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Sample GSM1048857 Query DataSets for GSM1048857
Status Public on Dec 05, 2012
Title NC rep1
Sample type RNA
 
Source name control
Organism Mus musculus
Characteristics treatment: control
cell line: RAW 264.7
Treatment protocol RAW264.7 cells were transfected with pRNAi-U6H1vector containing Tim-3 siRNA or control siRNA. The siRNA duplex giving maximal knockdown was selected. Raw264.7 cell clones stably express Tim-3 SiRNA were selected after continued culture with selecting drugs (G418, Sigma-Aldrich), and were analyzed for Tim-3 expression.
Growth protocol Tim-3 knockdown and control RAW264.7 cells were maintained in DMEM supplemented with 10% heat-inactivated FBS, 100 units/ml of penicillin, and 100 units/ml of streptomycin in a humidified 5% CO2 atmosphere at 37 °C.
Extracted molecule total RNA
Extraction protocol Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description This sample is of control siRNA transfected RAW264.7 cells. It is the first of three negative control (NC) biological replicates used in this experiment, each from separate cultures.
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5 (Roche NimbleGen, Inc.). All gene level files were imported into Agilent GeneSpring GX software(version 11.5.1) for further analysis. Genes that at least 3 out of 6 samples have values greater than or equal to lower cut-off: 100.0 were chosen for differentially expressed gene screening.
 
Submission date Dec 04, 2012
Last update date Dec 05, 2012
Contact name Gencheng HAN
Organization name Beijing Institute of Basic Medical Sciences
Department Department of Immunology
Street address 27 Taiping Road, Haidian District
City Beijing
ZIP/Postal code 100850
Country China
 
Platform ID GPL10192
Series (1)
GSE42729 Expression analysis of Tim-3 knockdown RAW264.7 cell

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity for 27,526 genes

Data table
ID_REF VALUE
AB000096 126.03051
AB000490 157.55203
AB001425 727.77423
AB001539 2817.5269
AB001750 1878.3235
AB001926 2555.9333
AB003502 8480.493
AB004048 304.76886
AB005662 2234.9385
AB008928 220.9168
AB009369 51.046997
AB010122 11021.12
AB011499 1330.5162
AB011812 5522.569
AB012265 1887.7325
AB012393 265.55292
AB012601 3401.008
AB012727 115.408714
AB012808 350.6966
AB013467 543.1145

Total number of rows: 27526

Table truncated, full table size 509 Kbytes.




Supplementary file Size Download File type/resource
GSM1048857_NC_1_532.pair.gz 2.6 Mb (ftp)(http) PAIR
GSM1048857_NC_1_532_RMA.calls.gz 466.2 Kb (ftp)(http) CALLS
GSM1048857_NC_1_532_norm_RMA.pair.gz 2.3 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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