SMED30011682

Overview
NameSMED30011682
Smed IDSMED30011682
Length (bp)887
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)



Explore this single cell expression dataset with our NB Cluster Shiny App



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30011682 (SMED30011682) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30011682 (SMED30011682) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30011682 (SMED30011682) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30011682 (SMED30011682) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30011682

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30011682 SmedASXL_018771SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30011682 dd_Smed_v4_399_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30011682 dd_Smed_v4_399_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30011682 dd_Smed_v6_399_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30011682 dd_Smed_v4_399_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal ventral margin of the whole animalSMED30011682 dd_Smed_v4_399_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30011682 vs. Planmine SMEST
Match: SMESG000045893.1 (SMESG000045893.1)

HSP 1 Score: 163.696 bits (413), Expect = 2.776e-51
Identity = 81/82 (98.78%), Postives = 82/82 (100.00%), Query Frame = 3 
Query:   96 MDDDVVTKIFKAVDKNKNGEISQDELKEYFKKTKMADCDIEKRITDWMGKFDTDSNKSISYSEMCKVVGIPENQNTKAMFKK 341
            MDDDVVTKIFKAVDKNKNGEISQDELKEYFKKTK+ADCDIEKRITDWMGKFDTDSNKSISYSEMCKVVGIPENQNTKAMFKK
Sbjct:    1 MDDDVVTKIFKAVDKNKNGEISQDELKEYFKKTKVADCDIEKRITDWMGKFDTDSNKSISYSEMCKVVGIPENQNTKAMFKK 82
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BLAST of SMED30011682 vs. Planmine SMEST
Match: SMESG000002907.1 (SMESG000002907.1)

HSP 1 Score: 65.4698 bits (158), Expect = 1.041e-13
Identity = 33/82 (40.24%), Postives = 54/82 (65.85%), Query Frame = 3 
Query:   96 MDDDVVTKIFKAVDKNKNGEISQDELKEYFKKTKMADCDIEKRITDWMGKFDTDSNKSISYSEMCKVVGIPENQNTKAMFKK 341
            M DD+ +K+F  +D NKNG IS DELK++  KT     ++++ I  ++  FD D +K+++Y E  K +GIP ++ T ++FKK
Sbjct:    1 MGDDIASKMFLKIDTNKNGVISIDELKQHCSKT----ANVDEAIKTFLKNFDKDKDKNVTYEEFAKALGIPVSEKTLSVFKK 78
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BLAST of SMED30011682 vs. Planmine SMEST
Match: SMESG000048475.1 (SMESG000048475.1)

HSP 1 Score: 61.6178 bits (148), Expect = 2.610e-12
Identity = 33/82 (40.24%), Postives = 51/82 (62.20%), Query Frame = 3 
Query:   96 MDDDVVTKIFKAVDKNKNGEISQDELKEYFKKTKMADCDIEKRITDWMGKFDTDSNKSISYSEMCKVVGIPENQNTKAMFKK 341
            M DD+ +K+F AVD NKNG IS +EL+++  K    D  +EK    ++  FDT+ ++ I+Y E    +G P N+ T A+F+K
Sbjct:    1 MGDDMASKMFLAVDINKNGIISVEELRKHCSKCSNVDEAVEK----FLKNFDTNRDREITYKEFADALGYPLNEKTLALFQK 78
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BLAST of SMED30011682 vs. Planmine SMEST
Match: SMESG000081370.1 (SMESG000081370.1)

HSP 1 Score: 48.1358 bits (113), Expect = 1.149e-6
Identity = 29/71 (40.85%), Postives = 40/71 (56.34%), Query Frame = 3 
Query:   99 DDDV--VTKIFKAVDKNKNGEISQDELKEYFKKTKMADCDIEKRITDWMGKFDTDSNKSISYSEMCKVVGI 305
            DDDV  + ++F  +D N N EIS+ EL++Y KK   +D D+EK    WM  FD D +  IS  E    + I
Sbjct:    7 DDDVQMLVELFYEIDANCNNEISRKELQDYMKKRGYSDNDVEK----WMQNFDVDHDGKISLEEFVSRLEI 73
[Close]
BLAST of SMED30011682 vs. Planmine SMEST
Match: SMESG000045029.1 (SMESG000045029.1)

