|
| Status |
Public on Sep 04, 2015 |
| Title |
BMDC_untreated_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Bone marrow derived dendritic cells unstimulated
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: BMDC
agent: control
|
| Treatment protocol |
Cells were treated with CpG or control (PBS alone)
|
| Growth protocol |
Bone marrow was flushed from tibias and femurs of mice with HBSS. Bone marrow cells were cultured at 2x106 cells/ml in 10 ml non-tissue culture treated dishes in RPMI 1640 containing 10% LPS-free FBS, Penicillin:streptomycin glutamine 2-mercaptoethanol (cRPMI), with 40ng/ml murine GM-CSF (Peprotech). On day 3 of cultures 10ml of fresh media was added also containing 40ng/ml GM-CSF. On days 6 and 8, 10ml of media was removed and centrifuged to collect cells, which were resuspended in 10ml fresh media containing GM-CSF and were added back to dishes. Non-adherent cells were isolated on day 9. DCs were plated in 24-well plates at 2x106 cells/ml in 1ml of cRPMI with or without the class B CpG ODN1826 (ACGT DNA Technologies corporation, Toronto, ON, Canada) at 10μM final concentration overnight.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mirVana miRNA isolation kit
|
| Label |
Cy3
|
| Label protocol |
Agilent miRNA Complete Labeling and Hyb Kit
|
| |
|
| Hybridization protocol |
Agilent miRNA Complete Labeling and Hyb Kit
|
| Scan protocol |
scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
|
| Description |
Whole RNA with miRNA
BMDC1
DC1_S01_1_3_
|
| Data processing |
GeneView intensity files were imported into R, values less than 0.01 were set to 0.01. Pearson correlations were calculated and outputted into correlation file MDS plot: pearson_plot_filter.png Hierarchical clustering of samples based on pearson correlation: 'HCL_sample_filter.png' Unsupervised Hierarchical clustering result: 'HCL_filter.png' linear fit was done by limma package from R/bioconductor.
FilteredIntensities_mirna_dc.txt is linked as a supplementary file on the Series record.
|
| |
|
| Submission date |
Sep 04, 2015 |
| Last update date |
Sep 04, 2015 |
| Contact name |
Evan F. Lind |
| E-mail(s) |
linde@ohsu.edu
|
| Phone |
503 494-1347
|
| Organization name |
Oregon Health & Science University
|
| Department |
Molecular Microbiology and Immunology
|
| Street address |
Mail Code L220, 3181 SW Sam Jackson Park Road
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
| |
|
| Platform ID |
GPL8824 |
| Series (1) |
| GSE72716 |
miRNA expression patterns in immature and CpG stimulated murine BMDCs |
|
