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Sample GSM601350 Query DataSets for GSM601350
Status Public on Sep 29, 2010
Title DEED+activin+RA (ExpIII)
Sample type RNA
Source name DEED+activin+RA (ExpIII)
Organism Xenopus laevis
Characteristics tissue: animal cap cells dissected from embryos injected with DEED antisense (DEED-As) nucleotide against Xenopus lhx1
treatment group: treated with activin and retinoic acid
Biomaterial provider Neil Hukriede's lab
Treatment protocol The embryos at two cell stage were injected with DEED-As nucleotide against Xenopus lhx1.The animal caps were dissected from the injected embryos at stage 9, and then treated with 1X10-4 M retinoic acid and 10ng/ml Activin.
Growth protocol The DEED-As injected animal caps were cultured in 1X Danilchik’s solution with 1X10-4 M retinoic acid and 10ng/ml Activin till the sibling embryos reached stage 12.5.
Extracted molecule total RNA
Extraction protocol The dissected explants were homogenized in Stat 60 (TEL TEST), RNA was precipitated by isopropanol, treated with DNase I, and purified using the RNeasy kit (Qiagen).
Label biotin
Label protocol Biotinylated probe was prepared from 100 ng total RNA using the OVATION RNA amplification system (Nugen Technologies, Inc).
Hybridization protocol Total 2.2 microgram fargmented, biotin labeled amplified cDNA was used for hybridization, and the hybridization last for 18 hours.
Scan protocol Scanning was performed by using GeneChip Scanner 3000 driven by GCOS1.4.
Description Animal caps were injected with DEED-As, and then treated with activin and retinoic acid in experiment III.
Data processing Single Array Analysis were performed by using GCOS1.4. Briefly, the “Target Signal” for “all probe set” was set to 500. Select “User Defined” and place a “1” as the "Normalization Value” in the “Normalization” tab. Detection p-value less than 0.04 is assigned a Present call, and above 0.06 is assigned an Absent call. Marginal calls are given to probe sets which have p-values between 0.04 and 0.06. 
Submission date Sep 28, 2010
Last update date Sep 28, 2010
Contact name Hui Zhao
Phone 0085239431344
Organization name The Chinese University of Hong Kong
Department School of Biomedical Sciences
Street address The Chinese University of Hong Kong
City Hong Kong
ZIP/Postal code 00000
Country Hong Kong
Platform ID GPL1318
Series (1)
GSE24392 Lhx1 is required for specification of renal progenitor cell field

Data table header descriptions
VALUE Signal value is calculated which assigns a relative measure of abundance to the transcript.
ABS_CALL Absent (A), Marginal (M), and Present (P)
DETECTION P-VALUE p-VALUE is a basic property of a probe pair that describes its ability to detect its intended target

Data table
AFFX-BioB-5_at 3322.57 P 4.42873e-05
AFFX-BioB-M_at 5374.74 P 4.42873e-05
AFFX-BioB-3_at 4074.39 P 4.42873e-05
AFFX-BioC-5_at 8414.98 P 4.42873e-05
AFFX-BioC-3_at 4308.64 P 4.42873e-05
AFFX-BioDn-5_at 12541.3 P 4.42873e-05
AFFX-BioDn-3_at 28273.9 P 4.42873e-05
AFFX-CreX-5_at 51323.1 P 4.42873e-05
AFFX-CreX-3_at 71176.9 P 4.42873e-05
AFFX-DapX-5_at 49.8055 A 0.165861
AFFX-DapX-M_at 74.1188 A 0.116113
AFFX-DapX-3_at 10.7458 A 0.712257
AFFX-LysX-5_at 5.77275 A 0.794268
AFFX-LysX-M_at 26.2921 A 0.617421
AFFX-LysX-3_at 58.055 A 0.287743
AFFX-PheX-5_at 9.19981 A 0.749204
AFFX-PheX-M_at 6.93055 A 0.772364
AFFX-PheX-3_at 2.37656 A 0.804734
AFFX-ThrX-5_at 3.14277 A 0.969024
AFFX-ThrX-M_at 46.7256 A 0.147918

Total number of rows: 15611

Table truncated, full table size 564 Kbytes.

Supplementary file Size Download File type/resource
GSM601350.CEL.gz 1.8 Mb (ftp)(http) CEL
GSM601350.CHP.gz 90.2 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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