HSP 1 Score: 46.9802 bits (110), Expect = 2.956e-6
Identity = 26/67 (38.81%), Postives = 38/67 (56.72%), Query Frame = 3 
Query:  105 DVVTKIFKAVDKNKNGEISQDELKEYFKKTKMADCDIEKRITDWMGKFDTDSNKSISYSEMCKVVGI 305
            D   + F A+D + +GEIS DEL +Y  K       I+K    W+  FD D++ +I+  E CKV+GI
Sbjct:    2 DSFIEAFFAIDTDSSGEISTDELSDYMNKNHYRSEFIKK----WLKIFDIDNSGTITLEEYCKVLGI 64
The following BLAST results are available for this feature:
BLAST of SMED30011682 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30011682 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30011682 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30011682 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30011682 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30011682 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30011682 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30011682 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30011682 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30011682 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30011682 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30011682 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30011682 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30011682 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000045893.12.776e-5198.78SMESG000045893.1[more]
SMESG000002907.11.041e-1340.24SMESG000002907.1[more]
SMESG000048475.12.610e-1240.24SMESG000048475.1[more]
SMESG000081370.11.149e-640.85SMESG000081370.1[more]
SMESG000045029.12.956e-638.81SMESG000045029.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011682 ID=SMED30011682|Name=SMED30011682|organism=Schmidtea mediterranea sexual|type=transcript|length=887bp
AAATAATTAGTTTGTTATTCAGTACACCATGAAGTATGAATATAAATTGA
CATAGAAAATCATACTGTGCAGTTTAACTGAAAATTTTCATAACCATGGA
TGATGATGTAGTCACAAAAATATTTAAAGCCGTCGACAAAAACAAGAACG
GAGAAATTTCCCAAGACGAATTGAAGGAATATTTTAAGAAAACAAAAATG
GCTGATTGCGACATTGAAAAACGAATTACTGATTGGATGGGAAAATTTGA
TACCGATTCAAACAAATCCATCAGCTATAGTGAGATGTGCAAGGTCGTTG
GAATACCTGAAAACCAGAATACCAAGGCGATGTTCAAGAAATAATTTATT
ATCCGTTTTTTCCTTGAAATCTTATTAGCATCCTTTAATTNNAANNNATA
ATAAATATTTATTNGTTTNAAANNNNNANCTTAAAAAATTACACATGCCG
CGAGTGGGATTATAATGCATTTTCAAAGTGGCGAATAAGATCATTTGATT
AGCCAGGCATGATCTATATTCTTCTTTTTCAAACAAAACCTTACCTAGGA
TAGGAAAATAATTGTTTTTCATGCCAACCGGTAGTAAATTTATTCTAGAA
AAATTTTGAAAAAACGATTGTAAAAAATGGACAGTAGGAACTAGCAAAAC
CTATGAGAAATGCTTGTGAACAGAGTGCTAATTCTATAATATAGCTTAAA
GCTGGTTTATTAAAATTAGCACAAAATTTTTGAAATTTATACGAAATATT
GTATTTTACGTGTAAAAGCCAATAACAGATAATAAGAAGATTATTATTGT
ATTCAATAATGTAAACGAAAATTTTGTTTAATTTAACTTTGAATAAATCA
AATGGCAGACACGAGCTAATTATGAGCCCAGGCGGTA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000043dorsal ventral margin of the whole animal
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR002048EF_hand_dom
IPR011992EF-hand-dom_pair
IPR018247EF_Hand_1_Ca_BS
Vocabulary: molecular function
TermDefinition
GO:0005509calcium ion binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR002048EF-hand domainSMARTSM00054efh_1coord: 5..33
e-value: 3.6E-4
score: 29.9
coord: 43..71
e-value: 5.4
score: 11.8
IPR002048EF-hand domainPFAMPF13499EF-hand_7coord: 6..67
e-value: 1.2E-11
score: 44.9
IPR002048EF-hand domainPROSITEPS50222EF_HAND_2coord: 39..74
score: 7.205
IPR002048EF-hand domainPROSITEPS50222EF_HAND_2coord: 1..36
score: 13.76
IPR002048EF-hand domainCDDcd00051EFhcoord: 6..68
e-value: 4.73745E-8
score: 43.3053
NoneNo IPR availableGENE3DG3DSA:1.10.238.10coord: 5..73
e-value: 6.1E-14
score: 53.5
IPR018247EF-Hand 1, calcium-binding sitePROSITEPS00018EF_HAND_1coord: 14..26
IPR018247EF-Hand 1, calcium-binding sitePROSITEPS00018EF_HAND_1coord: 52..64
IPR011992EF-hand domain pairSUPERFAMILYSSF47473EF-handcoord: 3..68