Result

Search results for the GEO ID: GSE31244

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Title

Source name

Description

Characteristics

GSM774510

GPL1261

Notch1 wildtype, replicate 1

Uterus

strain: C57Bl/6J age: 6 weeks Sex: Female genotype: Notch1 f/f (floxed, wild type) tissue: Uterus

flox/flox, uterus

Sample_geo_accession	GSM774510
Sample_status	Public on Aug 09 2011
Sample_submission_date	Aug 07 2011
Sample_last_update_date	Aug 09 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Amplification conditions include: holding for 10 min at 95°C, 40 thermal cycles of denaturing for 15 sec at 95°C, and annealing/extending for 1 min at 60°C. A SYBR Green dissociation step was added to the end of the PCR cycle. Relative fold induction levels were calculated using the comparative threshold cycle method for separate tube amplification.
Sample_growth_protocol_ch1	The RNA was pooled from the uteri of three mice per genotype and treatment.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Six-week old mice were ovariectomized. Two weeks later, ovariectomized mice were treated with three daily injections of 100ng/mouse/day estradiol (E2) per mouse. After two day of rest, mice were then treated with three daily injections of 1.0mg/mouse/day methoxyprogesterone acetate (MPA) and 6.7ng/mouse/day E2, by subcutaneous injection. Six-hours following final injection, unilateral scratching on the anti-mesometrial lumen induced a decidual reaction. Mice were then given daily sc injections of 1.0mg/mouse/day MPA and 6.7ng/mouse/day E2 for 1-5 days after stimulation that followed the induction of the uterine decidual response. Mice were anesthetized with Avertin (2,2-tribromoethyl alcohol; Sigma-Aldrich) and sacrificed by cervical dislocation to collect the uteri. Uterine tissues was flash frozen and stored at -80°C until RNA isolation. Total RNA was extracted from mouse uteri using TrIzol reagent (Invitrogen, Carlsbad, Ca, USA). RT PCR was performed using iScript (Bio-Rad, Hercules, Ca, USA) according to manufacturers’ instructions
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Approximately 5-20 µg of total RNA were processed to produce biotinylated cRNA targets.
Sample_hyb_protocol	Standard Affymetrix procedures for the Affymetrix murine genome 430 2.0 mouse oligonucleotide arrays.
Sample_scan_protocol	Standard Affymetrix procedures for the Affymetrix murine genome 430 2.0 mouse oligonucleotide arrays.
Sample_data_processing	The gene expression data were normalized and background corrected with the RMA (Robust Multichip Average) method in R/Bioconductor.
Sample_platform_id	GPL1261
Sample_contact_name	Damian,S,Roqueiro
Sample_contact_phone	312-413-4819
Sample_contact_laboratory	Laboratory of Computational Functional Genomics
Sample_contact_department	Bioengineering
Sample_contact_institute	University of Illinois at Chicago
Sample_contact_address	820 S. Wood St, Suite W103
Sample_contact_city	Chicago
Sample_contact_state	Illinois
Sample_contact_zip/postal_code	60612
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774510/suppl/GSM774510.cel.gz
Sample_series_id	GSE31244
Sample_data_row_count	45101

GSM774511

GPL1261

Notch1 wildtype, replicate 2

Uterus

strain: C57Bl/6J age: 6 weeks Sex: Female genotype: Notch1 f/f (floxed, wild type) tissue: Uterus

