Human Omics database for
the Generation of iPS and Normal Cells
Release notes
Statistics
Document manuals
FAQ
All Modules
Cell Taxonomy(Human cell)
Cell Taxonomy(C. Elegans cell)
Cell Taxonomy(Sea Urchin cell)
Transcriptome Sample(Single-cell)
Transcriptome Project(Single-cell)
Methylome Sample(Single-cell)
Methylome Project(Single-cell)
Cell Conversion(Differentiation)
Cell Conversion(Transdifferentiation)
Cell Marker(from literature)
Cell Image
Tissue Image
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
7
Postnatal
8
Neonatal
9
Infant
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