SMED30000378

Overview
NameSMED30000378
Smed IDSMED30000378
Length (bp)688
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 SMED30000378 (SMED30000378) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30000378 (SMED30000378) 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 SMED30000378 (SMED30000378) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30000378 (SMED30000378) 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




SMED30000378

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



PAGE Curations: 15

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30000378 SmedASXL_007952SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
protonephridiaSMED30000378 dd_Smed_v4_512_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30000378 dd_Smed_v4_512_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30000378 dd_Smed_v4_512_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30000378 dd_Smed_v4_512_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30000378 dd_Smed_v4_512_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30000378 dd_Smed_v4_512_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
muscle cellSMED30000378 dd_Smed_v4_512_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30000378 dd_Smed_v4_512_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30000378 dd_Smed_v4_512_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neural progenitor cellSMED30000378 dd_Smed_v6_512_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30000378 dd_Smed_v6_512_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30000378 dd_Smed_v6_512_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cholinergic neuronSMED30000378 dd_Smed_v6_512_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 2 cellSMED30000378 dd_Smed_v4_512_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
Alignments
SMED30000378 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000868:120580..121310 -3400
Homology
BLAST of SMED30000378 vs. TrEMBL
Match: A0A267FUI9 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig015490g3 PE=4 SV=1)

HSP 1 Score: 80.8777 bits (198), Expect = 6.627e-16
Identity = 43/89 (48.31%), Postives = 64/89 (71.91%), Query Frame = 2
Query:   83 FSVMSTNLEKRCSGGYAFEVGIEDIGCKSPSSGKPKHVFERLGDSVDLSPEDLEQKLKNAEERRKAQENDKVKKVQEHNARVERIAKEV 349
             S   ++ +++ SGG AFEV ++D    SP SGKP H+ ERL D  +LSPE++E++L+ AEERRK  E D +K+V EHN +VE+++K+V
Sbjct:   19 LSTEMSDEQQQHSGGVAFEVSVDDENI-SPRSGKPHHLEERLEDR-NLSPEEIEKRLQEAEERRKKMEEDMLKRVSEHNDKVEKVSKDV 105          
BLAST of SMED30000378 vs. TrEMBL
Match: A0A1I8HPD2 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 81.2629 bits (199), Expect = 6.655e-16
Identity = 46/103 (44.66%), Postives = 69/103 (66.99%), Query Frame = 2
Query:   41 YSVNK*ECMHCLNYFSVMSTNLEKRCSGGYAFEVGIEDIGCKSPSSGKPKHVFERLGDSVDLSPEDLEQKLKNAEERRKAQENDKVKKVQEHNARVERIAKEV 349
            +S+       C    + MS + +++ SGG AFEV ++D    SP SGKP H+ ERL D  +LSPE++E++L+ AEERRK  E D +K+V EHN +VE+++K+V
Sbjct:    9 FSIANPAAQTCCRLSTEMS-DEQQQHSGGVAFEVSVDDENI-SPRSGKPHHLEERLEDR-NLSPEEIEKRLQEAEERRKKMEEDMLKRVSEHNDKVEKVSKDV 108          
BLAST of SMED30000378 vs. TrEMBL
Match: A0A1I8JEV9 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 63.929 bits (154), Expect = 1.653e-9
Identity = 36/82 (43.90%), Postives = 52/82 (63.41%), Query Frame = 2
Query:  122 GGYAFEVGIEDIGCKSPSSGKPKHVFERLGDSV-DLSPEDLEQKLKNAEERRKAQENDKVKKVQEHNARVERIAKEVAKEEK 364
            GG AFEV + D G  +P S KP H+  RLGD     +P+ + ++ + AE RRK QE + +K+V  HN RVER+A+E  + +K
Sbjct:   28 GGVAFEVAL-DSGNVTPRSRKPHHLERRLGDDARPTTPDLIAKRQREAEARRKKQEAETIKRVGRHNDRVERLAREAEQRKK 108          
BLAST of SMED30000378 vs. TrEMBL
Match: A0A1I8HLC7 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 63.5438 bits (153), Expect = 3.902e-9
Identity = 36/82 (43.90%), Postives = 52/82 (63.41%), Query Frame = 2
Query:  122 GGYAFEVGIEDIGCKSPSSGKPKHVFERLGDSV-DLSPEDLEQKLKNAEERRKAQENDKVKKVQEHNARVERIAKEVAKEEK 364
            GG AFEV + D G  +P S KP H+  RLGD     +P+ + ++ + AE RRK QE + +K+V  HN RVER+A+E  + +K
Sbjct:   56 GGVAFEVAL-DSGNVTPRSRKPHHLERRLGDDARPTTPDLIAKRQREAEARRKKQEAETIKRVGRHNDRVERLAREAEQRKK 136          
BLAST of SMED30000378 vs. TrEMBL
Match: A0A1I8JI23 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 63.1586 bits (152), Expect = 1.081e-8
Identity = 35/77 (45.45%), Postives = 49/77 (63.64%), Query Frame = 2
Query:  122 GGYAFEVGIEDIGCKSPSSGKPKHVFERLGDSV-DLSPEDLEQKLKNAEERRKAQENDKVKKVQEHNARVERIAKEV 349
            GG AFEV + D G  +P S KP H+  RLGD     +P+ + ++ + AE RRK QE + +K+V  HN RVER+A+E 
Sbjct:   56 GGVAFEVAL-DSGNVTPRSRKPHHLERRLGDDARPTTPDLIAKRQREAEARRKKQEAETIKRVGRHNDRVERLAREA 131          
BLAST of SMED30000378 vs. Planmine SMEST
Match: SMESG000061591.1 (SMESG000061591.1)

