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Sample GSM1026692 Query DataSets for GSM1026692
Status Public on Oct 23, 2015
Title Sputum_R21
Sample type RNA
 
Source name Sputum sample from R21 (group:Asthma)
Organism Homo sapiens
Characteristics age: 54
Sex: Female
disease: Asthma
tissue: Sputum
subtype: eosino
Extracted molecule total RNA
Extraction protocol Total RNA 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.
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.
 
Submission date Oct 26, 2012
Last update date Oct 23, 2015
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 (1)
GSE41863 Sputum gene expression profiling in asthmatics

Data table header descriptions
ID_REF
VALUE log2 RMA signal intensity

Data table
ID_REF VALUE
231211_s_at 4.17304
244279_at 5.14
1552256_a_at 5.85092
1552263_at 7.13253
1552264_a_at 7.73535
1552274_at 5.05309
1552275_s_at 6.61431
1552278_a_at 6.65669
1552279_a_at 5.4614
1552280_at 7.27075
1552283_s_at 5.21181
1552286_at 5.83596
1552291_at 6.53234
1552295_a_at 5.1215
1552299_at 4.59024
1552301_a_at 4.49273
1552307_a_at 5.51412
1552309_a_at 6.7786
1552310_at 5.99815
1552311_a_at 4.80169

Total number of rows: 21767

Table truncated, full table size 398 Kbytes.




Supplementary file Size Download File type/resource
GSM1026692__52001900911217062614417436060856.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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