SMED30030213

Overview
NameSMED30030213
Smed IDSMED30030213
Length (bp)560
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 SMED30030213 (SMED30030213) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30030213 (SMED30030213) 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 SMED30030213 (SMED30030213) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30030213 (SMED30030213) 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



SMED30030213

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 cellSMED30030213h1SMcG0006120 SmedASXL_055178SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
cephalic gangliaSMED30030213h1SMcG0006120 dd_Smed_v4_4581_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30030213h1SMcG0006120 dd_Smed_v4_4581_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30030213h1SMcG0006120 dd_Smed_v4_4581_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
SMED30030213 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003913:28922..29610 +2667
Homology
[Close]
BLAST of SMED30030213 vs. Ensembl Nematostella
Match: EDO37175 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SGL7])

HSP 1 Score: 50.8322 bits (120), Expect = 7.057e-8
Identity = 26/71 (36.62%), Postives = 37/71 (52.11%), Query Frame = 1 
Query:   43 MSTSYGANGETLVRCPINPREILKLRSLQTHLFKVHKDC--TDFVRCPYNFSHVIKIHEIEKHYDECRDRT 249
            M+   G NGE LV CP +P  I+  +  Q H+ K  K+    DFV CP+N  H++   ++  H   C DR 
Sbjct:    1 MALPVGPNGEMLV-CPYDPVHIISAKRFQYHILKCRKNHPDKDFVTCPFNAKHIMLRPDLRHHIARCPDRA 70
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BLAST of SMED30030213 vs. Planmine SMEST
Match: SMESG000012962.1 (SMESG000012962.1)

HSP 1 Score: 290.426 bits (742), Expect = 4.355e-102
Identity = 138/138 (100.00%), Postives = 138/138 (100.00%), Query Frame = 1 
Query:   43 MSTSYGANGETLVRCPINPREILKLRSLQTHLFKVHKDCTDFVRCPYNFSHVIKIHEIEKHYDECRDRTLDQDTKFPIVTGYVGKPVYGGTDYFETHDTFNDMNKKTYENLVMKTPMTNLPFIESSLQRGRMERRGVN 456
            MSTSYGANGETLVRCPINPREILKLRSLQTHLFKVHKDCTDFVRCPYNFSHVIKIHEIEKHYDECRDRTLDQDTKFPIVTGYVGKPVYGGTDYFETHDTFNDMNKKTYENLVMKTPMTNLPFIESSLQRGRMERRGVN
Sbjct:    1 MSTSYGANGETLVRCPINPREILKLRSLQTHLFKVHKDCTDFVRCPYNFSHVIKIHEIEKHYDECRDRTLDQDTKFPIVTGYVGKPVYGGTDYFETHDTFNDMNKKTYENLVMKTPMTNLPFIESSLQRGRMERRGVN 138
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BLAST of SMED30030213 vs. Planmine SMEST
Match: SMESG000027366.1 (SMESG000027366.1)

HSP 1 Score: 224.172 bits (570), Expect = 6.970e-76
Identity = 99/138 (71.74%), Postives = 122/138 (88.41%), Query Frame = 1 
Query:   43 MSTSYGANGETLVRCPINPREILKLRSLQTHLFKVHKDCTDFVRCPYNFSHVIKIHEIEKHYDECRDRTLDQDTKFPIVTGYVGKPVYGGTDYFETHDTFNDMNKKTYENLVMKTPMTNLPFIESSLQRGRMERRGVN 456
            M+TSYG++G+TL+RCPINP EILKL+SLQ HL KVHK+ TDFVRC YNFSH+IKIHEI+KHY+ECRDRTL+QDT  PIV G+VGKP+YGGTDYFET DTFN++N +TY+NL+++ P+TNLP    SL+RGR ERRG+N
Sbjct:    1 MTTSYGSDGDTLIRCPINPTEILKLKSLQNHLLKVHKNNTDFVRCCYNFSHIIKIHEIQKHYEECRDRTLNQDTNLPIVAGFVGKPIYGGTDYFETRDTFNNINNETYQNLIVRNPVTNLPVSGKSLKRGRNERRGIN 138
The following BLAST results are available for this feature:
BLAST of SMED30030213 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 SMED30030213 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 SMED30030213 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 SMED30030213 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 SMED30030213 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 SMED30030213 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 SMED30030213 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 SMED30030213 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 SMED30030213 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 SMED30030213 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 SMED30030213 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 SMED30030213 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO371757.057e-836.62Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30030213 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 SMED30030213 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000012962.14.355e-102100.00SMESG000012962.1[more]
SMESG000027366.16.970e-7671.74SMESG000027366.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030213 ID=SMED30030213|Name=SMED30030213|organism=Schmidtea mediterranea sexual|type=transcript|length=560bp
CCGATCTTTTGAATAATTATTTTGAATAAGAATTCATTTTTTATGTCTAC
ATCATACGGTGCTAATGGTGAAACTCTTGTTCGATGTCCTATTAATCCTA
GAGAAATATTAAAACTGCGGAGTCTTCAAACTCACTTGTTTAAAGTTCAC
AAAGACTGTACTGATTTTGTTCGATGTCCTTACAATTTTAGTCATGTCAT
TAAAATACATGAAATAGAAAAACATTACGATGAGTGCCGTGATCGAACGC
TAGATCAAGATACTAAATTTCCTATTGTTACTGGATATGTTGGGAAGCCA
GTTTATGGCGGTACTGATTATTTTGAAACTCACGATACATTTAATGACAT
GAACAAGAAAACTTACGAAAATTTGGTTATGAAAACTCCAATGACTAATT
TGCCTTTTATTGAATCATCATTACAAAGAGGTAGAATGGAACGACGTGGA
GTAAATTAATTTGAATTGATGTTAATAGTGTTATGTATTCTATAATATAA
TTTTTATGTTGATATTTTCATTTTCGTAATTGTTTCCATTGAATTTTCTA
TGATTTTTTG
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protein sequence of SMED30030213-orf-1

>SMED30030213-orf-1 ID=SMED30030213-orf-1|Name=SMED30030213-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=139bp
MSTSYGANGETLVRCPINPREILKLRSLQTHLFKVHKDCTDFVRCPYNFS
HVIKIHEIEKHYDECRDRTLDQDTKFPIVTGYVGKPVYGGTDYFETHDTF
NDMNKKTYENLVMKTPMTNLPFIESSLQRGRMERRGVN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000429neoblast
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR022776TRM13/UPF0224_CHHC_Znf_dom
IPR036236Znf_C2H2_sf
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR022776TRM13/UPF0224 family, U11-48K-like CHHC zinc finger domainPROSITEPS51800ZF_CHHC_U11_48Kcoord: 12..39
score: 8.722
IPR022776TRM13/UPF0224 family, U11-48K-like CHHC zinc finger domainPROSITEPS51800ZF_CHHC_U11_48Kcoord: 42..69
score: 13.208
IPR036236Zinc finger C2H2 superfamilySUPERFAMILYSSF57667beta-beta-alpha zinc fingerscoord: 41..71