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Sample GSM98575 Query DataSets for GSM98575
Status Public on Mar 20, 2006
Title ES 10pg amplified, technical rep8
Sample type RNA
 
Source name Total RNA from Embryonic Stem cell culture diluted to 10 pg
Organism Mus musculus
Characteristics Line: E14tg2a
Extracted molecule total RNA
Extraction protocol The total RNA was prepared by the RNeasy Mini Kit (Qiagen) according to the manufacturer's instruction
Label biotin
Label protocol Biotinylated cRNA were prepared from the PCR-amplified double-starnded cDNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay)
 
Hybridization protocol Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization)
Scan protocol The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix)
Description Gene expression data to verify the PCR-based single-cell cDNA amplification method (the V1V3 method)
Data processing CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data obtained from the eight amplified samples (ES-10pg-amplified-rep1:8) were normalized together with the default settings. The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.
 
Submission date Feb 27, 2006
Last update date Aug 28, 2018
Contact name Kazuki Kurimoto
E-mail(s) kurimoto@anat2.med.kyoto-u.ac.jp
Organization name Kyoto University
Department Graduate school of medicine
Lab Department of anatomy and cell biology
Street address Yoshida-Konoe-cho, Sakyo-ku
City Kyoto
ZIP/Postal code 606-8501
Country Japan
 
Platform ID GPL1261
Series (2)
GSE4308 Expression data for validation of single cell cDNA amplification method (V1V3 method)
GSE4309 An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE Model-based Expression Index calculated with dCHIP
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)

Data table
ID_REF VALUE ABS_CALL
AFFX-TrpnX-M_at 29.07162883 A
AFFX-TrpnX-5_at 63.27396067 P
AFFX-TrpnX-3_at 52.34682026 A
AFFX-TransRecMur/X57349_M_at 62.67420995 A
AFFX-TransRecMur/X57349_5_at 32.21922753 A
AFFX-TransRecMur/X57349_3_at 52.40200108 A
AFFX-ThrX-M_at 54.8998385 A
AFFX-ThrX-5_at 12.07457077 A
AFFX-ThrX-3_at 1 A
AFFX-r2-P1-cre-5_at 8268.443166 P
AFFX-r2-P1-cre-3_at 11556.36455 P
AFFX-r2-Ec-bioD-5_at 3673.653902 P
AFFX-r2-Ec-bioD-3_at 3822.232971 P
AFFX-r2-Ec-bioC-5_at 622.6078687 P
AFFX-r2-Ec-bioC-3_at 1096.127572 P
AFFX-r2-Ec-bioB-M_at 399.5549174 P
AFFX-r2-Ec-bioB-5_at 264.306849 P
AFFX-r2-Ec-bioB-3_at 330.4824843 P
AFFX-r2-Bs-thr-M_s_at 23.73509633 A
AFFX-r2-Bs-thr-5_s_at 20.70575638 A

Total number of rows: 45101

Table truncated, full table size 1081 Kbytes.




Supplementary file Size Download File type/resource
GSM98575.CEL.gz 5.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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