Search results for the GEO ID: GSE26787  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM659103 | GPL570 |
|
RT3E10
|
fertile
|
gender: female
tissue: endometrium
|
Fertiles 1
|
| Sample_geo_accession | GSM659103
| | Sample_status | Public on Jan 22 2011
| | Sample_submission_date | Jan 21 2011
| | Sample_last_update_date | Jan 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy mini kit (Qiagen, Courtabeuf, France) including the RNase-Free DNAse set.Genomic DNA contamination was eliminated with RNAse inhibitor.RNA quantity and quality were confirmed by the analysis with an Experion system and RNA StdSens analysis kit (Bio-Rad)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Four micrograms of total RNA were labeled using the GeneChip® Expression 3’ Amplification One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).The cRNA was hybridized to Genechip Human Genome U133 Plus 2.0 Array (Affymetrix)
| | Sample_hyb_protocol | double-stranded cDNA was synthesized from 4 µg of total RNA primed with a poly-(dT)-T7 oligonucteotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotyin-labeled modified nucleotides during 16 hours at 37°C. Biotinylated cRNA was purified and then fragmented (35-200 nucleotides) together with hybridization controls and hybridized to the microarrays for 16 hours at 45°C. Using Fluidics Station (Affymetrix), the hybridized biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated anti-strepatvidine antibody and streptavidine R-phycoerythrin conjugate.
| | Sample_scan_protocol | The arrays were finally scanned with an affymetrix/Hewlett-Packard GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were read and pre-processed using the R sofware (http://www.R-project.org/) and especially using packages from the Bioconductor project (http://www.bioconductor.org). CEL data files were read using the affy package. Data were normalized by condition using the GC-RMA method implemented in the gcrma package. This method performs a Background Adjustment Using Sequence Information before normalized the data using the rma method (which is a quantile normalisation followed by a summarization of probes by median polish). Differential analysis was performed with the anapuce package of R2 [ http://www.agroparistech.fr/mia/doku.php?id=productions:logiciels]. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance [7]. The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.01.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nathalie,,Lédée
| | Sample_contact_email | nathalie-ledee@orange.fr
| | Sample_contact_phone | 331 45 37 44 50
| | Sample_contact_fax | 33 1 45 37 44 50
| | Sample_contact_laboratory | implantation et dialogue mother-conceptus
| | Sample_contact_department | Hopital Antoine Béclère, Pavillon Jean Dalsace
| | Sample_contact_institute | INSERM UMRS-783, université Paris XI
| | Sample_contact_address | 157 rue de la porte de trivaux
| | Sample_contact_city | Clamart
| | Sample_contact_zip/postal_code | 92141
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659103/suppl/GSM659103.CEL.gz
| | Sample_series_id | GSE26787
| | Sample_data_row_count | 54675
| | |
|
GSM659104 | GPL570 |
|
RT5E01
|
fertile
|
gender: female
tissue: endometrium
|
Fertiles 2
|
| Sample_geo_accession | GSM659104
| | Sample_status | Public on Jan 22 2011
| | Sample_submission_date | Jan 21 2011
| | Sample_last_update_date | Jan 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy mini kit (Qiagen, Courtabeuf, France) including the RNase-Free DNAse set.Genomic DNA contamination was eliminated with RNAse inhibitor.RNA quantity and quality were confirmed by the analysis with an Experion system and RNA StdSens analysis kit (Bio-Rad)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Four micrograms of total RNA were labeled using the GeneChip® Expression 3’ Amplification One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).The cRNA was hybridized to Genechip Human Genome U133 Plus 2.0 Array (Affymetrix)
| | Sample_hyb_protocol | double-stranded cDNA was synthesized from 4 µg of total RNA primed with a poly-(dT)-T7 oligonucteotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotyin-labeled modified nucleotides during 16 hours at 37°C. Biotinylated cRNA was purified and then fragmented (35-200 nucleotides) together with hybridization controls and hybridized to the microarrays for 16 hours at 45°C. Using Fluidics Station (Affymetrix), the hybridized biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated anti-strepatvidine antibody and streptavidine R-phycoerythrin conjugate.
