|
| Status |
Public on Aug 22, 2008 |
| Title |
single cell from PGCs (E8.25), biological rep5 |
| Sample type |
RNA |
| |
|
| Source name |
single cell from primordial germ cell (PGCs) at Embryonic day (E) 8.25(Blimp1+, stella+)
|
| Organism |
Mus musculus |
| Characteristics |
Strain: C57BL/6
Genotype: Wild type
cDNA amplified from single cellular RNA
|
| 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.
|
| 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)
|
| |
|
| 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 PGCs (E8.25)
|
| 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.
|
| |
|
| 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) |
|
| Relations |
| Reanalyzed by |
GSE119085 |