flox/flox, uterus

Sample_geo_accession	GSM774511
Sample_status	Public on Aug 09 2011
Sample_submission_date	Aug 07 2011
Sample_last_update_date	Aug 09 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Amplification conditions include: holding for 10 min at 95°C, 40 thermal cycles of denaturing for 15 sec at 95°C, and annealing/extending for 1 min at 60°C. A SYBR Green dissociation step was added to the end of the PCR cycle. Relative fold induction levels were calculated using the comparative threshold cycle method for separate tube amplification.
Sample_growth_protocol_ch1	The RNA was pooled from the uteri of three mice per genotype and treatment.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Six-week old mice were ovariectomized. Two weeks later, ovariectomized mice were treated with three daily injections of 100ng/mouse/day estradiol (E2) per mouse. After two day of rest, mice were then treated with three daily injections of 1.0mg/mouse/day methoxyprogesterone acetate (MPA) and 6.7ng/mouse/day E2, by subcutaneous injection. Six-hours following final injection, unilateral scratching on the anti-mesometrial lumen induced a decidual reaction. Mice were then given daily sc injections of 1.0mg/mouse/day MPA and 6.7ng/mouse/day E2 for 1-5 days after stimulation that followed the induction of the uterine decidual response. Mice were anesthetized with Avertin (2,2-tribromoethyl alcohol; Sigma-Aldrich) and sacrificed by cervical dislocation to collect the uteri. Uterine tissues was flash frozen and stored at -80°C until RNA isolation. Total RNA was extracted from mouse uteri using TrIzol reagent (Invitrogen, Carlsbad, Ca, USA). RT PCR was performed using iScript (Bio-Rad, Hercules, Ca, USA) according to manufacturers’ instructions
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Approximately 5-20 µg of total RNA were processed to produce biotinylated cRNA targets.
Sample_hyb_protocol	Standard Affymetrix procedures for the Affymetrix murine genome 430 2.0 mouse oligonucleotide arrays.
Sample_scan_protocol	Standard Affymetrix procedures for the Affymetrix murine genome 430 2.0 mouse oligonucleotide arrays.
Sample_data_processing	The gene expression data were normalized and background corrected with the RMA (Robust Multichip Average) method in R/Bioconductor.
Sample_platform_id	GPL1261
Sample_contact_name	Damian,S,Roqueiro
Sample_contact_phone	312-413-4819
Sample_contact_laboratory	Laboratory of Computational Functional Genomics
Sample_contact_department	Bioengineering
Sample_contact_institute	University of Illinois at Chicago
Sample_contact_address	820 S. Wood St, Suite W103
Sample_contact_city	Chicago
Sample_contact_state	Illinois
Sample_contact_zip/postal_code	60612
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774511/suppl/GSM774511.cel.gz
Sample_series_id	GSE31244
Sample_data_row_count	45101

GSM774512

GPL1261

Notch1 wildtype, replicate 3

Uterus

strain: C57Bl/6J age: 6 weeks Sex: Female genotype: Notch1 f/f (floxed, wild type) tissue: Uterus

flox/flox, uterus

Sample_geo_accession	GSM774512
Sample_status	Public on Aug 09 2011
Sample_submission_date	Aug 07 2011
Sample_last_update_date	Aug 09 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Amplification conditions include: holding for 10 min at 95°C, 40 thermal cycles of denaturing for 15 sec at 95°C, and annealing/extending for 1 min at 60°C. A SYBR Green dissociation step was added to the end of the PCR cycle. Relative fold induction levels were calculated using the comparative threshold cycle method for separate tube amplification.
Sample_growth_protocol_ch1	The RNA was pooled from the uteri of three mice per genotype and treatment.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Six-week old mice were ovariectomized. Two weeks later, ovariectomized mice were treated with three daily injections of 100ng/mouse/day estradiol (E2) per mouse. After two day of rest, mice were then treated with three daily injections of 1.0mg/mouse/day methoxyprogesterone acetate (MPA) and 6.7ng/mouse/day E2, by subcutaneous injection. Six-hours following final injection, unilateral scratching on the anti-mesometrial lumen induced a decidual reaction. Mice were then given daily sc injections of 1.0mg/mouse/day MPA and 6.7ng/mouse/day E2 for 1-5 days after stimulation that followed the induction of the uterine decidual response. Mice were anesthetized with Avertin (2,2-tribromoethyl alcohol; Sigma-Aldrich) and sacrificed by cervical dislocation to collect the uteri. Uterine tissues was flash frozen and stored at -80°C until RNA isolation. Total RNA was extracted from mouse uteri using TrIzol reagent (Invitrogen, Carlsbad, Ca, USA). RT PCR was performed using iScript (Bio-Rad, Hercules, Ca, USA) according to manufacturers’ instructions
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Approximately 5-20 µg of total RNA were processed to produce biotinylated cRNA targets.
Sample_hyb_protocol	Standard Affymetrix procedures for the Affymetrix murine genome 430 2.0 mouse oligonucleotide arrays.
Sample_scan_protocol	Standard Affymetrix procedures for the Affymetrix murine genome 430 2.0 mouse oligonucleotide arrays.
Sample_data_processing	The gene expression data were normalized and background corrected with the RMA (Robust Multichip Average) method in R/Bioconductor.
Sample_platform_id	GPL1261
Sample_contact_name	Damian,S,Roqueiro
Sample_contact_phone	312-413-4819
Sample_contact_laboratory	Laboratory of Computational Functional Genomics
Sample_contact_department	Bioengineering
Sample_contact_institute	University of Illinois at Chicago
Sample_contact_address	820 S. Wood St, Suite W103
Sample_contact_city	Chicago
Sample_contact_state	Illinois
Sample_contact_zip/postal_code	60612
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774512/suppl/GSM774512.cel.gz
Sample_series_id	GSE31244
Sample_data_row_count	45101

