NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM541790 Query DataSets for GSM541790
Status Public on Apr 12, 2011
Title 4_day_old_Prnp_knockout_mouse_rep2
Sample type RNA
 
Source name hippocampus
Organism Mus musculus
Characteristics strain: FVB
developmental stage: newborn (4-day-old)
tissue: hippocampus
genotype/variation: Prnp0/0
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, treated with DnaseI (Ambion) and purified with the RNeasy Mini kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified with a NanoDrop 1000 spectrophotometer (Thermo Scientific).
Label biotin
Label protocol A 10μg-amount of each total RNA sample was labeled according to the standard one-cycle amplification and labeling protocol (Affymetrix, Santa Clara, CA).
 
Hybridization protocol Labeled cRNA was hybridized on Affymetrix GeneChip Mouse Genome 430A 2.0 Arrays, containing 22,690 probesets corresponding to approximately 14,000 well-characterized mouse genes. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).
Scan protocol Hybridized arrays were scanned with the GeneChip Scanner 3000 7G.
Data processing Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment (http://www.r-project.org/) version 2.8.0 with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Data were then filtered based on Affymetrix detection call and probeset intensity, so that only probesets that had a present call and intensity value >100 in at least one of the arrays were retained. Statistical analysis was performed with limma. P-values were adjusted for multiple testing using Benjamini and Hochberg’s method to control the false discovery rate. Genes with adjusted P values below 0.05 were considered differentially expressed.
 
Submission date May 06, 2010
Last update date Apr 12, 2011
Contact name Paola Roncaglia
Organization name SISSA/ISAS (International School for Advanced Studies)
Department Neurobiology
Street address via Bonomea 265
City Trieste
State/province TS
ZIP/Postal code 34136
Country Italy
 
Platform ID GPL8321
Series (1)
GSE21718 Developmental influence of the cellular prion protein on the gene expression profile in mouse hippocampus

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
1415670_at 11.18546134
1415671_at 13.67864903
1415672_at 13.14604516
1415673_at 10.74244801
1415674_a_at 12.50885153
1415675_at 11.19603363
1415676_a_at 13.14413
1415677_at 11.82058111
1415678_at 13.18829691
1415679_at 12.55082652
1415680_at 10.43735471
1415681_at 12.28148919
1415682_at 10.21476493
1415683_at 12.50457688
1415684_at 10.84480839
1415685_at 11.31163961
1415686_at 12.8795592
1415687_a_at 13.4988057
1415688_at 13.11083681
1415689_s_at 11.63734013

Total number of rows: 22690

Table truncated, full table size 521 Kbytes.




Supplementary file Size Download File type/resource
GSM541790.CEL.gz 2.4 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap