GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM927628 Query DataSets for GSM927628
Status Public on May 05, 2012
Title Xenopus laevis inner ear_ biological rep2
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 XIE2
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
Fax 575-646-5665
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
VALUE GCRMA log2 transformed intensity values

Data table
AFFX-BioB-3_at 7.045849353 P
AFFX-BioB-5_at 8.198350637 P
AFFX-BioB-M_at 7.991211115 P
AFFX-BioC-3_at 9.821839985 P
AFFX-BioC-5_at 9.31676467 P
AFFX-BioDn-3_at 11.62548276 P
AFFX-BioDn-5_at 10.45418667 P
AFFX-CreX-3_at 14.03229074 P
AFFX-CreX-5_at 13.19801624 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
GSM927628_A6250_XIE2.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap