Search results for the GEO ID: GSE39402  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM967430 | GPL1261 |
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flox_control_ovary_5months_age
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ovary_mouse 5 months old
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strain: C57BL/6
gender: female
tissue: ovary
genotype: era f/f_estrogen receptor alpha flox
age: 5 months
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| Sample_geo_accession | GSM967430
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Jul 16 2012
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Ovarian tumor tissue and normal ovarian tissue was snap frozen in liquid nitrogen and then homogenized using a bead beater.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from ovarian tumor tissue or normal ovary tissue after tissue was homogenized using a bead beater. Total RNA was cleaned up using Qiagen kit and protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Microarrays were processed by the W. M. Keck Center for Comparative and Functional Genomics in the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign. Labeled antisense RNA was prepared utilizing the GeneChip 3' IVT Express Kit Labeling and Control Reagents kit (Affymetrix, Inc., Santa Clara, CA), according to the manufacturer’s manual P/N 702646 Revision 1. Briefly, 100 nanograms of total RNA was spiked with four prokaryotic polyadenylated sense RNA controls, primed with a T7-(dT) oligonucleotide containing a T7 promoter sequence, and reverse transcribed to synthesize first-strand DNA. A double-stranded DNA template was then synthesized with DNA polymerase along with RNase H to degrade RNA. The resulting cDNA was in vitro transcribed with the addition of a biotinylated ribonucleotide analog, and amplified at 40°C for 14 hours. The resulting biotin-labeled antisense RNA was purified with magnetic beads, quantified, and fragmented to produce lengths of less than 200 nucleotides.
| | Sample_hyb_protocol | The Affymetrix Alternative Protocol for Eukaryotic Target Hybridization manual P/N 702232 Revision 2 Appendices B and C was utilized for hybridization, washing, and staining. A cocktail was prepared with 15 micrograms of aRNA, adding biotinylated, fragmented hybridization controls: four prokaryotic antisense RNAs and one synthetic oligonucleotide. Following a 16-hour hybridization to an Affymetrix GeneChip 3’ Expression Mouse Genome 430 2.0 Array at 45°C and 60 rpm in a GeneChip model 640 oven, the chip was washed, and stained first with streptavidin-conjugated phycoerythrin dye (Invitrogen Corporation, Carlsbad, CA). The stain was enhanced with biotinylated goat anti-streptavidin antibody (Vector Laboratories, Burlingame, CA), and counterstained with additional conjugated phycoerythrin utilizing a GeneChip Fluidics Station model 450 and the GeneChip Command Console (AGCC) Fluidics Control software version 1.0.
| | Sample_scan_protocol | The chip was scanned with a GeneChip Scanner model 3000 7G Plus. Raw fluorescence signals for pixels within each probe feature in the image (DAT) file were converted to a single feature fluorescence value utilizing the Cell Analysis algorithm incorporated in the AGCC Scan Control version 1.0 to generate a fluorescence intensity (CEL) file. The quality of the image file was evaluated visually before further processing.
| | Sample_data_processing | The CEL files in each experiment were analyzed with Affymetrix Expression Console version 1.1 utilizing the MAS5 algorithm, selecting the scaling parameter for all probe sets, and an arbitrary target value of 150 to generate chip and report files. A quality control summary of metrics, labeling and hybridization controls, and housekeeping genes for all files within the experiment was generated by the Keck Center Functional Genomics staff and results were evaluated for accuracy and consistency.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mary,,Laws
| | Sample_contact_email | maryjolaws@gmail.com
| | Sample_contact_institute | University of Illinois
| | Sample_contact_address | 2001 S. Lincoln Ave.
