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Sample GSM3840150 Query DataSets for GSM3840150
Status Public on Jun 01, 2019
Title KO-P13
Sample type RNA
 
Source name frontal lobe (brain)
Organism Mus musculus
Characteristics genotype/variation: KO
age: P13
tissue: Frontal lobe (brain)
sequencing batch: 2015-04-07
Extracted molecule total RNA
Extraction protocol Twenty milligrams of the frontal lobe of P14 mice of WT, Het, KO and treated KO (n=6 per genotype) was immediately removed after euthanizing the mice with isoflurane. RNA extraction was performed following the manufacturer’s instructions (RNeasy mini kit, Qiagen, Hilden, Germany) and DNase treatment (Roche, Basel, Switzerland) was applied.
Label biotin
Label protocol RNA was transcribed to double-stranded cRNA using MessageAmp Premier RNA Amplification Kit (Life Technologies, Carlsbad, CA) with an oligo(dT) primer following the manufacturer’s instructions. Following fragmentation, 11 µg of biotin-labeled cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 430 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix), then scanned with the Affymetrix GeneChip Scanner 3000 G7 (Affymetrix).
 
Hybridization protocol Following fragmentation, 11 µg of biotin-labeled cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 430 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix), then scanned with the Affymetrix GeneChip Scanner 3000 G7 (Affymetrix).
Scan protocol GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix), then scanned with the Affymetrix GeneChip Scanner 3000 G7 (Affymetrix).
Description Array hybridization was done by the UCLA Clinical Microarray Core using their protocols.
Data processing Raw fluorescence data was stored as .CEL.gz files was loaded into R as an AffyBatch object (using the affy package in R). This object was then processed using Robust Multi-Array Average (RMA) normalization, also part of the affy package, which removed background ‘noise’ and converted data to a log2 scale. ComBat from the sva R package was then applied to the normalized data to adjust for batch effects. Affymetrix probes were summarized and re-annotated with Ensembl gene names from the Ensembl July 2015 archive (Ensembl version 81). Finally, the dataset was filtered so that genes with a standard deviation in the 5th quantile or lower were removed.
 
Submission date May 31, 2019
Last update date Jun 01, 2019
Contact name Gerald Lipshutz
E-mail(s) GLipshutz@mednet.ucla.edu
Organization name UCLA
Department Surgery
Lab Lipshutz
Street address 650 CE Young Drive, Box 957054, UCLA School of Medicine
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL26724
Series (1)
GSE132058 Hepatic arginase deficiency fosters dysmyelination during postnatal CNS development

Data table header descriptions
ID_REF
VALUE Log2 RMA

Data table
ID_REF VALUE
ENSMUSG00000000001 9.57236256
ENSMUSG00000000003 3.17912192
ENSMUSG00000000028 5.552878015
ENSMUSG00000000031 6.510169023
ENSMUSG00000000037 4.768711131
ENSMUSG00000000049 5.97791985
ENSMUSG00000000056 9.028976043
ENSMUSG00000000058 9.493272424
ENSMUSG00000000078 8.724151371
ENSMUSG00000000085 8.121864923
ENSMUSG00000000093 4.438452555
ENSMUSG00000000094 4.075550597
ENSMUSG00000000103 3.604105053
ENSMUSG00000000120 6.539284807
ENSMUSG00000000125 2.904759265
ENSMUSG00000000126 7.98230763
ENSMUSG00000000127 6.446572499
ENSMUSG00000000131 8.652911385
ENSMUSG00000000134 8.120458325
ENSMUSG00000000142 7.558560754

Total number of rows: 18057

Table truncated, full table size 544 Kbytes.




Supplementary file Size Download File type/resource
GSM3840150_KO_P13.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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