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
Image : Cell Image ID 313
No.
SHOGoiN cell id
Image (Image ID)
Title
Sample
Method
Contact
Morphologic Feature
Note
1
8010000000000000000000-006
313
Immune system (blood):Macrophage:Human
Location
Large intestine
Age
49
Sex
male
Race
Japanese
Disease
carcinoid of rectum
Cause Of Death
-
Date
2010.12.10
Condition
normal tissue or mild epithelial hyperplasia
Embedding Mehtod
Staining Mehtod
Hematoxylin
Microscope
OLYMPUS DX50
Camera
OLYMPUS DP20
Image Size (pixels)
1200x1600
Resolution (ppi)
72
magnification
400
Person
Koji Yamanegi
E-mail
yamanegi@hyo-med.ac.jp
Telephone
0798-45-6432
Fax
0798-45-6431
Affiliation
Department of clinical pathology, Hyogo collage of medicine
Address
1-1, Mukogawa, Nishinomiya, Hyogo
Cell
Nucleus
Nucleus/Cell
Area
6519.5
406.5
Area ratio
0.0623514
Circularity
0.501874
0.853672
Eccentricity1
0.234599
Convex area
7382
449
Eccentricity2
0.223788
Bending energy
3.41003
1.34328
Eccentricity3
0.984436
Elliptic long axis
93.8386
24.3847
Eccentricity3
0.984436
Inertia moment
6978950
26829.4
Eccentricity4
0.861196
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
4
Mesodermal
4
Terminally differentiated
6
Fetus
7
Postnatal
8
Neonatal
9
Infant
10
Juvenile
11
Adult
8010000000000000000000
006
Immune system class
Blood
Macrophage
CL:0000235
51
,
137
,
171
,
311
,
312
,
313
,
625
,
626
,
627
,
659
,
660
SHOGoiN Cell Marker
Cell Type Name
Immune system/blood cell
Immune system/blood cell
Immune system/blood cell
Cell Type Subclass
Macrophage
Macrophage
Macrophage
SHOGoiN Cell Id
8010000000000000000000-006
8010000000000000000000-006
8010000000000000000000-006
Anatomical Location
Blood
Blood
Blood
Marker Molecule:name
C-X-C chemokine receptor type 4 (CXC-R4, CXCR-4, FB22, Fusin, HM89, LCR1, Leukocyte-derived seven transmembrane domain receptor, LESTR, Lipopolysaccharide-associated protein 3, LAP-3, LPS-associated p
Stage-specific embryonic antigen 1 (SSEA1, CD15)
Leukosialin (Galactoglycoprotein, CD43)
Marker Molecule:type
Protein
Protein
Protein
Marker Molecule:category
CD molecule
CD molecule
CD molecule
Subcellular Localization
Plasma membrane
Plasma membrane
Plasma membrane
Uniprot Id
P61073
P16150
Gene Id
Source Organism
Human
Human
Human
Reference
http://www.bdbiosciences.com/documents/cd_marker_handbook.pdf
http://www.miltenyibiotec.com/en/products-and-services/macs-cell-separation/cell-separation-reagents/b-cells/cd43-microbeads-human.aspx
Image
SHOGoiN Cell Id
8010000000000000000000-006
8010000000000000000000-006
8010000000000000000000-006
8010000000000000000000-006
8010000000000000000000-006
8010000000000000000000-006
8010000000000000000000-006
8010000000000000000000-006
8010000000000000000000-006
8010000000000000000000-006
8010000000000000000000-006
Image Id
51
137
171
311
312
313
625
626
627
659
660
Tissue
Bone
Immune system (blood)
Immune system (blood)
