Search results for the GEO ID: GSE35830  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM875816 | GPL570 |
|
control replicate 1
|
Ect1 cells
|
treatment: medium alone
cell line: Ect1
treatment time: 10 h
|
|
| Sample_geo_accession | GSM875816
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 14 2012
| | Sample_last_update_date | Feb 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Quadruplicates wells containing 1 x 10^5 cells in 500 µl of KSFM in 1.5 ml culture wells (Nunc) were incubated at 37 C/5% CO2 for 2-3 days to generate a confluent monolayer, then the medium was replaced with 500 µl of KSFM containing TGFβ3 (5 ng/ml), 10% pooled human seminal plasma (v/v), or medium alone for 10h before termination of the experiment and extraction of mRNA.
| | Sample_growth_protocol_ch1 | Ect1 cells were propagated in keratinocyte serum–free media (Gibco, Mount Waverley, Australia) supplemented with 0.1 ng/ml rhEGF (Gibco), 0.05 mg/ml bovine pituitary extract (Gibco) and 0.4 mM CaCl2 (KSFM).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from Ect1 cells using Trizol® (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions, and purified using RNeasy micro kits (Qiagen, Doncaster, Australia). Prior to hybridization, RNA underwent further purification using RNeasy Mini Spin columns (Qiagen, Valencia, CA, USA) and eluted into RNAse-free milli-Q water according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.
| | Sample_hyb_protocol | Genechips were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.
| | Sample_scan_protocol | Genechips were scanned using the Affymetrix GSC3000 scanner.
| | Sample_data_processing | RNA integrity analysis, hybridization and washing were performed according to the manufacturer’s instructions. GCOS 1.4 software (Affymetrix) using MAS 5.0 was used to generate CEL files for each chip. Quality control was assessed using the affyQCreport package in R (v2.6.1). The array data was initially examined using Partek Genomics Suite (Partek Inc, MO), after CEL files were imported using RMA background correction, GC content correction, and mean probe summarization, to generate dendrogram hierarchical clustering analysis and principal components analysis (PCA). Non-log2 transformed expression values for each chip were submitted to IlluminaGUI (free software implemented by R 2.6.1) after substituting Illumina probe IDs for Affymetrix IDs. Two contrasts were analysed; seminal plasma versus control, and TGFβ3 versus control. In both cases, differentially expressed probes were identified using default high stringency parameters (≥2.0-fold change, t-test p <0.05, >100 difference between mean expression intensity). The Kyoto Encyclopedia of Genes and Genomics (KEGG) database and Pathway Express and OntoExpress analysis software were utilized to assign genes to cytokine–cytokine receptor interaction, TGFβ signalling, JAK/STAT signalling or VEGF signalling pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,Anne,Robertson
| | Sample_contact_email | sarah.robertson@adelaide.edu.au
| | Sample_contact_phone | 61 8 83034094
| | Sample_contact_fax | 61 8 8303 4099
| | Sample_contact_laboratory | Reproductive Immunology
| | Sample_contact_department | paediatrics and Reproductive Health
| | Sample_contact_institute | University of Adelaide
| | Sample_contact_address | Frome Rd
| | Sample_contact_city | Adelaide
| | Sample_contact_state | SA
| | Sample_contact_zip/postal_code | 5005
| | Sample_contact_country | Australia
| | Sample_contact_web_link | http://www.adelaide.edu.au/directory/sarah.robertson
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM875nnn/GSM875816/suppl/GSM875816.CEL.gz
| | Sample_series_id | GSE35830
| | Sample_data_row_count | 54613
| | |
|
GSM875817 | GPL570 |
|
control replicate 2
|
Ect1 cells
|
treatment: medium alone
cell line: Ect1
treatment time: 10 h
|
|
| Sample_geo_accession | GSM875817
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 14 2012
| | Sample_last_update_date | Feb 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Quadruplicates wells containing 1 x 10^5 cells in 500 µl of KSFM in 1.5 ml culture wells (Nunc) were incubated at 37 C/5% CO2 for 2-3 days to generate a confluent monolayer, then the medium was replaced with 500 µl of KSFM containing TGFβ3 (5 ng/ml), 10% pooled human seminal plasma (v/v), or medium alone for 10h before termination of the experiment and extraction of mRNA.
| | Sample_growth_protocol_ch1 | Ect1 cells were propagated in keratinocyte serum–free media (Gibco, Mount Waverley, Australia) supplemented with 0.1 ng/ml rhEGF (Gibco), 0.05 mg/ml bovine pituitary extract (Gibco) and 0.4 mM CaCl2 (KSFM).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from Ect1 cells using Trizol® (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions, and purified using RNeasy micro kits (Qiagen, Doncaster, Australia). Prior to hybridization, RNA underwent further purification using RNeasy Mini Spin columns (Qiagen, Valencia, CA, USA) and eluted into RNAse-free milli-Q water according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.
| | Sample_hyb_protocol | Genechips were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.
| | Sample_scan_protocol | Genechips were scanned using the Affymetrix GSC3000 scanner.
