SHOGoiN Cell ID: 9010000-769

SHOGoiN Cell Taxonomy

Homo sapiens & Mus musculus cell

No.Germ LayerDifferentiation StateSource AgeAnatomy IdCell Type IdAnatomy:level 1Anatomy:level 2Anatomy:level 3Anatomy:level 4-1Anatomy:level 4-2Anatomy:level 5-1Anatomy:level 5-2Anatomy:level 5-3Anatomy:level 6Cell TypeSynonymCL IdUBERON IdImage IdTissue Image ID
11:Non-layered1:Totipotent1:Embryonic9010000769EmbryoZygoteZygote

SHOGoiN Cell Transcriptome

Expression Profile

GSM1160115

GSM1160116

GSM1160117

GSM1160118

GSM1160119

GSM1112766

GSM1112767

GSM1112768

GSM1112769

SHOGoiN Cell Id9010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-769
Project NameSequence Read ArchiveSequence Read ArchiveSequence Read ArchiveSequence Read ArchiveSequence Read ArchiveSequence Read ArchiveSequence Read ArchiveSequence Read ArchiveSequence Read Archive
Project IdSRP018525SRP018525SRP018525SRP018525SRP018525SRP020490SRP020490SRP020490SRP020490
Assay IdSRP018525_T19SRP018525_T20SRP018525_T21SRP018525_T22SRP018525_T23SRP020490_T277SRP020490_T278SRP020490_T279SRP020490_T280
Project:project TitleGenetic Programs in Human and Mouse Early Embryos Revealed by Single-Cell RNA-SequencingGenetic Programs in Human and Mouse Early Embryos Revealed by Single-Cell RNA-SequencingGenetic Programs in Human and Mouse Early Embryos Revealed by Single-Cell RNA-SequencingGenetic Programs in Human and Mouse Early Embryos Revealed by Single-Cell RNA-SequencingGenetic Programs in Human and Mouse Early Embryos Revealed by Single-Cell RNA-SequencingSingle-cell RNA-Seq reveals dynamic, random monoallelic gene expression in mammalian cellsSingle-cell RNA-Seq reveals dynamic, random monoallelic gene expression in mammalian cellsSingle-cell RNA-Seq reveals dynamic, random monoallelic gene expression in mammalian cellsSingle-cell RNA-Seq reveals dynamic, random monoallelic gene expression in mammalian cells
Project:project Descriptionhttp://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE44183http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE44183http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE44183http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE44183http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE44183http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45719http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45719http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45719http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45719
Project:project Submission Date19-Jul-1319-Jul-1319-Jul-1319-Jul-1319-Jul-1310-Jan-1410-Jan-1410-Jan-1410-Jan-14
Project:organization NameHuman Genetics, UCLAHuman Genetics, UCLAHuman Genetics, UCLAHuman Genetics, UCLAHuman Genetics, UCLAKarolinska InstitutetKarolinska InstitutetKarolinska InstitutetKarolinska Institutet
Project:stable Contact InformationKevin HuangKevin HuangKevin HuangKevin HuangKevin HuangDaniel Ramsk_ld, daniel.ramskold@licr.ki.seDaniel Ramsk_ld, daniel.ramskold@licr.ki.seDaniel Ramsk_ld, daniel.ramskold@licr.ki.seDaniel Ramsk_ld, daniel.ramskold@licr.ki.se
Project:reference Submission StatusPublishedPublishedPublishedPublishedPublishedPublishedPublishedPublishedPublished
Project:reference AuthorsXue Z, Huang K, Cai C, Cai L et al.Xue Z, Huang K, Cai C, Cai L et al.Xue Z, Huang K, Cai C, Cai L et al.Xue Z, Huang K, Cai C, Cai L et al.Xue Z, Huang K, Cai C, Cai L et al.Deng Q, Ramsk_ld D, Reinius B, Sandberg R. Deng Q, Ramsk_ld D, Reinius B, Sandberg R. Deng Q, Ramsk_ld D, Reinius B, Sandberg R. Deng Q, Ramsk_ld D, Reinius B, Sandberg R.
Project:reference TitleGenetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.
Project:reference Pubmed Id238927782389277823892778238927782389277824408435244084352440843524408435
Assay:assay TypeTranscriptomeTranscriptomeTranscriptomeTranscriptomeTranscriptomeTranscriptomeTranscriptomeTranscriptomeTranscriptome
Assay:assay Factor9010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-769
Source Cell:sample IdGSM1160115GSM1160116GSM1160117GSM1160118GSM1160119GSM1112766GSM1112767GSM1112768GSM1112769
Source Cell:SHOGoiN Cell Id9010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-769
Source Cell:source Cell TypeTwo-pronuclear zygoteTwo-pronuclear zygoteTwo-pronuclear zygoteZygote (Zygote)Zygote (Zygote)Zygote (Zygote)Zygote (Zygote)Zygote (Zygote)Zygote (Zygote)
Source Cell:source OrganismHumanHumanHumanHumanHumanMouseMouseMouseMouse
Source Cell:race Or StrainHan ChinaseHan ChinaseHan ChinaseHan ChinaseHan ChinaseCAST/EiJ(mother) x C57BL/6J(father), first generation crossCAST/EiJ(mother) x C57BL/6J(father), first generation crossCAST/EiJ(mother) x C57BL/6J(father), first generation crossCAST/EiJ(mother) x C57BL/6J(father), first generation cross
Source Cell:age Or Stage
Source Cell:source Tissue Or OrganEarly embryonic tissueEarly embryonic tissueEarly embryonic tissueEarly embryonic tissueEarly embryonic tissueEarly embryonic tissueEarly embryonic tissueEarly embryonic tissueEarly embryonic tissue
Source Cell:source Cell Karyotype
Source Cell:cell Lineage
Source Cell:organism Genetic Information
Source Cell:health Status
Source Cell:source Provider
Technology:assay TechnologyRNA-seqRNA-seqRNA-seqRNA-seqRNA-seqRNA-SeqRNA-SeqRNA-SeqRNA-Seq
Technology:assay Detection InstrumentationHiSeq 2000HiSeq 2000HiSeq 2000HiSeq 2000HiSeq 2000HiSeq 2000HiSeq 2000HiSeq 2000HiSeq 2000
Technology:assay Detection Instrument VendorIlluminaIlluminaIlluminaIlluminaIlluminaIlluminaIlluminaIlluminaIllumina
Technology:assessed MaterialpolyA RNApolyA RNApolyA RNApolyA RNApolyA RNApolyA RNApolyA RNApolyA RNApolyA RNA
Technology:source Cell Format
Technology:source Cell Preparation MethodSingle cell, dissociatedSingle cell, dissociatedSingle cell, dissociatedSingle cell, dissociatedSingle cell, dissociatedSingle cell, dissociatedSingle cell, dissociatedSingle cell, dissociatedSingle cell, dissociated
Technology:source Cell Identidication Method
Technology:source Cell Treatment
Data:data IdSRR893049SRR893050SRR893051SRR893052SRR893053SRR805449SRR805450SRR805451SRR805452
Data:data TypeSequenceSequenceSequenceSequenceSequenceSequenceSequenceSequenceSequence
Data:data Processing Method
Data:data Processing Software And Version
Data:data Normalization MethodRPKMRPKMRPKMRPKMRPKMRPKM RPKM RPKM RPKM
Data:data Normalization Software Name And Version
Data:data Analytical Software And Versionbowtie 0.12.7bowtie 0.12.7bowtie 0.12.7bowtie 0.12.7
Data:reference Sequence Sourcehg19hg19hg19hg19hg19mm9mm9mm9mm9
Data:genome Annotation Ref

