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Sample GSM4774222 Query DataSets for GSM4774222
Status Public on Sep 10, 2020
Title Day 6 Mature DC_Patient 5
Sample type RNA
 
Source name Dendritic Cell, Melanoma
Organism Homo sapiens
Characteristics subject id: Patient 5
patient diagnosis: melanoma
cell type: Dendritic Cell
dc subtype: day 6 mDC
clinical outcome: PD
overall survival (months): 0.67
Treatment protocol Matured DC (mDC) were transduced with the recombinant Adenovirus vaccine (encoding three full length antigens: Tyrosinase, MART-1, MAGE-A6) for 3hrs at 37°C.
Growth protocol Patient immature dendritic cells were generated from elutriated monocytes using GM-CSF and IL-4 for 5 days. On day 6, immature DC were matured using IFNG and LPS for 24hrs. 24hrs. Post-maturation, mDC were transduced with the adenovirus vaccine for 3hrs.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by using RNeasy kit (Qiagen, Germantown, , MD, USA). The RNA concentration was measured using Nano Drop ND-1000 Spectrophotometer (Nano Drop Technologies, Wilmington, DE, USA) and RNA quality was assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). 300ng of total RNA per sample was amplified according to manufacturer's instructions (Ambion WT Expression Kit).
Label biotin
Label protocol cDNAs were fragmented, biotinylated, and hybridized to the GeneChip Human Gene 2.0 ST Arrays (Affymetrix WT Terminal Labeling Kit).
 
Hybridization protocol the arrays were washed and stained on a GeneChip Fluidics Station 450
Scan protocol Scanning was carried out with the GeneChip Scanner 3000 and image analysis with the Affymetrix GeneChip Command Console Scan Control(all from Affymetrix, Santa Clara, CA).
Description Gene expression data from mDC, melanoma
Data processing R/Bioconductor was used for the primary analysis. (Oligo & Limma Packages)
 
Submission date Sep 09, 2020
Last update date Sep 10, 2020
Contact name Deena Marie Maurer
E-mail(s) [email protected]
Organization name University of Pittsburgh
Department Immunology
Street address 200 Lothrop Street
City Pittsburgh
ZIP/Postal code 15213
Country USA
 
Platform ID GPL16686
Series (1)
GSE157738 Monocyte-derived DC Expression Data from Advanced Staged Melanoma Patients

Data table header descriptions
ID_REF
VALUE Log 2 RMA Normalization

Data table
ID_REF VALUE
16650001 1.376771738
16650003 1.890466128
16650005 3.239641765
16650007 2.099351899
16650009 1.319284396
16650011 2.085690607
16650013 4.508327481
16650015 4.604516881
16650017 2.203364849
16650019 4.095408455
16650021 3.391469414
16650023 2.204394911
16650025 3.631565665
16650027 1.484758999
16650029 3.400416304
16650031 3.313228759
16650033 2.027292211
16650035 1.509598322
16650037 2.542493715
16650041 4.886068526

Total number of rows: 53617

Table truncated, full table size 1093 Kbytes.




Supplementary file Size Download File type/resource
GSM4774222_mDC_5.CEL.gz 7.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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