Search results for the GEO ID: GSE33168  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM821262 | GPL570 |
|
second_trimester_euploid_AF_normalAFstudy_female1
|
second_trimester_euploid_AF_normalAFstudy_female
|
gender: female
developmental stage: fetus
rna source: cell free mRNA from second trimester amniotic fluid
|
femaleAF1
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM821262
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Jan 11 2012
| | 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 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (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 | Donna,K,Slonim
| | Sample_contact_email | Donna.Slonim@tufts.edu
| | Sample_contact_fax | (617) 627-2227
| | Sample_contact_department | 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 | 01845
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821262/suppl/GSM821262_femaleAF1.cel.gz
| | Sample_relation | Reanalysis of: GSM629855
| | Sample_series_id | GSE33168
| | Sample_data_row_count | 54675
| | |
|
GSM821263 | GPL570 |
|
second_trimester_euploid_AF_normalAFstudy_female2
|
second_trimester_euploid_AF_normalAFstudy_female
|
gender: female
developmental stage: fetus
rna source: cell free mRNA from second trimester amniotic fluid
|
femaleAF2
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM821263
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Jan 11 2012
| | 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 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (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 | Donna,K,Slonim
| | Sample_contact_email | Donna.Slonim@tufts.edu
| | Sample_contact_fax | (617) 627-2227
| | Sample_contact_department | 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 | 01845
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821263/suppl/GSM821263_femaleAF2.cel.gz
| | Sample_relation | Reanalysis of: GSM629856
| | Sample_series_id | GSE33168
| | Sample_data_row_count | 54675
| | |
|
GSM821264 | GPL570 |
|
second_trimester_euploid_AF_normalAFstudy_female3
|
second_trimester_euploid_AF_normalAFstudy_female
|
gender: female
developmental stage: fetus
rna source: cell free mRNA from second trimester amniotic fluid
|
femaleAF3
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM821264
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Jan 11 2012
| | 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 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (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 | Donna,K,Slonim
| | Sample_contact_email | Donna.Slonim@tufts.edu
| | Sample_contact_fax | (617) 627-2227
| | Sample_contact_department | 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 | 01845
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821264/suppl/GSM821264_femaleAF3.cel.gz
| | Sample_relation | Reanalysis of: GSM406286
| | Sample_series_id | GSE33168
| | Sample_data_row_count | 54675
| | |
|
GSM821265 | GPL570 |
|
second_trimester_euploid_AF_normalAFstudy_female4
|
second_trimester_euploid_AF_normalAFstudy_female
|
gender: female
developmental stage: fetus
rna source: cell free mRNA from second trimester amniotic fluid
|
femaleAF4
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM821265
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Jan 11 2012
| | 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 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (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 | Donna,K,Slonim
| | Sample_contact_email | Donna.Slonim@tufts.edu
| | Sample_contact_fax | (617) 627-2227
| | Sample_contact_department | 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 | 01845
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821265/suppl/GSM821265_femaleAF4.cel.gz
| | Sample_relation | Reanalysis of: GSM629858
| | Sample_series_id | GSE33168
| | Sample_data_row_count | 54675
| | |
|
GSM821266 | GPL570 |
|
second_trimester_euploid_AF_normalAFstudy_female5
|
second_trimester_euploid_AF_normalAFstudy_female
|
gender: female
developmental stage: fetus
rna source: cell free mRNA from second trimester amniotic fluid
|
femaleAF5
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM821266
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Jan 11 2012
| | 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 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (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 | Donna,K,Slonim
| | Sample_contact_email | Donna.Slonim@tufts.edu
| | Sample_contact_fax | (617) 627-2227
| | Sample_contact_department | 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 | 01845
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821266/suppl/GSM821266_femaleAF5.cel.gz
| | Sample_relation | Reanalysis of: GSM406288
| | Sample_series_id | GSE33168
| | Sample_data_row_count | 54675
| | |
|
GSM821267 | GPL570 |
|
second_trimester_euploid_AF_normalAFstudy_female6
|
second_trimester_euploid_AF_normalAFstudy_female
|
gender: female
developmental stage: fetus
rna source: cell free mRNA from second trimester amniotic fluid
|
femaleAF6
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM821267
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Jan 11 2012
| | 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 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (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 | Donna,K,Slonim
| | Sample_contact_email | Donna.Slonim@tufts.edu
| | Sample_contact_fax | (617) 627-2227
| | Sample_contact_department | 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 | 01845
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821267/suppl/GSM821267_femaleAF6.cel.gz
| | Sample_relation | Reanalysis of: GSM629860
| | Sample_series_id | GSE33168