SHOGoiN Cell Methylome

Methylation Profile

GSM1147594

GSM1147595

GSM1147601

GSM1147602

GSM1147603

GSM1147604

GSM1147605

GSM1147606

GSM1147607

GSM1147608

GSM1147609

GSM1147610

SHOGoiN Cell Id9010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-769
Project NameSequence Read ArchiveSequence Read ArchiveSequence Read ArchiveSequence Read ArchiveSequence Read ArchiveSequence Read ArchiveSequence Read ArchiveSequence Read ArchiveSequence Read ArchiveSequence Read ArchiveSequence Read ArchiveSequence Read Archive
Project IdSRP023116SRP023116SRP023116SRP023116SRP023116SRP023116SRP023116SRP023116SRP023116SRP023116SRP023116SRP023116
Assay IdSRP023116_M11SRP023116_M12SRP023116_M18SRP023116_M19SRP023116_M20SRP023116_M21SRP023116_M22SRP023116_M23SRP023116_M24SRP023116_M25SRP023116_M26SRP023116_M27
Project:project TitleSingle cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencingSingle cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencingSingle cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencingSingle cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencingSingle cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencingSingle cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencingSingle cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencingSingle cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencingSingle cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencingSingle cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencingSingle cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencingSingle cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed by reduced representation bisulfite sequencing
Project:project Descriptionhttp://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47343http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47343http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47343http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47343http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47343http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47343http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47343http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47343http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47343http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47343http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47343http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47343
Project:project Submission Date31-Aug-1331-Aug-1331-Aug-1331-Aug-1331-Aug-1331-Aug-1331-Aug-1331-Aug-1331-Aug-1331-Aug-1331-Aug-1331-Aug-13
Project:organization NameBiodynamics Optical Imaging Center, Peking UniversityBiodynamics Optical Imaging Center, Peking UniversityBiodynamics Optical Imaging Center, Peking UniversityBiodynamics Optical Imaging Center, Peking UniversityBiodynamics Optical Imaging Center, Peking UniversityBiodynamics Optical Imaging Center, Peking UniversityBiodynamics Optical Imaging Center, Peking UniversityBiodynamics Optical Imaging Center, Peking UniversityBiodynamics Optical Imaging Center, Peking UniversityBiodynamics Optical Imaging Center, Peking UniversityBiodynamics Optical Imaging Center, Peking UniversityBiodynamics Optical Imaging Center, Peking University
Project:stable Contact InformationHongshan Guo, guo-hs@pku.edu.cnHongshan Guo, guo-hs@pku.edu.cnHongshan Guo, guo-hs@pku.edu.cnHongshan Guo, guo-hs@pku.edu.cnHongshan Guo, guo-hs@pku.edu.cnHongshan Guo, guo-hs@pku.edu.cnHongshan Guo, guo-hs@pku.edu.cnHongshan Guo, guo-hs@pku.edu.cnHongshan Guo, guo-hs@pku.edu.cnHongshan Guo, guo-hs@pku.edu.cnHongshan Guo, guo-hs@pku.edu.cnHongshan Guo, guo-hs@pku.edu.cn
Project:reference Submission StatusPublishedPublishedPublishedPublishedPublishedPublishedPublishedPublishedPublishedPublishedPublishedPublished
