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Sample GSM98563 Query DataSets for GSM98563
Status Public on Mar 20, 2006
Title single cell from ICM E3.5, biological rep16
Sample type RNA
Source name Single cell from ICM in blastocyst at E3.5
Organism Mus musculus
Characteristics Strain: C57BL/6
Extracted molecule total RNA
Extraction protocol Single cell was lysed by adding to the tube containing cell lysis buffer, and the clude lysate was used for cDNA synthesis and amplification without purification.
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 from single ICM cells (E3.5)
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)
GSE4307 Expression data from single cells from ICMs of mouse blastocysts at E3.5
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-BioB-5_at 244.1747146 P
AFFX-BioB-M_at 336.2126041 P
AFFX-BioB-3_at 267.078494 P
AFFX-BioC-5_at 528.9985655 P
AFFX-BioC-3_at 835.0449217 P
AFFX-BioDn-5_at 1565.491544 P
AFFX-BioDn-3_at 2638.86165 P
AFFX-CreX-5_at 6488.638156 P
AFFX-CreX-3_at 7410.730267 P
AFFX-DapX-5_at 28.41202983 A
AFFX-DapX-M_at 702.5124583 P
AFFX-DapX-3_at 1768.609711 P
AFFX-LysX-5_at 2180.283464 P
AFFX-LysX-M_at 3770.917834 P
AFFX-LysX-3_at 5856.812527 P
AFFX-PheX-5_at 1 A
AFFX-PheX-M_at 179.5136825 P
AFFX-PheX-3_at 175.2693599 P
AFFX-ThrX-5_at 21.3069177 A
AFFX-ThrX-M_at 26.06135156 A

Total number of rows: 45101

Table truncated, full table size 1066 Kbytes.

Supplementary file Size Download File type/resource
GSM98563.CEL.gz 5.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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