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Sample GSM212561 Query DataSets for GSM212561
Status Public on Jul 25, 2007
Title Gene expression profiling of Phgdh knockout embryo KO2
Sample type RNA
 
Source name Head RNA of Phgdh Knockout@E13.5 No.2
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 58.2134 P 0.00141043
AFFX-BioB-M_at 58.7255 P 0.000753643
AFFX-BioB-3_at 29.1632 P 0.00844047
AFFX-BioC-5_at 193.879 P 8.14279e-05
AFFX-BioC-3_at 192.5 P 5.16732e-05
AFFX-BioDn-5_at 293.388 P 4.42873e-05
AFFX-BioDn-3_at 764.647 P 0.000146581
AFFX-CreX-5_at 2004.78 P 4.42873e-05
AFFX-CreX-3_at 2687.47 P 4.42873e-05
AFFX-DapX-5_at 0.805203 A 0.559354
AFFX-DapX-M_at 5.03601 A 0.672921
AFFX-DapX-3_at 0.969783 A 0.963431
AFFX-LysX-5_at 3.59007 A 0.425962
AFFX-LysX-M_at 0.814127 A 0.824693
AFFX-LysX-3_at 1.04125 A 0.440641
AFFX-PheX-5_at 0.994728 A 0.904333
AFFX-PheX-M_at 0.744484 A 0.921998
AFFX-PheX-3_at 1.7488 A 0.804734
AFFX-ThrX-5_at 4.10107 A 0.686277
AFFX-ThrX-M_at 1.26286 A 0.824672

Total number of rows: 45101

Table truncated, full table size 1374 Kbytes.




Supplementary file Size Download File type/resource
GSM212561.CEL.gz 6.0 Mb (ftp)(http) CEL
GSM212561.CHP.gz 10.6 Mb (ftp)(http) CHP
GSM212561.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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