| | Sample_contact_city | Urbana
| | Sample_contact_zip/postal_code | 61802
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967430/suppl/GSM967430_3590_E_F5_Mouse430_2_.150.mas5.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967430/suppl/GSM967430_3590_E_F5_Mouse430_2_.CEL.gz
| | Sample_series_id | GSE39402
| | Sample_data_row_count | 45101
| | |
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GSM967431 | GPL1261 |
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flox_control_ovary_10months_age
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ovary_mouse 10 months old
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strain: C57BL/6
gender: female
tissue: ovary
genotype: era f/f_estrogen receptor alpha flox
age: 5 months
|
|
| Sample_geo_accession | GSM967431
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Jul 16 2012
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Ovarian tumor tissue and normal ovarian tissue was snap frozen in liquid nitrogen and then homogenized using a bead beater.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from ovarian tumor tissue or normal ovary tissue after tissue was homogenized using a bead beater. Total RNA was cleaned up using Qiagen kit and protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Microarrays were processed by the W. M. Keck Center for Comparative and Functional Genomics in the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign. Labeled antisense RNA was prepared utilizing the GeneChip 3' IVT Express Kit Labeling and Control Reagents kit (Affymetrix, Inc., Santa Clara, CA), according to the manufacturer’s manual P/N 702646 Revision 1. Briefly, 100 nanograms of total RNA was spiked with four prokaryotic polyadenylated sense RNA controls, primed with a T7-(dT) oligonucleotide containing a T7 promoter sequence, and reverse transcribed to synthesize first-strand DNA. A double-stranded DNA template was then synthesized with DNA polymerase along with RNase H to degrade RNA. The resulting cDNA was in vitro transcribed with the addition of a biotinylated ribonucleotide analog, and amplified at 40°C for 14 hours. The resulting biotin-labeled antisense RNA was purified with magnetic beads, quantified, and fragmented to produce lengths of less than 200 nucleotides.
| | Sample_hyb_protocol | The Affymetrix Alternative Protocol for Eukaryotic Target Hybridization manual P/N 702232 Revision 2 Appendices B and C was utilized for hybridization, washing, and staining. A cocktail was prepared with 15 micrograms of aRNA, adding biotinylated, fragmented hybridization controls: four prokaryotic antisense RNAs and one synthetic oligonucleotide. Following a 16-hour hybridization to an Affymetrix GeneChip 3’ Expression Mouse Genome 430 2.0 Array at 45°C and 60 rpm in a GeneChip model 640 oven, the chip was washed, and stained first with streptavidin-conjugated phycoerythrin dye (Invitrogen Corporation, Carlsbad, CA). The stain was enhanced with biotinylated goat anti-streptavidin antibody (Vector Laboratories, Burlingame, CA), and counterstained with additional conjugated phycoerythrin utilizing a GeneChip Fluidics Station model 450 and the GeneChip Command Console (AGCC) Fluidics Control software version 1.0.
| | Sample_scan_protocol | The chip was scanned with a GeneChip Scanner model 3000 7G Plus. Raw fluorescence signals for pixels within each probe feature in the image (DAT) file were converted to a single feature fluorescence value utilizing the Cell Analysis algorithm incorporated in the AGCC Scan Control version 1.0 to generate a fluorescence intensity (CEL) file. The quality of the image file was evaluated visually before further processing.
| | Sample_data_processing | The CEL files in each experiment were analyzed with Affymetrix Expression Console version 1.1 utilizing the MAS5 algorithm, selecting the scaling parameter for all probe sets, and an arbitrary target value of 150 to generate chip and report files. A quality control summary of metrics, labeling and hybridization controls, and housekeeping genes for all files within the experiment was generated by the Keck Center Functional Genomics staff and results were evaluated for accuracy and consistency.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mary,,Laws
| | Sample_contact_email | maryjolaws@gmail.com
| | Sample_contact_institute | University of Illinois
| | Sample_contact_address | 2001 S. Lincoln Ave.
