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Sample GSM189303 Query DataSets for GSM189303
Status Public on Jun 01, 2007
Title ERaKO-OVX-1
Sample type RNA
 
Source name the left femurs from ovariectomized osteoclast specific ERaKO mouse
Organism Mus musculus
Characteristics Strain: C57BL/6
Gender: female
Tissue: the left femurs
Extracted molecule total RNA
Extraction protocol The distal 5 mm of the left femurs were harvested after sacrificing by cervical dislocation. Samples were then homogenized in ISOGEN(Nippon gene, Japan) and total RNA extracted according to the manufacturer’s instructions. The extracted total RNA was cleaned up and concentrated using the RNeasy MinElute Cleanup Kit (QIAGEN, Valencia, CA) for GeneChip analysis (Proc Natl Acad Sci U S A. 2006;103(1):224-9.).
Label Biotin
Label protocol Total RNA was purified by using an RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. First-strand cDNA was synthesized from 5 µg of RNA by using 200 units of SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA), 100 pmol T7-(dT)24 primer [5'-GGCCAGTGA AT TGTA ATACGACTCACTATAGGGAGGCGG-(dT)24-3'], 1x first-strand buffer, and 0.5 mM dNTPs at 42°C for 1 h. Second-strand synthesis was performed by incubating first-strand cDNA with 10 units of Escherichia coli ligase (Invitrogen), 40 units of DNA polymerase I (Invitrogen), 2 units of RNase H (Invitrogen), 1x reaction buffer, and 0.2 mM dNTPs at 16°C for 2 h, followed by 10 units of T4 DNA polymerase (Invitrogen) and incubation for another 5 min at 16°C. Double-stranded cDNA was purified by using GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions and labeled by in vitro transcription by using a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY). Briefly, dsDNA was mixed with 1x HY reaction buffer, 1x biotin-labeled ribonucleotides (NTPs with Bio-UTP and BioCTP), 1x DTT, 1x RNase inhibitor mix, and 1x T7 RNA polymerase and incubated at 37°C for 4 h. Labeled cRNA was then purified by using GeneChip Sample Cleanup Module and fragmented in 1x fragmentation buffer at 94°C for 35 min.
 
Hybridization protocol For hybridization to the GeneChip Mouse Expression Array 430A or 430B or Mouse Genome 430 2.0 Array (Affymetrix), 15 µg of fragmented cRNA probe was incubated with 50 pM control oligonucleotide B2, 1x eukaryotic hybridization control, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, and 1x hybridization buffer in a 45°C rotisserie oven for 16 h. Washing and staining were performed by using a GeneChip Fluidic Station (Affymetrix) according to the manufacturer's protocol.
Scan protocol Phycoerythrin-stained arrays were scanned as digital image files with GeneChip Scanner 3000 7G with AutoLoader.
Description Osteoclast-specific estrogen receptor alpha knock-out mice that were ovariectomized
Data processing Data transformation algorithm and normalization was done by Affymetrix GCOS.
Scaling:All Probe Sets, Target Signal=500
Normalization value:1
Parameters: defalut settings
 
Submission date May 15, 2007
Last update date Aug 28, 2018
Contact name KATSUHIDE IGARASHI
E-mail(s) k-igarashi@hoshi.ac.jp
Phone +81-3-3786-1011
Organization name Hoshi University School of Pharmacy and Pharmaceutical Science
Department Life Science Tokyo Advanced Research center (L-StaR)
Street address 2-4-41 Ebara
City Shinagawa-ku
State/province Tokyo
ZIP/Postal code 142-8501
Country Japan
 
Platform ID GPL1261
Series (1)
GSE7798 Osteoclastic estrogen receptor alpha mediates the osteoprotective estrogen action through Fas ligand signaling
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE A measure of the abundance of a transcript
ABS_CALL Detection call that indicates whether the transcript of a particular probe set reliably detected by the probe array
DETECTION P-VALUE p-value that indicates the significance level of the Detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 999.671 P 0.000753643
AFFX-BioB-M_at 2060.62 P 7.00668e-05
AFFX-BioB-3_at 1534.44 P 0.000224668
AFFX-BioC-5_at 3447.84 P 5.16732e-05
AFFX-BioC-3_at 4399.32 P 4.42873e-05
AFFX-BioDn-5_at 7825.18 P 4.42873e-05
AFFX-BioDn-3_at 18870.1 P 4.42873e-05
AFFX-CreX-5_at 45794.3 P 5.16732e-05
AFFX-CreX-3_at 46138.2 P 4.42873e-05
AFFX-DapX-5_at 8.00425 A 0.440646
AFFX-DapX-M_at 3.67936 A 0.699394
AFFX-DapX-3_at 5.66838 A 0.98333
AFFX-LysX-5_at 2.70649 A 0.794268
AFFX-LysX-M_at 3.49667 A 0.960391
AFFX-LysX-3_at 9.25111 A 0.5
AFFX-PheX-5_at 2.63989 A 0.960339
AFFX-PheX-M_at 24.4064 A 0.544587
AFFX-PheX-3_at 57.6032 A 0.250796
AFFX-ThrX-5_at 7.52233 A 0.945787
AFFX-ThrX-M_at 5.21404 A 0.712257

Total number of rows: 45101

Table truncated, full table size 1373 Kbytes.




Supplementary file Size Download File type/resource
GSM189303.CEL.gz 3.7 Mb (ftp)(http) CEL
GSM189303.CHP.gz 241.7 Kb (ftp)(http) CHP
GSM189303.xml.gz 5.5 Kb (ftp)(http) XML
Processed data included within Sample table
Processed data provided as supplementary file

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