SHOGoiN Cell ID: 3110001010000000000000-067

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 state 7 Postnatal state 8 Neonatal state 9 Infant state 10 Juvenile 11 Adult	3110001010000000000000	067	Trunk	Pancreas		Endocrine pancreas	Islet of Langerhans							Delta cell		CL:0000173		393, 394, 395	t072

SHOGoiN Cell Transcriptome

Expression Profile	GSM1901457	GSM1901462
SHOGoiN Cell Id	3110001010000000000000-067	3110001010000000000000-067
Project Name	Sequence Read Archive	Sequence Read Archive
Project Id	SRP064464	SRP064464
Assay Id	SRP064464_T3	SRP064464_T8
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
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
Project:project Submission Date	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
Project:stable Contact Information	Christoph Bock, cbock@cemm.oeaw.ac.at	Christoph Bock, cbock@cemm.oeaw.ac.at
Project:reference Submission Status	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.
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.
Project:reference Pubmed Id	26691212	26691212
Assay:assay Type	Transcriptome	Transcriptome
Assay:assay Factor	3110001010000000000000-067	3110001010000000000000-067
Source Cell:sample Id	GSM1901457	GSM1901462
Source Cell:SHOGoiN Cell Id	3110001010000000000000-067	3110001010000000000000-067
Source Cell:source Cell Type	Delta cell (Pancreatic islet)	Delta cell (Pancreatic islet)
Source Cell:source Organism	Human	Human
Source Cell:race Or Strain	Male	Male
Source Cell:age Or Stage	37 y/o	37 y/o
Source Cell:source Tissue Or Organ	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
Source Cell:source Provider
Technology:assay Technology	RNA-Seq	RNA-Seq
Technology:assay Detection Instrumentation	HiSeq 2000	HiSeq 2000
Technology:assay Detection Instrument Vendor	Illumina	Illumina
Technology:assessed Material	polyA RNA	polyA RNA
Technology:source Cell Format
Technology:source Cell Preparation Method	Single cell, cultured	Single cell, cultured
Technology:source Cell Identidication Method
Technology:source Cell Treatment
Data:data Id	SRR2558113	SRR2558118
Data:data Type	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
Data:data Normalization Software Name And Version
Data:data Analytical Software And Version
Data:reference Sequence Source	hg19	hg19
Data:genome Annotation Ref

SHOGoiN Cell Marker

Cell Type Name	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell	Delta cell
Cell Type Subclass
SHOGoiN Cell Id	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067
Anatomical Location	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	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans	Pancreas, islet of Langerhans
Marker Molecule:name	somatostatin	Protein patched homolog 1	Proteoglycan 4 (Lubricin, Megakaryocyte-stimulating factor, Superficial zone proteoglycan, PRG4, MSF, SZP)	Leptin receptor (LEP-R, HuB219, OB receptor, OB-R, CD295, LEPR, DB, OBR)	Retinol-binding protein 4 (Plasma retinol-binding protein, PRBP, RBP, RBP4)	Cholinesterase (Acylcholine acylhydrolase, Butyrylcholine esterase, Choline esterase II, Pseudocholinesterase, BCHE, CHE1)	Hematopoietically-expressed homeobox protein HHEX (Homeobox protein HEX, Homeobox protein PRH, HHEX, PRH, PRHX)	Secreted frizzled-related protein 3 (sFRP-3, Frezzled, Fritz, Frizzled-related protein 1, FrzB-1, FRZB, FIZ, FRE, FRP, FRZB1, SFRP3)	Neuroendocrine convertase 1 (NEC 1, Prohormone convertase 1, Proprotein convertase 1, PC1, PCSK1, NEC1)	Regulator of G-protein signaling 2 (RGS2, Cell growth-inhibiting gene 31 protein, G0/G1 switch regulatory protein 8, RGS2, G0S8)	Gamma-aminobutyric acid receptor subunit gamma-2 (GABA(A) receptor subunit gamma-2, GABRG2)	Hematopoietically-expressed homeobox protein HHEX (Homeobox protein HEX, Homeobox protein PRH, HHEX, PRH, PRHX)	Receptor tyrosine-protein kinase erbB-4 (Proto-oncogene-like protein c-ErbB-4, Tyrosine kinase-type cell surface receptor HER4, p180erbB4, ERBB4, HER4)	POU domain, class 3, transcription factor 1 (Octamer-binding protein 6, Oct-6, Octamer-binding transcription factor 6, OTF-6, POU domain transcription factor SCIP, POU3F1, OCT6, OTF6)	Insulin gene enhancer protein ISL-1 (Islet-1, ISL1)	PC4 and SFRS1-interacting protein (CLL-associated antigen KW-7, Dense fine speckles 70 kDa protein, DFS 70, Lens epithelium-derived growth factor, Transcriptional coactivator p75/p52, PSIP1, DFS70, LE	Class E basic helix-loop-helix protein 41 (bHLHe41, Class B basic helix-loop-helix protein 3, bHLHb3, Differentially expressed in chondrocytes protein 2, hDEC2, Enhancer-of-split and hairy-related pro	PDZ and LIM domain protein 4 (LIM protein RIL, Reversion-induced LIM protein, PDLIM4, RIL)	ETS homologous factor (hEHF, ETS domain-containing transcription factor, Epithelium-specific Ets transcription factor 3, ESE-3, EHF, ESE3, ESE3B, ESEJ)	Ligand-dependent nuclear receptor corepressor-like protein (LCoR-like protein, LCORL)	ETS translocation variant 1 (Ets-related protein 81, ETV1, ER81)
Marker Molecule:type	Peptide hormone	Protein	Gene	Gene	Gene	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
Subcellular Localization	Endprasmic reticulum	Plasma membrane	Secreted	Plasma membrane	Secreted	Secreted	Nucleus	Secreted	Cytoplasmic vesicle	Plasma membrane	Plasma membrane	Nucleus	Plasma membrane	Nucleus	Nucleus	Nucleus	Nucleus	Nucleus	Nucleus	Nucleus	Nucleus
Uniprot Id	P61278	Q13635	Q92954	P48357	P02753	P06276	Q03014	Q92765	P29120	P41220	P18507	Q03014	Q15303	Q03052	P61371	O75475	Q9C0J9	P50479	Q9NZC4	Q8N3X6	P50549
Gene Id			10216	3953	5950	590	3087	2487	5122	5997	2566	3087	2066	5453	3670	11168	79365	8572	26298	254251	2115
Source Organism	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human	Human
Reference	PMID:22069255	PMID:22069255	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	PMID:27693023	PMID:27693023	PMID:27693023

Image

SHOGoiN Cell Id	3110001010000000000000-067	3110001010000000000000-067	3110001010000000000000-067
Image Id	393	394	395
Tissue	Pancreas	Pancreas	Pancreas
Cell Type	Delta cell	Delta cell	Delta 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