| | Sample_data_processing | RNA integrity analysis, hybridization and washing were performed according to the manufacturer’s instructions. GCOS 1.4 software (Affymetrix) using MAS 5.0 was used to generate CEL files for each chip. Quality control was assessed using the affyQCreport package in R (v2.6.1). The array data was initially examined using Partek Genomics Suite (Partek Inc, MO), after CEL files were imported using RMA background correction, GC content correction, and mean probe summarization, to generate dendrogram hierarchical clustering analysis and principal components analysis (PCA). Non-log2 transformed expression values for each chip were submitted to IlluminaGUI (free software implemented by R 2.6.1) after substituting Illumina probe IDs for Affymetrix IDs. Two contrasts were analysed; seminal plasma versus control, and TGFβ3 versus control. In both cases, differentially expressed probes were identified using default high stringency parameters (≥2.0-fold change, t-test p <0.05, >100 difference between mean expression intensity). The Kyoto Encyclopedia of Genes and Genomics (KEGG) database and Pathway Express and OntoExpress analysis software were utilized to assign genes to cytokine–cytokine receptor interaction, TGFβ signalling, JAK/STAT signalling or VEGF signalling pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,Anne,Robertson
| | Sample_contact_email | sarah.robertson@adelaide.edu.au
| | Sample_contact_phone | 61 8 83034094
| | Sample_contact_fax | 61 8 8303 4099
| | Sample_contact_laboratory | Reproductive Immunology
| | Sample_contact_department | paediatrics and Reproductive Health
| | Sample_contact_institute | University of Adelaide
| | Sample_contact_address | Frome Rd
| | Sample_contact_city | Adelaide
| | Sample_contact_state | SA
| | Sample_contact_zip/postal_code | 5005
| | Sample_contact_country | Australia
| | Sample_contact_web_link | http://www.adelaide.edu.au/directory/sarah.robertson
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM875nnn/GSM875817/suppl/GSM875817.CEL.gz
| | Sample_series_id | GSE35830
| | Sample_data_row_count | 54613
| | |
|
GSM875818 | GPL570 |
|
control replicate 3
|
Ect1 cells
|
treatment: medium alone
cell line: Ect1
treatment time: 10 h
|
|
| Sample_geo_accession | GSM875818
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 14 2012
| | Sample_last_update_date | Feb 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Quadruplicates wells containing 1 x 10^5 cells in 500 µl of KSFM in 1.5 ml culture wells (Nunc) were incubated at 37 C/5% CO2 for 2-3 days to generate a confluent monolayer, then the medium was replaced with 500 µl of KSFM containing TGFβ3 (5 ng/ml), 10% pooled human seminal plasma (v/v), or medium alone for 10h before termination of the experiment and extraction of mRNA.
| | Sample_growth_protocol_ch1 | Ect1 cells were propagated in keratinocyte serum–free media (Gibco, Mount Waverley, Australia) supplemented with 0.1 ng/ml rhEGF (Gibco), 0.05 mg/ml bovine pituitary extract (Gibco) and 0.4 mM CaCl2 (KSFM).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from Ect1 cells using Trizol® (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions, and purified using RNeasy micro kits (Qiagen, Doncaster, Australia). Prior to hybridization, RNA underwent further purification using RNeasy Mini Spin columns (Qiagen, Valencia, CA, USA) and eluted into RNAse-free milli-Q water according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.
| | Sample_hyb_protocol | Genechips were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.
| | Sample_scan_protocol | Genechips were scanned using the Affymetrix GSC3000 scanner.
| | Sample_data_processing | RNA integrity analysis, hybridization and washing were performed according to the manufacturer’s instructions. GCOS 1.4 software (Affymetrix) using MAS 5.0 was used to generate CEL files for each chip. Quality control was assessed using the affyQCreport package in R (v2.6.1). The array data was initially examined using Partek Genomics Suite (Partek Inc, MO), after CEL files were imported using RMA background correction, GC content correction, and mean probe summarization, to generate dendrogram hierarchical clustering analysis and principal components analysis (PCA). Non-log2 transformed expression values for each chip were submitted to IlluminaGUI (free software implemented by R 2.6.1) after substituting Illumina probe IDs for Affymetrix IDs. Two contrasts were analysed; seminal plasma versus control, and TGFβ3 versus control. In both cases, differentially expressed probes were identified using default high stringency parameters (≥2.0-fold change, t-test p <0.05, >100 difference between mean expression intensity). The Kyoto Encyclopedia of Genes and Genomics (KEGG) database and Pathway Express and OntoExpress analysis software were utilized to assign genes to cytokine–cytokine receptor interaction, TGFβ signalling, JAK/STAT signalling or VEGF signalling pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,Anne,Robertson
| | Sample_contact_email | sarah.robertson@adelaide.edu.au
| | Sample_contact_phone | 61 8 83034094
| | Sample_contact_fax | 61 8 8303 4099
| | Sample_contact_laboratory | Reproductive Immunology
| | Sample_contact_department | paediatrics and Reproductive Health
| | Sample_contact_institute | University of Adelaide
| | Sample_contact_address | Frome Rd
| | Sample_contact_city | Adelaide
| | Sample_contact_state | SA
| | Sample_contact_zip/postal_code | 5005
| | Sample_contact_country | Australia
| | Sample_contact_web_link | http://www.adelaide.edu.au/directory/sarah.robertson
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM875nnn/GSM875818/suppl/GSM875818.CEL.gz
| | Sample_series_id | GSE35830
| | Sample_data_row_count | 54613
| | |
|
GSM875819 | GPL570 |
|
control replicate 4
|
Ect1 cells
|
treatment: medium alone
cell line: Ect1
treatment time: 10 h
|
|
| Sample_geo_accession | GSM875819
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 14 2012
| | Sample_last_update_date | Feb 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Quadruplicates wells containing 1 x 10^5 cells in 500 µl of KSFM in 1.5 ml culture wells (Nunc) were incubated at 37 C/5% CO2 for 2-3 days to generate a confluent monolayer, then the medium was replaced with 500 µl of KSFM containing TGFβ3 (5 ng/ml), 10% pooled human seminal plasma (v/v), or medium alone for 10h before termination of the experiment and extraction of mRNA.
