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Sample GSM1264249 Query DataSets for GSM1264249
Status Public on Aug 26, 2014
Title f-MDSC, before contact, replicate 4
Sample type RNA
 
Source name UCB derided CD33+IL4Rα+ sorted and incubated for 4 days with GM-CSF and G-CSF
Organism Homo sapiens
Characteristics treatment: Before contact
cell state: Preactivated cells
cell type: UCB derided CD33+IL4Rα+ sorted and incubated for 4 days with GM-CSF and G-CSF
Treatment protocol Sterilely sorted CD33 and IL-4Rα positive cells before and after been co-culture with autologous CD3+ T cells were lysed with TRIZOL and stored at -80◦C till RNA extraction was performed. TRIZOL samples preservation was also used for the control cells line HEK-293.
Growth protocol Human Umbilical cord blood (UCB) samples underwent Ficoll-Paque gradient separation and ACK red cell lysis, and then were cultured for 4 days in the presence of GM-CSF and G-CSF (40ng/ml). CD33 and IL-4Rα positive cells were sterilely sorted, part of the cells stored for RNA extraction, and part co-cultured for 3 days with autologous PHA activated CFSE labeled CD3+ T cells either in cell to cell contact (CONTACT) or using a transwell device to avoid cell contact (TRANSWELL). HEK-293 cells were maintained in complete RPMI-140 10% FBS.
Extracted molecule total RNA
Extraction protocol RNA was purified using the miRNA easy kit from Qiagen and following the manufacture instruction.
Label biotin
Label protocol Affymetrix GeneChip WT Terminal Labeling Kit - sense-strand cDNA is fragmented with a combination of uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 and its yield is further labeled by terminal deoxynucleotidyl transferase (TdT) with the Affymetrix® proprietary DNA Labeling Reagent that is covalently linked to biotin.
 
Hybridization protocol GeneChip® Hybridization, Wash, and Stain Kit - Following labeling, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 ST arrays. GeneChips were washed and stained (streptavidin,R-phycoerythrin conjugate and biotinylated anti-streptavidin) in the Affymetrix Fluidics Station 400.
Scan protocol Standard Affymetrix scanning procedures on a GeneChip® Scanner 3000 7G . Affymetrix GeneChip® Command Console® Software (AGCC)- used to view CEL file images.
Description Gene expression data of CD33+IL4Ra+ sorted cell before contact with autologus PHA activated CD3+ T cells
Data processing RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
 
Submission date Nov 14, 2013
Last update date Aug 26, 2014
Contact name Silvio Bicciato
E-mail(s) silvio.bicciato@unipd.it
Phone +39-049-827-6108
Organization name University of Padova
Department Molecular Medicine
Street address via U. Bassi 59/b
City Padova
ZIP/Postal code 35131
Country Italy
 
Platform ID GPL17930
Series (1)
GSE52376 Molecular and cellular characterization of Cord Blood derived, IDO expressing human fibrocystic Myeloid Derived Suppressor Cells

Data table header descriptions
ID_REF
VALUE RMA-calculated signal intensity (log2)

Data table
ID_REF VALUE
1_at 6.096357365
10_at 4.227434348
100_at 7.874549185
1000_at 4.794442508
10000_at 6.643099148
100009613_at 4.945445104
100009676_at 7.072756231
10001_at 9.195231303
10002_at 5.935452985
10003_at 3.066226095
100033413_at 5.156066974
100033422_at 4.456954002
100033423_at 3.707529842
100033424_at 3.984080999
100033425_at 2.722470416
100033426_at 8.33687749
100033427_at 10.06028718
100033428_at 2.272171693
100033430_at 2.616213258
100033431_at 6.414304583

Total number of rows: 23786

Table truncated, full table size 494 Kbytes.




Supplementary file Size Download File type/resource
GSM1264249_b_13.CEL.gz 8.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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