Search results for the GEO ID: GSE46286  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1128138 | GPL570 |
|
Term_AF_sample_1_male_37_weeks
|
cell free mRNA from term amniotic fluid
|
gender: male
Stage: term
|
gene expression data from normal term fetus
|
| Sample_geo_accession | GSM1128138
| | Sample_status | Public on Apr 23 2013
| | Sample_submission_date | Apr 22 2013
| | Sample_last_update_date | Apr 23 2013
| | 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 | RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
| | Sample_hyb_protocol | Arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Heather,C,Wick
| | Sample_contact_email | hwick@cs.tufts.edu
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | Tufts University
| | Sample_contact_address | 161 College Ave
| | Sample_contact_city | Medford
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02155
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://dflat.cs.tufts.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1128nnn/GSM1128138/suppl/GSM1128138_Term_AF_sample_1_male_37_weeks.CEL.gz
| | Sample_series_id | GSE46286
| | Sample_data_row_count | 54675
| | |
|
GSM1128139 | GPL570 |
|
Term_AF_sample_2_female_37_weeks
|
cell free mRNA from term amniotic fluid
|
gender: female
Stage: term
|
gene expression data from normal term fetus
|
| Sample_geo_accession | GSM1128139
| | Sample_status | Public on Apr 23 2013
| | Sample_submission_date | Apr 22 2013
| | Sample_last_update_date | Apr 23 2013
| | 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 | RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
| | Sample_hyb_protocol | Arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Heather,C,Wick
| | Sample_contact_email | hwick@cs.tufts.edu
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | Tufts University
| | Sample_contact_address | 161 College Ave
| | Sample_contact_city | Medford
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02155
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://dflat.cs.tufts.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1128nnn/GSM1128139/suppl/GSM1128139_Term_AF_sample_2_female_37_weeks.CEL.gz
| | Sample_series_id | GSE46286
| | Sample_data_row_count | 54675
| | |
|
GSM1128140 | GPL570 |
|
Term_AF_sample_3_male_39_weeks
|
cell free mRNA from term amniotic fluid
|
gender: male
Stage: term
|
gene expression data from normal term fetus
|
| Sample_geo_accession | GSM1128140
| | Sample_status | Public on Apr 23 2013
| | Sample_submission_date | Apr 22 2013
| | Sample_last_update_date | Apr 23 2013
| | 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 | RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
| | Sample_hyb_protocol | Arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Heather,C,Wick
| | Sample_contact_email | hwick@cs.tufts.edu
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | Tufts University
| | Sample_contact_address | 161 College Ave
| | Sample_contact_city | Medford
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02155
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://dflat.cs.tufts.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1128nnn/GSM1128140/suppl/GSM1128140_Term_AF_sample_3_male_39_weeks.CEL.gz
| | Sample_series_id | GSE46286
| | Sample_data_row_count | 54675
| | |
|
GSM1128141 | GPL570 |
|
Term_AF_sample_4_male_37_weeks
|
cell free mRNA from term amniotic fluid
|
gender: male
Stage: term
|
gene expression data from normal term fetus
|
| Sample_geo_accession | GSM1128141
| | Sample_status | Public on Apr 23 2013
| | Sample_submission_date | Apr 22 2013
| | Sample_last_update_date | Apr 23 2013
| | 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 | RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
| | Sample_hyb_protocol | Arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Heather,C,Wick
| | Sample_contact_email | hwick@cs.tufts.edu
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | Tufts University
| | Sample_contact_address | 161 College Ave
| | Sample_contact_city | Medford
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02155
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://dflat.cs.tufts.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1128nnn/GSM1128141/suppl/GSM1128141_Term_AF_sample_4_male_37_weeks.CEL.gz
| | Sample_series_id | GSE46286
| | Sample_data_row_count | 54675
| | |
|
GSM1128142 | GPL570 |
|
Term_AF_sample_5_male_39_weeks
|
cell free mRNA from term amniotic fluid
|
gender: male
Stage: term
|
gene expression data from normal term fetus
|
| Sample_geo_accession | GSM1128142
| | Sample_status | Public on Apr 23 2013
| | Sample_submission_date | Apr 22 2013
| | Sample_last_update_date | Apr 23 2013
| | 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 | RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
| | Sample_hyb_protocol | Arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Heather,C,Wick
| | Sample_contact_email | hwick@cs.tufts.edu
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | Tufts University
| | Sample_contact_address | 161 College Ave
| | Sample_contact_city | Medford
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02155
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://dflat.cs.tufts.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1128nnn/GSM1128142/suppl/GSM1128142_Term_AF_sample_5_male_39_weeks.CEL.gz
| | Sample_series_id | GSE46286
| | Sample_data_row_count | 54675
| | |
|
GSM1128143 | GPL570 |
|
Term_AF_sample_6_male_37_weeks
|
cell free mRNA from term amniotic fluid
|
gender: male
Stage: term
|
gene expression data from normal term fetus
|
| Sample_geo_accession | GSM1128143
| | Sample_status | Public on Apr 23 2013
| | Sample_submission_date | Apr 22 2013
| | Sample_last_update_date | Apr 23 2013
| | 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 | RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
| | Sample_hyb_protocol | Arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Heather,C,Wick
| | Sample_contact_email | hwick@cs.tufts.edu
