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Sample GSM1401302 Query DataSets for GSM1401302
Status Public on May 21, 2015
Title IL2 knockout GM-DCs treated with curdlan for 6 hours, replicate 3
Sample type RNA
 
Source name GM-DC derived from bone marrow and selected using CD11c microbeads
Organism Mus musculus
Characteristics strain: B6.129P2-Il2tm1Hor/J
cell type: GM-CSF myeloid dendritic cells
genotype: IL2 knockout
Treatment protocol Wt and IL-2-/- GM-DCs were treated or not with curdlan for 6h and processed for microarray
Growth protocol Bone marrow was flushed with IMDM medium with GM-CSF (200ng/ml), 1% Penicillin-Streptomycin, 10% Serum, 1% L-Glutamine and 0.1% β-Mercaptoethanol and cells were cultured for 7d The suspension cells were harvested on d7 and purified by positive selection using CD11c microbeads (Miltenyi Biotec) according to the manufacturer’s protocol. GM-DC (CD11c+, MHCII aI-A/I-E +) purity determined by FACS was routinely >95%.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted following the double extraction protocol using Trizol and Qiagen RNeasy Micro Extraction Kit. Total RNA integrity was assessed by Agilent Bioanalyzer.
Label biotin
Label protocol Single-stranded DNA were prepared according to the Ambion WT Expression Kit from 100ng of total RNA. 5.5ug of ssDNA were fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit.
 
Hybridization protocol Fragmented samples were hybridized according to Affymetrix guidelines for 17hr in 45°C on GeneChip Mouse Gene 1.0 ST Array; The arrays were then washed and stained using the standard fluidics protocol (FS450_0007) for gene arrays on the GeneChip Fluidics Station 450.
Scan protocol The mouse gene chips were scanned using GeneChip Scanner 3000. The images were analyzed using Expression Console and standard array quality controls analyses were carried out according to the instructions provided by Affymetrix.
Data processing CEL files were processed in Bioconductor using the xps package. Expression data was summarized at the transcript level and normalized using RMA. Log2 transformation was applied to the expression data.
 
Submission date May 30, 2014
Last update date May 22, 2015
Contact name Bernett Lee
E-mail(s) bernett_lee@immunol.a-star.edu.sg
Organization name Singapore Immunology Network
Street address 8A Biomedical Grove #03-06 Immunos
City NA
ZIP/Postal code 138648
Country Singapore
 
Platform ID GPL6246
Series (1)
GSE58120 Dendritic cell-derived IL-2 promotes apoptosis of terminally mature cells via a novel autocrine signaling pathway

Data table header descriptions
ID_REF
VALUE log2 RMA normalized expression values

Data table
ID_REF VALUE
10338001 11.73694965
10338003 10.0589157
10338004 8.913187649
10338017 12.79017504
10338025 8.813491006
10338026 13.04538384
10338029 9.843281702
10338035 8.807382899
10338036 9.28420304
10338037 4.265821936
10338041 11.03688654
10338042 10.03779963
10338044 12.0784912
10338047 7.522260362
10338056 3.982667574
10338059 13.01281478
10338060 4.212586013
10338063 4.154681956
10338064 6.465719442
10338065 7.49369933

Total number of rows: 34760

Table truncated, full table size 709 Kbytes.




Supplementary file Size Download File type/resource
GSM1401302_M3163.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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