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Sample GSM705320 Query DataSets for GSM705320
Status Public on Jan 23, 2012
Title Eosinophils rep4 mRNA (Roche)
Sample type RNA
 
Source name Eosinophils from healthy donor pool 8
Organism Homo sapiens
Characteristics cell type: Eosinophils
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 Isolated using EasySep® Human Eosinophil Enrichment Kit (Stem Cell Technologies)
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 4.88618
1560369_at 4.63886
235614_at 4.83716
1552256_a_at 4.75825
1552263_at 6.85292
1552264_a_at 6.84162
1552274_at 6.91741
1552275_s_at 4.65201
1552279_a_at 5.21731
1552281_at 5.91005
1552286_at 4.31084
1552291_at 7.57759
1552295_a_at 4.76546
1552307_a_at 3.98384
1552309_a_at 4.05791
1552310_at 5.16042
1552311_a_at 5.67054
1552312_a_at 4.75946
1552315_at 3.30951
1552316_a_at 2.64253

Total number of rows: 20367

Table truncated, full table size 372 Kbytes.




Supplementary file Size Download File type/resource
GSM705320_mRNA_EOSINO_EXP8.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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