|
| Status |
Public on Jan 04, 2013 |
| Title |
NN_4 |
| Sample type |
RNA |
| |
|
| Source name |
Naïve mouse
|
| Organism |
Mus musculus |
| Characteristics |
strain background: BALB/c
group: BM naïve neutrophils
control group: yes
replicates: yes
class: clonal
sample id: NN_4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Gene expression was analyzed in neutrophils from 3 different populations – 7 isolated from bone marrow of naïve mice (NN), 4 isolated from spleens of tumor bearing mice (Granulocytic myeloid derived suppressor cells, G-MDSC), and 4 isolated from flank AB12 tumors (Tumor associated neutrophils, TAN). All neutrophil populations were defined as Ly6G+. Neutrophils were isolated following preparation of single cell suspension, using CD11b-Miltenni beads for enrichment, followed by flow-sorting of the Ly6G+ cells. RNA was processed as previously described and hybridized on Illumina Mouse Ref-8 v2 microarray chips.
|
| Label |
biotin
|
| Label protocol |
Biotin Labeling of RNA at 250ng with Ambion Illumina® TotalPrep RNA Amplification Kit (Cat #AMIL1791)
|
| |
|
| Hybridization protocol |
Hyb on Illumina Mouse Ref-8 v2 Expression BeadChip Kit using Illumina whole-Genome Gene Exprssion with Intellihyb Seal system which detect signal with streptavidin-Cy3.
|
| Scan protocol |
Illumina Setting with PMTFactor=2
|
| Data processing |
Array data were processed by Illumina’s BeadStudio software and expression levels exported for analysis. The gene-wise, median correlation of each array compared to all other arrays was computed to ensure that no outliers existed within the data. The expression levels were then quantile normalized using Matlab software (2010b) and non-informative probes (those with detection p-value >0.05 in all samples) were removed to reduce experimental noise. Ultimately, 16,322 probes were used in our analysis.
|
| |
|
| Submission date |
Jan 02, 2013 |
| Last update date |
Jan 04, 2013 |
| Contact name |
Louise C Showe |
| E-mail(s) |
lshowe@wistar.org
|
| Phone |
215-898-3791
|
| Organization name |
The Wistar Institute
|
| Lab |
Dr. Louise Showe
|
| Street address |
3601 Spruce St
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE43254 |
Transcriptomic Analysis Comparing Tumor-Associated Neutrophils with Granulocytic Myeloid-Derived Suppressor Cells and Normal Neutrophils |
|
