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Sample GSM868907 Query DataSets for GSM868907
Status Public on Jul 12, 2012
Title blood-cd1c-dc-4
Sample type RNA
 
Source name healthy donor, dendritic cell, CD1c
Organism Homo sapiens
Characteristics tissue: blood
cell type: dendritic cell
cell subtype: CD1c
disease state: healthy
Treatment protocol None.
Growth protocol Monocytes and dendritic cell subsets were purified by FACS sorting from primary samples for transcription analysis.
Extracted molecule total RNA
Extraction protocol RNA was extracted from monocytes using an RNeasy Mini Kit (Qiagen) as per manufacturer's specifications. Extracted RNA was runned and quantified on a Bioanalyser (Agilent) for quality control and used subsequently in a microarray assay.
Label biotin
Label protocol Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).
 
Hybridization protocol According to BeadChip array manufacturer's protocol.
Scan protocol According to BeadChip array manufacturer's protocol.
Description BD_CD1c_DC_III
healthy donor, dendritic cell, CD1c,Homo sapiens,blood,dendritic cell,CD1c,total RNA,biotin
Data processing Array data were extracted at the probeset level with no background correction using Illumina's BeadStudio software. These raw data were normalised using the Loess method within the LUMI package in R/Bioconductor v2.13.1. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate, and probesets with corrected p-value less than 0.05 were considered.
 
Submission date Jan 31, 2012
Last update date Oct 23, 2015
Contact name Pavandip Singh Wasan
E-mail(s) [email protected]
Organization name Singapore Immunology Network
Department Bioinformatics
Street address 8A Biomedical Grove, #03-06, Immunos
City Singapore
ZIP/Postal code 138648
Country Singapore
 
Platform ID GPL10558
Series (2)
GSE35457 Transcriptome profiles of mouse and human monocyte and dendritic cell subsets (human data)
GSE35459 Transcriptome profiles of mouse and human monocyte and dendritic cell subsets
Relations
Reanalyzed by GSE74316

Data table header descriptions
ID_REF
VALUE Non-background-corrected, loess-normalised signal intensity from using the lumiN function within the LUMI package of R/Bioconductor
Detection_Pval

Data table
ID_REF VALUE Detection_Pval
ILMN_1762337 137.2385285 0.4194805
ILMN_2055271 184.4610754 0.01688312
ILMN_1736007 119.8156842 0.7324675
ILMN_2383229 140.9387252 0.374026
ILMN_1806310 114.6437685 0.7857143
ILMN_1779670 113.1254395 0.7727273
ILMN_1653355 150.2618858 0.2285714
ILMN_1717783 87.17931788 0.9727273
ILMN_1705025 137.4064498 0.4142857
ILMN_1814316 137.8268585 0.4103896
ILMN_2359168 96.79049278 0.9168831
ILMN_1731507 97.89689004 0.8974026
ILMN_1787689 142.1278634 0.3077922
ILMN_3241953 983.7027424 0
ILMN_1745607 192.9437321 0.002597403
ILMN_2136495 98.1680229 0.8935065
ILMN_1668111 112.7251856 0.8181818
ILMN_2295559 148.1453888 0.2636364
ILMN_1735045 120.31645 0.651948
ILMN_1680754 178.1263074 0.03116883

Total number of rows: 47323

Table truncated, full table size 1532 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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