SMED30027585

Overview
NameSMED30027585
Smed IDSMED30027585
Length (bp)447
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 SMED30027585 (SMED30027585) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30027585 (SMED30027585) 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.
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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



SMED30027585

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
gutSMED30027585 dd_Smed_v4_28726_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30027585 dd_Smed_v4_28726_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30027585 dd_Smed_v4_28726_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30027585 dd_Smed_v4_28726_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30027585 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001701:73348..73942 +2224
v31.002468:41408..42005 +1776
v31.005148:8886..9477 -1680
v31.001513:57058..57642 +1618
v31.015084:9652..10232 +1604
v31.019025:2372..2952 -1586
v31.003422:15008..15580 +1581
v31.004829:31965..32538 +1580
v31.000338:96294..96868 +1031
Homology
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BLAST of SMED30027585 vs. Planmine SMEST
Match: SMESG000003988.1 (SMESG000003988.1)

HSP 1 Score: 92.4337 bits (228), Expect = 4.768e-29
Identity = 44/81 (54.32%), Postives = 60/81 (74.07%), Query Frame = 1 
Query:  211 DRGYTLSTFGSKKWLYWNMRQDDEVEFPSIAIKREPGKNPVREIRHQTEVTLH-LKYMERKFGWQANMMR--RRLARINAD 444
            DRGYTLST+G  +W + NM QDD+V FPSIAIKREPG+NPVREIR + EVTL  L+++E+K G  ++     ++L  +N +
Sbjct:  874 DRGYTLSTYGRNEWPHRNMNQDDKVVFPSIAIKREPGRNPVREIRQKAEVTLQRLEHLEKKHGGDSDTRSELKKLHHVNTE 954

HSP 2 Score: 52.373 bits (124), Expect = 4.768e-29
Identity = 31/70 (44.29%), Postives = 38/70 (54.29%), Query Frame = 2 
Query:   17 KKRDNRSANQKLVKSDQPL-----VGENPDYDQIDHGQGLNPTELEWSDDSRVTLTVPGRYAAQYHQVLW 211
            KK  NR+  +  V S Q +          +   +   + LN TE EWSDDSRV LTVP R+AAQY Q LW
Sbjct:  804 KKEKNRNVLRHTVASKQKMRDKVNFKSRTERQPMKFSKVLNSTEFEWSDDSRVALTVPVRHAAQYRQALW 873
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BLAST of SMED30027585 vs. Planmine SMEST
Match: SMESG000010307.1 (SMESG000010307.1)

HSP 1 Score: 85.5001 bits (210), Expect = 7.620e-23
Identity = 41/81 (50.62%), Postives = 60/81 (74.07%), Query Frame = 1 
Query:  211 DRGYTLSTFGSKKWLYWN-MRQDDEVEFPSIAIKREPGKNPVREIRHQTEVTL-HLKYMERKFGWQANMMRRRLARINADI 447
            D  Y+LST+G+ +W   + +R D++VE PS+AIKREPG+N  R+IRH+ EV L    ++ERK+ W+A++ R+RL RIN DI
Sbjct:   85 DGVYSLSTYGTSEWPNRSRIRHDEDVELPSLAIKREPGRNTARKIRHEAEVALQQFDHLERKYRWKASLQRKRLMRINKDI 165

HSP 2 Score: 38.5058 bits (88), Expect = 7.620e-23
Identity = 13/28 (46.43%), Postives = 18/28 (64.29%), Query Frame = 2 
Query:  137 EWSDDSRVTLTVPGRYAAQYHQVLWIAV 220
            +W DD R TL +P ++A +Y Q LW  V
Sbjct:   60 QWKDDERTTLIIPSKFAGRYRQALWDGV 87
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BLAST of SMED30027585 vs. Planmine SMEST
Match: SMESG000010307.1 (SMESG000010307.1)

HSP 1 Score: 85.1149 bits (209), Expect = 7.875e-23
Identity = 41/81 (50.62%), Postives = 60/81 (74.07%), Query Frame = 1 
Query:  211 DRGYTLSTFGSKKWLYWN-MRQDDEVEFPSIAIKREPGKNPVREIRHQTEVTL-HLKYMERKFGWQANMMRRRLARINADI 447
            D  Y+LST+G+ +W   + +R D++VE PS+AIKREPG+N  R+IRH+ EV L    ++ERK+ W+A++ R+RL RIN DI
Sbjct:   83 DGVYSLSTYGTSEWPNRSRIRHDEDVELPSLAIKREPGRNTARKIRHEAEVALQQFDHLERKYRWKASLQRKRLMRINKDI 163

