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Sample GSM4774192 Query DataSets for GSM4774192
Status Public on Sep 10, 2020
Title Day 5 Immature DC_Patient 9
Sample type RNA
 
Source name Dendritic Cell, Melanoma
Organism Homo sapiens
Characteristics subject id: Patient 9
patient diagnosis: melanoma
cell type: Dendritic Cell
dc subtype: day 5 iDC
clinical outcome: SD
overall survival (months): 27.43
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 monocyte-derived iDC, 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 1.939971642
16650003 1.62342513
16650005 4.234157552
16650007 1.687184041
16650009 1.551173774
16650011 1.755621839
16650013 3.690990117
16650015 3.113235183
16650017 2.826352242
16650019 1.344475808
16650021 2.852245156
16650023 2.62023485
16650025 2.777102637
16650027 1.82106337
16650029 3.328873905
16650031 2.699844087
16650033 1.860083691
16650035 1.36178559
16650037 1.860083691
16650041 3.907856354

Total number of rows: 53617

Table truncated, full table size 1093 Kbytes.




Supplementary file Size Download File type/resource
GSM4774192_iDC_9.CEL.gz 7.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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