SHOGoiN Cell ID: 3110001010000000000000-026

SHOGoiN Cell Taxonomy

Homo sapiens & Mus musculus cell

Differentiated (1)
Stem (0)
Embryo (0)

No.	Germ Layer	Differentiation State	Source Age	Anatomy Id	Cell Type Id	Anatomy:body Part	Anatomy:organ	Anatomy:sub-organ	Anatomy:tissue 1	Anatomy:tissue 2	Anatomy:tissue 3	Anatomy:tissue 4	Anatomy:tissue 5-1	Anatomy:tissue 5-2	Anatomy:tissue 5-3	Anatomy:tissue 5-4	Cell Type	Synonym	CL Id	UBERON Id	Image Id	Tissue Image ID
1	3 Endodermal	4 Terminally differentiated	6 Fetus 7 Postnatal 8 Neonatal 9 Infant 10 Juvenile 11 Adult	3110001010000000000000	026	Trunk	Pancreas		Endocrine pancreas	Islet of Langerhans							Beta cell		CL:0000169		387, 388, 389	t072

SHOGoiN Cell Transcriptome

Expression Profile	GSM1901465	GSM1901469	GSM1901482	GSM1901490	GSM1901496	GSM1901506	GSM1901509	GSM1901517	GSM1901518	GSM1901519	GSM1901520	GSM1901523
SHOGoiN Cell Id	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026
Project Name	Sequence Read Archive	Sequence Read Archive	Sequence Read Archive	Sequence Read Archive	Sequence Read Archive	Sequence Read Archive	Sequence Read Archive	Sequence Read Archive	Sequence Read Archive	Sequence Read Archive	Sequence Read Archive	Sequence Read Archive
Project Id	SRP064464	SRP064464	SRP064464	SRP064464	SRP064464	SRP064464	SRP064464	SRP064464	SRP064464	SRP064464	SRP064464	SRP064464
Assay Id	SRP064464_T11	SRP064464_T15	SRP064464_T26	SRP064464_T34	SRP064464_T40	SRP064464_T47	SRP064464_T50	SRP064464_T57	SRP064464_T58	SRP064464_T59	SRP064464_T60	SRP064464_T63
Project:project Title	Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes	Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes	Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes	Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes	Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes	Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes	Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes	Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes	Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes	Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes	Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes	Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes
Project:project Description	http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73727	http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73727	http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73727	http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73727	http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73727	http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73727	http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73727	http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73727	http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73727	http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73727	http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73727	http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73727
Project:project Submission Date	5-Oct-15	5-Oct-15	5-Oct-15	5-Oct-15	5-Oct-15	5-Oct-15	5-Oct-15	5-Oct-15	5-Oct-15	5-Oct-15	5-Oct-15	5-Oct-15
Project:organization Name	CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences	CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences	CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences	CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences	CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences	CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences	CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences	CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences	CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences	CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences	CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences	CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Project:stable Contact Information	Christoph Bock, cbock@cemm.oeaw.ac.at	Christoph Bock, cbock@cemm.oeaw.ac.at	Christoph Bock, cbock@cemm.oeaw.ac.at	Christoph Bock, cbock@cemm.oeaw.ac.at	Christoph Bock, cbock@cemm.oeaw.ac.at	Christoph Bock, cbock@cemm.oeaw.ac.at	Christoph Bock, cbock@cemm.oeaw.ac.at	Christoph Bock, cbock@cemm.oeaw.ac.at	Christoph Bock, cbock@cemm.oeaw.ac.at	Christoph Bock, cbock@cemm.oeaw.ac.at	Christoph Bock, cbock@cemm.oeaw.ac.at	Christoph Bock, cbock@cemm.oeaw.ac.at
Project:reference Submission Status	Published	Published	Published	Published	Published	Published	Published	Published	Published	Published	Published	Published
Project:reference Authors	Li J, Klughammer J, Farlik M, Penz T et al.	Li J, Klughammer J, Farlik M, Penz T et al.	Li J, Klughammer J, Farlik M, Penz T et al.	Li J, Klughammer J, Farlik M, Penz T et al.	Li J, Klughammer J, Farlik M, Penz T et al.	Li J, Klughammer J, Farlik M, Penz T et al.	Li J, Klughammer J, Farlik M, Penz T et al.	Li J, Klughammer J, Farlik M, Penz T et al.	Li J, Klughammer J, Farlik M, Penz T et al.	Li J, Klughammer J, Farlik M, Penz T et al.	Li J, Klughammer J, Farlik M, Penz T et al.	Li J, Klughammer J, Farlik M, Penz T et al.