| | Sample_growth_protocol_ch1 | Ect1 cells were propagated in keratinocyte serum–free media (Gibco, Mount Waverley, Australia) supplemented with 0.1 ng/ml rhEGF (Gibco), 0.05 mg/ml bovine pituitary extract (Gibco) and 0.4 mM CaCl2 (KSFM).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from Ect1 cells using Trizol® (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions, and purified using RNeasy micro kits (Qiagen, Doncaster, Australia). Prior to hybridization, RNA underwent further purification using RNeasy Mini Spin columns (Qiagen, Valencia, CA, USA) and eluted into RNAse-free milli-Q water according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.
| | Sample_hyb_protocol | Genechips were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.
| | Sample_scan_protocol | Genechips were scanned using the Affymetrix GSC3000 scanner.
| | Sample_data_processing | RNA integrity analysis, hybridization and washing were performed according to the manufacturer’s instructions. GCOS 1.4 software (Affymetrix) using MAS 5.0 was used to generate CEL files for each chip. Quality control was assessed using the affyQCreport package in R (v2.6.1). The array data was initially examined using Partek Genomics Suite (Partek Inc, MO), after CEL files were imported using RMA background correction, GC content correction, and mean probe summarization, to generate dendrogram hierarchical clustering analysis and principal components analysis (PCA). Non-log2 transformed expression values for each chip were submitted to IlluminaGUI (free software implemented by R 2.6.1) after substituting Illumina probe IDs for Affymetrix IDs. Two contrasts were analysed; seminal plasma versus control, and TGFβ3 versus control. In both cases, differentially expressed probes were identified using default high stringency parameters (≥2.0-fold change, t-test p <0.05, >100 difference between mean expression intensity). The Kyoto Encyclopedia of Genes and Genomics (KEGG) database and Pathway Express and OntoExpress analysis software were utilized to assign genes to cytokine–cytokine receptor interaction, TGFβ signalling, JAK/STAT signalling or VEGF signalling pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,Anne,Robertson
| | Sample_contact_email | sarah.robertson@adelaide.edu.au
| | Sample_contact_phone | 61 8 83034094
| | Sample_contact_fax | 61 8 8303 4099
| | Sample_contact_laboratory | Reproductive Immunology
| | Sample_contact_department | paediatrics and Reproductive Health
| | Sample_contact_institute | University of Adelaide
| | Sample_contact_address | Frome Rd
| | Sample_contact_city | Adelaide
| | Sample_contact_state | SA
| | Sample_contact_zip/postal_code | 5005
| | Sample_contact_country | Australia
| | Sample_contact_web_link | http://www.adelaide.edu.au/directory/sarah.robertson
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM875nnn/GSM875819/suppl/GSM875819.CEL.gz
| | Sample_series_id | GSE35830
| | Sample_data_row_count | 54613
| | |
|
GSM875820 | GPL570 |
|
seminal plasma replicate 1
|
Ect1 cells
|
treatment: 10% seminal plasma
cell line: Ect1
treatment time: 10 h
|
|
| Sample_geo_accession | GSM875820
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 14 2012
| | Sample_last_update_date | Feb 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Quadruplicates wells containing 1 x 10^5 cells in 500 µl of KSFM in 1.5 ml culture wells (Nunc) were incubated at 37 C/5% CO2 for 2-3 days to generate a confluent monolayer, then the medium was replaced with 500 µl of KSFM containing TGFβ3 (5 ng/ml), 10% pooled human seminal plasma (v/v), or medium alone for 10h before termination of the experiment and extraction of mRNA.
| | Sample_growth_protocol_ch1 | Ect1 cells were propagated in keratinocyte serum–free media (Gibco, Mount Waverley, Australia) supplemented with 0.1 ng/ml rhEGF (Gibco), 0.05 mg/ml bovine pituitary extract (Gibco) and 0.4 mM CaCl2 (KSFM).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from Ect1 cells using Trizol® (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions, and purified using RNeasy micro kits (Qiagen, Doncaster, Australia). Prior to hybridization, RNA underwent further purification using RNeasy Mini Spin columns (Qiagen, Valencia, CA, USA) and eluted into RNAse-free milli-Q water according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.
| | Sample_hyb_protocol | Genechips were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.
| | Sample_scan_protocol | Genechips were scanned using the Affymetrix GSC3000 scanner.
