Cell Institute and Braman Family Breast Cancer Institute, Miller School of Medicine, University of Miami
Sample_contact_address	1501 NW 10th Avenue, Suite 913
Sample_contact_city	Miami
Sample_contact_state	FL
Sample_contact_zip/postal_code	33136
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178819/suppl/GSM1178819_AR2006011302.CEL.gz
Sample_series_id	GSE48444
Sample_data_row_count	54675

GSM1178820

GPL570

BPLER3_R3NX4

Primary tumor explants

tumorigenic cell type: BPLER host strain: NOD/SCID mice

R3NX4

Sample_geo_accession	GSM1178820
Sample_status	Public on Jul 02 2013
Sample_submission_date	Jul 01 2013
Sample_last_update_date	Jul 02 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	No treatment
Sample_growth_protocol_ch1	Cells injected in matrigel in immunocompromised mice
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The standard protocols followed were per Affymetrix’s instructions (Genechip Expression Analysis Technical Manual 701021 Rev 4). Briefly, total RNA was isolated from tumors using Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s instructions. The RNA pellet was resuspended in 100 ul of RNAse free water. The RNeasy Clean-up kit (Qiagen, Valencia, CA) was utilized per manufacturer’s instructions resulting in 30 ul total RNA sample. The total RNA concentration and 260/280 ratio was evaluated on a NanoDrop ND- 1000 UV-Vis Spectrophotomter (NanoDrop Technologies, Rockland, DE). Only samples with a 260/280 ratio greater than 1.9 were further processed. An aliquot of 1 ul from each of the samples was diluted to be within the dynamic range of the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto, CA), with a target of 100 ng. The Nano Labchip protocol was followed as per manufacturer’s instructions and was placed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for evaluation. Samples with the highest concentration, only 2 distinct 18 S and 28 S peaks, and no evidence of degradation were further processed. Six hundred units of SuperScript II reverse transcriptase were used for the first strand cDNA synthesis reaction. The second strand DNA synthesis, the clean-up of the double-stranded cDNA, the synthesis of the biotin-labeled cRNA, and the clean-up of the biotin-labeled cRNA were per Affymetrix instructions. The Genechip Sample Cleanup module was used for the clean-up steps of the double stranded cDNA and the biotin-labeled cRNA. Quantification of the cRNA was evaluated on the NanoDrop.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	As per Affymetrix instructions
Sample_hyb_protocol	Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
Sample_scan_protocol	The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
Sample_data_processing	MAS5, R (v.2.15.2)/Bioconductor (v.2.11)
Sample_platform_id	GPL570
Sample_contact_name	Tan,A,Ince
Sample_contact_email	TInce@med.miami.edu
Sample_contact_department	Department of Pathology
Sample_contact_institute	Interdisciplinary Stem Cell Institute and Braman Family Breast Cancer Institute, Miller School of Medicine, University of Miami
Sample_contact_address	1501 NW 10th Avenue, Suite 913
Sample_contact_city	Miami
Sample_contact_state	FL
Sample_contact_zip/postal_code	33136
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178820/suppl/GSM1178820_AR2006011303.CEL.gz
Sample_series_id	GSE48444
Sample_data_row_count	54675

