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Sample GSM1547485 Query DataSets for GSM1547485
Status Public on Jan 05, 2015
Title Thyroid female 2
Sample type RNA
 
Source name normal thyroid
Organism Rattus norvegicus
Characteristics tissue: thyroid
Sex: female
strain: Han Wistar-derived rats (AlpkHsdBrlHan:WIST)
Treatment protocol Rats were humanely killed at a designated establishment by halothane inhalation, which is an appropriate method under Schedule 1 of the Act.Organs and tissues were removed and cleaned of extraneous tissue by a 5-person necropsy team within 5 min of death, then frozen in liquid nitrogen. Pancreas was prioritized for rapid freezing, since its mRNA is known to be particularly vulnerable to degredation. Tissue samples from each animal weighing 100-250 mg were taken from frozen samples and homogenized immediately in RNeasy lysis buffer. Care was taken to ensure samples were taken consistently from the same region of tissue for each individual, and that they were representative of the whole organ (e.g. radial segments of kidney were taken from the equator in each case).
Growth protocol Rats were housed 2-3 per cage
Extracted molecule total RNA
Extraction protocol RNA was purified from lysates using Qiagen RNeasy mini columns according to the manufacturer’s instructions. Nucleic acid (RNA) purity was determined according to the 260/280nM absorbance ratio using a Nanodrop-1000 (Thermo Scientific). Samples were accepted only if the ratio fell between 1.8 and 2.2. Otherwise, RNA was re-extracted from new samples of frozen tissue. RNA integrity was assessed using the 2100 Bioanalyser (Agilent). Samples with an RNA integrity number (RIN) <7 were rejected, and re-processed.
Label biotin
Label protocol cDNA, biotin-labelled cRNA and fragmented hybridization probes were prepared using the Affymetrix IVT kit (Affymetrix CA.).
 
Hybridization protocol Hybridization mixes including control oligos and biotin-labelled cRNA were prepared following the Affymetrix protocol. Hybridisation to Affymetrix RAE230_2 rat genechips® was carried out overnight at 45oC rotating at 60 rpm. Bound biotinylated probes were revealed with strptavidin-phycoerythrin complex according to the Affymetrix protocol.
Scan protocol Scanning was carried out with an Affymetric 3000 scanner using the RAE_230_V2 protocol
Data processing R bioconductor was used for primary analysis, analysis was using GC-RMA-s
 
Submission date Nov 17, 2014
Last update date Jan 05, 2015
Contact name Russell Huby
Organization name AstraZeneca
Street address Alderley Park
City Macclesfield
State/province Cheshire
ZIP/Postal code SK10 4TG
Country United Kingdom
 
Platform ID GPL1355
Series (1)
GSE63362 Identification of sexually dimorphically expressed genes in rat tissues

Data table header descriptions
ID_REF
VALUE Data in the matrix table are log2 GC-RMA values

Data table
ID_REF VALUE
1367452_at 11.816665
1367453_at 10.3558445
1367454_at 10.385286
1367455_at 11.730155
1367456_at 11.783349
1367457_at 9.86919
1367458_at 7.6255713
1367459_at 12.743999
1367460_at 11.826248
1367461_at 10.103453
1367462_at 11.828209
1367463_at 11.151852
1367464_at 10.362538
1367465_at 11.390912
1367466_at 10.195852
1367467_at 11.507164
1367468_at 9.343628
1367469_at 12.77819
1367470_at 10.513915
1367471_at 9.951821

Total number of rows: 31042

Table truncated, full table size 626 Kbytes.




Supplementary file Size Download File type/resource
GSM1547485_NRTP_-_3107_-_Thyroid.CEL.gz 2.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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