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Sample GSM705403 Query DataSets for GSM705403
Status Public on Jan 23, 2012
Title B cells rep2 mRNA (HUG)
Sample type RNA
 
Source name CD19+ B cells
Organism Homo sapiens
Characteristics cell type: CD19+ B cells
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 at University Hospital of Geneva (HUG)
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 18,391 out of 54,675 probesets passed the QC and curation processes.
 
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)
GSE28491 mRNA expression profiling of human immune cell subsets (HUG)
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 4.862844938
1560369_at 4.518987413
235614_at 4.665906311
1552256_a_at 4.830443298
1552263_at 4.470151237
1552264_a_at 4.542279809
1552271_at 4.890945824
1552274_at 5.698275883
1552275_s_at 4.665840544
1552279_a_at 5.154690539
1552281_at 5.818696922
1552286_at 5.723565029
1552291_at 2.927189722
1552295_a_at 5.182753356
1552307_a_at 5.157274931
1552310_at 4.422645884
1552311_a_at 5.810471927
1552315_at 4.144337277
1552316_a_at 2.770244467
1552318_at 3.984611699

Total number of rows: 18391

Table truncated, full table size 408 Kbytes.




Supplementary file Size Download File type/resource
GSM705403_B_05_08_10.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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