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Status |
Public on Aug 22, 2008 |
Title |
single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep1 |
Sample type |
RNA |
|
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Source name |
single cell from lineage-restricted PGC precursors at Late-Streak/0-Bud stage(Blimp1+, Oct4+)
|
Organism |
Mus musculus |
Characteristics |
Strain: C57BL/6 Genotype: Wild type cDNA amplified from single cellular RNA
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Treatment protocol |
Embryos were dissected in DMEM/BSA. Embryonic fragments containing primordial germ cells (PGCs) or PGC precursors were cut out by glass needle and incubated with 0.05% trypsin/0.5 mM EDTA for 7 min, followed by dissociation into single cells by mouth pipette. Dissociated single cells were randomly picked up for single cell cDNA amplification.
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Growth protocol |
Mice were sacrified and embryos were collected in Dulbecco’s modified Eagle Medium supplemented with 0.5% BSA (DMEM/BSA) at different days post coitum (dpc). Noon of the day when the vaginal plugs of the mated females were identified was scored as 0.5 dpc.
|
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)
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Hybridization protocol |
Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization)
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Scan protocol |
The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix)
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Description |
Gene expression data from single lineage-restricted PGC precursors (Late-Streak/0-Bud stage)
|
Data processing |
CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software. Data 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. The absolute calls were calculated using MAS5.0 algorism with dCHIP default settings.
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Submission date |
Apr 10, 2008 |
Last update date |
Aug 28, 2018 |
Contact name |
Kazuki Kurimoto |
E-mail(s) |
kurimoto@naramed-u.ac.jp
|
Organization name |
Nara Medical University
|
Department |
School of medicine
|
Lab |
Department of Embryology
|
Street address |
840 Shijo-Cho, Kashihara
|
City |
Nara |
ZIP/Postal code |
634-8521 |
Country |
Japan |
|
|
Platform ID |
GPL1261 |
Series (1) |
GSE11128 |
Expression data from single cells from mouse primordial germ cell lineage (E6.25-E8.25, wild type and Blimp1KO) |
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Relations |
Reanalyzed by |
GSE119085 |