SMED30029293

Overview
NameSMED30029293
Smed IDSMED30029293
Length (bp)507
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 SMED30029293 (SMED30029293) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30029293 (SMED30029293) 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 SMED30029293 (SMED30029293) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30029293 (SMED30029293) 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



SMED30029293

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30029293 SmedASXL_005523SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
epidermisSMED30029293 dd_Smed_v4_5527_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
body wall musculatureSMED30029293 dd_Smed_v4_5527_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 2 cellSMED30029293 dd_Smed_v4_5527_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
SMED30029293 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000583:53452..54000 +2487
Homology
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BLAST of SMED30029293 vs. TrEMBL
Match: A0A0L8GI73 (Uncharacterized protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22033073mg PE=4 SV=1)

HSP 1 Score: 54.299 bits (129), Expect = 4.989e-6
Identity = 28/90 (31.11%), Postives = 51/90 (56.67%), Query Frame = 3 
Query:   36 HYFPFELKSELNKIDLKTYFLSCVRKNENNKGITYFGSFRGRPLSGCVVKPVPSYSGMIISPEN--LSRQNVTKYQVNEVFPQYTHWNLG 299
            HY P  +K    + + + YF + ++++++ K +T   SFRGRPL+G ++ P   Y  MI+  +   LS +   ++ +    PQ+T+WNL 
Sbjct:   20 HYMPCIIKYS-GETNAEKYFETTIQEDDDKKELT--ASFRGRPLNGKILTPPQGYESMIVKEKKVPLSEEEDRQFSIVARVPQFTYWNLD 106
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BLAST of SMED30029293 vs. Ensembl Nematostella
Match: EDO28923 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7T538])

HSP 1 Score: 45.4394 bits (106), Expect = 6.606e-7
Identity = 33/108 (30.56%), Postives = 54/108 (50.00%), Query Frame = 3 
Query:   78 DLKTYFLSCVRKNENNKGITYFGSFRGRPLSGCVVKPVPSYSGMIISPENLSRQNVTKYQ-----VNEVFPQYTHWNL-----GLDINEKEHKFFEEWIEISTILNSE 371
            ++  +F   +RKNE  +      SFRGR L G V++P   YSG I+  +   RQ  T+ Q     V + F ++ +WNL     G D   K      +WI ++++L+ +
Sbjct:   12 NVANFFDPTIRKNEGTEQ-DISASFRGRKLRGAVMQPPAGYSGFILRED---RQPTTEEQDHHLKVTKKFNKFHYWNLETPPSGNDAVAKAM----QWITLASVLHGQ 111
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BLAST of SMED30029293 vs. Ensembl Nematostella
Match: EDO27966 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7T7T3])

HSP 1 Score: 44.2838 bits (103), Expect = 1.175e-6
Identity = 29/92 (31.52%), Postives = 47/92 (51.09%), Query Frame = 3 
Query:   36 HYFPFELKSELNKIDLKTYFLSCVRKNENNKGITYFGSFRGRPLSGCVVKPVPSYSGMIISPENLSRQNVTKYQ-----VNEVFPQYTHWNL 296
            H+ P ++ +     ++  +F   +RKNE  +      SFRGR L G V++P   YSG I+  +   RQ  T+ Q     V + F ++ +WNL
Sbjct:    3 HWMPCQI-THNGDANVANFFDPTIRKNEGTEQ-DISASFRGRKLRGAVMQPPAGYSGFILRED---RQPTTEEQDHHLKVTKKFNKFHYWNL 89
[Close]
BLAST of SMED30029293 vs. Planmine SMEST
Match: SMESG000064498.1 (SMESG000064498.1)

HSP 1 Score: 239.58 bits (610), Expect = 1.306e-82
Identity = 114/115 (99.13%), Postives = 115/115 (100.00%), Query Frame = 3 
Query:   27 MDAHYFPFELKSELNKIDLKTYFLSCVRKNENNKGITYFGSFRGRPLSGCVVKPVPSYSGMIISPENLSRQNVTKYQVNEVFPQYTHWNLGLDINEKEHKFFEEWIEISTILNSE 371
            MDAHYFPFELKSELNKIDLKTYFLSCVRKNENNKGITYFGSFRGRPLSGCVVKPVPSYSGMIISPENLSRQNVTKYQVNE+FPQYTHWNLGLDINEKEHKFFEEWIEISTILNSE
Sbjct:    1 MDAHYFPFELKSELNKIDLKTYFLSCVRKNENNKGITYFGSFRGRPLSGCVVKPVPSYSGMIISPENLSRQNVTKYQVNEIFPQYTHWNLGLDINEKEHKFFEEWIEISTILNSE 115
The following BLAST results are available for this feature:
BLAST of SMED30029293 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 SMED30029293 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 SMED30029293 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 SMED30029293 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 SMED30029293 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 SMED30029293 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 SMED30029293 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 SMED30029293 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A0L8GI734.989e-631.11Uncharacterized protein OS=Octopus bimaculoides OX... [more]
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BLAST of SMED30029293 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 SMED30029293 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 SMED30029293 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 SMED30029293 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 2
Match NameE-valueIdentityDescription
EDO289236.606e-730.56Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
EDO279661.175e-631.52Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30029293 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 SMED30029293 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000064498.11.306e-8299.13SMESG000064498.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029293 ID=SMED30029293|Name=SMED30029293|organism=Schmidtea mediterranea sexual|type=transcript|length=507bp
CGGATTTTTAAAAAAAAAAATTTAAAATGGATGCTCATTATTTTCCATTT
GAATTGAAGTCAGAACTAAACAAAATCGATTTAAAAACATATTTTCTTTC
TTGTGTCAGGAAAAATGAAAATAATAAAGGTATAACATATTTTGGTTCTT
TTCGTGGCAGACCATTATCTGGATGTGTAGTTAAACCAGTTCCTAGCTAT
TCTGGAATGATAATATCTCCAGAAAATTTGTCACGTCAAAATGTTACAAA
ATATCAAGTTAATGAAGTATTTCCTCAATACACTCACTGGAATTTAGGAT
TAGATATTAATGAAAAAGAGCATAAGTTCTTTGAAGAATGGATTGAGATA
TCCACAATTTTAAATTCTGAATAAGCTTCTTTGTGATGTTGTGTGTGGCT
AAATGCATTTATTACATTTTATATATATGGGTTAAGATTTTTTAACGATA
TAAATTAGTCATTTATAATTAAAATCGGTGGTATAATTCAGATATTGAAA
AGATAAT
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protein sequence of SMED30029293-orf-1

>SMED30029293-orf-1 ID=SMED30029293-orf-1|Name=SMED30029293-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=116bp
MDAHYFPFELKSELNKIDLKTYFLSCVRKNENNKGITYFGSFRGRPLSGC
VVKPVPSYSGMIISPENLSRQNVTKYQVNEVFPQYTHWNLGLDINEKEHK
FFEEWIEISTILNSE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000028Category 2 cell
PLANA:0000240body wall musculature
PLANA:0002109X1 cell
Vocabulary: biological process
TermDefinition
GO:0006401RNA catabolic process
Vocabulary: cellular component
TermDefinition
GO:0032299ribonuclease H2 complex
Vocabulary: INTERPRO
TermDefinition
IPR013924RNase_H2_suC
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR013924Ribonuclease H2, subunit CPFAMPF08615RNase_H2_suCcoord: 3..70
e-value: 1.4E-4
score: 22.1
NoneNo IPR availableGENE3DG3DSA:3.30.200.130coord: 1..115
e-value: 2.5E-10
score: 41.9