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Sample GSM212565 Query DataSets for GSM212565
Status Public on Jul 25, 2007
Title Gene expression profiling of Phgdh knockout embryo KO4
Sample type RNA
 
Source name Head RNA of Phgdh Knockout@E13.5 No.4
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 95.4909 P 0.000224668
AFFX-BioB-M_at 184.443 P 5.16732e-05
AFFX-BioB-3_at 104.735 P 4.42873e-05
AFFX-BioC-5_at 323.893 P 4.42873e-05
AFFX-BioC-3_at 402.745 P 4.42873e-05
AFFX-BioDn-5_at 840.117 P 4.42873e-05
AFFX-BioDn-3_at 1385.04 P 4.42873e-05
AFFX-CreX-5_at 4053.07 P 5.16732e-05
AFFX-CreX-3_at 4449.51 P 4.42873e-05
AFFX-DapX-5_at 154.54 P 6.02111e-05
AFFX-DapX-M_at 304.205 P 0.00010954
AFFX-DapX-3_at 362.371 P 4.42873e-05
AFFX-LysX-5_at 15.7234 P 0.000753643
AFFX-LysX-M_at 31.4294 P 0.000972149
AFFX-LysX-3_at 67.7421 P 9.4506e-05
AFFX-PheX-5_at 30.8493 P 0.000224668
AFFX-PheX-M_at 46.4703 P 0.000169227
AFFX-PheX-3_at 44.7514 P 0.000169227
AFFX-ThrX-5_at 36.9166 P 0.000389797
AFFX-ThrX-M_at 62.434 P 7.00668e-05

Total number of rows: 45101

Table truncated, full table size 1397 Kbytes.




Supplementary file Size Download File type/resource
GSM212565.CEL.gz 5.8 Mb (ftp)(http) CEL
GSM212565.CHP.gz 10.2 Mb (ftp)(http) CHP
GSM212565.EXP.gz 496 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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