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Sample GSM1059408 Query DataSets for GSM1059408
Status Public on Jan 04, 2013
Title TAN_3
Sample type RNA
 
Source name tumor-associated neutrophils (TAN)
Organism Mus musculus
Characteristics strain background: BALB/c
group: neutrophils from tumor
control group: No
replicates: yes
class: clonal
sample id: TAN_3
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

Data table header descriptions
ID_REF
VALUE normalized data

Data table
ID_REF VALUE
ILMN_2707227 126.653
ILMN_2896528 1611.83
ILMN_2721178 423.513
ILMN_1227723 784.292
ILMN_3033922 1298.31
ILMN_3092673 3428.35
ILMN_2730714 8782.51
ILMN_3162224 1252.87
ILMN_2816356 95.403
ILMN_2808939 460.816
ILMN_2634564 375.277
ILMN_1216623 526.813
ILMN_1215157 571.209
ILMN_1228777 94.981
ILMN_2734484 450.484
ILMN_2952292 142.964
ILMN_2660815 1860.62
ILMN_1243593 2713.22
ILMN_1219797 120.089
ILMN_1231132 284.884

Total number of rows: 16322

Table truncated, full table size 332 Kbytes.




Supplementary file Size Download File type/resource
GSM1059408_TAN_3_Raw.txt.gz 197.3 Kb (ftp)(http) TXT
Processed data included within Sample table

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