Result

Search results for the GEO ID: GSE25881

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Title

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Description

Characteristics

GSM635410

GPL1261

Control stromal cells

uterine stromal cells from Floxed control mice on day4 of pregnancy

sample type: uterus, D4 of pregnancy, implantation, stromal-epithelial communication, FGFs genotype: Hand2 Floxed cell type: uterine stromal cell age: day 4 of pregnancy genetic background: Prcre, C57BL/6, SV129 mixed background

Sample_geo_accession	GSM635410
Sample_status	Public on Jun 03 2011
Sample_submission_date	Dec 06 2010
Sample_last_update_date	Jun 03 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Hand2-null mice (n=5) and the corresponding controls (n=5) were mated to fertile male mice. The presence of vaginal plug after mating was designated as Day1 of pregnancy. On day4 of pregnancy, uterine horns were excised and cut into 3-5 mm pieces, then placed in HBSS containing 6g/L dispase (Gibico BRL), 25g/L pancreatin (Sigma), and 100 U/L penicillin, 0.1 g/L streptomycin, 1.25 mg/L fungizone (Gibico BRL) for 1h on ice followed by 1h at room temperature and then 10 min at 37⁰C. The tubes were gently mixed and the supernatant was discarded to remove the emdometrial epithelial clumps. The partially digested tissues were then washed twice in HBSS and placed in HBSS containing 0.5g/L collagenase (Sigma). After incubation for 45 min at 37⁰C, the tubes were mixed for 10-12 seconds by vortexing until the supernatant became turbid with dispersed endometrial stromal cells. The content of the tube was then passed through a 70 m gauze filter (Millipore). After washing with HBSS, cells were suspended in Dulbecco’s modified Eagle’s Medium-F12 medium containing 2% heat-inactivated fetal calf serum and then allowed to attch to the culture plates for 1 h at 37⁰C. Unattached Cells were removed prior to RNA extraction.
Sample_growth_protocol_ch1	Mice were maintained in the designated animal care facility at University of Illinois at Urbana-Champaign according to the institutional guidelines for the care and use of laboratory animals. Hand2 floxed mice obtained from Dr. Deepak Srivastava (University of California) were crossed with PRcre mice (provided by Dr. Francceso DeMayo, (Baylor College of Medicine) to conditionally ablate Hand2 in the uterus.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from uterine stromal cells (n=4 for each genotype) using the Qiagen RNAeasy total RNA isolation kit according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Keck Center Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign prepared amplified, biotin-labeled, fragmented antisense RNA from 100 nanograms of sample total RNA using the Affymetrix 3' Express Kit (Affymetrix, Inc., Santa Clara, CA) according to manufacturer’s instructions.
Sample_hyb_protocol	10 micrograms of labeled aRNA were hybridized to a Mouse Genome 430 2.0 Affymetrix 3' Expression Analysis Array. Wash and stain were performed on Affymetrix Fluidics Station 450 with protocol EukGE_WS2v5 using Affymetrix GeneChip Command Console Fluidics Control software and solutions prepared by Keck Center,Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign.
Sample_scan_protocol	Arrays were scanned on Affymetrix GeneChip Scanner model 3000 7G Plus using GeneChip Command Console Scan Control software to generate DAT and CEL files.
Sample_data_processing	To generate quality control metrics the Keck Center generated CHP files using the MAS5 algorithm with Affymetrix Expression Console version 1_1.
Sample_platform_id	GPL1261
Sample_contact_name	Quanxi,,Li
Sample_contact_email	quanxili@Illinois.edu
Sample_contact_phone	217-333-1731
Sample_contact_laboratory	Dr. Bagchi
Sample_contact_department	Comparative Bioscience
Sample_contact_institute	Universit of Illinois at Urbana-Champaign
Sample_contact_address	2001 S lincoln Avenue
Sample_contact_city	Urbana
Sample_contact_state	IL
Sample_contact_zip/postal_code	61802
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM635nnn/GSM635410/suppl/GSM635410_FF_stroma.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM635nnn/GSM635410/suppl/GSM635410_FF_stroma.CHP.gz
Sample_series_id	GSE25881
Sample_data_row_count	45101

