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Sample GSM98564 Query DataSets for GSM98564
Status Public on Mar 20, 2006
Title single cell from ICM E3.5, biological rep17
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 405.6382813 P
AFFX-BioB-M_at 554.191203 P
AFFX-BioB-3_at 443.5583214 P
AFFX-BioC-5_at 870.433336 P
AFFX-BioC-3_at 1261.303719 P
AFFX-BioDn-5_at 2176.357733 P
AFFX-BioDn-3_at 3503.06004 P
AFFX-CreX-5_at 7954.745174 P
AFFX-CreX-3_at 8579.037009 P
AFFX-DapX-5_at 20.72427891 P
AFFX-DapX-M_at 101.1701585 A
AFFX-DapX-3_at 579.1125694 P
AFFX-LysX-5_at 3802.150701 P
AFFX-LysX-M_at 6025.227499 P
AFFX-LysX-3_at 7866.466344 P
AFFX-PheX-5_at 275.5270208 P
AFFX-PheX-M_at 711.7910587 P
AFFX-PheX-3_at 865.7339944 P
AFFX-ThrX-5_at 28.50493882 A
AFFX-ThrX-M_at 43.01685062 A

Total number of rows: 45101

Table truncated, full table size 1055 Kbytes.

Supplementary file Size Download File type/resource
GSM98564.CEL.gz 5.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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