| | Sample_data_processing | RNA integrity analysis, hybridization and washing were performed according to the manufacturer’s instructions. GCOS 1.4 software (Affymetrix) using MAS 5.0 was used to generate CEL files for each chip. Quality control was assessed using the affyQCreport package in R (v2.6.1). The array data was initially examined using Partek Genomics Suite (Partek Inc, MO), after CEL files were imported using RMA background correction, GC content correction, and mean probe summarization, to generate dendrogram hierarchical clustering analysis and principal components analysis (PCA). Non-log2 transformed expression values for each chip were submitted to IlluminaGUI (free software implemented by R 2.6.1) after substituting Illumina probe IDs for Affymetrix IDs. Two contrasts were analysed; seminal plasma versus control, and TGFβ3 versus control. In both cases, differentially expressed probes were identified using default high stringency parameters (≥2.0-fold change, t-test p <0.05, >100 difference between mean expression intensity). The Kyoto Encyclopedia of Genes and Genomics (KEGG) database and Pathway Express and OntoExpress analysis software were utilized to assign genes to cytokine–cytokine receptor interaction, TGFβ signalling, JAK/STAT signalling or VEGF signalling pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,Anne,Robertson
| | Sample_contact_email | sarah.robertson@adelaide.edu.au
| | Sample_contact_phone | 61 8 83034094
| | Sample_contact_fax | 61 8 8303 4099
| | Sample_contact_laboratory | Reproductive Immunology
| | Sample_contact_department | paediatrics and Reproductive Health
| | Sample_contact_institute | University of Adelaide
| | Sample_contact_address | Frome Rd
| | Sample_contact_city | Adelaide
| | Sample_contact_state | SA
| | Sample_contact_zip/postal_code | 5005
| | Sample_contact_country | Australia
| | Sample_contact_web_link | http://www.adelaide.edu.au/directory/sarah.robertson
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM875nnn/GSM875820/suppl/GSM875820.CEL.gz
| | Sample_series_id | GSE35830
| | Sample_data_row_count | 54613
| | |
|
GSM875821 | GPL570 |
|
seminal plasma replicate 2
|
Ect1 cells
|
treatment: 10% seminal plasma
cell line: Ect1
treatment time: 10 h
|
|
| Sample_geo_accession | GSM875821
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 14 2012
| | Sample_last_update_date | Feb 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Quadruplicates wells containing 1 x 10^5 cells in 500 µl of KSFM in 1.5 ml culture wells (Nunc) were incubated at 37 C/5% CO2 for 2-3 days to generate a confluent monolayer, then the medium was replaced with 500 µl of KSFM containing TGFβ3 (5 ng/ml), 10% pooled human seminal plasma (v/v), or medium alone for 10h before termination of the experiment and extraction of mRNA.
| | Sample_growth_protocol_ch1 | Ect1 cells were propagated in keratinocyte serum–free media (Gibco, Mount Waverley, Australia) supplemented with 0.1 ng/ml rhEGF (Gibco), 0.05 mg/ml bovine pituitary extract (Gibco) and 0.4 mM CaCl2 (KSFM).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from Ect1 cells using Trizol® (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions, and purified using RNeasy micro kits (Qiagen, Doncaster, Australia). Prior to hybridization, RNA underwent further purification using RNeasy Mini Spin columns (Qiagen, Valencia, CA, USA) and eluted into RNAse-free milli-Q water according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.
| | Sample_hyb_protocol | Genechips were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.
| | Sample_scan_protocol | Genechips were scanned using the Affymetrix GSC3000 scanner.
| | Sample_data_processing | RNA integrity analysis, hybridization and washing were performed according to the manufacturer’s instructions. GCOS 1.4 software (Affymetrix) using MAS 5.0 was used to generate CEL files for each chip. Quality control was assessed using the affyQCreport package in R (v2.6.1). The array data was initially examined using Partek Genomics Suite (Partek Inc, MO), after CEL files were imported using RMA background correction, GC content correction, and mean probe summarization, to generate dendrogram hierarchical clustering analysis and principal components analysis (PCA). Non-log2 transformed expression values for each chip were submitted to IlluminaGUI (free software implemented by R 2.6.1) after substituting Illumina probe IDs for Affymetrix IDs. Two contrasts were analysed; seminal plasma versus control, and TGFβ3 versus control. In both cases, differentially expressed probes were identified using default high stringency parameters (≥2.0-fold change, t-test p <0.05, >100 difference between mean expression intensity). The Kyoto Encyclopedia of Genes and Genomics (KEGG) database and Pathway Express and OntoExpress analysis software were utilized to assign genes to cytokine–cytokine receptor interaction, TGFβ signalling, JAK/STAT signalling or VEGF signalling pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,Anne,Robertson
| | Sample_contact_email | sarah.robertson@adelaide.edu.au
| | Sample_contact_phone | 61 8 83034094
| | Sample_contact_fax | 61 8 8303 4099
| | Sample_contact_laboratory | Reproductive Immunology
| | Sample_contact_department | paediatrics and Reproductive Health
| | Sample_contact_institute | University of Adelaide
| | Sample_contact_address | Frome Rd
| | Sample_contact_city | Adelaide
| | Sample_contact_state | SA
| | Sample_contact_zip/postal_code | 5005
| | Sample_contact_country | Australia
| | Sample_contact_web_link | http://www.adelaide.edu.au/directory/sarah.robertson
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM875nnn/GSM875821/suppl/GSM875821.CEL.gz
| | Sample_series_id | GSE35830
| | Sample_data_row_count | 54613
| | |
|
GSM875822 | GPL570 |
|
seminal plasma replicate 3
|
Ect1 cells
|
treatment: 10% seminal plasma
cell line: Ect1
treatment time: 10 h
|
|
| Sample_geo_accession | GSM875822
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 14 2012
| | Sample_last_update_date | Feb 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Quadruplicates wells containing 1 x 10^5 cells in 500 µl of KSFM in 1.5 ml culture wells (Nunc) were incubated at 37 C/5% CO2 for 2-3 days to generate a confluent monolayer, then the medium was replaced with 500 µl of KSFM containing TGFβ3 (5 ng/ml), 10% pooled human seminal plasma (v/v), or medium alone for 10h before termination of the experiment and extraction of mRNA.