Immune system (blood)
Immune system (blood)
Immune system (blood)
Immune system (blood)
Immune system (blood)
Immune system (blood)
Immune system (blood)
Immune system (blood)
Cell Type
Macrophage
Macrophage
Macrophage
Macrophage
Macrophage
Macrophage
Macrophage
Macrophage
Macrophage
Macrophage
Macrophage
Organism
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Human
Cell Strain
Location
Bone
Mammary gland
Penis
Large intestine
Large intestine
Large intestine
Immune system
Immune system
Immune system
Immune system
Immune system
Karyotype
Race
Japanese
Japanese
Japanese
Japanese
Japanese
Japanese
Japanese
Japanese
Japanese
Japanese
Age
44
58
49
49
49
79
79
79
79
79
Sex
female
Male
male
male
male
Female
Female
Female
Female
Female
Medium
Serum
Other Chemical
Feeder
Other Treatment
Culture Period
Differentiaion
Self Renewal Ability
Onocogenic Transformation
Knock Out Gene
Knock In Gene
Disease
breast cancer
squamous cell carcinoma
carcinoid of rectum
carcinoid of rectum
carcinoid of rectum
Ascending colon cancer
Ascending colon cancer
Ascending colon cancer
Ascending colon cancer
Ascending colon cancer
Cod
Shooting Date
2005.8.12
2009.2.19
2009.11.25
2010.12.10
2010.12.10
2010.12.10
2013.08.01
2013.08.01
2013.08.01
2013.08.01
2013.08.01
Shooting Condition
normal tissue or mild epithelial hyperplasia
normal tissue from the resected cancerous fragment
normal tissue or mild epithelial hyperplasia
normal tissue or mild epithelial hyperplasia
normal tissue or mild epithelial hyperplasia
Embedding
Paraffin
Paraffin
Paraffin
Paraffin
Paraffin
Paraffin
Paraffin
Staining
Hematoxylin
Hematoxylin
Hematoxylin
Hematoxylin
Hematoxylin
Hematoxylin
Hematoxylin
Hematoxylin
Hematoxylin
Hematoxylin
Microscope
OLYMPUS DX50
OLYMPUS DX50
OLYMPUS DX50
OLYMPUS DX50
OLYMPUS DX50
OLYMPUS DX50
OLYMPUS DX50
OLYMPUS DX50
OLYMPUS DX50
OLYMPUS DX50
Camera
OLYMPUS DP20
OLYMPUS DP20
OLYMPUS DP20
OLYMPUS DP20
OLYMPUS DP20
OLYMPUS DP20
OLYMPUS DP20
OLYMPUS DP20
OLYMPUS DP20
OLYMPUS DP20
Image Size X
1600
1600
1600
1600
1600
1600
1600
1600
1600
1600
Image Size Y
1392
1200
1200
1200
1200
1200
1200
1200
1200
1200
1200
Resolution
1040
72
72
72
72
72
72
72
72
72
72
Magnification
400
400
400
400
400
400
400
400
400
400
Contact Person
Takayuki Masuda
Koji Yamanegi
Koji Yamanegi
Koji Yamanegi
Koji Yamanegi
Koji Yamanegi
Koji Yamanegi
Koji Yamanegi
Koji Yamanegi
Koji Yamanegi
Koji Yamanegi
Email
masudat@mail.tains.tohoku.ac.jp
yamanegi@hyo-med.ac.jp
yamanegi@hyo-med.ac.jp
yamanegi@hyo-med.ac.jp
yamanegi@hyo-med.ac.jp
yamanegi@hyo-med.ac.jp
yamanegi@hyo-med.ac.jp
yamanegi@hyo-med.ac.jp
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
0798-45-6432
0798-45-6432
0798-45-6432
0798-45-6432
0798-45-6432
0798-45-6432
0798-45-6432
Fax
0798-45-6431
0798-45-6431
0798-45-6431
0798-45-6431
0798-45-6431
0798-45-6431
0798-45-6431
0798-45-6431
0798-45-6431
0798-45-6431
Affiliation