| | Sample_scan_protocol | The arrays were finally scanned with an affymetrix/Hewlett-Packard GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were read and pre-processed using the R sofware (http://www.R-project.org/) and especially using packages from the Bioconductor project (http://www.bioconductor.org). CEL data files were read using the affy package. Data were normalized by condition using the GC-RMA method implemented in the gcrma package. This method performs a Background Adjustment Using Sequence Information before normalized the data using the rma method (which is a quantile normalisation followed by a summarization of probes by median polish). Differential analysis was performed with the anapuce package of R2 [ http://www.agroparistech.fr/mia/doku.php?id=productions:logiciels]. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance [7]. The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.01.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nathalie,,Lédée
| | Sample_contact_email | nathalie-ledee@orange.fr
| | Sample_contact_phone | 331 45 37 44 50
| | Sample_contact_fax | 33 1 45 37 44 50
| | Sample_contact_laboratory | implantation et dialogue mother-conceptus
| | Sample_contact_department | Hopital Antoine Béclère, Pavillon Jean Dalsace
| | Sample_contact_institute | INSERM UMRS-783, université Paris XI
| | Sample_contact_address | 157 rue de la porte de trivaux
| | Sample_contact_city | Clamart
| | Sample_contact_zip/postal_code | 92141
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659104/suppl/GSM659104.CEL.gz
| | Sample_series_id | GSE26787
| | Sample_data_row_count | 54675
| | |
|
GSM659105 | GPL570 |
|
RT5E21
|
fertile
|
gender: female
tissue: endometrium
|
Fertiles 3
|
| Sample_geo_accession | GSM659105
| | Sample_status | Public on Jan 22 2011
| | Sample_submission_date | Jan 21 2011
| | Sample_last_update_date | Jan 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy mini kit (Qiagen, Courtabeuf, France) including the RNase-Free DNAse set.Genomic DNA contamination was eliminated with RNAse inhibitor.RNA quantity and quality were confirmed by the analysis with an Experion system and RNA StdSens analysis kit (Bio-Rad)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Four micrograms of total RNA were labeled using the GeneChip® Expression 3’ Amplification One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).The cRNA was hybridized to Genechip Human Genome U133 Plus 2.0 Array (Affymetrix)
| | Sample_hyb_protocol | double-stranded cDNA was synthesized from 4 µg of total RNA primed with a poly-(dT)-T7 oligonucteotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotyin-labeled modified nucleotides during 16 hours at 37°C. Biotinylated cRNA was purified and then fragmented (35-200 nucleotides) together with hybridization controls and hybridized to the microarrays for 16 hours at 45°C. Using Fluidics Station (Affymetrix), the hybridized biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated anti-strepatvidine antibody and streptavidine R-phycoerythrin conjugate.
| | Sample_scan_protocol | The arrays were finally scanned with an affymetrix/Hewlett-Packard GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were read and pre-processed using the R sofware (http://www.R-project.org/) and especially using packages from the Bioconductor project (http://www.bioconductor.org). CEL data files were read using the affy package. Data were normalized by condition using the GC-RMA method implemented in the gcrma package. This method performs a Background Adjustment Using Sequence Information before normalized the data using the rma method (which is a quantile normalisation followed by a summarization of probes by median polish). Differential analysis was performed with the anapuce package of R2 [ http://www.agroparistech.fr/mia/doku.php?id=productions:logiciels]. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance [7]. The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.01.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nathalie,,Lédée
| | Sample_contact_email | nathalie-ledee@orange.fr
| | Sample_contact_phone | 331 45 37 44 50
| | Sample_contact_fax | 33 1 45 37 44 50
| | Sample_contact_laboratory | implantation et dialogue mother-conceptus
| | Sample_contact_department | Hopital Antoine Béclère, Pavillon Jean Dalsace
| | Sample_contact_institute | INSERM UMRS-783, université Paris XI
| | Sample_contact_address | 157 rue de la porte de trivaux
| | Sample_contact_city | Clamart
| | Sample_contact_zip/postal_code | 92141
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659105/suppl/GSM659105.CEL.gz
| | Sample_series_id | GSE26787
| | Sample_data_row_count | 54675
| | |
|
GSM659106 | GPL570 |
|
RT5E27
|
fertile
|
gender: female
tissue: endometrium
|
Fertiles 4
|
| Sample_geo_accession | GSM659106
| | Sample_status | Public on Jan 22 2011
| | Sample_submission_date | Jan 21 2011
| | Sample_last_update_date | Jan 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy mini kit (Qiagen, Courtabeuf, France) including the RNase-Free DNAse set.Genomic DNA contamination was eliminated with RNAse inhibitor.RNA quantity and quality were confirmed by the analysis with an Experion system and RNA StdSens analysis kit (Bio-Rad)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Four micrograms of total RNA were labeled using the GeneChip® Expression 3’ Amplification One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).The cRNA was hybridized to Genechip Human Genome U133 Plus 2.0 Array (Affymetrix)
| | Sample_hyb_protocol | double-stranded cDNA was synthesized from 4 µg of total RNA primed with a poly-(dT)-T7 oligonucteotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotyin-labeled modified nucleotides during 16 hours at 37°C. Biotinylated cRNA was purified and then fragmented (35-200 nucleotides) together with hybridization controls and hybridized to the microarrays for 16 hours at 45°C. Using Fluidics Station (Affymetrix), the hybridized biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated anti-strepatvidine antibody and streptavidine R-phycoerythrin conjugate.