GSM774513

GPL1261

Notch1 knockout, replicate 1

Uterus

strain: C57Bl/6J age: 6 weeks Sex: Female genotype: Notch1 d/d (knockout) tissue: Uterus

PRCre/+, uterus

Sample_geo_accession	GSM774513
Sample_status	Public on Aug 09 2011
Sample_submission_date	Aug 07 2011
Sample_last_update_date	Aug 09 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Amplification conditions include: holding for 10 min at 95°C, 40 thermal cycles of denaturing for 15 sec at 95°C, and annealing/extending for 1 min at 60°C. A SYBR Green dissociation step was added to the end of the PCR cycle. Relative fold induction levels were calculated using the comparative threshold cycle method for separate tube amplification.
Sample_growth_protocol_ch1	The RNA was pooled from the uteri of three mice per genotype and treatment.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Six-week old mice were ovariectomized. Two weeks later, ovariectomized mice were treated with three daily injections of 100ng/mouse/day estradiol (E2) per mouse. After two day of rest, mice were then treated with three daily injections of 1.0mg/mouse/day methoxyprogesterone acetate (MPA) and 6.7ng/mouse/day E2, by subcutaneous injection. Six-hours following final injection, unilateral scratching on the anti-mesometrial lumen induced a decidual reaction. Mice were then given daily sc injections of 1.0mg/mouse/day MPA and 6.7ng/mouse/day E2 for 1-5 days after stimulation that followed the induction of the uterine decidual response. Mice were anesthetized with Avertin (2,2-tribromoethyl alcohol; Sigma-Aldrich) and sacrificed by cervical dislocation to collect the uteri. Uterine tissues was flash frozen and stored at -80°C until RNA isolation. Total RNA was extracted from mouse uteri using TrIzol reagent (Invitrogen, Carlsbad, Ca, USA). RT PCR was performed using iScript (Bio-Rad, Hercules, Ca, USA) according to manufacturers’ instructions
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Approximately 5-20 µg of total RNA were processed to produce biotinylated cRNA targets.
Sample_hyb_protocol	Standard Affymetrix procedures for the Affymetrix murine genome 430 2.0 mouse oligonucleotide arrays.
Sample_scan_protocol	Standard Affymetrix procedures for the Affymetrix murine genome 430 2.0 mouse oligonucleotide arrays.
Sample_data_processing	The gene expression data were normalized and background corrected with the RMA (Robust Multichip Average) method in R/Bioconductor.
Sample_platform_id	GPL1261
Sample_contact_name	Damian,S,Roqueiro
Sample_contact_phone	312-413-4819
Sample_contact_laboratory	Laboratory of Computational Functional Genomics
Sample_contact_department	Bioengineering
Sample_contact_institute	University of Illinois at Chicago
Sample_contact_address	820 S. Wood St, Suite W103
Sample_contact_city	Chicago
Sample_contact_state	Illinois
Sample_contact_zip/postal_code	60612
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774513/suppl/GSM774513.cel.gz
Sample_series_id	GSE31244
Sample_data_row_count	45101

GSM774514

GPL1261

Notch1 knockout, replicate 2

Uterus

strain: C57Bl/6J age: 6 weeks Sex: Female genotype: Notch1 d/d (knockout) tissue: Uterus

