SMED30000795

Overview
NameSMED30000795
Smed IDSMED30000795
Length (bp)449
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30000795 (SMED30000795) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30000795 (SMED30000795) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30000795

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X2 cellSMED30000795 SmedASXL_077910SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30000795 vs. Planmine SMEST
Match: SMESG000027872.1 (SMESG000027872.1)

HSP 1 Score: 207.994 bits (528), Expect = 1.603e-69
Identity = 103/129 (79.84%), Postives = 110/129 (85.27%), Query Frame = 2 
Query:    2 DTDLPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQTKLQVRRAQQHLDEINRDIANGLIPSTNGYVPPYNTSFNLDDPRLNLPTEAINVVVPRQIWPERSRRANEPSNTHREHPYARGIPRRSSNR 388
            D DLPFVAIKREPGRNPAREIRGQA+ LLARLEEHQRQT  Q+RRAQ+HLDEINRDIA GLIPSTNGY PPYNTSFNLDDPR N PTEAINVVVPRQ+W  R  R  E   T+REHPYARG PR +S+R
Sbjct:   56 DVDLPFVAIKREPGRNPAREIRGQAKHLLARLEEHQRQTAQQIRRAQRHLDEINRDIAVGLIPSTNGYAPPYNTSFNLDDPRFNRPTEAINVVVPRQLWTGRGERTYEAPTTNREHPYARGPPRTNSDR 184
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BLAST of SMED30000795 vs. Planmine SMEST
Match: SMESG000032540.1 (SMESG000032540.1)

HSP 1 Score: 176.022 bits (445), Expect = 7.932e-57
Identity = 87/128 (67.97%), Postives = 101/128 (78.91%), Query Frame = 2 
Query:    2 DTDLPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQTKLQVRRAQQHLDEINRDIANGLIPSTNGYVPPYNTSFNLDDPRLNLPTEAINVVVPRQIWPERSRRANEPSNTHREHPYARGIPRRSSN 385
            D DLPFVAIKREPGRNPAREIRGQAE+LLARLEEH+RQT  +V +A++HL+EIN DIA G+IPST+GY PPYNT FNLDDPRLN  + A+ VVVPR+        ANEP+N H +HPYAR  P R  N
Sbjct:   54 DVDLPFVAIKREPGRNPAREIRGQAEYLLARLEEHKRQTDHEVDKARRHLEEINWDIAAGIIPSTDGYAPPYNTPFNLDDPRLNRSSSAMKVVVPRETLIRGWGEANEPANEHHDHPYARERPSRRDN 181
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BLAST of SMED30000795 vs. Planmine SMEST
Match: SMESG000066467.1 (SMESG000066467.1)

HSP 1 Score: 176.792 bits (447), Expect = 3.003e-54
Identity = 84/131 (64.12%), Postives = 99/131 (75.57%), Query Frame = 2 
Query:    2 DTDLPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQTKLQVRRAQQHLDEINRDIANGLIPSTNGYVPPYNTSFNLDDPRLNLPTEAINVVVPRQIWPERSRRANEPSNTHREHPYARGIPRRSSNR*H 394
            + +LPFVAIKREPGRNPAREIRGQ EFLLARLEEHQRQT LQV RA+ +L  +N DIA G I  T+GY PPYNTSFNLDD RLN+  EA+NVV+PR+  P + RR   P+  H EHPYAR + +  S + H
Sbjct:  263 EVELPFVAIKREPGRNPAREIRGQTEFLLARLEEHQRQTNLQVARARLYLANVNEDIAAGRIACTDGYAPPYNTSFNLDDERLNVNAEAMNVVIPRKALPRKMRRNEGPAERHNEHPYARTVSKSDSFQHH 393
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BLAST of SMED30000795 vs. Planmine SMEST
Match: SMESG000066467.1 (SMESG000066467.1)