| | Sample_growth_protocol_ch1 | Ect1 cells were propagated in keratinocyte serum–free media (Gibco, Mount Waverley, Australia) supplemented with 0.1 ng/ml rhEGF (Gibco), 0.05 mg/ml bovine pituitary extract (Gibco) and 0.4 mM CaCl2 (KSFM).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from Ect1 cells using Trizol® (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions, and purified using RNeasy micro kits (Qiagen, Doncaster, Australia). Prior to hybridization, RNA underwent further purification using RNeasy Mini Spin columns (Qiagen, Valencia, CA, USA) and eluted into RNAse-free milli-Q water according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.
| | Sample_hyb_protocol | Genechips were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.
| | Sample_scan_protocol | Genechips were scanned using the Affymetrix GSC3000 scanner.
| | Sample_data_processing | RNA integrity analysis, hybridization and washing were performed according to the manufacturer’s instructions. GCOS 1.4 software (Affymetrix) using MAS 5.0 was used to generate CEL files for each chip. Quality control was assessed using the affyQCreport package in R (v2.6.1). The array data was initially examined using Partek Genomics Suite (Partek Inc, MO), after CEL files were imported using RMA background correction, GC content correction, and mean probe summarization, to generate dendrogram hierarchical clustering analysis and principal components analysis (PCA). Non-log2 transformed expression values for each chip were submitted to IlluminaGUI (free software implemented by R 2.6.1) after substituting Illumina probe IDs for Affymetrix IDs. Two contrasts were analysed; seminal plasma versus control, and TGFβ3 versus control. In both cases, differentially expressed probes were identified using default high stringency parameters (≥2.0-fold change, t-test p <0.05, >100 difference between mean expression intensity). The Kyoto Encyclopedia of Genes and Genomics (KEGG) database and Pathway Express and OntoExpress analysis software were utilized to assign genes to cytokine–cytokine receptor interaction, TGFβ signalling, JAK/STAT signalling or VEGF signalling pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,Anne,Robertson
| | Sample_contact_email | sarah.robertson@adelaide.edu.au
| | Sample_contact_phone | 61 8 83034094
| | Sample_contact_fax | 61 8 8303 4099
| | Sample_contact_laboratory | Reproductive Immunology
| | Sample_contact_department | paediatrics and Reproductive Health
| | Sample_contact_institute | University of Adelaide
| | Sample_contact_address | Frome Rd
| | Sample_contact_city | Adelaide
| | Sample_contact_state | SA
| | Sample_contact_zip/postal_code | 5005
| | Sample_contact_country | Australia
| | Sample_contact_web_link | http://www.adelaide.edu.au/directory/sarah.robertson
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM875nnn/GSM875822/suppl/GSM875822.CEL.gz
| | Sample_series_id | GSE35830
| | Sample_data_row_count | 54613
| | |
|
GSM875823 | GPL570 |
|
seminal plasma replicate 4
|
Ect1 cells
|
treatment: 10% seminal plasma
cell line: Ect1
treatment time: 10 h
|
|
| Sample_geo_accession | GSM875823
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 14 2012
| | Sample_last_update_date | Feb 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Quadruplicates wells containing 1 x 10^5 cells in 500 µl of KSFM in 1.5 ml culture wells (Nunc) were incubated at 37 C/5% CO2 for 2-3 days to generate a confluent monolayer, then the medium was replaced with 500 µl of KSFM containing TGFβ3 (5 ng/ml), 10% pooled human seminal plasma (v/v), or medium alone for 10h before termination of the experiment and extraction of mRNA.
| | Sample_growth_protocol_ch1 | Ect1 cells were propagated in keratinocyte serum–free media (Gibco, Mount Waverley, Australia) supplemented with 0.1 ng/ml rhEGF (Gibco), 0.05 mg/ml bovine pituitary extract (Gibco) and 0.4 mM CaCl2 (KSFM).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from Ect1 cells using Trizol® (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions, and purified using RNeasy micro kits (Qiagen, Doncaster, Australia). Prior to hybridization, RNA underwent further purification using RNeasy Mini Spin columns (Qiagen, Valencia, CA, USA) and eluted into RNAse-free milli-Q water according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.
| | Sample_hyb_protocol | Genechips were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.
| | Sample_scan_protocol | Genechips were scanned using the Affymetrix GSC3000 scanner.