HSP 2 Score: 38.5058 bits (88), Expect = 7.875e-23
Identity = 13/28 (46.43%), Postives = 18/28 (64.29%), Query Frame = 2 
Query:  137 EWSDDSRVTLTVPGRYAAQYHQVLWIAV 220
            +W DD R TL +P ++A +Y Q LW  V
Sbjct:   58 QWKDDERTTLIIPSKFAGRYRQALWDGV 85
[Close]
BLAST of SMED30027585 vs. Planmine SMEST
Match: SMESG000003895.1 (SMESG000003895.1)

HSP 1 Score: 90.5077 bits (223), Expect = 2.884e-22
Identity = 43/80 (53.75%), Postives = 63/80 (78.75%), Query Frame = 1 
Query:  211 DRGYTLSTFGSKKWLYWNMRQDDEVEFPSIAIKREPGKNPVREIRHQTEVTLH-LKYMERKFGWQANMMRRRLARINADI 447
            DR Y+L+T G+ +W   ++ +D+E E PS+AIKREPG+NP R+IR + + TL+ L+ +++KF W+ANM RR+LARINADI
Sbjct:  162 DRQYSLATCGNDEWPCRSISRDNETELPSVAIKREPGRNPSRQIRQKAKFTLYRLENLKKKFRWRANMARRKLARINADI 241
[Close]
BLAST of SMED30027585 vs. Planmine SMEST
Match: SMESG000050791.1 (SMESG000050791.1)

HSP 1 Score: 85.1149 bits (209), Expect = 1.013e-21
Identity = 39/60 (65.00%), Postives = 50/60 (83.33%), Query Frame = 1 
Query:  271 QDDEVEFPSIAIKREPGKNPVREIRHQTEVTL-HLKYMERKFGWQANMMRRRLARINADI 447
            QD+EVE PS++IKREPG+NP REIRH+ EV L   +++E KF W+AN+ RRRLARIN+DI
Sbjct:    6 QDEEVEIPSLSIKREPGRNPAREIRHEAEVMLQQFEHLEMKFRWKANLQRRRLARINSDI 65
The following BLAST results are available for this feature:
BLAST of SMED30027585 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 SMED30027585 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 SMED30027585 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 SMED30027585 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 SMED30027585 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 SMED30027585 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 SMED30027585 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 SMED30027585 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 SMED30027585 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 SMED30027585 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 SMED30027585 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 SMED30027585 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 SMED30027585 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 SMED30027585 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000003988.14.768e-2954.32SMESG000003988.1[more]
SMESG000010307.17.620e-2350.62SMESG000010307.1[more]
SMESG000010307.17.875e-2350.62SMESG000010307.1[more]
SMESG000003895.12.884e-2253.75SMESG000003895.1[more]
SMESG000050791.11.013e-2165.00SMESG000050791.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027585 ID=SMED30027585|Name=SMED30027585|organism=Schmidtea mediterranea sexual|type=transcript|length=447bp
GGATAACACAGCCAACAAAAAACGAGACAATAGAAGTGCGAACCAAAAAC
TAGTCAAATCCGACCAACCTTTGGTGGGAGAAAATCCAGACTACGACCAG
ATCGACCATGGACAAGGATTAAACCCAACCGAGCTCGAGTGGTCCGACGA
TTCCCGAGTTACTCTGACTGTTCCAGGTCGATATGCAGCACAGTACCACC
AAGTTCTCTGGATCGCGGTTATACCTTATCTACATTCGGAAGTAAAAAAT
GGCTATACTGGAACATGCGACAGGACGATGAGGTGGAATTCCCAAGCATT
GCCATAAAACGGGAACCGGGTAAAAACCCCGTCAGAGAAATCCGGCACCA
AACTGAAGTTACGTTACATCTGAAATACATGGAGAGAAAATTCGGCTGGC
AAGCTAACATGATGAGGAGACGGCTGGCACGAATAAACGCCGACATC
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protein sequence of SMED30027585-orf-1

>SMED30027585-orf-1 ID=SMED30027585-orf-1|Name=SMED30027585-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
DNTANKKRDNRSANQKLVKSDQPLVGENPDYDQIDHGQGLNPTELEWSDD
SRVTLTVPGRYAAQYHQVLWIAVIPYLHSEVKNGYTGTCDRTMRWNSQAL
P*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0003116parenchymal cell