| | Sample_contact_city | Urbana
| | Sample_contact_zip/postal_code | 61802
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967431/suppl/GSM967431_3593_E_F10_Mouse430_2_.150.mas5.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967431/suppl/GSM967431_3593_E_F10_Mouse430_2_.CEL.gz
| | Sample_series_id | GSE39402
| | Sample_data_row_count | 45101
| | |
|
GSM967432 | GPL1261 |
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erad/d_ovarian tumor_5 months_age
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ovarian tumor from era d/d mouse 5 months old
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strain: C57BL/6
gender: female
tissue: ovarian tumor
genotype: era d/d_conditional deletion of estrogen receptor alpha mediated by cre driven by progestrogen receptor
age: 10 months
|
|
| Sample_geo_accession | GSM967432
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Jul 16 2012
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Ovarian tumor tissue and normal ovarian tissue was snap frozen in liquid nitrogen and then homogenized using a bead beater.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from ovarian tumor tissue or normal ovary tissue after tissue was homogenized using a bead beater. Total RNA was cleaned up using Qiagen kit and protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Microarrays were processed by the W. M. Keck Center for Comparative and Functional Genomics in the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign. Labeled antisense RNA was prepared utilizing the GeneChip 3' IVT Express Kit Labeling and Control Reagents kit (Affymetrix, Inc., Santa Clara, CA), according to the manufacturer’s manual P/N 702646 Revision 1. Briefly, 100 nanograms of total RNA was spiked with four prokaryotic polyadenylated sense RNA controls, primed with a T7-(dT) oligonucleotide containing a T7 promoter sequence, and reverse transcribed to synthesize first-strand DNA. A double-stranded DNA template was then synthesized with DNA polymerase along with RNase H to degrade RNA. The resulting cDNA was in vitro transcribed with the addition of a biotinylated ribonucleotide analog, and amplified at 40°C for 14 hours. The resulting biotin-labeled antisense RNA was purified with magnetic beads, quantified, and fragmented to produce lengths of less than 200 nucleotides.
| | Sample_hyb_protocol | The Affymetrix Alternative Protocol for Eukaryotic Target Hybridization manual P/N 702232 Revision 2 Appendices B and C was utilized for hybridization, washing, and staining. A cocktail was prepared with 15 micrograms of aRNA, adding biotinylated, fragmented hybridization controls: four prokaryotic antisense RNAs and one synthetic oligonucleotide. Following a 16-hour hybridization to an Affymetrix GeneChip 3’ Expression Mouse Genome 430 2.0 Array at 45°C and 60 rpm in a GeneChip model 640 oven, the chip was washed, and stained first with streptavidin-conjugated phycoerythrin dye (Invitrogen Corporation, Carlsbad, CA). The stain was enhanced with biotinylated goat anti-streptavidin antibody (Vector Laboratories, Burlingame, CA), and counterstained with additional conjugated phycoerythrin utilizing a GeneChip Fluidics Station model 450 and the GeneChip Command Console (AGCC) Fluidics Control software version 1.0.
| | Sample_scan_protocol | The chip was scanned with a GeneChip Scanner model 3000 7G Plus. Raw fluorescence signals for pixels within each probe feature in the image (DAT) file were converted to a single feature fluorescence value utilizing the Cell Analysis algorithm incorporated in the AGCC Scan Control version 1.0 to generate a fluorescence intensity (CEL) file. The quality of the image file was evaluated visually before further processing.
| | Sample_data_processing | The CEL files in each experiment were analyzed with Affymetrix Expression Console version 1.1 utilizing the MAS5 algorithm, selecting the scaling parameter for all probe sets, and an arbitrary target value of 150 to generate chip and report files. A quality control summary of metrics, labeling and hybridization controls, and housekeeping genes for all files within the experiment was generated by the Keck Center Functional Genomics staff and results were evaluated for accuracy and consistency.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mary,,Laws
| | Sample_contact_email | maryjolaws@gmail.com
| | Sample_contact_institute | University of Illinois
| | Sample_contact_address | 2001 S. Lincoln Ave.