Microbiology and Immunology, Department. of Medical Technology, School of Medicine, Tohoku University
Department of clinical pathology, Hyogo collage of medicine
Department of clinical pathology, Hyogo collage of medicine
Department of clinical pathology, Hyogo collage of medicine
Department of clinical pathology, Hyogo collage of medicine
Department of clinical pathology, Hyogo collage of medicine
Department of clinical pathology, Hyogo collage of medicine
Department of clinical pathology, Hyogo collage of medicine
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
980-8575
663-8501
663-8501
663-8501
663-8501
663-8501
663-8501
663-8501
663-8501
663-8501
663-8501
Address
2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi
1-1, Mukogawa, Nishinomiya, Hyogo
1-1, Mukogawa, Nishinomiya, Hyogo
1-1, Mukogawa, Nishinomiya, Hyogo
1-1, Mukogawa, Nishinomiya, Hyogo
1-1, Mukogawa, Nishinomiya, Hyogo
1-1, Mukogawa, Nishinomiya, Hyogo
1-1, Mukogawa, Nishinomiya, Hyogo
1-1, Mukogawa, Nishinomiya, Hyogo
1-1, Mukogawa, Nishinomiya, Hyogo
1-1, Mukogawa, Nishinomiya, Hyogo
Country
Japan
Japan
Japan
Japan
Japan
Japan
Japan
Japan
Japan
Japan
Japan
Note
Nucleous Area
640.5
549
1300.5
348.5
493
406.5
4548.5
2152.5
1120.5
3152.5
565
Nucleous Circularity
0.89
0.850149
0.850611
0.513767
0.876272
0.853672
0.35617
0.555065
0.45674
0.42728
0.48451
Nucleous Bending
693
2.47368
3.47826
0.831169
1.82857
1.34328
1.5047
3.23316
4.40816
2.33716
3.60784
Nucleous Convex Area
66159
602
1380
393
539
449
5368
2423
1350
3737
728
Nucleous Ellipse Long Axis
30.7
30.4396
43.9928
35.6632
25.4626
24.3847
153.577
69.0388
42.1624
98.0194
33.4329
Nucleous Inertia
1.01
50130.6
275912
31775.6
39483
26829.4
7.36E+06
859259
207206
2.31E+06
55770.6
Cell Area
3403
5413.5
2097.5
1772
4432
6519.5
365.5
1737
755.5
465.5
393
Cell Circularity
0.78
0.623047
0.654021
0.380521
0.503661
0.501874
0.486602
0.78405
0.87229
0.752235
0.85315
Cell Bending
2.05
2.41155
2.86705
4.21212
2.50355
3.41003
0.814815
1.49296
2.69663
2.44156
1.25806
Cell Convex Area
3660
5948
2287
2282
5206
7382
419
1837
814
526
427
Cell Ellipse Long Axis
68.45
96.6378
53.1736
76.9439
81.7142
93.8386
42.7701
62.4078
35.0024
28.9788
26.6317
Cell Inertia
1.88E+06
4.98E+06
705993
823651
3289350
6978950
44171.1
562758
93770.1
37952.4
26252.9
Cell-nucleous Area Ratio
0.19
0.101413
0.620024
0.19667
0.111236
0.0623514
12.4446
1.23921
1.48312
6.77229
1.43766
Cell-nucleous Eccentricity1
0.15
0.144526
0.0595199
0.0646352
0.0765719
0.234599
4.77119
0.0280484
0.0362779
1.16008
0.0741046
Cell-nucleous Eccentricity2
0.14
0.108035
0.056419
0.025993
0.0659024
0.223788
1.24271
0.0160237
0.0285695
0.845974
0.0531026
Cell-nucleous Eccentricity3
0.37
0.453505
0.0788611
0.149357
0.215247
0.984436
1.31734
0.0248133
0.0285535
0.590992
0.0604981
Cell-nucleous Eccentricity4
0.32
0.342984
0.0681929
0.0560802
0.211493
0.861196
0.346085
0.0144846
0.0237178
0.250107
0.0423001