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Sample GSM98578 Query DataSets for GSM98578
Status Public on Mar 20, 2006
Title ES 5ug nonamplified, technical rep3
Sample type RNA
Source name Total RNA from Embryonic Stem cell culture (5ug)
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 total RNA from cultured ES cells 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
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
Reanalyzed by GSE119085

Data table header descriptions
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
AFFX-TrpnX-M_at 16.33075969 A
AFFX-TrpnX-5_at 28.46150409 P
AFFX-TrpnX-3_at 53.48639264 A
AFFX-TransRecMur/X57349_M_at 284.3551257 P
AFFX-TransRecMur/X57349_5_at 339.7594811 P
AFFX-TransRecMur/X57349_3_at 692.3750849 P
AFFX-ThrX-M_at 88.72876605 P
AFFX-ThrX-5_at 89.79666749 P
AFFX-ThrX-3_at 175.4662801 P
AFFX-r2-P1-cre-5_at 6540.113691 P
AFFX-r2-P1-cre-3_at 8087.622815 P
AFFX-r2-Ec-bioD-5_at 2343.257849 P
AFFX-r2-Ec-bioD-3_at 2365.123822 P
AFFX-r2-Ec-bioC-5_at 451.5900848 P
AFFX-r2-Ec-bioC-3_at 706.492287 P
AFFX-r2-Ec-bioB-M_at 238.8382346 P
AFFX-r2-Ec-bioB-5_at 262.3956513 P
AFFX-r2-Ec-bioB-3_at 250.8376329 P
AFFX-r2-Bs-thr-M_s_at 151.8612523 P
AFFX-r2-Bs-thr-5_s_at 115.3152895 P

Total number of rows: 45101

Table truncated, full table size 1103 Kbytes.

Supplementary file Size Download File type/resource
GSM98578.CEL.gz 5.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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