| | Sample_scan_protocol | The arrays were finally scanned with an affymetrix/Hewlett-Packard GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were read and pre-processed using the R sofware (http://www.R-project.org/) and especially using packages from the Bioconductor project (http://www.bioconductor.org). CEL data files were read using the affy package. Data were normalized by condition using the GC-RMA method implemented in the gcrma package. This method performs a Background Adjustment Using Sequence Information before normalized the data using the rma method (which is a quantile normalisation followed by a summarization of probes by median polish). Differential analysis was performed with the anapuce package of R2 [ http://www.agroparistech.fr/mia/doku.php?id=productions:logiciels]. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance [7]. The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.01.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nathalie,,Lédée
| | Sample_contact_email | nathalie-ledee@orange.fr
| | Sample_contact_phone | 331 45 37 44 50
| | Sample_contact_fax | 33 1 45 37 44 50
| | Sample_contact_laboratory | implantation et dialogue mother-conceptus
| | Sample_contact_department | Hopital Antoine Béclère, Pavillon Jean Dalsace
| | Sample_contact_institute | INSERM UMRS-783, université Paris XI
| | Sample_contact_address | 157 rue de la porte de trivaux
| | Sample_contact_city | Clamart
| | Sample_contact_zip/postal_code | 92141
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659106/suppl/GSM659106.CEL.gz
| | Sample_series_id | GSE26787
| | Sample_data_row_count | 54675
| | |
|
GSM659107 | GPL570 |
|
RT3E35
|
fertile
|
gender: female
tissue: endometrium
|
Fertiles 5
|
| Sample_geo_accession | GSM659107
| | Sample_status | Public on Jan 22 2011
| | Sample_submission_date | Jan 21 2011
| | Sample_last_update_date | Jan 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy mini kit (Qiagen, Courtabeuf, France) including the RNase-Free DNAse set.Genomic DNA contamination was eliminated with RNAse inhibitor.RNA quantity and quality were confirmed by the analysis with an Experion system and RNA StdSens analysis kit (Bio-Rad)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Four micrograms of total RNA were labeled using the GeneChip® Expression 3’ Amplification One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).The cRNA was hybridized to Genechip Human Genome U133 Plus 2.0 Array (Affymetrix)
| | Sample_hyb_protocol | double-stranded cDNA was synthesized from 4 µg of total RNA primed with a poly-(dT)-T7 oligonucteotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotyin-labeled modified nucleotides during 16 hours at 37°C. Biotinylated cRNA was purified and then fragmented (35-200 nucleotides) together with hybridization controls and hybridized to the microarrays for 16 hours at 45°C. Using Fluidics Station (Affymetrix), the hybridized biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated anti-strepatvidine antibody and streptavidine R-phycoerythrin conjugate.
| | Sample_scan_protocol | The arrays were finally scanned with an affymetrix/Hewlett-Packard GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were read and pre-processed using the R sofware (http://www.R-project.org/) and especially using packages from the Bioconductor project (http://www.bioconductor.org). CEL data files were read using the affy package. Data were normalized by condition using the GC-RMA method implemented in the gcrma package. This method performs a Background Adjustment Using Sequence Information before normalized the data using the rma method (which is a quantile normalisation followed by a summarization of probes by median polish). Differential analysis was performed with the anapuce package of R2 [ http://www.agroparistech.fr/mia/doku.php?id=productions:logiciels]. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance [7]. The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.01.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nathalie,,Lédée
| | Sample_contact_email | nathalie-ledee@orange.fr
| | Sample_contact_phone | 331 45 37 44 50
| | Sample_contact_fax | 33 1 45 37 44 50
| | Sample_contact_laboratory | implantation et dialogue mother-conceptus
| | Sample_contact_department | Hopital Antoine Béclère, Pavillon Jean Dalsace
| | Sample_contact_institute | INSERM UMRS-783, université Paris XI
| | Sample_contact_address | 157 rue de la porte de trivaux
| | Sample_contact_city | Clamart
| | Sample_contact_zip/postal_code | 92141
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659107/suppl/GSM659107.CEL.gz
| | Sample_series_id | GSE26787
| | Sample_data_row_count | 54675
| | |
|
GSM659108 | GPL570 |
|
RT2E10
|
implantation failure
|
gender: female
tissue: endometrium
|
echec 1
|
| Sample_geo_accession | GSM659108
| | Sample_status | Public on Jan 22 2011
| | Sample_submission_date | Jan 21 2011
| | Sample_last_update_date | Jan 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy mini kit (Qiagen, Courtabeuf, France) including the RNase-Free DNAse set.Genomic DNA contamination was eliminated with RNAse inhibitor.RNA quantity and quality were confirmed by the analysis with an Experion system and RNA StdSens analysis kit (Bio-Rad)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Four micrograms of total RNA were labeled using the GeneChip® Expression 3’ Amplification One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).The cRNA was hybridized to Genechip Human Genome U133 Plus 2.0 Array (Affymetrix)
| | Sample_hyb_protocol | double-stranded cDNA was synthesized from 4 µg of total RNA primed with a poly-(dT)-T7 oligonucteotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotyin-labeled modified nucleotides during 16 hours at 37°C. Biotinylated cRNA was purified and then fragmented (35-200 nucleotides) together with hybridization controls and hybridized to the microarrays for 16 hours at 45°C. Using Fluidics Station (Affymetrix), the hybridized biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated anti-strepatvidine antibody and streptavidine R-phycoerythrin conjugate.
