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Sample GSM4774218 Query DataSets for GSM4774218
Status Public on Sep 10, 2020
Title Day 6 Mature DC_Patient 33
Sample type RNA
 
Source name Dendritic Cell, Melanoma
Organism Homo sapiens
Characteristics subject id: Patient 33
patient diagnosis: melanoma
cell type: Dendritic Cell
dc subtype: day 6 mDC
clinical outcome: PD
overall survival (months): 1.67
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 2.046341662
16650003 3.290828363
16650005 2.704424387
16650007 2.348185533
16650009 1.84417299
16650011 2.739596777
16650013 3.192832674
16650015 5.371912215
16650017 2.382471192
16650019 4.094980821
16650021 2.72041342
16650023 2.168681614
16650025 3.328038613
16650027 2.289661127
16650029 3.950682066
16650031 3.537518202
16650033 1.354311493
16650035 1.584570101
16650037 1.694242196
16650041 3.584992034

Total number of rows: 53617

Table truncated, full table size 1093 Kbytes.




Supplementary file Size Download File type/resource
GSM4774218_mDC_33.CEL.gz 7.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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