SMED30026018

Overview
NameSMED30026018
Smed IDSMED30026018
Length (bp)1313
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 SMED30026018 (SMED30026018) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30026018 (SMED30026018) 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 SMED30026018 (SMED30026018) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30026018 (SMED30026018) 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



SMED30026018

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30026018 SmedASXL_077058SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30026018 SmedASXL_077887SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30026018 SmedASXL_077887SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30026018 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004065:5154..6436 -5852
Homology
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BLAST of SMED30026018 vs. Planmine SMEST
Match: SMESG000050731.1 (SMESG000050731.1)

HSP 1 Score: 130.183 bits (326), Expect = 2.985e-36
Identity = 67/101 (66.34%), Postives = 78/101 (77.23%), Query Frame = 1 
Query:  532 MESSVLTGDLAENVRRITTRGKGKKSARRALPKRPQEVQDKEIRRYDGKCTKEAEKWIQVIDDCIGRNDLKRTEAFDFLLSDKTATLWKNFKTKKTTHNIA 834
            MESSVL GD  ENV  +TT G+GKKSAR AL KR Q+  D EIRRYD +CTKEAEKWI+ I+D IG+NDLKRT AFDFLL ++ AT W NFK ++TT  IA
Sbjct:    1 MESSVLAGDNDENVHTMTTLGEGKKSARDALSKRAQKPPDMEIRRYDRRCTKEAEKWIKAINDWIGQNDLKRTGAFDFLLCNEAATPWTNFKRERTTDKIA 101
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BLAST of SMED30026018 vs. Planmine SMEST
Match: SMESG000056605.1 (SMESG000056605.1)

HSP 1 Score: 102.449 bits (254), Expect = 7.869e-25
Identity = 53/85 (62.35%), Postives = 61/85 (71.76%), Query Frame = 1 
Query:  580 ITTRGKGKKSARRALPKRPQEVQDKEIRRYDGKCTKEAEKWIQVIDDCIGRNDLKRTEAFDFLLSDKTATLWKNFKTKKTTHNIA 834
            ++TRG+G             E+ D EIRRYDG+CTKEAE WIQ IDD IGRNDLKRTEAF+FLL +  ATLWK FKT+KTT  IA
Sbjct:    1 MSTRGEGGNLQEMHCQ---NELLDMEIRRYDGRCTKEAEIWIQAIDDWIGRNDLKRTEAFNFLLCNNAATLWKIFKTEKTTDKIA 82
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BLAST of SMED30026018 vs. Planmine SMEST
Match: SMESG000056626.1 (SMESG000056626.1)

HSP 1 Score: 99.3673 bits (246), Expect = 8.108e-24
Identity = 48/66 (72.73%), Postives = 54/66 (81.82%), Query Frame = 1 
Query:  637 QEVQDKEIRRYDGKCTKEAEKWIQVIDDCIGRNDLKRTEAFDFLLSDKTATLWKNFKTKKTTHNIA 834
             E+ D EIRRYDG+CTKEAE WIQ I+D IGRNDLKRTEAF+FLL +  ATLWK FKT+KTT  IA
Sbjct:    5 NELLDMEIRRYDGRCTKEAEIWIQAIEDWIGRNDLKRTEAFNFLLCNNGATLWKIFKTEKTTDKIA 70
[Close]
BLAST of SMED30026018 vs. Planmine SMEST
Match: SMESG000074507.1 (SMESG000074507.1)

HSP 1 Score: 102.064 bits (253), Expect = 8.553e-24
Identity = 48/62 (77.42%), Postives = 54/62 (87.10%), Query Frame = 1 
Query:  649 DKEIRRYDGKCTKEAEKWIQVIDDCIGRNDLKRTEAFDFLLSDKTATLWKNFKTKKTTHNIA 834
            DK+IRRYDGKCTKEAE+W Q IDD IGRNDLKRT AFDF+L D+TA LWKNFKT+ TT+ IA
Sbjct:   74 DKQIRRYDGKCTKEAERWTQAIDDWIGRNDLKRTVAFDFILCDETAKLWKNFKTEITTNKIA 135
[Close]
BLAST of SMED30026018 vs. Planmine SMEST
Match: SMESG000052773.1 (SMESG000052773.1)