| | Sample_scan_protocol | The arrays were finally scanned with an affymetrix/Hewlett-Packard GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were read and pre-processed using the R sofware (http://www.R-project.org/) and especially using packages from the Bioconductor project (http://www.bioconductor.org). CEL data files were read using the affy package. Data were normalized by condition using the GC-RMA method implemented in the gcrma package. This method performs a Background Adjustment Using Sequence Information before normalized the data using the rma method (which is a quantile normalisation followed by a summarization of probes by median polish). Differential analysis was performed with the anapuce package of R2 [ http://www.agroparistech.fr/mia/doku.php?id=productions:logiciels]. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance [7]. The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.01.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nathalie,,Lédée
| | Sample_contact_email | nathalie-ledee@orange.fr
| | Sample_contact_phone | 331 45 37 44 50
| | Sample_contact_fax | 33 1 45 37 44 50
| | Sample_contact_laboratory | implantation et dialogue mother-conceptus
| | Sample_contact_department | Hopital Antoine Béclère, Pavillon Jean Dalsace
| | Sample_contact_institute | INSERM UMRS-783, université Paris XI
| | Sample_contact_address | 157 rue de la porte de trivaux
| | Sample_contact_city | Clamart
| | Sample_contact_zip/postal_code | 92141
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659108/suppl/GSM659108.CEL.gz
| | Sample_series_id | GSE26787
| | Sample_data_row_count | 54675
| | |
|
GSM659109 | GPL570 |
|
RT4E01
|
implantation failure
|
gender: female
tissue: endometrium
|
echec 2
|
| Sample_geo_accession | GSM659109
| | Sample_status | Public on Jan 22 2011
| | Sample_submission_date | Jan 21 2011
| | Sample_last_update_date | Jan 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy mini kit (Qiagen, Courtabeuf, France) including the RNase-Free DNAse set.Genomic DNA contamination was eliminated with RNAse inhibitor.RNA quantity and quality were confirmed by the analysis with an Experion system and RNA StdSens analysis kit (Bio-Rad)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Four micrograms of total RNA were labeled using the GeneChip® Expression 3’ Amplification One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).The cRNA was hybridized to Genechip Human Genome U133 Plus 2.0 Array (Affymetrix)
| | Sample_hyb_protocol | double-stranded cDNA was synthesized from 4 µg of total RNA primed with a poly-(dT)-T7 oligonucteotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotyin-labeled modified nucleotides during 16 hours at 37°C. Biotinylated cRNA was purified and then fragmented (35-200 nucleotides) together with hybridization controls and hybridized to the microarrays for 16 hours at 45°C. Using Fluidics Station (Affymetrix), the hybridized biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated anti-strepatvidine antibody and streptavidine R-phycoerythrin conjugate.
| | Sample_scan_protocol | The arrays were finally scanned with an affymetrix/Hewlett-Packard GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were read and pre-processed using the R sofware (http://www.R-project.org/) and especially using packages from the Bioconductor project (http://www.bioconductor.org). CEL data files were read using the affy package. Data were normalized by condition using the GC-RMA method implemented in the gcrma package. This method performs a Background Adjustment Using Sequence Information before normalized the data using the rma method (which is a quantile normalisation followed by a summarization of probes by median polish). Differential analysis was performed with the anapuce package of R2 [ http://www.agroparistech.fr/mia/doku.php?id=productions:logiciels]. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance [7]. The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.01.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nathalie,,Lédée
| | Sample_contact_email | nathalie-ledee@orange.fr
| | Sample_contact_phone | 331 45 37 44 50
| | Sample_contact_fax | 33 1 45 37 44 50
| | Sample_contact_laboratory | implantation et dialogue mother-conceptus
| | Sample_contact_department | Hopital Antoine Béclère, Pavillon Jean Dalsace
| | Sample_contact_institute | INSERM UMRS-783, université Paris XI
| | Sample_contact_address | 157 rue de la porte de trivaux
| | Sample_contact_city | Clamart
| | Sample_contact_zip/postal_code | 92141
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659109/suppl/GSM659109.CEL.gz
| | Sample_series_id | GSE26787
| | Sample_data_row_count | 54675
| | |
|
GSM659110 | GPL570 |
|
RT4E10
|
implantation failure
|
gender: female
tissue: endometrium
|
echec 3
|
| Sample_geo_accession | GSM659110
| | Sample_status | Public on Jan 22 2011
| | Sample_submission_date | Jan 21 2011
| | Sample_last_update_date | Jan 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy mini kit (Qiagen, Courtabeuf, France) including the RNase-Free DNAse set.Genomic DNA contamination was eliminated with RNAse inhibitor.RNA quantity and quality were confirmed by the analysis with an Experion system and RNA StdSens analysis kit (Bio-Rad)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Four micrograms of total RNA were labeled using the GeneChip® Expression 3’ Amplification One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).The cRNA was hybridized to Genechip Human Genome U133 Plus 2.0 Array (Affymetrix)
| | Sample_hyb_protocol | double-stranded cDNA was synthesized from 4 µg of total RNA primed with a poly-(dT)-T7 oligonucteotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotyin-labeled modified nucleotides during 16 hours at 37°C. Biotinylated cRNA was purified and then fragmented (35-200 nucleotides) together with hybridization controls and hybridized to the microarrays for 16 hours at 45°C. Using Fluidics Station (Affymetrix), the hybridized biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated anti-strepatvidine antibody and streptavidine R-phycoerythrin conjugate.