Project:reference Title	Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types.	Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types.	Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types.	Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types.	Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types.	Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types.	Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types.	Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types.	Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types.	Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types.	Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types.	Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types.
Project:reference Pubmed Id	26691212	26691212	26691212	26691212	26691212	26691212	26691212	26691212	26691212	26691212	26691212	26691212
Assay:assay Type	Transcriptome	Transcriptome	Transcriptome	Transcriptome	Transcriptome	Transcriptome	Transcriptome	Transcriptome	Transcriptome	Transcriptome	Transcriptome	Transcriptome
Assay:assay Factor	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026
Source Cell:sample Id	GSM1901465	GSM1901469	GSM1901482	GSM1901490	GSM1901496	GSM1901506	GSM1901509	GSM1901517	GSM1901518	GSM1901519	GSM1901520	GSM1901523
Source Cell:SHOGoiN Cell Id	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026
Source Cell:source Cell Type	Beta cell (Pancreatic islet)	Beta cell (Pancreatic islet)	Beta cell (Pancreatic islet)	Beta cell (Pancreatic islet)	Beta cell (Pancreatic islet)	Beta cell (Pancreatic islet)	Beta cell (Pancreatic islet)	Beta cell (Pancreatic islet)	Beta cell (Pancreatic islet)	Beta cell (Pancreatic islet)	Beta cell (Pancreatic islet)	Beta cell (Pancreatic islet)
Source Cell:source Organism	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human
Source Cell:race Or Strain	Male	Male	Male	Male	Male	Male	Male	Male	Male	Male	Male	Male
Source Cell:age Or Stage	37 y/o	37 y/o	37 y/o	37 y/o	37 y/o	37 y/o	37 y/o	37 y/o	37 y/o	37 y/o	37 y/o	37 y/o
Source Cell:source Tissue Or Organ	Pancreas	Pancreas	Pancreas	Pancreas	Pancreas	Pancreas	Pancreas	Pancreas	Pancreas	Pancreas	Pancreas	Pancreas
Source Cell:source Cell Karyotype
Source Cell:cell Lineage
Source Cell:organism Genetic Information
Source Cell:health Status	BMI was 22	BMI was 22	BMI was 22	BMI was 22	BMI was 22	BMI was 22	BMI was 22	BMI was 22	BMI was 22	BMI was 22	BMI was 22	BMI was 22
Source Cell:source Provider
Technology:assay Technology	RNA-Seq	RNA-Seq	RNA-Seq	RNA-Seq	RNA-Seq	RNA-Seq	RNA-Seq	RNA-Seq	RNA-Seq	RNA-Seq	RNA-Seq	RNA-Seq
Technology:assay Detection Instrumentation	HiSeq 2000	HiSeq 2000	HiSeq 2000	HiSeq 2000	HiSeq 2000	HiSeq 2000	HiSeq 2000	HiSeq 2000	HiSeq 2000	HiSeq 2000	HiSeq 2000	HiSeq 2000
Technology:assay Detection Instrument Vendor	Illumina	Illumina	Illumina	Illumina	Illumina	Illumina	Illumina	Illumina	Illumina	Illumina	Illumina	Illumina
Technology:assessed Material	polyA RNA	polyA RNA	polyA RNA	polyA RNA	polyA RNA	polyA RNA	polyA RNA	polyA RNA	polyA RNA	polyA RNA	polyA RNA	polyA RNA
Technology:source Cell Format
Technology:source Cell Preparation Method	Single cell, cultured	Single cell, cultured	Single cell, cultured	Single cell, cultured	Single cell, cultured	Single cell, cultured	Single cell, cultured	Single cell, cultured	Single cell, cultured	Single cell, cultured	Single cell, cultured	Single cell, cultured
Technology:source Cell Identidication Method
Technology:source Cell Treatment
Data:data Id	SRR2558121	SRR2558125	SRR2558138	SRR2558146	SRR2558152	SRR2558162	SRR2558165	SRR2558173	SRR2558174	SRR2558175	SRR2558176	SRR2558179
Data:data Type	Sequence	Sequence	Sequence	Sequence	Sequence	Sequence	Sequence	Sequence	Sequence	Sequence	Sequence	Sequence
Data:data Processing Method
Data:data Processing Software And Version
Data:data Normalization Method	Tab-delimited text files include transcript-wise RPKM values or read counts for each sample	Tab-delimited text files include transcript-wise RPKM values or read counts for each sample	Tab-delimited text files include transcript-wise RPKM values or read counts for each sample	Tab-delimited text files include transcript-wise RPKM values or read counts for each sample	Tab-delimited text files include transcript-wise RPKM values or read counts for each sample	Tab-delimited text files include transcript-wise RPKM values or read counts for each sample	Tab-delimited text files include transcript-wise RPKM values or read counts for each sample	Tab-delimited text files include transcript-wise RPKM values or read counts for each sample	Tab-delimited text files include transcript-wise RPKM values or read counts for each sample	Tab-delimited text files include transcript-wise RPKM values or read counts for each sample	Tab-delimited text files include transcript-wise RPKM values or read counts for each sample	Tab-delimited text files include transcript-wise RPKM values or read counts for each sample
Data:data Normalization Software Name And Version
Data:data Analytical Software And Version
Data:reference Sequence Source	hg19	hg19	hg19	hg19	hg19	hg19	hg19	hg19	hg19	hg19	hg19	hg19
Data:genome Annotation Ref