| | Sample_data_processing | RNA integrity analysis, hybridization and washing were performed according to the manufacturer’s instructions. GCOS 1.4 software (Affymetrix) using MAS 5.0 was used to generate CEL files for each chip. Quality control was assessed using the affyQCreport package in R (v2.6.1). The array data was initially examined using Partek Genomics Suite (Partek Inc, MO), after CEL files were imported using RMA background correction, GC content correction, and mean probe summarization, to generate dendrogram hierarchical clustering analysis and principal components analysis (PCA). Non-log2 transformed expression values for each chip were submitted to IlluminaGUI (free software implemented by R 2.6.1) after substituting Illumina probe IDs for Affymetrix IDs. Two contrasts were analysed; seminal plasma versus control, and TGFβ3 versus control. In both cases, differentially expressed probes were identified using default high stringency parameters (≥2.0-fold change, t-test p <0.05, >100 difference between mean expression intensity). The Kyoto Encyclopedia of Genes and Genomics (KEGG) database and Pathway Express and OntoExpress analysis software were utilized to assign genes to cytokine–cytokine receptor interaction, TGFβ signalling, JAK/STAT signalling or VEGF signalling pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,Anne,Robertson
| | Sample_contact_email | sarah.robertson@adelaide.edu.au
| | Sample_contact_phone | 61 8 83034094
| | Sample_contact_fax | 61 8 8303 4099
| | Sample_contact_laboratory | Reproductive Immunology
| | Sample_contact_department | paediatrics and Reproductive Health
| | Sample_contact_institute | University of Adelaide
| | Sample_contact_address | Frome Rd
| | Sample_contact_city | Adelaide
| | Sample_contact_state | SA
| | Sample_contact_zip/postal_code | 5005
| | Sample_contact_country | Australia
| | Sample_contact_web_link | http://www.adelaide.edu.au/directory/sarah.robertson
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM875nnn/GSM875823/suppl/GSM875823.CEL.gz
| | Sample_series_id | GSE35830
| | Sample_data_row_count | 54613
| | |
|
GSM875824 | GPL570 |
|
TGFB replicate 1
|
Ect1 cells
|
treatment: rec human TGFβ3 (5 ng/ml)
cell line: Ect1
treatment time: 10 h
|
|
| Sample_geo_accession | GSM875824
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 14 2012
| | Sample_last_update_date | Feb 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Quadruplicates wells containing 1 x 10^5 cells in 500 µl of KSFM in 1.5 ml culture wells (Nunc) were incubated at 37 C/5% CO2 for 2-3 days to generate a confluent monolayer, then the medium was replaced with 500 µl of KSFM containing TGFβ3 (5 ng/ml), 10% pooled human seminal plasma (v/v), or medium alone for 10h before termination of the experiment and extraction of mRNA.
| | Sample_growth_protocol_ch1 | Ect1 cells were propagated in keratinocyte serum–free media (Gibco, Mount Waverley, Australia) supplemented with 0.1 ng/ml rhEGF (Gibco), 0.05 mg/ml bovine pituitary extract (Gibco) and 0.4 mM CaCl2 (KSFM).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from Ect1 cells using Trizol® (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions, and purified using RNeasy micro kits (Qiagen, Doncaster, Australia). Prior to hybridization, RNA underwent further purification using RNeasy Mini Spin columns (Qiagen, Valencia, CA, USA) and eluted into RNAse-free milli-Q water according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.
| | Sample_hyb_protocol | Genechips were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.
| | Sample_scan_protocol | Genechips were scanned using the Affymetrix GSC3000 scanner.
| | Sample_data_processing | RNA integrity analysis, hybridization and washing were performed according to the manufacturer’s instructions. GCOS 1.4 software (Affymetrix) using MAS 5.0 was used to generate CEL files for each chip. Quality control was assessed using the affyQCreport package in R (v2.6.1). The array data was initially examined using Partek Genomics Suite (Partek Inc, MO), after CEL files were imported using RMA background correction, GC content correction, and mean probe summarization, to generate dendrogram hierarchical clustering analysis and principal components analysis (PCA). Non-log2 transformed expression values for each chip were submitted to IlluminaGUI (free software implemented by R 2.6.1) after substituting Illumina probe IDs for Affymetrix IDs. Two contrasts were analysed; seminal plasma versus control, and TGFβ3 versus control. In both cases, differentially expressed probes were identified using default high stringency parameters (≥2.0-fold change, t-test p <0.05, >100 difference between mean expression intensity). The Kyoto Encyclopedia of Genes and Genomics (KEGG) database and Pathway Express and OntoExpress analysis software were utilized to assign genes to cytokine–cytokine receptor interaction, TGFβ signalling, JAK/STAT signalling or VEGF signalling pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,Anne,Robertson
| | Sample_contact_email | sarah.robertson@adelaide.edu.au
| | Sample_contact_phone | 61 8 83034094
| | Sample_contact_fax | 61 8 8303 4099
| | Sample_contact_laboratory | Reproductive Immunology
| | Sample_contact_department | paediatrics and Reproductive Health
| | Sample_contact_institute | University of Adelaide
| | Sample_contact_address | Frome Rd
| | Sample_contact_city | Adelaide
| | Sample_contact_state | SA
| | Sample_contact_zip/postal_code | 5005
| | Sample_contact_country | Australia
| | Sample_contact_web_link | http://www.adelaide.edu.au/directory/sarah.robertson
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM875nnn/GSM875824/suppl/GSM875824.CEL.gz
| | Sample_series_id | GSE35830
| | Sample_data_row_count | 54613
| | |
|
GSM875825 | GPL570 |
|
TGFB replicate 2
|
Ect1 cells
|
treatment: rec human TGFβ3 (5 ng/ml)
cell line: Ect1
treatment time: 10 h
|
|
| Sample_geo_accession | GSM875825
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 14 2012
| | Sample_last_update_date | Feb 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Quadruplicates wells containing 1 x 10^5 cells in 500 µl of KSFM in 1.5 ml culture wells (Nunc) were incubated at 37 C/5% CO2 for 2-3 days to generate a confluent monolayer, then the medium was replaced with 500 µl of KSFM containing TGFβ3 (5 ng/ml), 10% pooled human seminal plasma (v/v), or medium alone for 10h before termination of the experiment and extraction of mRNA.
