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Sample GSM1103584 Query DataSets for GSM1103584
Status Public on Jun 01, 2013
Title Foxp3- activated in vitro_Polysome-associated RNA_12
Sample type RNA
 
Source name Cells isolated from lymph nodes and spleens
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Foxp3-
condition: Activated in vitro for 36 hrs with plate bound CD3 and CD28 antibodies (BD Bioscience) (5µg/ml) in the presence of recombinant hIL-2 ([100U/ml]
isolated rna: Polysome-associated RNA
Treatment protocol For the naïve cells all buffers and media were supplemented with cycloheximide (Sigma, St. Louis, MO) (100µg/ml). For the activated samples cells were activated for 36h with plate bound CD3 and CD28 antibodies (BD Bioscience) (5µg/ml) in the presence of recombinant hIL-2 ([100U/ml]
Growth protocol Cells isolated from lymph nodes and spleens were stained with PE conjugated CD4 antibody (GK1.5, eBioscience, San Diego, CA) and MACS purified. Thereafter TFoxp3+ and TFoxp3- cells were sorted based on CD4 and GFP-Foxp3 expression using a FACSAria to obtain cell populations of high purity (>97%). For the activated samples cells were activated for 36h with plate bound CD3 and CD28 antibodies (BD Bioscience) (5µg/ml) in the presence of recombinant hIL-2 ([100U/ml]
Extracted molecule total RNA
Extraction protocol Cytosolic and polysome-associated RNA were prepared directly ex vivo or post-activation in vitro as described previously (Larsson O, 2007 ancer Res 67: 6814-6824). For cells isolated directly ex vivo, RNA from two experiments was pooled for each sample.
Label biotin
Label protocol Ovation Pico WTA system (NuGEN) according to the manufacturer’s instructions.
 
Hybridization protocol Samples were hybridized with the Affymetrix GeneChip Mouse Genome 430 2.0 Array according the instructions of the manufacturer
Scan protocol Arrays were scanned using the GeneArray Scanner 3000 according to the instructions from the manufacturer.
Description Gene expression data from Foxp3- cells Activated in vitro for 36 h using RNA isolated from Polysome-associated RNA
@52002900806613121411408986822861.CEL
Data processing Data were extracted and normalized using a custom CDF and Robust Multi-array Average (RMA) in R (r-project.org) with default settings.
 
Submission date Mar 21, 2013
Last update date Jun 01, 2013
Contact name Ola Larsson
E-mail(s) ola.larsson@ki.se
Phone +46 (0)8 517 73280
Organization name Karolinska Institutet
Department Department of oncology-pathology
Street address CCK, R8:01
City Stockholm
ZIP/Postal code 171 76
Country Sweden
 
Platform ID GPL7546
Series (1)
GSE45401 Distinct translational control in CD4+ T-cell subsets

Data table header descriptions
ID_REF
VALUE Log2 RMA signal

Data table
ID_REF VALUE
100009600_at 4.983406284
100012_at 2.484082101
100017_at 5.25275586
100019_at 5.907733307
100034251_at 5.975220978
100036521_at 3.174476571
100037258_at 7.894306969
100037278_at 2.339920823
100038570_at 4.506239538
100038635_at 3.953825851
100038680_at 3.151984423
100038887_at 12.38374913
100038959_at 3.278162466
100039026_at 9.279093933
100039027_at 3.697280979
100039094_at 4.75980505
100039235_at 6.093373386
100039282_at 2.725493399
100039284_at 2.925708887
100039307_at 4.654670614

Total number of rows: 16539

Table truncated, full table size 343 Kbytes.




Supplementary file Size Download File type/resource
GSM1103584__52002900806613121411408986822861.CEL.gz 3.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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