SHOGoiN Cell Marker

Cell Type Name	Beta cell	Beta cell	Beta cell	Beta cell	Beta cell	Beta cell	Beta cell	Bata cell	Bata cell	Bata cell	Bata cell	Bata cell	Bata cell	Bata cell	Bata cell	Bata cell	Bata cell	Bata cell	Bata cell	Bata cell	Bata cell	Bata cell	Bata cell
Cell Type Subclass
SHOGoiN Cell Id	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026
Anatomical Location	Pancreas	Pancreas	Pancreas	Pancreas	Pancreas	Pancreas	Pancreas	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans
Marker Molecule:name	Insulin	Motor neuron and pancreas homeobox protein 1 (Hlxb9)	Transcription factor MafA	Homeobox protein CDX-2 (Cdx2/3)	Solute carrier family 2, facilitated glucose transporter member 2 (Glucose transporter 2, GLUT2)	Homeobox protein Nkx-6.1 (Homeobox protein NK-6 homolog A)	insulin (INS)	Islet amyloid polypeptide (Amylin, Diabetes-associated peptide, DAP, Insulinoma amyloid peptide, IAPP)	Neuronal pentraxin-2 (NP2, Neuronal pentraxin II, NP-II, NPTX2)	Protein delta homolog 1 (DLK-1, pG2, DLK1, DLK)	Pituitary adenylate cyclase-activating polypeptide (PACAP, ADCYAP1)	6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 2 (6PF-2-K/Fru-2,6-P2ase 2, PFK/FBPase 2, 6PF-2-K/Fru-2,6-P2ase heart-type isozyme, PFKFB2)	Pancreas/duodenum homeobox protein 1 (PDX-1, Glucose-sensitive factor, GSF, Insulin promoter factor 1, IPF-1, Insulin upstream factor 1, IUF-1, Islet/duodenum homeobox-1, IDX-1, Somatostatin-transacti	Transforming growth factor beta receptor type 3 (TGF-beta receptor type 3, TGFR-3, Betaglycan, Transforming growth factor beta receptor III, TGF-beta receptor type III, TGFBR3)	Synaptotagmin-13 (Synaptotagmin XIII, SytXIII, SYT13, KIAA1427)	Pancreas/duodenum homeobox protein 1 (PDX-1, Glucose-sensitive factor, GSF, Insulin promoter factor 1, IPF-1, Insulin upstream factor 1, IUF-1, Islet/duodenum homeobox-1, IDX-1, Somatostatin-transacti	Mothers against decapentaplegic homolog 9 (MAD homolog 9, Mothers against DPP homolog 9, Madh6, SMAD family member 9, SMAD 9, Smad9, SMAD9, MADH6, MADH9)	Cyclin-dependent kinase inhibitor 1C (Cyclin-dependent kinase inhibitor p57, p57Kip2, CDKN1C, KIP2)	Transcription factor CP2-like protein 1 (CP2-related transcriptional repressor 1, CRTR-1, Transcription factor LBP-9, TFCP2L1, CRTR1, LBP9)	Homeobox protein SIX3 (Sine oculis homeobox homolog 3, SIX3)	Homeobox protein SIX2 (Sine oculis homeobox homolog 2, SIX2)	Bone morphogenetic protein 5 (BMP-5)	Pirin (Probable quercetin 2,3-dioxygenase PIR, Probable quercetinase, PIR)
Marker Molecule:type	Peptide hormone	Protein	Protein	Protein	Protein	Protein	Protein	Gene	Gene	Gene	Gene	Gene	Gene	Gene	Gene	Gene	Gene	Gene	Gene	Gene	Gene	Gene	Gene
Marker Molecule:category	Secreted	Transcription factor	Transcription factor	Transcription factor		Transcription factor										Transcription factor	Transcription factor	Transcription factor	Transcription factor	Transcription factor	Transcription factor	Transcription factor	Transcription factor
Subcellular Localization	Endprasmic reticulum	Nucleus	Nucleus	Nucleus	Plasma membrane	Nucleus	Secreted	Secreted	Secreted	Plasma membrane	Secreted		Nucleus, Cytosol	Secreted, Plasma membrane	Plasma membrane	Nucleus, Cytosol	Nucleus, Cytosol	Nucleus	Nucleus	Nucleus	Nucleus	Secreted	Nucleus, Cytosol
Uniprot Id	P01308	P50219	Q8NHW3	Q99626	P11168	P78426	P01308	P10997	P47972	P80370	P18509	O60825	P52945	Q03167	Q7L8C5	P52945	O15198	P49918	Q9NZI6	O95343	Q9NPC8	P22003	O00625
Gene Id							3630	3375	4885	8788	116	5208	3651	7049	57586	3651	4093	1028	29842	6496	10736	653	8544
Source Organism	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human
Reference	PMID:22974359	PMID:10471501	PMID:22974359	PMID:22974359	PMID:22974359	PMID:24035389	PMID:26691212	PMID:27693023	PMID:27693023	PMID:27693023	PMID:27693023	PMID:27693023	PMID:27693023	PMID:27693023	PMID:27693023	PMID:27693023	PMID:27693023	PMID:27693023	PMID:27693023	PMID:27693023	PMID:27693023	PMID:27693023	PMID:27693023