| | Sample_scan_protocol | The arrays were finally scanned with an affymetrix/Hewlett-Packard GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were read and pre-processed using the R sofware (http://www.R-project.org/) and especially using packages from the Bioconductor project (http://www.bioconductor.org). CEL data files were read using the affy package. Data were normalized by condition using the GC-RMA method implemented in the gcrma package. This method performs a Background Adjustment Using Sequence Information before normalized the data using the rma method (which is a quantile normalisation followed by a summarization of probes by median polish). Differential analysis was performed with the anapuce package of R2 [ http://www.agroparistech.fr/mia/doku.php?id=productions:logiciels]. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance [7]. The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.01.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nathalie,,Lédée
| | Sample_contact_email | nathalie-ledee@orange.fr
| | Sample_contact_phone | 331 45 37 44 50
| | Sample_contact_fax | 33 1 45 37 44 50
| | Sample_contact_laboratory | implantation et dialogue mother-conceptus
| | Sample_contact_department | Hopital Antoine Béclère, Pavillon Jean Dalsace
| | Sample_contact_institute | INSERM UMRS-783, université Paris XI
| | Sample_contact_address | 157 rue de la porte de trivaux
| | Sample_contact_city | Clamart
| | Sample_contact_zip/postal_code | 92141
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659110/suppl/GSM659110.CEL.gz
| | Sample_series_id | GSE26787
| | Sample_data_row_count | 54675
| | |
|
GSM659111 | GPL570 |
|
RT5E35
|
implantation failure
|
gender: female
tissue: endometrium
|
echec 4
|
| Sample_geo_accession | GSM659111
| | Sample_status | Public on Jan 22 2011
| | Sample_submission_date | Jan 21 2011
| | Sample_last_update_date | Jan 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy mini kit (Qiagen, Courtabeuf, France) including the RNase-Free DNAse set.Genomic DNA contamination was eliminated with RNAse inhibitor.RNA quantity and quality were confirmed by the analysis with an Experion system and RNA StdSens analysis kit (Bio-Rad)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Four micrograms of total RNA were labeled using the GeneChip® Expression 3’ Amplification One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).The cRNA was hybridized to Genechip Human Genome U133 Plus 2.0 Array (Affymetrix)
| | Sample_hyb_protocol | double-stranded cDNA was synthesized from 4 µg of total RNA primed with a poly-(dT)-T7 oligonucteotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotyin-labeled modified nucleotides during 16 hours at 37°C. Biotinylated cRNA was purified and then fragmented (35-200 nucleotides) together with hybridization controls and hybridized to the microarrays for 16 hours at 45°C. Using Fluidics Station (Affymetrix), the hybridized biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated anti-strepatvidine antibody and streptavidine R-phycoerythrin conjugate.
| | Sample_scan_protocol | The arrays were finally scanned with an affymetrix/Hewlett-Packard GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were read and pre-processed using the R sofware (http://www.R-project.org/) and especially using packages from the Bioconductor project (http://www.bioconductor.org). CEL data files were read using the affy package. Data were normalized by condition using the GC-RMA method implemented in the gcrma package. This method performs a Background Adjustment Using Sequence Information before normalized the data using the rma method (which is a quantile normalisation followed by a summarization of probes by median polish). Differential analysis was performed with the anapuce package of R2 [ http://www.agroparistech.fr/mia/doku.php?id=productions:logiciels]. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance [7]. The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.01.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nathalie,,Lédée
| | Sample_contact_email | nathalie-ledee@orange.fr
| | Sample_contact_phone | 331 45 37 44 50
| | Sample_contact_fax | 33 1 45 37 44 50
| | Sample_contact_laboratory | implantation et dialogue mother-conceptus
| | Sample_contact_department | Hopital Antoine Béclère, Pavillon Jean Dalsace
| | Sample_contact_institute | INSERM UMRS-783, université Paris XI
| | Sample_contact_address | 157 rue de la porte de trivaux
| | Sample_contact_city | Clamart
| | Sample_contact_zip/postal_code | 92141
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659111/suppl/GSM659111.CEL.gz
| | Sample_series_id | GSE26787
| | Sample_data_row_count | 54675
| | |
|
GSM659112 | GPL570 |
|
RT5E47
|
implantation failure
|
gender: female
tissue: endometrium
|
echec 5
|
| Sample_geo_accession | GSM659112
| | Sample_status | Public on Jan 22 2011
| | Sample_submission_date | Jan 21 2011
| | Sample_last_update_date | Jan 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy mini kit (Qiagen, Courtabeuf, France) including the RNase-Free DNAse set.Genomic DNA contamination was eliminated with RNAse inhibitor.RNA quantity and quality were confirmed by the analysis with an Experion system and RNA StdSens analysis kit (Bio-Rad)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Four micrograms of total RNA were labeled using the GeneChip® Expression 3’ Amplification One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).The cRNA was hybridized to Genechip Human Genome U133 Plus 2.0 Array (Affymetrix)
| | Sample_hyb_protocol | double-stranded cDNA was synthesized from 4 µg of total RNA primed with a poly-(dT)-T7 oligonucteotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotyin-labeled modified nucleotides during 16 hours at 37°C. Biotinylated cRNA was purified and then fragmented (35-200 nucleotides) together with hybridization controls and hybridized to the microarrays for 16 hours at 45°C. Using Fluidics Station (Affymetrix), the hybridized biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated anti-strepatvidine antibody and streptavidine R-phycoerythrin conjugate.
