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Sample GSM7676816 Query DataSets for GSM7676816
Status Public on Sep 30, 2023
Title Donor 4 unstimulated BDCA3
Sample type RNA
 
Source name Blood
Organism Homo sapiens
Characteristics cell type: cDC1 (BDCA3+ DC)
treatment: None
Treatment protocol DCs were stimulated with: pRNA (15μg/ ml) and Hiltonol (10 μg/ml) for 16 hours.
Growth protocol Cells were obtained from aphaeresis of 5 different donors. Peripheral blood mononuclear cells (PBMCs) were isolated by using Ficoll density centrifugation (Lymphoprep; Axis-Shield PoC AS, Oslo, Anti-Human Lineage Cocktail 1 in FITC (LIN1) (BD Bioscience Pharmingen, San Jose, CA) containing antibodies for CD3, CD14, CD16, CD19, CD20, CD56 receptors, together with the anti-FITC conjugated magnetic microbeads of Miltenyi Biotec (Bergisch-Gladbach, Germany) were used to deplete the LIN1+ cell fraction, by following manufacturer’s instructions. Next, CDC1were further purified by sorting (flowcytometry) using anti–BDCA-3–APC combined with anti-HLA-DR-PE-Vio770 (Miltenyi Biotec) to a purity of 99.9%. DCs were cultured in X-VIVO-15 medium (Lonza, Basel, Switzerland) supplemented with 2% human serum (Sanquin).
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol (Invitrogen, MA, USA), following the standard protocol. Quality control of the isolated RNA (concentration, RIN, 28S/18S and size) was performed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol by ThermoFisher (Clariom D Expression Analysis Technical Manual revision B.0, ThermoFisher).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol According to the standard Affymetrix protocol by ThermoFisher (Clariom D Expression Analysis Technical Manual revision B.0, ThermoFisher).
Data processing Expression intensities from CEL files were converted to an expression matrix using the bioconductor packages affycoretools, version 1.70.0, and oligo, version 1.62.2.
 
Submission date Aug 02, 2023
Last update date Sep 30, 2023
Contact name Johannes Textor
E-mail(s) johannes.textor@radboudumc.nl
Organization name Radboud University Medical Center
Street address Geert Groteplein 26-28
City Nijmegen
ZIP/Postal code 6525 GA
Country Netherlands
 
Platform ID GPL23126
Series (2)
GSE239895 Hiltonol and pRNA stimuli induce an immune activating profile in the transcriptomics of cDC1s [Affy]
GSE239899 Hiltonol and pRNA stimuli induce an immune activating profile in the transcriptomics of cDC1s

Data table header descriptions
ID_REF
VALUE Normalized signal intensity as computed by RMA algorithm (Bioconductor package oligo, version 1.62.2)

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 1.664269585
AFFX-BkGr-GC04_st 1.508696496
AFFX-BkGr-GC05_st 1.52203896
AFFX-BkGr-GC06_st 1.585614877
AFFX-BkGr-GC07_st 1.617719305
AFFX-BkGr-GC08_st 1.61606328
AFFX-BkGr-GC09_st 1.653782583
AFFX-BkGr-GC10_st 1.755422651
AFFX-BkGr-GC11_st 1.806843834
AFFX-BkGr-GC12_st 2.003750732
AFFX-BkGr-GC13_st 2.212439444
AFFX-BkGr-GC14_st 2.490750766
AFFX-BkGr-GC15_st 2.704580168
AFFX-BkGr-GC16_st 3.434249694
AFFX-BkGr-GC17_st 3.821276482
AFFX-BkGr-GC18_st 4.379156381
AFFX-BkGr-GC19_st 4.97265579
AFFX-BkGr-GC20_st 5.225645522
AFFX-BkGr-GC21_st 5.473840038
AFFX-BkGr-GC22_st 5.781744056

Total number of rows: 138745

Table truncated, full table size 4075 Kbytes.




Supplementary file Size Download File type/resource
GSM7676816_SMP4_0021941A_B01.CEL.gz 22.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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