Project:reference AuthorsGuo H, Zhu P, Tang F, Wu X, Wen L, Li XGuo H, Zhu P, Tang F, Wu X, Wen L, Li XGuo H, Zhu P, Tang F, Wu X, Wen L, Li XGuo H, Zhu P, Tang F, Wu X, Wen L, Li XGuo H, Zhu P, Tang F, Wu X, Wen L, Li XGuo H, Zhu P, Tang F, Wu X, Wen L, Li XGuo H, Zhu P, Tang F, Wu X, Wen L, Li XGuo H, Zhu P, Tang F, Wu X, Wen L, Li XGuo H, Zhu P, Tang F, Wu X, Wen L, Li XGuo H, Zhu P, Tang F, Wu X, Wen L, Li XGuo H, Zhu P, Tang F, Wu X, Wen L, Li XGuo H, Zhu P, Tang F, Wu X, Wen L, Li X
Project:reference TitleSingle-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.
Project:reference Pubmed Id241791432417914324179143241791432417914324179143241791432417914324179143241791432417914324179143
Assay:assay TypeMethylomeMethylomeMethylomeMethylomeMethylomeMethylomeMethylomeMethylomeMethylomeMethylomeMethylomeMethylome
Assay:assay FactorCell typeCell typeCell typeCell typeCell typeCell typeCell typeCell typeCell typeCell typeCell typeCell type
Source Cell:sample IdGSM1147594GSM1147595GSM1147601GSM1147602GSM1147603GSM1147604GSM1147605GSM1147606GSM1147607GSM1147608GSM1147609GSM1147610
Source Cell:SHOGoiN Cell Id9010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-7699010000-769
Source Cell:source Cell TypeFirst polar body (Zygote)First polar body (Zygote)Male pronucleus (Zygote)Female pronucleus (Zygote)Male pronucleus (Zygote)Female pronucleus (Zygote)Male pronucleus (Zygote)Female pronucleus (Zygote)Male pronucleus (Zygote)Female pronucleus (Zygote)Male pronucleus (Zygote)Female pronucleus (Zygote)
Source Cell:source OrganismMouseMouseMouseMouseMouseMouseMouseMouseMouseMouseMouseMouse
Source Cell:race Or StrainC57BL/6NC57BL/6NC57BL/6N X 129S2/SvC57BL/6N X 129S2/SvC57BL/6N X 129S2/SvC57BL/6N X 129S2/SvC57BL/6N X 129S2/SvC57BL/6N X 129S2/SvC57BL/6N X 129S2/SvC57BL/6N X 129S2/SvC57BL/6N X 129S2/SvC57BL/6N X 129S2/Sv
Source Cell:age Or Stage
Source Cell:source Tissue Or OrganEarly embryonic tissueEarly embryonic tissueEarly embryonic tissueEarly embryonic tissueEarly embryonic tissueEarly embryonic tissueEarly embryonic tissueEarly embryonic tissueEarly embryonic tissueEarly embryonic tissueEarly embryonic tissueEarly embryonic tissue
Source Cell:source Cell Karyotype
Source Cell:cell Lineage
Source Cell:organism Genetic Information
Source Cell:health Status
Source Cell:source Providor
Technology:assay TechnologyBisulfite-Seq (RRBS)Bisulfite-Seq (RRBS)Bisulfite-Seq (RRBS)Bisulfite-Seq (RRBS)Bisulfite-Seq (RRBS)Bisulfite-Seq (RRBS)Bisulfite-Seq (RRBS)Bisulfite-Seq (RRBS)Bisulfite-Seq (RRBS)Bisulfite-Seq (RRBS)Bisulfite-Seq (RRBS)Bisulfite-Seq (RRBS)
Technology:assay Detection InstrumentationHiSeq 2000HiSeq 2000HiSeq 2000HiSeq 2000HiSeq 2000HiSeq 2000HiSeq 2000HiSeq 2000HiSeq 2000HiSeq 2000HiSeq 2000HiSeq 2000
Technology:assay Detection Instrument VendorIllumina Illumina Illumina Illumina Illumina Illumina Illumina Illumina Illumina Illumina Illumina Illumina
Technology:assesed MaterialGenomic DNAGenomic DNAGenomic DNAGenomic DNAGenomic DNAGenomic DNAGenomic DNAGenomic DNAGenomic DNAGenomic DNAGenomic DNAGenomic DNA
Technology:source Cell FormatSingle cellSingle cellSingle cellSingle cellSingle cellSingle cellSingle cellSingle cellSingle cellSingle cellSingle cellSingle cell
Technology:source Cell Preparation Method
Technology:source Cell Identidication Method
Technology:source Cell Treatment
Data:data IdSRR867083SRR867084SRR867090SRR867091SRR867092SRR867093SRR867094SRR867095SRR867096SRR867097SRR867098SRR867099
Data:data TypeSequenceSequenceSequenceSequenceSequenceSequenceSequenceSequenceSequenceSequenceSequenceSequence
Data:data Processing Method
Data:data Processing Software And Version
Data:data Normalization Method
Data:data Normalization Software Name And Version
Data:data Analytical Software And Version
Data:reference Sequence Sourcemm9mm9mm9mm9mm9mm9mm9mm9mm9mm9mm9mm9
Data:genome Annotation Ref