| | Sample_contact_city | Urbana
| | Sample_contact_zip/postal_code | 61802
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967432/suppl/GSM967432_3592_E_E5_Mouse430_2_.150.mas5.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967432/suppl/GSM967432_3592_E_E5_Mouse430_2_.CEL.gz
| | Sample_series_id | GSE39402
| | Sample_data_row_count | 45101
| | |
|
GSM967433 | GPL1261 |
|
erad/d_ovarian tumor_10 months_age
|
ovarian tumor from era d/d mouse 10 months old
|
strain: C57BL/6
gender: female
tissue: ovarian tumor
genotype: era d/d_conditional deletion of estrogen receptor alpha mediated by cre driven by progestrogen receptor
age: 10 months
|
|
| Sample_geo_accession | GSM967433
| | Sample_status | Public on Aug 06 2013
| | Sample_submission_date | Jul 16 2012
| | Sample_last_update_date | Aug 06 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Ovarian tumor tissue and normal ovarian tissue was snap frozen in liquid nitrogen and then homogenized using a bead beater.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated from ovarian tumor tissue or normal ovary tissue after tissue was homogenized using a bead beater. Total RNA was cleaned up using Qiagen kit and protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Microarrays were processed by the W. M. Keck Center for Comparative and Functional Genomics in the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign. Labeled antisense RNA was prepared utilizing the GeneChip 3' IVT Express Kit Labeling and Control Reagents kit (Affymetrix, Inc., Santa Clara, CA), according to the manufacturer’s manual P/N 702646 Revision 1. Briefly, 100 nanograms of total RNA was spiked with four prokaryotic polyadenylated sense RNA controls, primed with a T7-(dT) oligonucleotide containing a T7 promoter sequence, and reverse transcribed to synthesize first-strand DNA. A double-stranded DNA template was then synthesized with DNA polymerase along with RNase H to degrade RNA. The resulting cDNA was in vitro transcribed with the addition of a biotinylated ribonucleotide analog, and amplified at 40°C for 14 hours. The resulting biotin-labeled antisense RNA was purified with magnetic beads, quantified, and fragmented to produce lengths of less than 200 nucleotides.
| | Sample_hyb_protocol | The Affymetrix Alternative Protocol for Eukaryotic Target Hybridization manual P/N 702232 Revision 2 Appendices B and C was utilized for hybridization, washing, and staining. A cocktail was prepared with 15 micrograms of aRNA, adding biotinylated, fragmented hybridization controls: four prokaryotic antisense RNAs and one synthetic oligonucleotide. Following a 16-hour hybridization to an Affymetrix GeneChip 3’ Expression Mouse Genome 430 2.0 Array at 45°C and 60 rpm in a GeneChip model 640 oven, the chip was washed, and stained first with streptavidin-conjugated phycoerythrin dye (Invitrogen Corporation, Carlsbad, CA). The stain was enhanced with biotinylated goat anti-streptavidin antibody (Vector Laboratories, Burlingame, CA), and counterstained with additional conjugated phycoerythrin utilizing a GeneChip Fluidics Station model 450 and the GeneChip Command Console (AGCC) Fluidics Control software version 1.0.
| | Sample_scan_protocol | The chip was scanned with a GeneChip Scanner model 3000 7G Plus. Raw fluorescence signals for pixels within each probe feature in the image (DAT) file were converted to a single feature fluorescence value utilizing the Cell Analysis algorithm incorporated in the AGCC Scan Control version 1.0 to generate a fluorescence intensity (CEL) file. The quality of the image file was evaluated visually before further processing.
| | Sample_data_processing | The CEL files in each experiment were analyzed with Affymetrix Expression Console version 1.1 utilizing the MAS5 algorithm, selecting the scaling parameter for all probe sets, and an arbitrary target value of 150 to generate chip and report files. A quality control summary of metrics, labeling and hybridization controls, and housekeeping genes for all files within the experiment was generated by the Keck Center Functional Genomics staff and results were evaluated for accuracy and consistency.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Mary,,Laws
| | Sample_contact_email | maryjolaws@gmail.com
| | Sample_contact_institute | University of Illinois
| | Sample_contact_address | 2001 S. Lincoln Ave.
| | Sample_contact_city | Urbana
| | Sample_contact_zip/postal_code | 61802
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967433/suppl/GSM967433_3591_E_E10_Mouse430_2_.150.mas5.CHP.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM967nnn/GSM967433/suppl/GSM967433_3591_E_E10_Mouse430_2_.CEL.gz
| | Sample_series_id | GSE39402
| | Sample_data_row_count | 45101
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