NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2253770 Query DataSets for GSM2253770
Status Public on Aug 01, 2017
Title mouse alveolar macrophage_young_rep4
Sample type RNA
 
Source name alveolar macrophage, from 2-4 month-old, PBS
Organism Mus musculus
Characteristics strain: C57B/6
young or aged: young
treatment: PBS
Treatment protocol C57B/6 mice of either 2-4 months-old or 22-24 months old were obtained from the National Institute of Aging rodent facility. Mice were infected with purified human influenza virus, A/Puerto Rico/8/34 (H1N1) (PR8) (Advanced Biotechnologies Inc.; MD, USA), by instillation of with 50μl PBS containing indicated dose of PR8 virus or 50μl PBS control intranasally. At day 3 post infection, the lungs were harvested and single-cell suspension was obtained by mechanical and enzymatic digestion. . After staining with fluorescent antibodies, Alveolar macrophages were sorted according to their forward- and side-scatter profiles and by their phenotype as follow: CD45+SiglecF+CD11chiF4/80+.
Growth protocol NA
Extracted molecule total RNA
Extraction protocol RNA was isolated using the miRNeasy micro kit (Qiagen, Valencia CA) by utilizing QIAcube (Qiagen, Valencia CA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent Tapestation 2200 Bioanalyzer with High Sensitivity RNA ScreenTape (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.25 ug RNA using the One-Color Low RNA Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression v2 8x60k microarray slides (G4852B) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software 12.0.0.7 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Jul 27, 2016
Last update date Aug 01, 2017
Contact name Koji Sakamoto
E-mail(s) koji.sakamoto@yale.edu
Organization name Yale University
Department Internal Medicine
Lab Naftali Kaminski
Street address 300 Cedar Street
City New Haven
State/province CT
ZIP/Postal code 06521
Country USA
 
Platform ID GPL21163
Series (1)
GSE84901 Gene expression in murine alveolar macrophage: effect of aging and influenza infection

Data table header descriptions
ID_REF
VALUE log2 normalized signal intensity

Data table
ID_REF VALUE
A_52_P40327 2.853354454
A_55_P2180181 2.516381264
A_51_P400375 8.852467537
A_55_P2052831 7.29895401
A_55_P2235911 5.56519413
A_55_P2385960 2.617319107
A_51_P262721 6.298360825
A_52_P257547 5.985274792
A_52_P293299 4.552555084
A_55_P2176430 7.642647266
A_51_P443618 6.666461945
A_51_P417279 4.832152843
A_52_P474699 2.748924732
A_52_P120740 5.466676235
A_55_P2742543 2.639692307
A_55_P2335933 2.658853054
A_52_P613953 5.755447865
A_55_P2508064 2.693561316
A_52_P498557 2.927055597
A_51_P305061 3.068710566

Total number of rows: 27067

Table truncated, full table size 669 Kbytes.




Supplementary file Size Download File type/resource
GSM2253770_YP4.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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