GSM1178821

GPL570

BPLER3_R3NX4C

Primary tumor explants

tumorigenic cell type: BPLER host strain: NOD/SCID mice

R3NX4C

Sample_geo_accession	GSM1178821
Sample_status	Public on Jul 02 2013
Sample_submission_date	Jul 01 2013
Sample_last_update_date	Jul 02 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	No treatment
Sample_growth_protocol_ch1	Cells injected in matrigel in immunocompromised mice
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The standard protocols followed were per Affymetrix’s instructions (Genechip Expression Analysis Technical Manual 701021 Rev 4). Briefly, total RNA was isolated from tumors using Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s instructions. The RNA pellet was resuspended in 100 ul of RNAse free water. The RNeasy Clean-up kit (Qiagen, Valencia, CA) was utilized per manufacturer’s instructions resulting in 30 ul total RNA sample. The total RNA concentration and 260/280 ratio was evaluated on a NanoDrop ND- 1000 UV-Vis Spectrophotomter (NanoDrop Technologies, Rockland, DE). Only samples with a 260/280 ratio greater than 1.9 were further processed. An aliquot of 1 ul from each of the samples was diluted to be within the dynamic range of the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto, CA), with a target of 100 ng. The Nano Labchip protocol was followed as per manufacturer’s instructions and was placed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for evaluation. Samples with the highest concentration, only 2 distinct 18 S and 28 S peaks, and no evidence of degradation were further processed. Six hundred units of SuperScript II reverse transcriptase were used for the first strand cDNA synthesis reaction. The second strand DNA synthesis, the clean-up of the double-stranded cDNA, the synthesis of the biotin-labeled cRNA, and the clean-up of the biotin-labeled cRNA were per Affymetrix instructions. The Genechip Sample Cleanup module was used for the clean-up steps of the double stranded cDNA and the biotin-labeled cRNA. Quantification of the cRNA was evaluated on the NanoDrop.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	As per Affymetrix instructions
Sample_hyb_protocol	Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
Sample_scan_protocol	The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
Sample_data_processing	MAS5, R (v.2.15.2)/Bioconductor (v.2.11)
Sample_platform_id	GPL570
Sample_contact_name	Tan,A,Ince
Sample_contact_email	TInce@med.miami.edu
Sample_contact_department	Department of Pathology
Sample_contact_institute	Interdisciplinary Stem Cell Institute and Braman Family Breast Cancer Institute, Miller School of Medicine, University of Miami
Sample_contact_address	1501 NW 10th Avenue, Suite 913
Sample_contact_city	Miami
Sample_contact_state	FL
Sample_contact_zip/postal_code	33136
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178821/suppl/GSM1178821_AR2006011304.CEL.gz
Sample_series_id	GSE48444
Sample_data_row_count	54675

GSM1178822

GPL570

BPLER2_R2NX

Primary tumor explants

tumorigenic cell type: BPLER host strain: NOD/SCID mice

R2NX

Sample_geo_accession	GSM1178822
Sample_status	Public on Jul 02 2013
Sample_submission_date	Jul 01 2013
Sample_last_update_date	Jul 02 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	No treatment
Sample_growth_protocol_ch1	Cells injected in matrigel in immunocompromised mice
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The standard protocols followed were per Affymetrix’s instructions (Genechip Expression Analysis Technical Manual 701021 Rev 4). Briefly, total RNA was isolated from tumors using Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s instructions. The RNA pellet was resuspended in 100 ul of RNAse free water. The RNeasy Clean-up kit (Qiagen, Valencia, CA) was utilized per manufacturer’s instructions resulting in 30 ul total RNA sample. The total RNA concentration and 260/280 ratio was evaluated on a NanoDrop ND- 1000 UV-Vis Spectrophotomter (NanoDrop Technologies, Rockland, DE). Only samples with a 260/280 ratio greater than 1.9 were further processed. An aliquot of 1 ul from each of the samples was diluted to be within the dynamic range of the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto, CA), with a target of 100 ng. The Nano Labchip protocol was followed as per manufacturer’s instructions and was placed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for evaluation. Samples with the highest concentration, only 2 distinct 18 S and 28 S peaks, and no evidence of degradation were further processed. Six hundred units of SuperScript II reverse transcriptase were used for the first strand cDNA synthesis reaction. The second strand DNA synthesis, the clean-up of the double-stranded cDNA, the synthesis of the biotin-labeled cRNA, and the clean-up of the biotin-labeled cRNA were per Affymetrix instructions. The Genechip Sample Cleanup module was used for the clean-up steps of the double stranded cDNA and the biotin-labeled cRNA. Quantification of the cRNA was evaluated on the NanoDrop.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	As per Affymetrix instructions
Sample_hyb_protocol	Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
Sample_scan_protocol	The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
Sample_data_processing	MAS5, R (v.2.15.2)/Bioconductor (v.2.11)
Sample_platform_id	GPL570
Sample_contact_name	Tan,A,Ince
Sample_contact_email	TInce@med.miami.edu
Sample_contact_department	Department of Pathology
Sample_contact_institute	Interdisciplinary Stem Cell Institute and Braman Family Breast Cancer Institute, Miller School of Medicine, University of Miami
Sample_contact_address	1501 NW 10th Avenue, Suite 913
Sample_contact_city	Miami
Sample_contact_state	FL
Sample_contact_zip/postal_code	33136
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178822/suppl/GSM1178822_AR2006011305.CEL.gz
Sample_series_id	GSE48444
Sample_data_row_count	54675

