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Sample GSM705292 Query DataSets for GSM705292
Status Public on Jan 23, 2012
Title Monocytes rep6 mRNA (Roche)
Sample type RNA
 
Source name CD14+ monocytes from healthy donor pool 18
Organism Homo sapiens
Characteristics cell type: Monocytes
Extracted molecule total RNA
Extraction protocol Total RNA, including small non-coding RNAs, was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.
Label Biotin
Label protocol Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).
 
Hybridization protocol Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.
Scan protocol GeneChips were scanned using the GC 30007G scanner.
Description CD14+ monocytes, CD8+ T cells, CD56+ NK cells and CD19 B cells were isolated using the Human CD14 positive Selection Kit, Human CD8+ T cells Enrichment Kit, EasySep® Human CD56+ NK cells Enrichment Kit, EasySep® Human CD19+ B cells Enrichment Kit (all from Stem Cell Technologies) respectively according to manufacturer’s instructions.
Data processing Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total of 20,367 out of 54,675 probesets passed the QC and curation processes, corresponding to 11,629 unique genes.
 
Submission date Apr 08, 2011
Last update date Sep 01, 2016
Contact name Donavan Cheng
E-mail(s) donavan.cheng@gmail.com
Organization name Hoffmann-LaRoche
Department Translational Research Sciences
Street address 340 Kingsland Ave
City Nutley
State/province NJ
ZIP/Postal code 07110
Country USA
 
Platform ID GPL570
Series (2)
GSE28490 mRNA expression profiling of human immune cell subset (Roche)
GSE28492 miRNA and mRNA expression profiling of human immune cell subsets
Relations
Reanalyzed by GSE86362

Data table header descriptions
ID_REF
VALUE log2 RMA signal intensity

Data table
ID_REF VALUE
231211_s_at 4.25247
1560369_at 3.61369
235614_at 4.36236
1552256_a_at 5.59181
1552263_at 7.34316
1552264_a_at 7.02492
1552274_at 7.3314
1552275_s_at 5.44803
1552279_a_at 4.9459
1552281_at 5.28773
1552286_at 5.51319
1552291_at 5.40927
1552295_a_at 5.10512
1552307_a_at 4.72651
1552309_a_at 5.48319
1552310_at 5.78137
1552311_a_at 5.47497
1552312_a_at 3.66828
1552315_at 7.43157
1552316_a_at 8.44393

Total number of rows: 20367

Table truncated, full table size 372 Kbytes.




Supplementary file Size Download File type/resource
GSM705292_mRNA_CD14_EXP18.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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