HSP 1 Score: 184.111 bits (466), Expect = 4.777e-60
Identity = 91/91 (100.00%), Postives = 91/91 (100.00%), Query Frame = 2
Query:   92 MSTNLEKRCSGGYAFEVGIEDIGCKSPSSGKPKHVFERLGDSVDLSPEDLEQKLKNAEERRKAQENDKVKKVQEHNARVERIAKEVAKEEK 364
            MSTNLEKRCSGGYAFEVGIEDIGCKSPSSGKPKHVFERLGDSVDLSPEDLEQKLKNAEERRKAQENDKVKKVQEHNARVERIAKEVAKEEK
Sbjct:    1 MSTNLEKRCSGGYAFEVGIEDIGCKSPSSGKPKHVFERLGDSVDLSPEDLEQKLKNAEERRKAQENDKVKKVQEHNARVERIAKEVAKEEK 91          
The following BLAST results are available for this feature:
BLAST of SMED30000378 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 SMED30000378 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 SMED30000378 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 SMED30000378 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 SMED30000378 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 SMED30000378 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 SMED30000378 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 SMED30000378 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267FUI96.627e-1648.31Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A1I8HPD26.655e-1644.66Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8JEV91.653e-943.90Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8HLC73.902e-943.90Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8JI231.081e-845.45Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of SMED30000378 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 SMED30000378 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 SMED30000378 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 SMED30000378 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 SMED30000378 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 SMED30000378 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000061591.14.777e-60100.00SMESG000061591.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000378 ID=SMED30000378|Name=SMED30000378|organism=Schmidtea mediterranea sexual|type=transcript|length=688bp
GGGAAATTCAAGACAGAAAATTGATGACTCACTCTTTTTCTACTCTGTAA
ATAAATAGGAATGCATGCATTGTTTAAATTATTTTTCTGTAATGTCAACA
AATTTGGAGAAGCGTTGTTCTGGTGGATATGCTTTTGAAGTTGGAATCGA
AGATATTGGTTGTAAATCACCGTCATCAGGAAAACCGAAACATGTTTTCG
AAAGATTGGGTGATTCTGTGGATCTTAGTCCCGAAGATTTGGAACAAAAG
TTAAAAAATGCCGAAGAAAGACGAAAGGCTCAAGAAAATGATAAAGTAAA
AAAAGTTCAAGAGCATAACGCCAGAGTTGAACGAATTGCGAAAGAAGTTG
CAAAAGAAGAGAAATAAACGACATTTGTAGAAATATTTTATTTTTTTGTT
AATATTTTAATTTTTATTGATTAAGTGGGTGTTGGAATGATCTATTGAAT
ATGAATAATGACTTATGAGTTATCGTATTTTATGTGTATCAGATTTGTTG
ATGTATTTTGTTTTATTTTTAGTTATTTTTGTTAAATAGATGTCATGAAA
AATATGGTTGACATTTATATTTTATTTTGTTAAGTGTTGCGAATAAACAT
TTAATGTTAATATCATTTAAAATTCCTGGCATAATTGCTACTGATTTAAA
TATATCACATTGACATATTAACAATTTTTCAATTTACC
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protein sequence of SMED30000378-orf-1

>SMED30000378-orf-1 ID=SMED30000378-orf-1|Name=SMED30000378-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=101bp
MHCLNYFSVMSTNLEKRCSGGYAFEVGIEDIGCKSPSSGKPKHVFERLGD
SVDLSPEDLEQKLKNAEERRKAQENDKVKKVQEHNARVERIAKEVAKEEK
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000012neural progenitor cell
PLANA:0000020protonephridia
PLANA:0000028Category 2 cell
PLANA:0000099neuron
PLANA:0000429neoblast
PLANA:0000463cholinergic neuron
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR036002Stathmin_sf
IPR000956Stathmin_fam
Vocabulary: biological process
TermDefinition
GO:0031110regulation of microtubule polymerization or depolymerization
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 56..100
NoneNo IPR availableGENE3DG3DSA:1.20.58.580coord: 55..99
e-value: 1.5E-6
score: 30.0
IPR000956Stathmin familyPFAMPF00836Stathmincoord: 15..99
e-value: 2.1E-11
score: 43.9
IPR036002Stathmin superfamilySUPERFAMILYSSF101494Stathmincoord: 13..94