PRCre/+, uterus

Sample_geo_accession	GSM774514
Sample_status	Public on Aug 09 2011
Sample_submission_date	Aug 07 2011
Sample_last_update_date	Aug 09 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Amplification conditions include: holding for 10 min at 95°C, 40 thermal cycles of denaturing for 15 sec at 95°C, and annealing/extending for 1 min at 60°C. A SYBR Green dissociation step was added to the end of the PCR cycle. Relative fold induction levels were calculated using the comparative threshold cycle method for separate tube amplification.
Sample_growth_protocol_ch1	The RNA was pooled from the uteri of three mice per genotype and treatment.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Six-week old mice were ovariectomized. Two weeks later, ovariectomized mice were treated with three daily injections of 100ng/mouse/day estradiol (E2) per mouse. After two day of rest, mice were then treated with three daily injections of 1.0mg/mouse/day methoxyprogesterone acetate (MPA) and 6.7ng/mouse/day E2, by subcutaneous injection. Six-hours following final injection, unilateral scratching on the anti-mesometrial lumen induced a decidual reaction. Mice were then given daily sc injections of 1.0mg/mouse/day MPA and 6.7ng/mouse/day E2 for 1-5 days after stimulation that followed the induction of the uterine decidual response. Mice were anesthetized with Avertin (2,2-tribromoethyl alcohol; Sigma-Aldrich) and sacrificed by cervical dislocation to collect the uteri. Uterine tissues was flash frozen and stored at -80°C until RNA isolation. Total RNA was extracted from mouse uteri using TrIzol reagent (Invitrogen, Carlsbad, Ca, USA). RT PCR was performed using iScript (Bio-Rad, Hercules, Ca, USA) according to manufacturers’ instructions
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Approximately 5-20 µg of total RNA were processed to produce biotinylated cRNA targets.
Sample_hyb_protocol	Standard Affymetrix procedures for the Affymetrix murine genome 430 2.0 mouse oligonucleotide arrays.
Sample_scan_protocol	Standard Affymetrix procedures for the Affymetrix murine genome 430 2.0 mouse oligonucleotide arrays.
Sample_data_processing	The gene expression data were normalized and background corrected with the RMA (Robust Multichip Average) method in R/Bioconductor.
Sample_platform_id	GPL1261
Sample_contact_name	Damian,S,Roqueiro
Sample_contact_phone	312-413-4819
Sample_contact_laboratory	Laboratory of Computational Functional Genomics
Sample_contact_department	Bioengineering
Sample_contact_institute	University of Illinois at Chicago
Sample_contact_address	820 S. Wood St, Suite W103
Sample_contact_city	Chicago
Sample_contact_state	Illinois
Sample_contact_zip/postal_code	60612
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774514/suppl/GSM774514.cel.gz
Sample_series_id	GSE31244
Sample_data_row_count	45101

GSM774515

GPL1261

Notch1 knockout, replicate 3

Uterus

strain: C57Bl/6J age: 6 weeks Sex: Female genotype: Notch1 d/d (knockout) tissue: Uterus

PRCre/+, uterus

Sample_geo_accession	GSM774515
Sample_status	Public on Aug 09 2011
Sample_submission_date	Aug 07 2011
Sample_last_update_date	Aug 09 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Amplification conditions include: holding for 10 min at 95°C, 40 thermal cycles of denaturing for 15 sec at 95°C, and annealing/extending for 1 min at 60°C. A SYBR Green dissociation step was added to the end of the PCR cycle. Relative fold induction levels were calculated using the comparative threshold cycle method for separate tube amplification.
Sample_growth_protocol_ch1	The RNA was pooled from the uteri of three mice per genotype and treatment.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Six-week old mice were ovariectomized. Two weeks later, ovariectomized mice were treated with three daily injections of 100ng/mouse/day estradiol (E2) per mouse. After two day of rest, mice were then treated with three daily injections of 1.0mg/mouse/day methoxyprogesterone acetate (MPA) and 6.7ng/mouse/day E2, by subcutaneous injection. Six-hours following final injection, unilateral scratching on the anti-mesometrial lumen induced a decidual reaction. Mice were then given daily sc injections of 1.0mg/mouse/day MPA and 6.7ng/mouse/day E2 for 1-5 days after stimulation that followed the induction of the uterine decidual response. Mice were anesthetized with Avertin (2,2-tribromoethyl alcohol; Sigma-Aldrich) and sacrificed by cervical dislocation to collect the uteri. Uterine tissues was flash frozen and stored at -80°C until RNA isolation. Total RNA was extracted from mouse uteri using TrIzol reagent (Invitrogen, Carlsbad, Ca, USA). RT PCR was performed using iScript (Bio-Rad, Hercules, Ca, USA) according to manufacturers’ instructions
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Approximately 5-20 µg of total RNA were processed to produce biotinylated cRNA targets.
Sample_hyb_protocol	Standard Affymetrix procedures for the Affymetrix murine genome 430 2.0 mouse oligonucleotide arrays.
Sample_scan_protocol	Standard Affymetrix procedures for the Affymetrix murine genome 430 2.0 mouse oligonucleotide arrays.
Sample_data_processing	The gene expression data were normalized and background corrected with the RMA (Robust Multichip Average) method in R/Bioconductor.
Sample_platform_id	GPL1261
Sample_contact_name	Damian,S,Roqueiro
Sample_contact_phone	312-413-4819
Sample_contact_laboratory	Laboratory of Computational Functional Genomics
Sample_contact_department	Bioengineering
Sample_contact_institute	University of Illinois at Chicago
Sample_contact_address	820 S. Wood St, Suite W103
Sample_contact_city	Chicago
Sample_contact_state	Illinois
Sample_contact_zip/postal_code	60612
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM774nnn/GSM774515/suppl/GSM774515.cel.gz
Sample_series_id	GSE31244
Sample_data_row_count	45101

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