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Sample GSM1289651 Query DataSets for GSM1289651
Status Public on Oct 01, 2015
Title Lung_4
Sample type RNA
 
Source name Lung M195-specific CD8+ T cells sorted from lungs of HMPV-infected mice at day 7 post-infection.
Organism Mus musculus
Characteristics strain background: C57BL6/J
gender: female
age: 8-12 weeks
genotype/variation: B6-Kb0Db0,B7.2 transgenic (B7tg) mice
infected with: human metapneumovirus (HMPV)
tissue: lung
cell type: Lung CD8+ T cells
Treatment protocol sort protocol: HMPV (pathogenic clinical strain TN/94-49, genotype A2) was grown and titered in LLC-MK2 cells. Mice were anesthetized with ketamine-xylazine and infected intranasally with 1x106 PFU of HMPV. Lymphocytes were isolated from spleens and lungs of infected animals. To obtain sufficient quantities of primary epitope-specific CD8+ T cells, on day 7 after HMPV infection the spleens and lungs from three mice were pooled together after processing. Samples were stained, sorted, and RNA purified on separate days in independent experiments. Cells were processed in ice-cold R10 media containing 10nM dasatinib to prevent activation and TCR signaling. Splenocytes were depleted of B cells by incubation on goat anti-mouse IgG and IgM coated (100μg/mL) T-75 flasks at 106 cells/mL for 1hr at 37C. Both lung and spleen cells were stained for viability, CD19, CD8, and M195-tetramers (both PE- and APC-conjugated). Surface/tetramer staining was performed for 1 hour at RT in PBS containing 1% FBS and 50nM dasatinib. Splenocytes were also stained for CD44 and CD62L to obtain control naïve cells. Dual-tetramer positive CD8+ T cells were sorted using a BD FACSAria III. Samples were maintained at 4C for the entirety of the sort and purity was 97–99% for all populations.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from sorted naive, spleen, lung, and secondary lung M195-specific CD8+ T cells using an RNeasy kit (QIAGEN) according to the manufacturer's instructions. On-column DNase digestion was performed and eluted RNA was quantified and checked for integrity using an Agilent 2100 Bioanalyzer. RNA was judged as suitable only if samples showed intact bands of 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RNA integrity number (RIN) above 8.0.
Label Biotin
Label protocol The FL-Ovation cDNA Biotin Molecule V2 (NuGen) was used to fragment and label single-stranded cDNA targets for subsequent hybridization.
 
Hybridization protocol The Affymetrix GeneChip Mouse Gene 1.1 ST 16-array plate consists of 16 single Gene 1.1 ST arrays arranged into the standard 96 well plate format. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.
Scan protocol Arrays were scanned on an Affymetrix GeneTitan instrument.
Description Lung M195-specific CD8+ T cells replicate #4
Data processing Microarray data were processed using the oligo package implementation of rma in R software.
 
Submission date Dec 16, 2013
Last update date Oct 01, 2015
Contact name Pengcheng Lu
E-mail(s) pengcheng.lu@vanderbilt.edu
Organization name Vanderbilt University
Street address 2200 Pierce Avenue
City Nashville
State/province TN
ZIP/Postal code 37232
Country USA
 
Platform ID GPL11533
Series (1)
GSE53349 CD8+ T cells during acute viral respiratory infection are uniquely differentiated and regulated by multiple inhibitory receptors

Data table header descriptions
ID_REF
VALUE RMA log2-signal intensity

Data table
ID_REF VALUE
10344614 4.330504279
10344616 2.136972197
10344620 2.442262003
10344622 3.004826297
10344624 8.161039523
10344633 7.757856057
10344637 6.821683718
10344653 2.257744553
10344658 6.471139856
10344674 2.624749331
10344679 2.877583252
10344707 6.932290945
10344713 8.573772599
10344715 3.21543469
10344717 2.654241139
10344719 4.021348
10344721 1.882399601
10344723 6.484158855
10344725 3.622261065
10344741 10.29666871

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM1289651_Lung_4.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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