| | Sample_scan_protocol | The arrays were finally scanned with an affymetrix/Hewlett-Packard GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were read and pre-processed using the R sofware (http://www.R-project.org/) and especially using packages from the Bioconductor project (http://www.bioconductor.org). CEL data files were read using the affy package. Data were normalized by condition using the GC-RMA method implemented in the gcrma package. This method performs a Background Adjustment Using Sequence Information before normalized the data using the rma method (which is a quantile normalisation followed by a summarization of probes by median polish). Differential analysis was performed with the anapuce package of R2 [ http://www.agroparistech.fr/mia/doku.php?id=productions:logiciels]. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance [7]. The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.01.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nathalie,,Lédée
| | Sample_contact_email | nathalie-ledee@orange.fr
| | Sample_contact_phone | 331 45 37 44 50
| | Sample_contact_fax | 33 1 45 37 44 50
| | Sample_contact_laboratory | implantation et dialogue mother-conceptus
| | Sample_contact_department | Hopital Antoine Béclère, Pavillon Jean Dalsace
| | Sample_contact_institute | INSERM UMRS-783, université Paris XI
| | Sample_contact_address | 157 rue de la porte de trivaux
| | Sample_contact_city | Clamart
| | Sample_contact_zip/postal_code | 92141
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659112/suppl/GSM659112.CEL.gz
| | Sample_series_id | GSE26787
| | Sample_data_row_count | 54675
| | |
|
GSM659113 | GPL570 |
|
RT4E11
|
recurrent spontaneous abortion
|
gender: female
tissue: endometrium
|
rsa 1
|
| Sample_geo_accession | GSM659113
| | Sample_status | Public on Jan 22 2011
| | Sample_submission_date | Jan 21 2011
| | Sample_last_update_date | Jan 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy mini kit (Qiagen, Courtabeuf, France) including the RNase-Free DNAse set.Genomic DNA contamination was eliminated with RNAse inhibitor.RNA quantity and quality were confirmed by the analysis with an Experion system and RNA StdSens analysis kit (Bio-Rad)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Four micrograms of total RNA were labeled using the GeneChip® Expression 3’ Amplification One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).The cRNA was hybridized to Genechip Human Genome U133 Plus 2.0 Array (Affymetrix)
| | Sample_hyb_protocol | double-stranded cDNA was synthesized from 4 µg of total RNA primed with a poly-(dT)-T7 oligonucteotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotyin-labeled modified nucleotides during 16 hours at 37°C. Biotinylated cRNA was purified and then fragmented (35-200 nucleotides) together with hybridization controls and hybridized to the microarrays for 16 hours at 45°C. Using Fluidics Station (Affymetrix), the hybridized biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated anti-strepatvidine antibody and streptavidine R-phycoerythrin conjugate.
| | Sample_scan_protocol | The arrays were finally scanned with an affymetrix/Hewlett-Packard GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were read and pre-processed using the R sofware (http://www.R-project.org/) and especially using packages from the Bioconductor project (http://www.bioconductor.org). CEL data files were read using the affy package. Data were normalized by condition using the GC-RMA method implemented in the gcrma package. This method performs a Background Adjustment Using Sequence Information before normalized the data using the rma method (which is a quantile normalisation followed by a summarization of probes by median polish). Differential analysis was performed with the anapuce package of R2 [ http://www.agroparistech.fr/mia/doku.php?id=productions:logiciels]. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance [7]. The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.01.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nathalie,,Lédée
| | Sample_contact_email | nathalie-ledee@orange.fr
| | Sample_contact_phone | 331 45 37 44 50
| | Sample_contact_fax | 33 1 45 37 44 50
| | Sample_contact_laboratory | implantation et dialogue mother-conceptus
| | Sample_contact_department | Hopital Antoine Béclère, Pavillon Jean Dalsace
| | Sample_contact_institute | INSERM UMRS-783, université Paris XI
| | Sample_contact_address | 157 rue de la porte de trivaux
| | Sample_contact_city | Clamart
| | Sample_contact_zip/postal_code | 92141
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659113/suppl/GSM659113.CEL.gz
| | Sample_series_id | GSE26787
| | Sample_data_row_count | 54675
| | |
|
GSM659114 | GPL570 |
|
RT5E03
|
recurrent spontaneous abortion
|
gender: female
tissue: endometrium
|
rsa 2
|
| Sample_geo_accession | GSM659114
| | Sample_status | Public on Jan 22 2011
| | Sample_submission_date | Jan 21 2011
| | Sample_last_update_date | Jan 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy mini kit (Qiagen, Courtabeuf, France) including the RNase-Free DNAse set.Genomic DNA contamination was eliminated with RNAse inhibitor.RNA quantity and quality were confirmed by the analysis with an Experion system and RNA StdSens analysis kit (Bio-Rad)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Four micrograms of total RNA were labeled using the GeneChip® Expression 3’ Amplification One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).The cRNA was hybridized to Genechip Human Genome U133 Plus 2.0 Array (Affymetrix)
| | Sample_hyb_protocol | double-stranded cDNA was synthesized from 4 µg of total RNA primed with a poly-(dT)-T7 oligonucteotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotyin-labeled modified nucleotides during 16 hours at 37°C. Biotinylated cRNA was purified and then fragmented (35-200 nucleotides) together with hybridization controls and hybridized to the microarrays for 16 hours at 45°C. Using Fluidics Station (Affymetrix), the hybridized biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated anti-strepatvidine antibody and streptavidine R-phycoerythrin conjugate.
| | Sample_scan_protocol | The arrays were finally scanned with an affymetrix/Hewlett-Packard GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were read and pre-processed using the R sofware (http://www.R-project.org/) and especially using packages from the Bioconductor project (http://www.bioconductor.org). CEL data files were read using the affy package. Data were normalized by condition using the GC-RMA method implemented in the gcrma package. This method performs a Background Adjustment Using Sequence Information before normalized the data using the rma method (which is a quantile normalisation followed by a summarization of probes by median polish). Differential analysis was performed with the anapuce package of R2 [ http://www.agroparistech.fr/mia/doku.php?id=productions:logiciels]. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance [7]. The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.01.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nathalie,,Lédée
| | Sample_contact_email | nathalie-ledee@orange.fr
| | Sample_contact_phone | 331 45 37 44 50
| | Sample_contact_fax | 33 1 45 37 44 50
| | Sample_contact_laboratory | implantation et dialogue mother-conceptus
| | Sample_contact_department | Hopital Antoine Béclère, Pavillon Jean Dalsace
| | Sample_contact_institute | INSERM UMRS-783, université Paris XI
| | Sample_contact_address | 157 rue de la porte de trivaux
| | Sample_contact_city | Clamart
| | Sample_contact_zip/postal_code | 92141
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659114/suppl/GSM659114.CEL.gz
| | Sample_series_id | GSE26787
| | Sample_data_row_count | 54675
| | |
|
GSM659115 | GPL570 |
|
RT6E07
|
recurrent spontaneous abortion
|
gender: female
tissue: endometrium
|
rsa 3
|
| Sample_geo_accession | GSM659115
| | Sample_status | Public on Jan 22 2011
| | Sample_submission_date | Jan 21 2011
| | Sample_last_update_date | Jan 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy mini kit (Qiagen, Courtabeuf, France) including the RNase-Free DNAse set.Genomic DNA contamination was eliminated with RNAse inhibitor.RNA quantity and quality were confirmed by the analysis with an Experion system and RNA StdSens analysis kit (Bio-Rad)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Four micrograms of total RNA were labeled using the GeneChip® Expression 3’ Amplification One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).The cRNA was hybridized to Genechip Human Genome U133 Plus 2.0 Array (Affymetrix)
| | Sample_hyb_protocol | double-stranded cDNA was synthesized from 4 µg of total RNA primed with a poly-(dT)-T7 oligonucteotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotyin-labeled modified nucleotides during 16 hours at 37°C. Biotinylated cRNA was purified and then fragmented (35-200 nucleotides) together with hybridization controls and hybridized to the microarrays for 16 hours at 45°C. Using Fluidics Station (Affymetrix), the hybridized biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated anti-strepatvidine antibody and streptavidine R-phycoerythrin conjugate.
| | Sample_scan_protocol | The arrays were finally scanned with an affymetrix/Hewlett-Packard GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were read and pre-processed using the R sofware (http://www.R-project.org/) and especially using packages from the Bioconductor project (http://www.bioconductor.org). CEL data files were read using the affy package. Data were normalized by condition using the GC-RMA method implemented in the gcrma package. This method performs a Background Adjustment Using Sequence Information before normalized the data using the rma method (which is a quantile normalisation followed by a summarization of probes by median polish). Differential analysis was performed with the anapuce package of R2 [ http://www.agroparistech.fr/mia/doku.php?id=productions:logiciels]. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance [7]. The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.01.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nathalie,,Lédée
| | Sample_contact_email | nathalie-ledee@orange.fr
| | Sample_contact_phone | 331 45 37 44 50
| | Sample_contact_fax | 33 1 45 37 44 50
| | Sample_contact_laboratory | implantation et dialogue mother-conceptus
| | Sample_contact_department | Hopital Antoine Béclère, Pavillon Jean Dalsace
| | Sample_contact_institute | INSERM UMRS-783, université Paris XI
| | Sample_contact_address | 157 rue de la porte de trivaux
| | Sample_contact_city | Clamart
| | Sample_contact_zip/postal_code | 92141
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659115/suppl/GSM659115.CEL.gz
| | Sample_series_id | GSE26787
| | Sample_data_row_count | 54675
| | |
|
GSM659116 | GPL570 |
|
RT4E05
|
recurrent spontaneous abortion
|
gender: female
tissue: endometrium
|
rsa 4
|
| Sample_geo_accession | GSM659116
| | Sample_status | Public on Jan 22 2011
| | Sample_submission_date | Jan 21 2011
| | Sample_last_update_date | Jan 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy mini kit (Qiagen, Courtabeuf, France) including the RNase-Free DNAse set.Genomic DNA contamination was eliminated with RNAse inhibitor.RNA quantity and quality were confirmed by the analysis with an Experion system and RNA StdSens analysis kit (Bio-Rad)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Four micrograms of total RNA were labeled using the GeneChip® Expression 3’ Amplification One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).The cRNA was hybridized to Genechip Human Genome U133 Plus 2.0 Array (Affymetrix)
| | Sample_hyb_protocol | double-stranded cDNA was synthesized from 4 µg of total RNA primed with a poly-(dT)-T7 oligonucteotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotyin-labeled modified nucleotides during 16 hours at 37°C. Biotinylated cRNA was purified and then fragmented (35-200 nucleotides) together with hybridization controls and hybridized to the microarrays for 16 hours at 45°C. Using Fluidics Station (Affymetrix), the hybridized biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated anti-strepatvidine antibody and streptavidine R-phycoerythrin conjugate.