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | Tufts University
| | Sample_contact_address | 161 College Ave
| | Sample_contact_city | Medford
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02155
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://dflat.cs.tufts.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1128nnn/GSM1128143/suppl/GSM1128143_Term_AF_sample_6_male_37_weeks.CEL.gz
| | Sample_series_id | GSE46286
| | Sample_data_row_count | 54675
| | |
|
GSM1128144 | GPL570 |
|
Term_AF_sample_7_female_39_weeks
|
cell free mRNA from term amniotic fluid
|
gender: female
Stage: term
|
gene expression data from normal term fetus
|
| Sample_geo_accession | GSM1128144
| | Sample_status | Public on Apr 23 2013
| | Sample_submission_date | Apr 22 2013
| | Sample_last_update_date | Apr 23 2013
| | 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 | RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
| | Sample_hyb_protocol | Arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Heather,C,Wick
| | Sample_contact_email | hwick@cs.tufts.edu
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | Tufts University
| | Sample_contact_address | 161 College Ave
| | Sample_contact_city | Medford
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02155
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://dflat.cs.tufts.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1128nnn/GSM1128144/suppl/GSM1128144_Term_AF_sample_7_female_39_weeks.CEL.gz
| | Sample_series_id | GSE46286
| | Sample_data_row_count | 54675
| | |
|
GSM1128145 | GPL570 |
|
Term_AF_sample_8_female_39_weeks
|
cell free mRNA from term amniotic fluid
|
gender: female
Stage: term
|
gene expression data from normal term fetus
|
| Sample_geo_accession | GSM1128145
| | Sample_status | Public on Apr 23 2013
| | Sample_submission_date | Apr 22 2013
| | Sample_last_update_date | Apr 23 2013
| | 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 | RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
| | Sample_hyb_protocol | Arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Heather,C,Wick
| | Sample_contact_email | hwick@cs.tufts.edu
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | Tufts University
| | Sample_contact_address | 161 College Ave
| | Sample_contact_city | Medford
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02155
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://dflat.cs.tufts.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1128nnn/GSM1128145/suppl/GSM1128145_Term_AF_sample_8_female_39_weeks.CEL.gz
| | Sample_series_id | GSE46286
| | Sample_data_row_count | 54675
| | |
|
GSM1128146 | GPL570 |
|
Midtrimester_AF_sample_1_male_16_weeks
|
cell free mRNA from second trimester amniotic fluid
|
gender: male
Stage: second trimester
|
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM1128146
| | Sample_status | Public on Apr 23 2013
| | Sample_submission_date | Apr 22 2013
| | Sample_last_update_date | Apr 23 2013
| | 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 | RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
| | Sample_hyb_protocol | Arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Heather,C,Wick
| | Sample_contact_email | hwick@cs.tufts.edu
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | Tufts University
| | Sample_contact_address | 161 College Ave
| | Sample_contact_city | Medford
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02155
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://dflat.cs.tufts.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1128nnn/GSM1128146/suppl/GSM1128146_Midtrimester_AF_sample_1_male_16_weeks.CEL.gz
| | Sample_series_id | GSE46286
| | Sample_data_row_count | 54675
| | |
|
GSM1128147 | GPL570 |
|
Midtrimester_AF_sample_2_female_19_weeks
|
cell free mRNA from second trimester amniotic fluid
|
gender: female
Stage: second trimester
|
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM1128147
| | Sample_status | Public on Apr 23 2013
| | Sample_submission_date | Apr 22 2013
| | Sample_last_update_date | Aug 14 2013
| | 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 | RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
| | Sample_hyb_protocol | Arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Heather,C,Wick
| | Sample_contact_email | hwick@cs.tufts.edu
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | Tufts University
| | Sample_contact_address | 161 College Ave
| | Sample_contact_city | Medford
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02155
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://dflat.cs.tufts.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1128nnn/GSM1128147/suppl/GSM1128147_Midtrimester_AF_sample_2_female_19_weeks.CEL.gz
| | Sample_relation | Alternative to: GSM1208973
| | Sample_series_id | GSE46286
| | Sample_data_row_count | 54675
| | |
|
GSM1128148 | GPL570 |
|
Midtrimester_AF_sample_3_female_18_weeks
|
cell free mRNA from second trimester amniotic fluid
|
gender: female
Stage: second trimester
|
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM1128148
| | Sample_status | Public on Apr 23 2013
| | Sample_submission_date | Apr 22 2013
| | Sample_last_update_date | Aug 14 2013
| | 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 | RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
| | Sample_hyb_protocol | Arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Heather,C,Wick
| | Sample_contact_email | hwick@cs.tufts.edu
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | Tufts University
| | Sample_contact_address | 161 College Ave
| | Sample_contact_city | Medford
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02155
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://dflat.cs.tufts.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1128nnn/GSM1128148/suppl/GSM1128148_Midtrimester_AF_sample_3_female_18_weeks.CEL.gz
| | Sample_relation | Alternative to: GSM1208974
| | Sample_series_id | GSE46286
| | Sample_data_row_count | 54675
| | |
|
