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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 31, 2010 |
| Title |
mouse blastomere in 4-cell embyro #2_4_cell_B6 |
| Sample type |
SRA |
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| Source name |
mouse blastomere in a 4-cell embyro
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| Organism |
Mus musculus |
| Characteristics |
cell type: mouse blastomere in 4-cell embyro #2
gender: female
strain: MF1 wild type
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Oocyte, Two-cell, Four-cell, and 8-cell stage embryos were recovered from MF1 females mated with MF1 male mice (Nagy et al. 2003). The zona pellucida was removed by treatment with acidic tyrode solution. The individual blastomeres were separated by gentle pipeting using a glass capillary. Whole transcriptome Amplification by RT-PCR from a single cell.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
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| Data processing |
Raw data is aligned to Mouse genome (Jul. 2007 assembly of the mouse genome: mm9, NCBI Build 37, with dbSNP128 positions replaced with IUB codes) using SOLiD whole transcriptome pipeline: http://solidsoftwaretools.com/gf/project/transcriptome/. Reads that aligned to a unique location are used for downstream analysis and saved in *_max.srf.tar files.
srf conversion is generated by SOLiD srt tool: http://solidsoftwaretools.com/gf/project/srf/
Algorithm description: Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, Lao K, Surani MA., mRNA-Seq whole-transcriptome analysis of a single cell, Nat Methods. 2009 May;6(5):377-82.
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| Submission date |
Jun 07, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Catalin Barbacioru |
| E-mail(s) |
catalin@appliedbiosystems.com
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| Organization name |
Applied Biosystems
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| Street address |
850 Lincoln Centre Dr
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| City |
Foster City |
| State/province |
CA |
| ZIP/Postal code |
94404 |
| Country |
USA |
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| Platform ID |
GPL9318 |
| Series (1) |
| GSE22182 |
Global Deterministic and Stochastic Allelic Specific Gene Expression in Single Blastomeres of Mouse Early Embryos |
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| Relations |
| SRA |
SRX022001 |
| BioSample |
SAMN00014866 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM552338_4cell_B6_max.srf.gz |
213.1 Mb |
(ftp)(http) |
SRF |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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