SMED30012172

Overview
NameSMED30012172
Smed IDSMED30012172
Length (bp)450
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 SMED30012172 (SMED30012172) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30012172 (SMED30012172) 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



SMED30012172

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
cephalic gangliaSMED30012172h1SMcG0007409 dd_Smed_v4_13852_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30012172h1SMcG0007409 dd_Smed_v4_13852_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
SMED30012172 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.013132:1215..1664 +2241
v31.016887:10939..11382 +2161
Homology
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BLAST of SMED30012172 vs. Planmine SMEST
Match: SMESG000067800.1 (SMESG000067800.1)

HSP 1 Score: 260.766 bits (665), Expect = 4.689e-91
Identity = 130/135 (96.30%), Postives = 133/135 (98.52%), Query Frame = 3 
Query:   45 MHLSSDHLYQTYSSEDCDDSYYLTPITSDHSCCFDFITESVEEGSRFLGISDSHEYLASHTESESVSISNSWDENENKYYDSSLDIYLDCPSAYSYSDPNNSRNIIYDETHYNELNCQGHRSMYKVECHLSDGMS 449
            MHLSSDHLYQTYSSEDCDDSYYLTPITSDHSCCFDFITESVEEGSRFLGISDSHEYLAS TESESVSISNSWDENENKYY+SSLDIYLDCPSAYSYSDPNNSRNIIY+ETHY ELNCQGHRS+YKVECHLSDGMS
Sbjct:    1 MHLSSDHLYQTYSSEDCDDSYYLTPITSDHSCCFDFITESVEEGSRFLGISDSHEYLASPTESESVSISNSWDENENKYYNSSLDIYLDCPSAYSYSDPNNSRNIIYEETHYKELNCQGHRSIYKVECHLSDGMS 135
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BLAST of SMED30012172 vs. Planmine SMEST
Match: SMESG000067796.1 (SMESG000067796.1)

HSP 1 Score: 205.682 bits (522), Expect = 2.428e-69
Identity = 104/107 (97.20%), Postives = 104/107 (97.20%), Query Frame = 3 
Query:    3 LDQGLCDLPSDYFEMHLSSDHLYQTYSSEDCDDSYYLTPITSDHSCCFDFITESVEEGSRFLGISDSHEYLASHTESESVSISNSWDENENKYYDSSLDIYLDCPSA 323
            LDQGLCDLPSDYFEMHLSSDHLYQTYSSEDCDDSYYLTPITSDHSCCFDFITES EE SRFLGISDSHEYLASHTESESVSISNSWDENENKYYDSSLDIYLDCPS 
Sbjct:   23 LDQGLCDLPSDYFEMHLSSDHLYQTYSSEDCDDSYYLTPITSDHSCCFDFITESAEECSRFLGISDSHEYLASHTESESVSISNSWDENENKYYDSSLDIYLDCPSG 129
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BLAST of SMED30012172 vs. Planmine SMEST
Match: SMESG000014110.1 (SMESG000014110.1)

HSP 1 Score: 126.716 bits (317), Expect = 1.151e-37
Identity = 70/143 (48.95%), Postives = 98/143 (68.53%), Query Frame = 3 
Query:   21 DLPSDYFEMHLSSDHLYQTYSSEDCDDSYYLTPITSDHSCCFDFITESVEEGSRFLGISDSHEYLASHTESESVSISNSWDENENKYYDSSLDIYLDCPSAYSYSDPNNSRNIIYDETHYNELNCQGHRSMYKVECHLSDGMS 449
            D    + E  LSSDH+Y +   E+CDDSYYLTP+TSD+S  FDF T+  E  +R+L I +++    S  +SE+ SISNS +E EN  Y+SS +I+ DCPS YS+ DPN S+NI  +E+ + E +C+    +Y+VECHLSDG+S
Sbjct:   25 DFQFGFSERSLSSDHIYSSCLFEECDDSYYLTPVTSDNSYSFDFFTKISESNTRYLDIVENNT-SGSSADSETSSISNSCNEKENDNYESSYNIHQDCPSIYSFRDPNISKNISGNESQFEESDCKSDTPIYRVECHLSDGVS 166
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BLAST of SMED30012172 vs. Planmine SMEST
Match: SMESG000034183.1 (SMESG000034183.1)

HSP 1 Score: 92.0485 bits (227), Expect = 2.824e-24
Identity = 60/133 (45.11%), Postives = 84/133 (63.16%), Query Frame = 3 
Query:   51 LSSDHLYQTYSSEDCDDSYYLTPITSDHSCCFDFITESVEEGSRFLGISDSHEYLASHTESESVSISNSWDENENKYYDSSLDIYLDCPSAYSYSDPNNSRNIIYDETHYNELNCQGHRSMYKVECHLSDGMS 449
            LSSD+ Y + S E  DDSYYLT  TSD+S   DFI++  E  S  + IS +H   +S  +SE+ S SNS++ ++N             PS YSYSDPN S+N   +E+H  EL+C+ H+ +Y++ECHLSDG+S
Sbjct:   30 LSSDYSYPSCSFEKFDDSYYLTKTTSDYSYGLDFISKKSENNSSLVDISGNHTNCSSSADSETSSFSNSFNIHQNG------------PSIYSYSDPNTSQNASDNESHCEELDCKSHKPIYRIECHLSDGVS 150
The following BLAST results are available for this feature:
BLAST of SMED30012172 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 SMED30012172 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 SMED30012172 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 SMED30012172 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 SMED30012172 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 SMED30012172 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 SMED30012172 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 SMED30012172 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 SMED30012172 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 SMED30012172 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 SMED30012172 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 SMED30012172 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 SMED30012172 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 SMED30012172 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000067800.14.689e-9196.30SMESG000067800.1[more]
SMESG000067796.12.428e-6997.20SMESG000067796.1[more]
SMESG000014110.11.151e-3748.95SMESG000014110.1[more]
SMESG000034183.12.824e-2445.11SMESG000034183.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012172 ID=SMED30012172|Name=SMED30012172|organism=Schmidtea mediterranea sexual|type=transcript|length=450bp
ATCTTGATCAAGGACTTTGTGATCTTCCATCTGATTATTTTGAAATGCAT
TTGTCTTCGGATCATTTATATCAGACATATTCATCAGAGGATTGTGATGA
TTCTTATTATCTGACTCCGATAACCTCTGATCATTCTTGCTGTTTTGACT
TCATCACAGAAAGCGTTGAAGAAGGTTCACGTTTTTTGGGCATCTCTGAC
AGCCACGAATACCTTGCTTCACATACTGAATCAGAGTCAGTTTCAATTTC
CAATAGTTGGGATGAAAACGAAAATAAATATTACGATTCATCGCTTGACA
TTTATCTAGATTGTCCCTCGGCATATTCCTATAGCGATCCGAATAACTCG
CGGAATATTATTTACGATGAAACCCACTATAACGAGTTGAACTGTCAAGG
CCACAGATCTATGTATAAGGTGGAATGCCATTTGTCTGACGGAATGTCCT
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protein sequence of SMED30012172-orf-1

>SMED30012172-orf-1 ID=SMED30012172-orf-1|Name=SMED30012172-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=149bp
LDQGLCDLPSDYFEMHLSSDHLYQTYSSEDCDDSYYLTPITSDHSCCFDF
ITESVEEGSRFLGISDSHEYLASHTESESVSISNSWDENENKYYDSSLDI
YLDCPSAYSYSDPNNSRNIIYDETHYNELNCQGHRSMYKVECHLSDGMS
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