GSM1178823

GPL570

BPLER2_R2NX3

Primary tumor explants

tumorigenic cell type: BPLER host strain: NOD/SCID mice

R2NX3

Sample_geo_accession	GSM1178823
Sample_status	Public on Jul 02 2013
Sample_submission_date	Jul 01 2013
Sample_last_update_date	Jul 02 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	No treatment
Sample_growth_protocol_ch1	Cells injected in matrigel in immunocompromised mice
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The standard protocols followed were per Affymetrix’s instructions (Genechip Expression Analysis Technical Manual 701021 Rev 4). Briefly, total RNA was isolated from tumors using Trizol (Invitrogen, Carlsbad, CA) as per manufacturer’s instructions. The RNA pellet was resuspended in 100 ul of RNAse free water. The RNeasy Clean-up kit (Qiagen, Valencia, CA) was utilized per manufacturer’s instructions resulting in 30 ul total RNA sample. The total RNA concentration and 260/280 ratio was evaluated on a NanoDrop ND- 1000 UV-Vis Spectrophotomter (NanoDrop Technologies, Rockland, DE). Only samples with a 260/280 ratio greater than 1.9 were further processed. An aliquot of 1 ul from each of the samples was diluted to be within the dynamic range of the Agilent RNA 6000 Nano Labchip kit (Agilent, Palo Alto, CA), with a target of 100 ng. The Nano Labchip protocol was followed as per manufacturer’s instructions and was placed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) for evaluation. Samples with the highest concentration, only 2 distinct 18 S and 28 S peaks, and no evidence of degradation were further processed. Six hundred units of SuperScript II reverse transcriptase were used for the first strand cDNA synthesis reaction. The second strand DNA synthesis, the clean-up of the double-stranded cDNA, the synthesis of the biotin-labeled cRNA, and the clean-up of the biotin-labeled cRNA were per Affymetrix instructions. The Genechip Sample Cleanup module was used for the clean-up steps of the double stranded cDNA and the biotin-labeled cRNA. Quantification of the cRNA was evaluated on the NanoDrop.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	As per Affymetrix instructions
Sample_hyb_protocol	Fragmentation, hybridization, washing, staining, and scanning were done according to the Affymetrix protocol. Briefly, reagent preparation included 12X MES stock (1.22 M MES, 0.89 M [Na+]) and 2X hybridization buffer (1X hybridization buffer: 100mMMES, 1M[Na+], 20mMEDTA, 0.01% Tween 20). The hybridization cocktail components and final concentrations consisted of fragmented cDNA (.05 µg/µl), control oligonucleotide B2 (50 pM), 20X eukaryotic hybridization controls bioB, bioC, bioD, and cre (1.5, 5, 25, 100 pM, respectively), herring sperm DNA(.1 mg/ml), acetylated BSA (.5 mg/ml), 1X hybridization buffer with a final volume of 300 µl. The GeneChip array was filled with 250 µl of the hybridization cocktail and hybridized for 16 hours, rotated at 60 RPM, and maintained at 45C. Reagents prepared for washing and staining included a nonstringent wash buffer (6X SSPE, .01% Tween 20), a stringent wash buffer (100mMMES, 0.1M[Na+], 0.01% Tween 20), and a 2X stain buffer (1X: 100 mM MES, 1 M [Na+], 0.05% Tween 20). The wash procedure was carried out in an Affymetrix Fluidics Station 400 controlled by Affymetrix Microarray Suite 5.0 software resident on a personal computer. The fluidics station first went through a priming step and subsequently did the washing and staining by a software protocol.
Sample_scan_protocol	The microarrays were scanned using the GeneArray scanner per manufacturer’s instructions (Affymetrix, Santa Clara, CA). The quality control algorithms for eliminating an array are based on recommendations in both the Affymetrix and dChip software packages.
Sample_data_processing	MAS5, R (v.2.15.2)/Bioconductor (v.2.11)
Sample_platform_id	GPL570
Sample_contact_name	Tan,A,Ince
Sample_contact_email	TInce@med.miami.edu
Sample_contact_department	Department of Pathology
Sample_contact_institute	Interdisciplinary Stem Cell Institute and Braman Family Breast Cancer Institute, Miller School of Medicine, University of Miami
Sample_contact_address	1501 NW 10th Avenue, Suite 913
Sample_contact_city	Miami
Sample_contact_state	FL
Sample_contact_zip/postal_code	33136
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1178nnn/GSM1178823/suppl/GSM1178823_AR2006011323.CEL.gz
Sample_series_id	GSE48444
Sample_data_row_count	54675

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