SHOGoiN Cell Marker

Cell Type NameZygoteZygote/PronucleateZygote/PronucleateZygote/PronucleateZygote/PronucleateZygote/Pronucleate
Cell Type Subclass
SHOGoiN Cell Id9010000-7699010000-7699010000-7699010000-7699010000-7699010000-769
Anatomical LocationEmbryoEmbryoEmbryoEmbryoEmbryoEmbryo
Marker Molecule:nameTranscription factor GATA-6 (GATA-binding factor 6, GATA6)OCT3B/4Homeobox protein NANOG (Homeobox protein NANOG, Homeobox transcription factor Nanog, hNanog, NANOG)Transcription initiation factor TFIID subunit 8 (Protein taube nuss, TBP-associated factor 43 kDa, TBP-associated factor 8, Transcription initiation factor TFIID 43 kDa subunit, TAFII-43, TAFII43, TAF8, TAFII43, TBN)Eukaryotic translation initiation factor 1A, X-chromosomal (eIF-1A X isoform, Eukaryotic translation initiation factor 4C, eIF-4C, EIF1AX, EIF1A, EIF4C)Receptor tyrosine-protein kinase erbB-4 (Proto-oncogene-like protein c-ErbB-4, Tyrosine kinase-type cell surface receptor HER4, p180erbB4, ERBB4, HER4)
Marker Molecule:typeGeneGeneGeneGeneGeneGene
Marker Molecule:categoryTranscription factor
Subcellular LocalizationNucleusNucleusNucleus, CytosolCytosolPlasma membrane
Uniprot IdQ92908Q9H9S0Q7Z7C8P47813Q15303
Gene Id26277992312968519642066
Source OrganismHumanHumanHumanHumanHumanHuman
Reference184114101841141018411410184114101841141018411410