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Sample GSM2580342 Query DataSets for GSM2580342
Status Public on Nov 01, 2017
Title WT neutrophils PBS rep4_miRNA
Sample type RNA
 
Source name Lung neutrophils isolated from WT mice given PBS
Organism Mus musculus
Characteristics tissue: Lung
cell type: neutrophils
genotype: Wild type (WT)
age: 6-12 weeks
Treatment protocol Anesthetized mice received PBS or a suspension containing S. pneumoniae instilled intratracheally into the left lung at a dose of 2.3 µl/g mouse body weight. Neutrophils were isolated using MACS beads (Miltenyi, Auburn, CA) according to the manufacturer’s instructions. Briefly, single cell suspensions were prepared from dissected mouse lungs. The cells were washed with PBS containing 2 mM EDTA and 0.5% bovine serum albumin, and incubated with biotin-anti-Ly6G and magnetic beads coated with anti-biotin. The samples were passed through a column in a magnetic field, and cells bound to beads were collected for further analysis. Cells were kept at 4-8°C during staining and magnetic bead isolation.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using miRNeasy kits from Qiagen (Valencia, CA, USA) according to the manufacturer's instructions.
Label Cy3
Label protocol 100 ng of total RNA from each sample was labeled with Cyanine 3-pCp using Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456) according to the manufacturer's instructions.
 
Hybridization protocol Labeled RNA was hybridized to Agilent SurePrint G3 Mouse miRNA 8X60K arrays for 20 hours at 55°C and 20 RPM. All reagents required for the labeling and hybridization steps were provided in Agilent’s miRNA Complete Labeling and Hyb Kit (p/n 5190-0456), and sample preparation and array processing were carried out according to the manufacturer's instructions.
Scan protocol Slides were scanned immediately after washing on an Agilent Microarray scanner using the default settings for the array format (AgilentG3_miRNA for the 8x60K format).
Description miR expression data from mouse lung neutrophils
Data processing MicroRNA expression signals were extracted from microarray images using Agilent Feature Extraction (FE) software, and normalized using either LVSmiRNA or AgiMicroRna package from Bioconductor. LVSmiRNA uses the least-variant set of miRs to normalize between the arrays (Calza, S., Valentini, D. & Pawitan, Y. BMC Bioinformatics 9, 140, doi:10.1186/1471-2105-9-140 (2008)), while AgiMicroRna uses RMA. Data analyses were carried out on both LVS and RMA normalized log2 intensities in parallel. Both LVS and RMA normalized values are available on the series record.
 
Submission date Apr 18, 2017
Last update date Nov 01, 2017
Contact name Claire M. Doerschuk
Organization name University of North Carolina at Chapel Hill
Department Marsico Lung Institute
Street address Marsico Hall 7205 CB#7248
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7248
Country USA
 
Platform ID GPL15547
Series (2)
GSE97921 The mRNA and microRNA (miR) transcriptome of lung neutrophils during S. pneumoniae (SP) pneumonia in wild type (WT) mice [miRNA]
GSE97922 The mRNA and microRNA (miR) transcriptome of lung neutrophils during S. pneumoniae pneumonia in wild type (WT) mice

Data table header descriptions
ID_REF
VALUE RMA normalized signal intensity

Data table
ID_REF VALUE
mmu-let-7g 12.977
mmu-let-7i 12.622
mmu-miR-1a 5.354
mmu-miR-15b 12.376
mmu-miR-23b 11.825
mmu-miR-27b 10.259
mmu-miR-29b 12.54
mmu-miR-30a 12.758
mmu-miR-30a* 8.948
mmu-miR-30b 11.328
mmu-miR-99a 9.534
mmu-miR-99b 8.373
mmu-miR-101a 9.948
mmu-miR-124 2.012
mmu-miR-125a-5p 8.646
mmu-miR-125b-5p 10.882
mmu-miR-126-5p 9.476
mmu-miR-126-3p 15.223
mmu-miR-127 4.168
mmu-miR-128 6.552

Total number of rows: 1079

Table truncated, full table size 20 Kbytes.




Supplementary file Size Download File type/resource
GSM2580342_miR_WT_PBS_C4.txt.gz 6.6 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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