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Sample GSM927627 Query DataSets for GSM927627
Status Public on May 05, 2012
Title Xenopus laevis inner ear_ biological rep1
Sample type RNA
 
Source name Xenopus laevis juveniles
Organism Xenopus laevis
Characteristics developmental stage: juvenile
age: ~1 month
tissue: inner ear
Growth protocol Juvenile Xenopus laevis (n = 21) were approximately 1 month old with an average weight of 2.4 ± 1.0 g and an average length of 2.7 ± 0.3 cm and obtained from Nasco (Fort Atkinson, WI). Animal husbandry and surgical procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of New Mexico State University.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA) as per Trujillo-Provencio C, Powers T, Sultemeier D, Serrano E: RNA isolation from Xenopus inner ear sensory endorgans for transcriptional profiling and molecular cloning. Methods Mol Biol 2009, 493:3-20.
Label biotin
Label protocol Biotinylated cRNA was prepared from each RNA replicate (~ 1 ug total RNA) using the GeneChip® One-Cycle Target Labelling kit following the manufacturer’s protocol (Affymetrix).
 
Hybridization protocol 20 ug of cRNA after fragmentation were hybridized following the manufacturer’s protocol (Affymetrix).
Scan protocol Xenopus laevis GeneChips were scanned by the GeneChip Scanner 3000 7G (Affymetrix).
Description XIE1
Data processing Bioconductor packages 'affy' and 'gcrma' were used to read in the CEL files and for preprocessing, respectively. Both packages were implemented in R.
 
Submission date May 04, 2012
Last update date May 05, 2012
Contact name Elba E. Serrano
E-mail(s) serrano@nmsu.edu
Fax 575-646-5665
URL http://biology-web.nmsu.edu/serrano/neurolab/neurolab.html
Organization name New Mexico State University
Department Biology
Street address 1200 S. Horseshoe, MSC 3AF
City Las Cruces
ZIP/Postal code 88005
Country USA
 
Platform ID GPL1318
Series (1)
GSE37767 Expression data from juvenile Xenopus laevis inner ear tissue

Data table header descriptions
ID_REF
VALUE GCRMA log2 transformed intensity values
Detection_CALL

Data table
ID_REF VALUE Detection_CALL
AFFX-BioB-3_at 6.889761775 P
AFFX-BioB-5_at 8.561371486 P
AFFX-BioB-M_at 7.991211115 P
AFFX-BioC-3_at 9.826015609 P
AFFX-BioC-5_at 9.31676467 P
AFFX-BioDn-3_at 11.55735117 P
AFFX-BioDn-5_at 10.52449078 P
AFFX-CreX-3_at 13.99886671 P
AFFX-CreX-5_at 13.28504563 P
AFFX-DapX-3_at 2.120208888 A
AFFX-DapX-5_at 2.120208888 A
AFFX-DapX-M_at 2.120208888 A
AFFX-LysX-3_at 2.120208888 A
AFFX-LysX-5_at 2.120208888 A
AFFX-LysX-M_at 2.120208888 A
AFFX-PheX-3_at 2.918329432 A
AFFX-PheX-5_at 2.120208888 A
AFFX-PheX-M_at 2.120208888 A
AFFX-ThrX-3_at 2.120208888 A
AFFX-ThrX-5_at 2.120208888 A

Total number of rows: 15611

Table truncated, full table size 466 Kbytes.




Supplementary file Size Download File type/resource
GSM927627_A6065_XIE1.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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