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Sample GSM316001 Query DataSets for GSM316001
Status Public on Sep 03, 2008
Title F1 hybrid Testis, biological rep 3
Sample type RNA
Source name F1 Hybrid (X.laevis female x X.borealis male), sexually mature testis
Organism Xenopus laevis x Xenopus borealis
Characteristics Mother: X.laevis (laboratory stock); Father: X.borealis (Kenya)
Age: 450 days
Treatment protocol Animal was immersed in MS222 and gonad was immediately extracted
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol® Reagent (Invitrogen Life Technologies) according to the manufacturer’s protocol and purified with RNeasy Mini Kit (Qiagen).
Label biotin
Label protocol Two micrograms of total RNA was used to prepare biotin labeled cRNA probes following the manufacturer’s (Affymetrix) protocol.
Hybridization protocol Hybridization to Affymetrix Xenopus laevis Genome expression array followed the manufacturer's (Affymetrix) protocol.
Scan protocol GeneChip was scanned using the Affymetrix GeneChip Scanner 3000 7G.
Description 1 of 3 biological replicates of gene expression data from sexually mature testis.
Data processing Data were RMA normalized using RMA Express and a probemask (based on perfect match probes for X.laevis and X.borealis).
Normalization of 3 biological replicates were performed with 3 biological replicates of X.laevis testis and 3 biological replicates of X.borealis testis.
Submission date Aug 29, 2008
Last update date Oct 17, 2008
Contact name Frederic Chain
Organization name McMaster University
Department Biology
Lab LSB 324
Street address 1280 Main Street West
City Hamilton
State/province Ontario
ZIP/Postal code L8S4K1
Country Canada
Platform ID GPL1318
Series (1)
GSE12625 Expression data for a study on cross-species hybridization on single-species microarrays

Data table header descriptions
VALUE RMA normalized (log2) using RMA express using "XB+XL perfect match probemask"

Data table
Xl.1.1.S1_s_at 12.65320368
Xl.10012.1.A1_at 8.419788902
Xl.10032.1.A1_s_at 9.783284039
Xl.10043.1.A1_at 7.173122965
Xl.10043.2.S1_at 4.704257637
Xl.10054.1.S1_at 9.105678382
Xl.10087.1.A1_at 8.76631278
Xl.10104.1.A1_at 6.356551624
Xl.10118.1.S1_at 5.588593219
Xl.1013.1.S1_at 6.174159563
Xl.10142.1.S1_at 8.325801657
Xl.1015.1.S1_at 9.396881001
Xl.10170.1.A1_at 8.056374506
Xl.10191.1.S1_at 9.221935697
Xl.10208.1.S1_at 6.778757027
Xl.10222.1.A1_at 6.916304956
Xl.10227.1.A1_at 8.382101782
Xl.10230.1.A1_at 8.175542819
Xl.10251.1.A1_at 5.792891029
Xl.10287.1.S1_at 8.738097088

Total number of rows: 2143

Table truncated, full table size 59 Kbytes.

Supplementary file Size Download File type/resource
GSM316001.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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