| | Sample_scan_protocol | The arrays were finally scanned with an affymetrix/Hewlett-Packard GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were read and pre-processed using the R sofware (http://www.R-project.org/) and especially using packages from the Bioconductor project (http://www.bioconductor.org). CEL data files were read using the affy package. Data were normalized by condition using the GC-RMA method implemented in the gcrma package. This method performs a Background Adjustment Using Sequence Information before normalized the data using the rma method (which is a quantile normalisation followed by a summarization of probes by median polish). Differential analysis was performed with the anapuce package of R2 [ http://www.agroparistech.fr/mia/doku.php?id=productions:logiciels]. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance [7]. The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.01.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nathalie,,Lédée
| | Sample_contact_email | nathalie-ledee@orange.fr
| | Sample_contact_phone | 331 45 37 44 50
| | Sample_contact_fax | 33 1 45 37 44 50
| | Sample_contact_laboratory | implantation et dialogue mother-conceptus
| | Sample_contact_department | Hopital Antoine Béclère, Pavillon Jean Dalsace
| | Sample_contact_institute | INSERM UMRS-783, université Paris XI
| | Sample_contact_address | 157 rue de la porte de trivaux
| | Sample_contact_city | Clamart
| | Sample_contact_zip/postal_code | 92141
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659116/suppl/GSM659116.CEL.gz
| | Sample_series_id | GSE26787
| | Sample_data_row_count | 54675
| | |
|
GSM659117 | GPL570 |
|
RT5E36
|
recurrent spontaneous abortion
|
gender: female
tissue: endometrium
|
rsa 5
|
| Sample_geo_accession | GSM659117
| | Sample_status | Public on Jan 22 2011
| | Sample_submission_date | Jan 21 2011
| | Sample_last_update_date | Jan 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with the Qiagen RNeasy mini kit (Qiagen, Courtabeuf, France) including the RNase-Free DNAse set.Genomic DNA contamination was eliminated with RNAse inhibitor.RNA quantity and quality were confirmed by the analysis with an Experion system and RNA StdSens analysis kit (Bio-Rad)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Four micrograms of total RNA were labeled using the GeneChip® Expression 3’ Amplification One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).The cRNA was hybridized to Genechip Human Genome U133 Plus 2.0 Array (Affymetrix)
| | Sample_hyb_protocol | double-stranded cDNA was synthesized from 4 µg of total RNA primed with a poly-(dT)-T7 oligonucteotide. The cDNA was used in an in vitro transcription reaction (IVT) in the presence of T7 RNA polymerase and biotyin-labeled modified nucleotides during 16 hours at 37°C. Biotinylated cRNA was purified and then fragmented (35-200 nucleotides) together with hybridization controls and hybridized to the microarrays for 16 hours at 45°C. Using Fluidics Station (Affymetrix), the hybridized biotin-labeled cRNA was revealed by successive reactions with streptavidin R-phycoerythrin conjugate, biotinylated anti-strepatvidine antibody and streptavidine R-phycoerythrin conjugate.
| | Sample_scan_protocol | The arrays were finally scanned with an affymetrix/Hewlett-Packard GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were read and pre-processed using the R sofware (http://www.R-project.org/) and especially using packages from the Bioconductor project (http://www.bioconductor.org). CEL data files were read using the affy package. Data were normalized by condition using the GC-RMA method implemented in the gcrma package. This method performs a Background Adjustment Using Sequence Information before normalized the data using the rma method (which is a quantile normalisation followed by a summarization of probes by median polish). Differential analysis was performed with the anapuce package of R2 [ http://www.agroparistech.fr/mia/doku.php?id=productions:logiciels]. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance [7]. The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.01.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Nathalie,,Lédée
| | Sample_contact_email | nathalie-ledee@orange.fr
| | Sample_contact_phone | 331 45 37 44 50
| | Sample_contact_fax | 33 1 45 37 44 50
| | Sample_contact_laboratory | implantation et dialogue mother-conceptus
| | Sample_contact_department | Hopital Antoine Béclère, Pavillon Jean Dalsace
| | Sample_contact_institute | INSERM UMRS-783, université Paris XI
| | Sample_contact_address | 157 rue de la porte de trivaux
| | Sample_contact_city | Clamart
| | Sample_contact_zip/postal_code | 92141
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM659nnn/GSM659117/suppl/GSM659117.CEL.gz
| | Sample_series_id | GSE26787
| | Sample_data_row_count | 54675
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