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Sample GSM1327511 Query DataSets for GSM1327511
Status Public on Jan 01, 2015
Title Nkx2.5-Cre; R26R-miR302-367, 3
Sample type RNA
 
Source name heart at postnatal day 14 heart
Organism Mus musculus
Characteristics tissue: heart
genotype: Nkx2.5-Cre; R26R-miR302-367
age: E14
strain: Mixed C57BL/6 x 129S6
Treatment protocol The mouse hearts were harvested at 14 days after birth
Extracted molecule total RNA
Extraction protocol RNA was extracted using Rneasy mini kit (Qiagene)
Label biotin
Label protocol 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter. Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.
 
Hybridization protocol cDNAs were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.
Scan protocol A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
Data processing Microarray data were analyzed using the Oligo package available at the Bioconductor website (www.bioconductor.org). The raw data were first background-corrected by the Robust Multichip Average (RMA) method and then normalized by an invariant set method. Probesets were considered expressed if at least one sample had a RMA expression value greater than the mean of the negative control probesets, 18,494 probesets were considered expressed. Differential gene expression between the control and mutant mice was analyzed by the Limma package available at the Bioconductor website. P-values obtained from the multiple comparison tests were corrected by false discovery rates. Heatmap displays were created using the freely available MeV package ( http://www.tm4.org/mev/).
 
Submission date Feb 13, 2014
Last update date Jan 01, 2015
Contact name Michael Patrick Morley
E-mail(s) mmorley@pennmedicine.upenn.edu
Phone 215-898-2026
Organization name Perelman School of Medicine at the University of Pennsylvania
Department Penn Cardiovascular Institute
Street address 3400 Civic Center Blvd, Bldg 421
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL16570
Series (1)
GSE54988 miR-302-367 regulates cardiomycyte proliferation and differentiation during development

Data table header descriptions
ID_REF
VALUE RMA log2 signal

Data table
ID_REF VALUE
17200001 6.987669007
17200003 6.736230519
17200005 4.414024471
17200007 4.883996856
17200009 6.232798658
17200011 5.618757574
17200013 6.040688969
17200015 5.310029527
17200017 2.867511635
17200019 4.26131498
17200021 4.871648435
17200023 7.866576464
17200025 5.828138838
17200027 5.745648442
17200029 5.21991792
17200031 3.793880122
17200033 3.113842019
17200035 4.988081063
17200037 5.780884654
17200039 3.346193869

Total number of rows: 41345

Table truncated, full table size 843 Kbytes.




Supplementary file Size Download File type/resource
GSM1327511_4761_48418_Mut3_MoGene2.0st.CEL.gz 9.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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