GSM635411

GPL1261

KO stromal cells

uterine stromal cells from KO mice on day4 of pregnancy

sample type: uterus, D4 of pregnancy, implantation, stromal-epithelial communication, FGFs genotype: Hand2-null cell type: uterine stromal cell age: day 4 of pregnancy genetic background: Prcre, C57BL/6, SV129 mixed background

Sample_geo_accession	GSM635411
Sample_status	Public on Jun 03 2011
Sample_submission_date	Dec 06 2010
Sample_last_update_date	Jun 03 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Hand2-null mice (n=5) and the corresponding controls (n=5) were mated to fertile male mice. The presence of vaginal plug after mating was designated as Day1 of pregnancy. On day4 of pregnancy, uterine horns were excised and cut into 3-5 mm pieces, then placed in HBSS containing 6g/L dispase (Gibico BRL), 25g/L pancreatin (Sigma), and 100 U/L penicillin, 0.1 g/L streptomycin, 1.25 mg/L fungizone (Gibico BRL) for 1h on ice followed by 1h at room temperature and then 10 min at 37⁰C. The tubes were gently mixed and the supernatant was discarded to remove the emdometrial epithelial clumps. The partially digested tissues were then washed twice in HBSS and placed in HBSS containing 0.5g/L collagenase (Sigma). After incubation for 45 min at 37⁰C, the tubes were mixed for 10-12 seconds by vortexing until the supernatant became turbid with dispersed endometrial stromal cells. The content of the tube was then passed through a 70 m gauze filter (Millipore). After washing with HBSS, cells were suspended in Dulbecco’s modified Eagle’s Medium-F12 medium containing 2% heat-inactivated fetal calf serum and then allowed to attch to the culture plates for 1 h at 37⁰C. Unattached Cells were removed prior to RNA extraction.
Sample_growth_protocol_ch1	Mice were maintained in the designated animal care facility at University of Illinois at Urbana-Champaign according to the institutional guidelines for the care and use of laboratory animals. Hand2 floxed mice obtained from Dr. Deepak Srivastava (University of California) were crossed with PRcre mice (provided by Dr. Francceso DeMayo, (Baylor College of Medicine) to conditionally ablate Hand2 in the uterus.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from uterine stromal cells (n=4 for each genotype) using the Qiagen RNAeasy total RNA isolation kit according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Keck Center Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign prepared amplified, biotin-labeled, fragmented antisense RNA from 100 nanograms of sample total RNA using the Affymetrix 3' Express Kit (Affymetrix, Inc., Santa Clara, CA) according to manufacturer’s instructions.
Sample_hyb_protocol	10 micrograms of labeled aRNA were hybridized to a Mouse Genome 430 2.0 Affymetrix 3' Expression Analysis Array. Wash and stain were performed on Affymetrix Fluidics Station 450 with protocol EukGE_WS2v5 using Affymetrix GeneChip Command Console Fluidics Control software and solutions prepared by Keck Center,Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign.
Sample_scan_protocol	Arrays were scanned on Affymetrix GeneChip Scanner model 3000 7G Plus using GeneChip Command Console Scan Control software to generate DAT and CEL files.
Sample_data_processing	To generate quality control metrics the Keck Center generated CHP files using the MAS5 algorithm with Affymetrix Expression Console version 1_1.
Sample_platform_id	GPL1261
Sample_contact_name	Quanxi,,Li
Sample_contact_email	quanxili@Illinois.edu
Sample_contact_phone	217-333-1731
Sample_contact_laboratory	Dr. Bagchi
Sample_contact_department	Comparative Bioscience
Sample_contact_institute	Universit of Illinois at Urbana-Champaign
Sample_contact_address	2001 S lincoln Avenue
Sample_contact_city	Urbana
Sample_contact_state	IL
Sample_contact_zip/postal_code	61802
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM635nnn/GSM635411/suppl/GSM635411_KO_stroma.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM635nnn/GSM635411/suppl/GSM635411_KO_stroma.CHP.gz
Sample_series_id	GSE25881
Sample_data_row_count	45101

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