| | Sample_growth_protocol_ch1 | Ect1 cells were propagated in keratinocyte serum–free media (Gibco, Mount Waverley, Australia) supplemented with 0.1 ng/ml rhEGF (Gibco), 0.05 mg/ml bovine pituitary extract (Gibco) and 0.4 mM CaCl2 (KSFM).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from Ect1 cells using Trizol® (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions, and purified using RNeasy micro kits (Qiagen, Doncaster, Australia). Prior to hybridization, RNA underwent further purification using RNeasy Mini Spin columns (Qiagen, Valencia, CA, USA) and eluted into RNAse-free milli-Q water according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.
| | Sample_hyb_protocol | Genechips were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.
| | Sample_scan_protocol | Genechips were scanned using the Affymetrix GSC3000 scanner.
| | Sample_data_processing | RNA integrity analysis, hybridization and washing were performed according to the manufacturer’s instructions. GCOS 1.4 software (Affymetrix) using MAS 5.0 was used to generate CEL files for each chip. Quality control was assessed using the affyQCreport package in R (v2.6.1). The array data was initially examined using Partek Genomics Suite (Partek Inc, MO), after CEL files were imported using RMA background correction, GC content correction, and mean probe summarization, to generate dendrogram hierarchical clustering analysis and principal components analysis (PCA). Non-log2 transformed expression values for each chip were submitted to IlluminaGUI (free software implemented by R 2.6.1) after substituting Illumina probe IDs for Affymetrix IDs. Two contrasts were analysed; seminal plasma versus control, and TGFβ3 versus control. In both cases, differentially expressed probes were identified using default high stringency parameters (≥2.0-fold change, t-test p <0.05, >100 difference between mean expression intensity). The Kyoto Encyclopedia of Genes and Genomics (KEGG) database and Pathway Express and OntoExpress analysis software were utilized to assign genes to cytokine–cytokine receptor interaction, TGFβ signalling, JAK/STAT signalling or VEGF signalling pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,Anne,Robertson
| | Sample_contact_email | sarah.robertson@adelaide.edu.au
| | Sample_contact_phone | 61 8 83034094
| | Sample_contact_fax | 61 8 8303 4099
| | Sample_contact_laboratory | Reproductive Immunology
| | Sample_contact_department | paediatrics and Reproductive Health
| | Sample_contact_institute | University of Adelaide
| | Sample_contact_address | Frome Rd
| | Sample_contact_city | Adelaide
| | Sample_contact_state | SA
| | Sample_contact_zip/postal_code | 5005
| | Sample_contact_country | Australia
| | Sample_contact_web_link | http://www.adelaide.edu.au/directory/sarah.robertson
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM875nnn/GSM875825/suppl/GSM875825.CEL.gz
| | Sample_series_id | GSE35830
| | Sample_data_row_count | 54613
| | |
|
GSM875826 | GPL570 |
|
TGFB replicate 3
|
Ect1 cells
|
treatment: rec human TGFβ3 (5 ng/ml)
cell line: Ect1
treatment time: 10 h
|
|
| Sample_geo_accession | GSM875826
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 14 2012
| | Sample_last_update_date | Feb 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Quadruplicates wells containing 1 x 10^5 cells in 500 µl of KSFM in 1.5 ml culture wells (Nunc) were incubated at 37 C/5% CO2 for 2-3 days to generate a confluent monolayer, then the medium was replaced with 500 µl of KSFM containing TGFβ3 (5 ng/ml), 10% pooled human seminal plasma (v/v), or medium alone for 10h before termination of the experiment and extraction of mRNA.
| | Sample_growth_protocol_ch1 | Ect1 cells were propagated in keratinocyte serum–free media (Gibco, Mount Waverley, Australia) supplemented with 0.1 ng/ml rhEGF (Gibco), 0.05 mg/ml bovine pituitary extract (Gibco) and 0.4 mM CaCl2 (KSFM).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from Ect1 cells using Trizol® (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions, and purified using RNeasy micro kits (Qiagen, Doncaster, Australia). Prior to hybridization, RNA underwent further purification using RNeasy Mini Spin columns (Qiagen, Valencia, CA, USA) and eluted into RNAse-free milli-Q water according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.
| | Sample_hyb_protocol | Genechips were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.
| | Sample_scan_protocol | Genechips were scanned using the Affymetrix GSC3000 scanner.
