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Sample GSM212563 Query DataSets for GSM212563
Status Public on Jul 25, 2007
Title Gene expression profiling of Phgdh knockout embryo KO3
Sample type RNA
 
Source name Head RNA of Phgdh Knockout@E13.5 No.3
Organism Mus musculus
Characteristics ES cells: E14 (129P2/OlaHsd background), Genotype: Knockout (Phgdh-/-), C57BL/6J background, Gestation: 13.5 days, Tissue: head
Biomaterial provider Shigeki Furuya
Treatment protocol Targeted disruption of D-3-Phosphoglycerate dehydrogenase (Phgdh; EC 1.1.1.95) in mice.
Growth protocol None
Extracted molecule total RNA
Extraction protocol Total RNA from embryo heads was extracted and purified using RNeasy Lipid Tissue kit (Qiagen Inc) according to the manufacturer’s instructions.
Label Biotin
Label protocol Labeling was carried out using Affymetrix GeneChip® One-Cycle Target Labeling kit, according to manufactuer's protocol.
 
Hybridization protocol Hybridization was carried out for 16 hr at 45 ºC according the Affymetrix GeneChip® Manual.
Scan protocol Scanning was carried out using Affymetrix® GeneChip® Scanner with GCOS software according to manufactuer's protocol.
Description Affymetrix GeneChip® Mouse Genome 430 2.0 Array
Data processing Fluorescent data were processed using the Microarray Suite (MAS) 5.0 software (Affymetrix) and then were transferred to GeneSpring 7.0 software (Agilent).
 
Submission date Jul 23, 2007
Last update date Aug 28, 2018
Contact name Shigeki Furuya
E-mail(s) shigekifur@brs.kyushu-u.ac.jp
Organization name Kyushu University
Department Bio-Architecture Center
Lab Furuya Laboratory
Street address 6-10-1 Hakozaki, Higashiku
City Fukuoka
State/province Fukuoka
ZIP/Postal code 812-8581
Country Japan
 
Platform ID GPL1261
Series (1)
GSE8555 Genome-wide analysis of Phgdh inactivation in murine embryonic head
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE Signal intensity
ABS_CALL Absolute Call: A (Absent), M (Marginal), or P (Present)
DETECTION P-VALUE P-value generated by MAS5

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 117.513 P 0.000224668
AFFX-BioB-M_at 206.766 P 5.16732e-05
AFFX-BioB-3_at 119.675 P 4.42873e-05
AFFX-BioC-5_at 416.374 P 5.16732e-05
AFFX-BioC-3_at 522.492 P 4.42873e-05
AFFX-BioDn-5_at 1023.78 P 4.42873e-05
AFFX-BioDn-3_at 1882.54 P 4.42873e-05
AFFX-CreX-5_at 4682.42 P 5.16732e-05
AFFX-CreX-3_at 5689.76 P 4.42873e-05
AFFX-DapX-5_at 200.461 P 4.42873e-05
AFFX-DapX-M_at 387.808 P 0.00010954
AFFX-DapX-3_at 389.811 P 4.42873e-05
AFFX-LysX-5_at 16.5192 P 0.000389797
AFFX-LysX-M_at 32.7014 P 0.00227496
AFFX-LysX-3_at 65.4803 P 4.42873e-05
AFFX-PheX-5_at 27.1854 P 0.000445901
AFFX-PheX-M_at 46.9594 P 5.16732e-05
AFFX-PheX-3_at 45.1819 P 0.000195116
AFFX-ThrX-5_at 48.0898 P 0.000340305
AFFX-ThrX-M_at 83.4558 P 6.02111e-05

Total number of rows: 45101

Table truncated, full table size 1397 Kbytes.




Supplementary file Size Download File type/resource
GSM212563.CEL.gz 5.8 Mb (ftp)(http) CEL
GSM212563.CHP.gz 10.3 Mb (ftp)(http) CHP
GSM212563.EXP.gz 495 b (ftp)(http) EXP
Processed data included within Sample table
Processed data provided as supplementary file
Raw data provided as supplementary file

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