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Sample GSM2333741 Query DataSets for GSM2333741
Status Public on Oct 04, 2016
Title Anxa2 knockout, biological replicate 4
Sample type RNA
 
Source name Anxa2 knockout, gastrocnemius skeletal muscle
Organism Mus musculus
Characteristics genotype: Anxa2 knockout
tissue: skeletal muscle, gastrocnemius
age: 24 weeks
genetic background: C57BL/6
Extracted molecule total RNA
Extraction protocol Directly following euthanasia, Gastrocnemius (GSC) muscles from the left hindlimb were directly frozen liquid nitrogen and stored at -80˚C. Total RNA was extracted from frozen GSC muscles using Trizol reagent (Life Technologies, USA) and cleaned up with RNeasy MinElute cleanup kit (Qiagen, USA) according to the manufacturers’ instructions, and then stored at -80oC until use.
Label biotin
Label protocol An aliquot of 250 ng of total high-quality RNA from each sample was used. cDNA and biotinylated cRNA were synthesized using the Affymetrix GeneChip® 3’ IVT Express Target Amplification, Labeling and Control Reagent kit according to manufacturer’s instructions.
 
Hybridization protocol 15.2 ug of biotinylated cRNA was fragmented and hybridized to Affymetrix Gene-Chips MG 430 2.0 for 16 hours. The arrays were then washed and stained on the Affymetrix Fluidics station 400.
Scan protocol Arrays were imaged using Hewlett Packard G2500A gene Array scanner according to manufacturer’s protocol
Description Gene expression data from Anxa2 knockout mouse
Data processing The R library affyQCReport was used for quality control. Raw CEL files were normalized using the RMA algorithm from affy library with Mouse4302_Mm_ENSG_v19.0.0 as custom Chip Description File (CDF) from the BRAINARRAY project (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/19.0.0/ensg.asp) (R version 3.1.2)
 
Submission date Oct 03, 2016
Last update date Oct 04, 2016
Contact name Jyoti K. Jaiswal
E-mail(s) jkjaiswal@cnmc.org
Organization name Children’s National Health System
Department Center for Genetic Medicine Research
Street address 111 Michigan Av NW
City Washington D. C.
ZIP/Postal code 20010
Country USA
 
Platform ID GPL22519
Series (1)
GSE87557 Role of annexin A2 in muscle repair

Data table header descriptions
ID_REF
VALUE Normalized using RMA

Data table
ID_REF VALUE
ENSMUSG00000000001_at 7.377248871
ENSMUSG00000000003_at 2.5643068
ENSMUSG00000000028_at 4.579267756
ENSMUSG00000000031_at 11.2720725
ENSMUSG00000000037_at 3.156531361
ENSMUSG00000000049_at 4.558128154
ENSMUSG00000000056_at 8.043507883
ENSMUSG00000000058_at 7.133539932
ENSMUSG00000000078_at 7.566380209
ENSMUSG00000000085_at 5.933177967
ENSMUSG00000000088_at 12.96947044
ENSMUSG00000000093_at 3.079739326
ENSMUSG00000000094_at 3.869746369
ENSMUSG00000000103_at 2.697935292
ENSMUSG00000000120_at 3.432408532
ENSMUSG00000000125_at 2.441406618
ENSMUSG00000000126_at 5.674347363
ENSMUSG00000000127_at 4.933275078
ENSMUSG00000000131_at 6.604469992
ENSMUSG00000000134_at 6.048453866

Total number of rows: 17352

Table truncated, full table size 574 Kbytes.




Supplementary file Size Download File type/resource
GSM2333741_JA2KM_ko-5mo-2_GAS-4m_Mouse430_2.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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