HSP 1 Score: 171.785 bits (434), Expect = 3.570e-52
Identity = 84/135 (62.22%), Postives = 101/135 (74.81%), Query Frame = 2 
Query:    2 DTDLPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQTKLQVRRAQQHLDEINRDIANGLIPSTNGYVPPYNTSFNLDDPRLNLPTEAINVVVPRQIWPERSRRANEPSNTHREHPYARGIPRRSSNR*HLRVN 406
            + +LPFVAIKREPGRNPAREIRGQ EFLLARLEEHQRQT LQV RA+ +L  +N DIA G I  T+GY PPYNTSFNLDD RLN+  EA+NVV+PR+  P + RR   P+  H EHPYAR + +  S + H + +
Sbjct:  263 EVELPFVAIKREPGRNPAREIRGQTEFLLARLEEHQRQTNLQVARARLYLANVNEDIAAGRIACTDGYAPPYNTSFNLDDERLNVNAEAMNVVIPRKALPRKMRRNEGPAERHNEHPYARTVSKSDSFQHHRKTD 397
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BLAST of SMED30000795 vs. Planmine SMEST
Match: SMESG000008989.1 (SMESG000008989.1)

HSP 1 Score: 162.925 bits (411), Expect = 4.000e-51
Identity = 79/121 (65.29%), Postives = 91/121 (75.21%), Query Frame = 2 
Query:   26 IKREPGRNPAREIRGQAEFLLARLEEHQRQTKLQVRRAQQHLDEINRDIANGLIPSTNGYVPPYNTSFNLDDPRLNLPTEAINVVVPRQIWPERSRRANEPSNTHREHPYARGIPRRSSNR 388
            + R P  N AREIRGQAE LLA LE+HQRQT  Q+R+AQQHLD+INRD A GLIP T+GY PPYNTSFNLDD R+N P + INV+VPR++W  R  R NE    HREHPYARG  R S +R
Sbjct:  103 LSRNPAENSAREIRGQAEHLLAILEKHQRQTAQQIRKAQQHLDDINRDNAAGLIPITDGYAPPYNTSFNLDDSRVNRPVDDINVIVPRRLWTGRGGRMNEEPKVHREHPYARGSSRASYDR 223
The following BLAST results are available for this feature:
BLAST of SMED30000795 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 SMED30000795 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 SMED30000795 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 SMED30000795 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 SMED30000795 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 SMED30000795 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 SMED30000795 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 SMED30000795 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 SMED30000795 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 SMED30000795 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 SMED30000795 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 SMED30000795 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 SMED30000795 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 SMED30000795 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000027872.11.603e-6979.84SMESG000027872.1[more]
SMESG000032540.17.932e-5767.97SMESG000032540.1[more]
SMESG000066467.13.003e-5464.12SMESG000066467.1[more]
SMESG000066467.13.570e-5262.22SMESG000066467.1[more]
SMESG000008989.14.000e-5165.29SMESG000008989.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000795 ID=SMED30000795|Name=SMED30000795|organism=Schmidtea mediterranea sexual|type=transcript|length=449bp
CGACACGGACCTTCCATTCGTCGCAATAAAGCGCGAACCCGGCCGGAATC
CGGCGCGGGAAATTAGAGGGCAAGCAGAGTTCCTCCTCGCGCGCTTAGAA
GAGCACCAGAGGCAAACCAAACTCCAAGTCCGGAGGGCACAACAGCATTT
GGATGAAATCAACCGAGACATAGCAAATGGGCTCATCCCAAGTACGAATG
GGTATGTCCCTCCGTACAACACGTCCTTCAATTTAGACGATCCCCGTCTA
AATCTCCCAACGGAAGCGATCAACGTGGTGGTTCCCCGCCAAATTTGGCC
AGAAAGATCAAGGAGAGCAAACGAACCATCCAACACCCATCGCGAACACC
CTTATGCTCGTGGAATTCCGCGAAGGAGTTCGAACCGATAACATCTGAGA
GTTAACTCACCTTGATGATTTTCCAGTGTTTAGTAAAAATATGTTTTAG
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protein sequence of SMED30000795-orf-1

>SMED30000795-orf-1 ID=SMED30000795-orf-1|Name=SMED30000795-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=130bp
DTDLPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQTKLQVRRAQQHL
DEINRDIANGLIPSTNGYVPPYNTSFNLDDPRLNLPTEAINVVVPRQIWP
ERSRRANEPSNTHREHPYARGIPRRSSNR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..28
score: 0.465