HSP 1 Score: 85.1149 bits (209), Expect = 1.582e-17
Identity = 43/55 (78.18%), Postives = 48/55 (87.27%), Query Frame = 1 
Query:  532 MESSVLTGDLAENVRRITTRGKGKKSARRALPKRPQEVQDKEIRRYDGKCTKEAE 696
            MESSVLTGD AENV+ +TTRG+GKKSAR ALPKR QE+ D EIRRYD +CTKEAE
Sbjct:    1 MESSVLTGDRAENVQTMTTRGEGKKSARDALPKRVQELLDIEIRRYDRRCTKEAE 55
The following BLAST results are available for this feature:
BLAST of SMED30026018 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 SMED30026018 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 SMED30026018 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 SMED30026018 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 SMED30026018 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 SMED30026018 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 SMED30026018 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 SMED30026018 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 SMED30026018 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 SMED30026018 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 SMED30026018 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 SMED30026018 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 SMED30026018 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 SMED30026018 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000050731.12.985e-3666.34SMESG000050731.1[more]
SMESG000056605.17.869e-2562.35SMESG000056605.1[more]
SMESG000056626.18.108e-2472.73SMESG000056626.1[more]
SMESG000074507.18.553e-2477.42SMESG000074507.1[more]
SMESG000052773.11.582e-1778.18SMESG000052773.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026018 ID=SMED30026018|Name=SMED30026018|organism=Schmidtea mediterranea sexual|type=transcript|length=1313bp
GTTACTGTTGGACTTTCAAAGAGAGGGTAAATTTTATGTTGTTTGTTTTT
CAATTAAATATATTAAAAAGATAATTTTGCGATCAAATTATTTTCATAAA
GAACTGTATTATTTAATGTGACAGACATATATCATTACTTATTTGTAAAA
AAATAAAGTGACACCATGGCAGTGTGGCTTAGCACACCACAACTAAAAGG
TTGCCGATCCCTGCTACAGAGTCTATAGTATAAGGACTTATCTAATGTCC
TGGTTATTATAAACACACGTATATGCGCGTCAACTGAATAACAACTTCTA
TAATAAACTGAAAAAACATTAACGTTGTACCAATGGGAATTAAATTAGAG
CTAAAAATGCAGCAAATGCATCTTATATTCAATCAAAAATCTAACCAGTA
ATGATATTACATTAAAGGTTAAAGACCAAATGTTAATCAGTTTAGTGTAT
ATTGCGCAACATAATTGATCGCGCAATATACACTAATATTTAAACAAGTG
GTCTTTTTATGTTTGTTTAATAAATATTTAGATGGAATCAAGTGTTTTAA
CTGGCGACCTAGCCGAAAATGTTCGCAGAATAACGACCCGAGGAAAAGGG
AAGAAATCTGCAAGACGTGCACTGCCAAAACGACCTCAAGAAGTCCAGGA
TAAGGAAATTAGAAGATACGATGGCAAATGTACCAAAGAAGCTGAAAAAT
GGATCCAAGTAATTGATGATTGTATCGGTCGAAATGACTTGAAGAGAACA
GAAGCATTCGATTTTCTTCTTAGCGACAAAACAGCTACGCTGTGGAAAAA
TTTTAAAACAAAAAAAACAACACATAACATAGCTAACATAGACTGAAACA
TTTACCATCAAATTAACTACTATAGACAAGACTAAGGAACTTGCTGCCAT
AAGTCAAGATGAAAGATACGCGACAGTTTACTTAACCAATAATAAATGTA
CATGTATGAGTCAAAGCCAAAATAGAATATCAATAAGACCTGGAACATAA
GGTAGGATCATATATTTTATGAGGGTTACGAAATTTCATGGCATAAGATT
TATTTTGAAACTAAAATAAATTTAATATTTCATAAGTTTTCAGAATAATT
TAAAAACCTCTAAAATTCATATATAAAGCAATTAAAAAATGCATGTTTAA
ATATAAAATTTTACTTAAAAACAAGTTAAAACATTTTAAAAATCCAGAGA
CTTATAGATTGTATCAAAGGTCGGATAAAATGACCCTTAGTATAAACGCT
ACATTATAGATAATCAAAGTGATAGAGAAATAAAATAATACACATTAACA
CAACCCATAATAA
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protein sequence of SMED30026018-orf-1

>SMED30026018-orf-1 ID=SMED30026018-orf-1|Name=SMED30026018-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=105bp
MESSVLTGDLAENVRRITTRGKGKKSARRALPKRPQEVQDKEIRRYDGKC
TKEAEKWIQVIDDCIGRNDLKRTEAFDFLLSDKTATLWKNFKTKKTTHNI
ANID*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 68..85
NoneNo IPR availableTMHMMTMhelixcoord: 10..32