| | Sample_data_row_count | 54675
| | |
|
GSM821268 | GPL570 |
|
second_trimester_euploid_AF_normalAFstudy_male1
|
second_trimester_euploid_AF_normalAFstudy_male
|
gender: male
developmental stage: fetus
rna source: cell free mRNA from second trimester amniotic fluid
|
maleAF1
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM821268
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Jan 11 2012
| | 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 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (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 | Donna,K,Slonim
| | Sample_contact_email | Donna.Slonim@tufts.edu
| | Sample_contact_fax | (617) 627-2227
| | Sample_contact_department | 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 | 01845
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821268/suppl/GSM821268_maleAF1.cel.gz
| | Sample_relation | Reanalysis of: GSM406294
| | Sample_series_id | GSE33168
| | Sample_data_row_count | 54675
| | |
|
GSM821269 | GPL570 |
|
second_trimester_euploid_AF_normalAFstudy_male2
|
second_trimester_euploid_AF_normalAFstudy_male
|
gender: male
developmental stage: fetus
rna source: cell free mRNA from second trimester amniotic fluid
|
maleAF2
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM821269
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Jan 11 2012
| | 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 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (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 | Donna,K,Slonim
| | Sample_contact_email | Donna.Slonim@tufts.edu
| | Sample_contact_fax | (617) 627-2227
| | Sample_contact_department | 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 | 01845
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821269/suppl/GSM821269_maleAF2.cel.gz
| | Sample_relation | Reanalysis of: GSM406296
| | Sample_series_id | GSE33168
| | Sample_data_row_count | 54675
| | |
|
GSM821270 | GPL570 |
|
second_trimester_euploid_AF_normalAFstudy_male3
|
second_trimester_euploid_AF_normalAFstudy_male
|
gender: male
developmental stage: fetus
rna source: cell free mRNA from second trimester amniotic fluid
|
maleAF3
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM821270
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Jan 11 2012
| | 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 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (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 | Donna,K,Slonim
| | Sample_contact_email | Donna.Slonim@tufts.edu
| | Sample_contact_fax | (617) 627-2227
| | Sample_contact_department | 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 | 01845
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821270/suppl/GSM821270_maleAF3.cel.gz
| | Sample_relation | Reanalysis of: GSM406292
| | Sample_series_id | GSE33168
| | Sample_data_row_count | 54675
| | |
|
GSM821271 | GPL570 |
|
second_trimester_euploid_AF_normalAFstudy_male4
|
second_trimester_euploid_AF_normalAFstudy_male
|
gender: male
developmental stage: fetus
rna source: cell free mRNA from second trimester amniotic fluid
|
maleAF4
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM821271
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Jan 11 2012
| | 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 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (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 | Donna,K,Slonim
| | Sample_contact_email | Donna.Slonim@tufts.edu
| | Sample_contact_fax | (617) 627-2227
| | Sample_contact_department | 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 | 01845
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821271/suppl/GSM821271_maleAF4.cel.gz
| | Sample_series_id | GSE33168
| | Sample_data_row_count | 54675
| | |
|
GSM821272 | GPL570 |
|
second_trimester_euploid_AF_normalAFstudy_male5
|
second_trimester_euploid_AF_normalAFstudy_male
|
gender: male
developmental stage: fetus
rna source: cell free mRNA from second trimester amniotic fluid
|
maleAF5
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM821272
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Jan 11 2012
| | 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 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (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 | Donna,K,Slonim
| | Sample_contact_email | Donna.Slonim@tufts.edu
| | Sample_contact_fax | (617) 627-2227
| | Sample_contact_department | 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 | 01845
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821272/suppl/GSM821272_maleAF5.cel.gz
| | Sample_relation | Reanalysis of: GSM406290
| | Sample_series_id | GSE33168
| | Sample_data_row_count | 54675
| | |
|
GSM821273 | GPL570 |
|
second_trimester_euploid_AF_normalAFstudy_male6
|
second_trimester_euploid_AF_normalAFstudy_male
|
gender: male
developmental stage: fetus
rna source: cell free mRNA from second trimester amniotic fluid
|
maleAF6
gene expression data from normal second trimester fetus
|
| Sample_geo_accession | GSM821273
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Oct 24 2011
| | Sample_last_update_date | Jan 11 2012
| | 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 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (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 | Donna,K,Slonim
| | Sample_contact_email | Donna.Slonim@tufts.edu
| | Sample_contact_fax | (617) 627-2227
| | Sample_contact_department | 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 | 01845
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM821nnn/GSM821273/suppl/GSM821273_maleAF6.cel.gz
| | Sample_relation | Reanalysis of: GSM406298
| | Sample_series_id | GSE33168
| | Sample_data_row_count | 54675
| | |
|
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