GSM1128149 | GPL570 |
|
Midtrimester_AF_sample_4_male_17_weeks
|
cell free mRNA from second trimester amniotic fluid
|
gender: male
Stage: second trimester
|
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM1128149
| | Sample_status | Public on Apr 23 2013
| | Sample_submission_date | Apr 22 2013
| | Sample_last_update_date | Aug 14 2013
| | 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 | RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
| | Sample_hyb_protocol | Arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Heather,C,Wick
| | Sample_contact_email | hwick@cs.tufts.edu
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | Tufts University
| | Sample_contact_address | 161 College Ave
| | Sample_contact_city | Medford
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02155
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://dflat.cs.tufts.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1128nnn/GSM1128149/suppl/GSM1128149_Midtrimester_AF_sample_4_male_17_weeks.CEL.gz
| | Sample_relation | Alternative to: GSM1208975
| | Sample_series_id | GSE46286
| | Sample_data_row_count | 54675
| | |
|
GSM1128150 | GPL570 |
|
Midtrimester_AF_sample_5_male_17_weeks
|
cell free mRNA from second trimester amniotic fluid
|
gender: male
Stage: second trimester
|
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM1128150
| | Sample_status | Public on Apr 23 2013
| | Sample_submission_date | Apr 22 2013
| | Sample_last_update_date | Aug 14 2013
| | 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 | RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
| | Sample_hyb_protocol | Arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Heather,C,Wick
| | Sample_contact_email | hwick@cs.tufts.edu
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | Tufts University
| | Sample_contact_address | 161 College Ave
| | Sample_contact_city | Medford
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02155
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://dflat.cs.tufts.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1128nnn/GSM1128150/suppl/GSM1128150_Midtrimester_AF_sample_5_male_17_weeks.CEL.gz
| | Sample_relation | Alternative to: GSM1208976
| | Sample_series_id | GSE46286
| | Sample_data_row_count | 54675
| | |
|
GSM1128151 | GPL570 |
|
Midtrimester_AF_sample_6_male_19_weeks
|
cell free mRNA from second trimester amniotic fluid
|
gender: male
Stage: second trimester
|
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM1128151
| | Sample_status | Public on Apr 23 2013
| | Sample_submission_date | Apr 22 2013
| | Sample_last_update_date | Aug 14 2013
| | 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 | RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
| | Sample_hyb_protocol | Arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Heather,C,Wick
| | Sample_contact_email | hwick@cs.tufts.edu
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | Tufts University
| | Sample_contact_address | 161 College Ave
| | Sample_contact_city | Medford
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02155
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://dflat.cs.tufts.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1128nnn/GSM1128151/suppl/GSM1128151_Midtrimester_AF_sample_6_male_19_weeks.CEL.gz
| | Sample_relation | Alternative to: GSM1208977
| | Sample_series_id | GSE46286
| | Sample_data_row_count | 54675
| | |
|
GSM1128152 | GPL570 |
|
Midtrimester_AF_sample_7_male_16_weeks
|
cell free mRNA from second trimester amniotic fluid
|
gender: male
Stage: second trimester
|
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM1128152
| | Sample_status | Public on Apr 23 2013
| | Sample_submission_date | Apr 22 2013
| | Sample_last_update_date | Apr 23 2013
| | 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 | RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
| | Sample_hyb_protocol | Arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Heather,C,Wick
| | Sample_contact_email | hwick@cs.tufts.edu
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | Tufts University
| | Sample_contact_address | 161 College Ave
| | Sample_contact_city | Medford
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02155
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://dflat.cs.tufts.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1128nnn/GSM1128152/suppl/GSM1128152_Midtrimester_AF_sample_7_male_16_weeks.CEL.gz
| | Sample_series_id | GSE46286
| | Sample_data_row_count | 54675
| | |
|
GSM1128153 | GPL570 |
|
Midtrimester_AF_sample_8_female_15_weeks
|
cell free mRNA from second trimester amniotic fluid
|
gender: female
Stage: second trimester
|
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM1128153
| | Sample_status | Public on Apr 23 2013
| | Sample_submission_date | Apr 22 2013
| | Sample_last_update_date | Apr 23 2013
| | 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 | RNA was extracted from 5-10 mL AF.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)
| | Sample_hyb_protocol | Arrays were washed and stained with streptavidin-phycoerythrin.
| | Sample_scan_protocol | Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method. To obtain detection calls consistent with those produced by Affymetrix' 5.0 software, we used the mas5calls function from the Bioconductor affy package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Heather,C,Wick
| | Sample_contact_email | hwick@cs.tufts.edu
| | Sample_contact_department | Department of Computer Science
| | Sample_contact_institute | Tufts University
| | Sample_contact_address | 161 College Ave
| | Sample_contact_city | Medford
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02155
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://dflat.cs.tufts.edu
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1128nnn/GSM1128153/suppl/GSM1128153_Midtrimester_AF_sample_8_female_15_weeks.CEL.gz
| | Sample_series_id | GSE46286
| | Sample_data_row_count | 54675
| | |
|
| |
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