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Sample GSM98551 Query DataSets for GSM98551
Status Public on Mar 20, 2006
Title single cell from ICM E3.5, biological rep4
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 294.1320122 P
AFFX-BioB-M_at 481.7697499 P
AFFX-BioB-3_at 333.4577108 P
AFFX-BioC-5_at 661.5608268 P
AFFX-BioC-3_at 1008.96471 P
AFFX-BioDn-5_at 1927.880616 P
AFFX-BioDn-3_at 3063.574033 P
AFFX-CreX-5_at 7278.371625 P
AFFX-CreX-3_at 7944.275832 P
AFFX-DapX-5_at 29.67322854 A
AFFX-DapX-M_at 862.786624 P
AFFX-DapX-3_at 889.1111654 P
AFFX-LysX-5_at 4654.788816 P
AFFX-LysX-M_at 6508.908869 P
AFFX-LysX-3_at 7826.762759 P
AFFX-PheX-5_at 404.717101 P
AFFX-PheX-M_at 430.0438609 P
AFFX-PheX-3_at 359.7298332 P
AFFX-ThrX-5_at 51.69740644 P
AFFX-ThrX-M_at 218.4198251 P

Total number of rows: 45101

Table truncated, full table size 1061 Kbytes.

Supplementary file Size Download File type/resource
GSM98551.CEL.gz 5.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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