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Sample GSM87677 Query DataSets for GSM87677
Status Public on May 01, 2006
Title HoxA11, D11 double null embryonic E11.5 Metanephric Mesenchyme replicate 1
Sample type RNA
 
Source name HoxA11, D11 null E11.5 MM rep1
Organism Mus musculus
Characteristics Hoxa11, Hoxd11 double null targeted embryonic metanephric mesenchyme at E11.5 isolated by laser capture microdissection, mixed C57, C3H and CF1 strain
Extracted molecule total RNA
Extraction protocol Urogenital ridges were dissected in ice-cold PBS then quick-frozen in Tissue-Tek® OCT compound (Sakura, Torrence, CA) using liquid nitrogen cooled 2-methylbutane isopentan. Serial sections (7 microns) were made using a Microm HM 550 cryostat (Richard-Allan Scientific, Kalamazoo, MI), collected on Fisher Superfrost plus precleaned slides (Hampton, NH), and stored at –80 C. Alternate sections were hematoxylin and eosin stained and used to help identify the UB and MM. For LCM the remaining sections were air dried at room temperature for 3 min, acetone fixed for 2 min, rinsed in ice cold 1/10 PBS for 3 min and then dehydrated in 75%, 95%, 100%, 100% ethanol, followed by two five minute rinses with xylene. Laser capture microdissection was performed using the Arcturus Pixcell II system, according to Arcturus protocols (Mountain View, California). RNA was prepared from collected tissue using the RNeasy Micro Kit (Qiagen, Valencia, CA), with 30 ng poly-inosine carrier (Epicentre, Madison, WI) added to the RLT buffer. Target RNA was prepared using the TargetAmp™ 2-Round aRNA Amplification Kit 1.0 (Epicentre, Madison, WI), and hybridized to Affymetrix MOE430_v2 microarrays.
Label biotin
Label protocol RNA collected from multiple sections of metanephric mesenchyme was prepared from collected tissue using the RNeasy Micro Kit (Qiagen, Valencia, CA), with 30 ng poly-inosine carrier (Epicentre, Madison, WI) added to the RLT buffer. Target RNA was prepared using the TargetAmp™ 2-Round aRNA Amplification Kit 1.0 (Epicentre, Madison, WI).
 
Hybridization protocol standard Affymetrix procedures
Scan protocol standard Affymetrix procedures
Description HoxA11, D11 double null embryonic E11.5 Metanephric Mesenchyme isolated by laser capture microdissection replicate 1
Data processing Affymetrix Microarray Suite version 5.0
 
Submission date Dec 14, 2005
Last update date Aug 28, 2018
Contact name Kristopher Robert Schwab
E-mail(s) kristopher.schwab@cchmc.org
Organization name Cincinnati Children's Hospital Research Foundation
Department Developmental Biology
Lab S. Steven Potter
Street address 3333 Burnett Ave
City Cincinnati
State/province OH
ZIP/Postal code 45229
Country USA
 
Platform ID GPL1261
Series (1)
GSE3822 Complete embryonic E11.5 metanephric kidney analysis of wild type and Hoxa11, Hoxd11 null targeted mice
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE '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 4159.2 P 0.000052
AFFX-BioB-M_at 7873.6 P 0.000044
AFFX-BioB-3_at 5210.8 P 0.000044
AFFX-BioC-5_at 9363.8 P 0.000044
AFFX-BioC-3_at 7870.9 P 0.000044
AFFX-BioDn-5_at 15352.6 P 0.000044
AFFX-BioDn-3_at 35376.9 P 0.000044
AFFX-CreX-5_at 83876 P 0.000044
AFFX-CreX-3_at 87043.9 P 0.000044
AFFX-DapX-5_at 12.6 A 0.737173
AFFX-DapX-M_at 50.6 A 0.60308
AFFX-DapX-3_at 26.3 A 0.834202
AFFX-LysX-5_at 3.8 A 0.973899
AFFX-LysX-M_at 7.5 A 0.910522
AFFX-LysX-3_at 50.9 A 0.354453
AFFX-PheX-5_at 13.2 A 0.783476
AFFX-PheX-M_at 4.7 A 0.932322
AFFX-PheX-3_at 71.5 A 0.287743
AFFX-ThrX-5_at 71.1 A 0.195266
AFFX-ThrX-M_at 4.7 A 0.921998

Total number of rows: 45101

Table truncated, full table size 1230 Kbytes.




Supplementary file Size Download File type/resource
GSM87677.CEL.gz 5.8 Mb (ftp)(http) CEL

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