| | Sample_data_processing | RNA integrity analysis, hybridization and washing were performed according to the manufacturer’s instructions. GCOS 1.4 software (Affymetrix) using MAS 5.0 was used to generate CEL files for each chip. Quality control was assessed using the affyQCreport package in R (v2.6.1). The array data was initially examined using Partek Genomics Suite (Partek Inc, MO), after CEL files were imported using RMA background correction, GC content correction, and mean probe summarization, to generate dendrogram hierarchical clustering analysis and principal components analysis (PCA). Non-log2 transformed expression values for each chip were submitted to IlluminaGUI (free software implemented by R 2.6.1) after substituting Illumina probe IDs for Affymetrix IDs. Two contrasts were analysed; seminal plasma versus control, and TGFβ3 versus control. In both cases, differentially expressed probes were identified using default high stringency parameters (≥2.0-fold change, t-test p <0.05, >100 difference between mean expression intensity). The Kyoto Encyclopedia of Genes and Genomics (KEGG) database and Pathway Express and OntoExpress analysis software were utilized to assign genes to cytokine–cytokine receptor interaction, TGFβ signalling, JAK/STAT signalling or VEGF signalling pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,Anne,Robertson
| | Sample_contact_email | sarah.robertson@adelaide.edu.au
| | Sample_contact_phone | 61 8 83034094
| | Sample_contact_fax | 61 8 8303 4099
| | Sample_contact_laboratory | Reproductive Immunology
| | Sample_contact_department | paediatrics and Reproductive Health
| | Sample_contact_institute | University of Adelaide
| | Sample_contact_address | Frome Rd
| | Sample_contact_city | Adelaide
| | Sample_contact_state | SA
| | Sample_contact_zip/postal_code | 5005
| | Sample_contact_country | Australia
| | Sample_contact_web_link | http://www.adelaide.edu.au/directory/sarah.robertson
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM875nnn/GSM875826/suppl/GSM875826.CEL.gz
| | Sample_series_id | GSE35830
| | Sample_data_row_count | 54613
| | |
|
GSM875827 | GPL570 |
|
TGFB replicate 4
|
Ect1 cells
|
treatment: rec human TGFβ3 (5 ng/ml)
cell line: Ect1
treatment time: 10 h
|
|
| Sample_geo_accession | GSM875827
| | Sample_status | Public on Feb 16 2012
| | Sample_submission_date | Feb 14 2012
| | Sample_last_update_date | Feb 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Quadruplicates wells containing 1 x 10^5 cells in 500 µl of KSFM in 1.5 ml culture wells (Nunc) were incubated at 37 C/5% CO2 for 2-3 days to generate a confluent monolayer, then the medium was replaced with 500 µl of KSFM containing TGFβ3 (5 ng/ml), 10% pooled human seminal plasma (v/v), or medium alone for 10h before termination of the experiment and extraction of mRNA.
| | Sample_growth_protocol_ch1 | Ect1 cells were propagated in keratinocyte serum–free media (Gibco, Mount Waverley, Australia) supplemented with 0.1 ng/ml rhEGF (Gibco), 0.05 mg/ml bovine pituitary extract (Gibco) and 0.4 mM CaCl2 (KSFM).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from Ect1 cells using Trizol® (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions, and purified using RNeasy micro kits (Qiagen, Doncaster, Australia). Prior to hybridization, RNA underwent further purification using RNeasy Mini Spin columns (Qiagen, Valencia, CA, USA) and eluted into RNAse-free milli-Q water according to the manufacturer’s instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.
| | Sample_hyb_protocol | Genechips were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.
| | Sample_scan_protocol | Genechips were scanned using the Affymetrix GSC3000 scanner.
| | Sample_data_processing | RNA integrity analysis, hybridization and washing were performed according to the manufacturer’s instructions. GCOS 1.4 software (Affymetrix) using MAS 5.0 was used to generate CEL files for each chip. Quality control was assessed using the affyQCreport package in R (v2.6.1). The array data was initially examined using Partek Genomics Suite (Partek Inc, MO), after CEL files were imported using RMA background correction, GC content correction, and mean probe summarization, to generate dendrogram hierarchical clustering analysis and principal components analysis (PCA). Non-log2 transformed expression values for each chip were submitted to IlluminaGUI (free software implemented by R 2.6.1) after substituting Illumina probe IDs for Affymetrix IDs. Two contrasts were analysed; seminal plasma versus control, and TGFβ3 versus control. In both cases, differentially expressed probes were identified using default high stringency parameters (≥2.0-fold change, t-test p <0.05, >100 difference between mean expression intensity). The Kyoto Encyclopedia of Genes and Genomics (KEGG) database and Pathway Express and OntoExpress analysis software were utilized to assign genes to cytokine–cytokine receptor interaction, TGFβ signalling, JAK/STAT signalling or VEGF signalling pathways.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sarah,Anne,Robertson
| | Sample_contact_email | sarah.robertson@adelaide.edu.au
| | Sample_contact_phone | 61 8 83034094
| | Sample_contact_fax | 61 8 8303 4099
| | Sample_contact_laboratory | Reproductive Immunology
| | Sample_contact_department | paediatrics and Reproductive Health
| | Sample_contact_institute | University of Adelaide
| | Sample_contact_address | Frome Rd
| | Sample_contact_city | Adelaide
| | Sample_contact_state | SA
| | Sample_contact_zip/postal_code | 5005
| | Sample_contact_country | Australia
| | Sample_contact_web_link | http://www.adelaide.edu.au/directory/sarah.robertson
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM875nnn/GSM875827/suppl/GSM875827.CEL.gz
| | Sample_series_id | GSE35830
| | Sample_data_row_count | 54613
| | |
|
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Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
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