Image

SHOGoiN Cell Id	3110001010000000000000-026	3110001010000000000000-026	3110001010000000000000-026
Image Id	387	388	389
Tissue	Pancreas	Pancreas	Pancreas
Cell Type	Beta cell	Beta cell	Beta cell
Organism	Human	Human	Human
Cell Strain
Location	Pancreas	Pancreas	Pancreas
Karyotype
Race	Japanese	Japanese	Japanese
Age	57	57	57
Sex	male	male	male
Medium
Serum
Other Chemical
Feeder
Other Treatment
Culture Period
Differentiaion
Self Renewal Ability
Onocogenic Transformation
Knock Out Gene
Knock In Gene
Disease	malignant pleural mesothelioma	malignant pleural mesothelioma	malignant pleural mesothelioma
Cod
Shooting Date	2010.12.10	2010.12.10	2010.12.10
Shooting Condition	normal tissue or mild fibrosing	normal tissue or mild fibrosing	normal tissue or mild fibrosing
Embedding	paraffin	paraffin	paraffin
Staining	hematoxylin	hematoxylin	hematoxylin
Microscope	OLYMPUS BX50	OLYMPUS BX50	OLYMPUS BX50
Camera	OLYMPUS DP20	OLYMPUS DP20	OLYMPUS DP20
Image Size X	1600	1600	1600
Image Size Y	1200	1200	1200
Resolution	72	72	72
Magnification	400	400	400
Contact Person	Koji Yamanegi	Koji Yamanegi	Koji Yamanegi
Email	yamanegi@hyo-med.ac.jp	yamanegi@hyo-med.ac.jp	yamanegi@hyo-med.ac.jp
Telephone	0798-45-6432	0798-45-6432	0798-45-6432
Fax	0798-45-6431	0798-45-6431	0798-45-6431
Affiliation	Department of clinical pathology, Hyogo collage of medicine	Department of clinical pathology, Hyogo collage of medicine	Department of clinical pathology, Hyogo collage of medicine
Zip Code	663-8501	663-8501	663-8501
Address	1-1, Mukogawa, Nishinomiya, Hyogo	1-1, Mukogawa, Nishinomiya, Hyogo	1-1, Mukogawa, Nishinomiya, Hyogo
Country	Japan	Japan	Japan
Note
Nucleous Area
Nucleous Circularity
Nucleous Bending
Nucleous Convex Area
Nucleous Ellipse Long Axis
Nucleous Inertia
Cell Area
Cell Circularity
Cell Bending
Cell Convex Area
Cell Ellipse Long Axis
Cell Inertia
Cell-nucleous Area Ratio
Cell-nucleous Eccentricity1
Cell-nucleous Eccentricity2
Cell-nucleous Eccentricity3
Cell-nucleous Eccentricity4