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Sample GSM612968 Query DataSets for GSM612968
Status Public on Dec 22, 2014
Title WT-SA_12_HR-1
Sample type RNA
 
Source name microglia, wild type control, 12hr
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: wild type
developmental stage: neonatal
age: 2-4 days
tissue: cerebral cortex
cell type: microglia from primary mixed glial culture
treatment: Staphylococcus aureus stimulation
time: 12 hours
Biomaterial provider Mice from Jackson Laboratories, Bar Harbor, ME.
Treatment protocol A USA300 community-acquired methicillin-resistant S. aureus (CA-MRSA) clinical isolate recovered from a patient with a fatal brain abscess was kindly provided by Dr. Costi Sifri (University of Virginia School of Medicine, Charlottesville). Bacterial strains were heat-inactivated and used to stimulate WT microglia at 107 colony forming units (cfu)/well for 6 or 12 hours.
Growth protocol Primary mixed glial cultures were prepared on the same day from the cerebral corticies of neonatal WT mice (2-4 days of age). Microglia were harvested from mixed glial cultures using a differential shaking technique with a purity of >98%.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the stimulated microglia using Trizol (Invitrogen). The quality and quantity of total RNA were analyzed by the Agilent 2100 Bioanalyzer using RNA 6000 nano chips (Agilent Technologies, Palo Alto, CA).
Label biotin
Label protocol Standard Illumina protocol using the Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791). In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double-stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.
 
Hybridization protocol Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's SentrixMouse Ref-8, v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3.
Scan protocol Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.
Description RNA from the S. aureus-stimulated microglia (12 hr) of WT C57BL/6 mice.
Data processing Data was extracted using the Illumina BeadStudio software (v3.4). Any spots at or in the Sample data table. the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented in the Sample data table. Z-score = (raw value - avg)/std. Complete data including detection p-values is included in the supplementary file that is linked to the Series record.
 
Submission date Oct 26, 2010
Last update date Jun 22, 2020
Contact name Supriyo De
Organization name NIA-IRP, NIH
Department Laboratory of Genetics and Genomics
Lab Computational Biology & Genomics Core
Street address 251 Bayview Blvd
City Baltimore
State/province Maryland
ZIP/Postal code 21224
Country USA
 
Platform ID GPL6885
Series (1)
GSE24935 Toll-like receptor 2 (TLR2)-TLR9 crosstalk dictates IL-12 family cytokine production in microglia

Data table header descriptions
ID_REF
RAW_VALUE Raw intensity value from Illumina GenomeStudio software
VALUE Z transformation of the natural log of the raw intensity values

Data table
ID_REF RAW_VALUE VALUE
ILMN_1212607 103.4044 -0.5211497
ILMN_1212612 89.85907 -0.6598336
ILMN_1212619 362.0607 0.71665358
ILMN_1212628 98.08637 -0.5733016
ILMN_1212632 86.59483 -0.6963825
ILMN_1212636 1673.955 2.22901775
ILMN_1212637 471.922 0.97840708
ILMN_1212645 192.0855 0.09055216
ILMN_1212648 327.4388 0.61737491
ILMN_1212653 115.8564 -0.4088395
ILMN_1212672 181.0495 0.03210734
ILMN_1212682 119.7592 -0.3761141
ILMN_1212683 82.44767 -0.7448573
ILMN_1212685 95.09302 -0.6039146
ILMN_1212692 99.80608 -0.556134
ILMN_1212693 142.2277 -0.2062755
ILMN_1212695 7224.31 3.67335626
ILMN_1212698 82.01993 -0.749995
ILMN_1212702 97.34879 -0.5807572
ILMN_1212703 156.7083 -0.1105072

Total number of rows: 25697

Table truncated, full table size 822 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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