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Sample GSM1252983 Query DataSets for GSM1252983
Status Public on Nov 09, 2013
Title NE 6hrs
Sample type RNA
 
Source name 6hrs with 0.001% NE treatment
Organism Mus musculus
Characteristics background strain: C57BL6
cell type: JAWS II dendritic cells
Treatment protocol JAWS II dendritic cells (10^7 cells/culture in 10 ml plates) were incubated with 0.001% W805EC NE alone or mixed with 10 µg/ml rPA. Control cultures were either untreated (PBS) or incubated with 10 µg/ml rPA or with 1 µg/ml of TLR4 ligand LPS K12
Growth protocol Jaws II cells were grown according ATCC protocol
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3’ IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3’ IVT Express kit Instruction Manual, P/N 702646 Rev. 5).
 
Hybridization protocol Following fragmentation, 16 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.
Description Global gene expression in vitro
Data processing Data was analyzed using the limma and affy bioconductor packages implemented in the R-statistical environment version 2.15.0. RMA was used to normalize the data and fit log2 transformed expression values.
 
Submission date Oct 28, 2013
Last update date Nov 09, 2013
Contact name Paul Edward Makidon
E-mail(s) pmakidon@gmail.com
Phone 734-277-5775
Organization name University of Michigan
Department Internal Medicine
Lab MNIMBS
Street address 9340 MSRB III, 1150 W. Medical Center Dr.
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platform ID GPL1261
Series (1)
GSE51804 Effect of W805EC nanoemulsion (NE) on global gene transcription in JawsII dendritic cells in vitro

Data table header descriptions
ID_REF
VALUE Log 2 Transformed RMA

Data table
ID_REF VALUE
1415670_at 10.632
1415671_at 12.789
1415672_at 12.421
1415673_at 8.824
1415674_a_at 10.246
1415675_at 9.798
1415676_a_at 12.413
1415677_at 10.487
1415678_at 10.823
1415679_at 12.197
1415680_at 11.239
1415681_at 11.488
1415682_at 9.478
1415683_at 12.485
1415684_at 10.569
1415685_at 9.981
1415686_at 11.036
1415687_a_at 13.549
1415688_at 11.011
1415689_s_at 9.789

Total number of rows: 45101

Table truncated, full table size 772 Kbytes.




Supplementary file Size Download File type/resource
GSM1252983_Baker_Jr_002_166_Mouse430_2_.CEL.gz 3.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table
Processed data are available on Series record

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