SMED30000746

Overview
NameSMED30000746
Smed IDSMED30000746
Length (bp)506
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 SMED30000746 (SMED30000746) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30000746 (SMED30000746) 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 SMED30000746 (SMED30000746) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30000746 (SMED30000746) 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



SMED30000746

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30000746SMESG000024821.1 SMESG000024754.1 SmedASXL_008207SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Category 3 cellSMED30000746SMESG000024821.1 SMESG000024754.1 SmedASXL_008207SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		whole organism asexual adult fluorescence in situ hybridization evidence
parenchymaSMED30000746SMESG000024821.1 SMESG000024754.1 SmedASXL_008207SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
epidermisSMED30000746SMESG000024821.1 SMESG000024754.1 dd_Smed_v4_306_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30000746SMESG000024821.1 SMESG000024754.1 dd_Smed_v4_306_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30000746SMESG000075824.1 SMESG000072099.1 SMESG000064652.1 SMESG000061492.1 SMESG000042033.1 SMESG000038610.1 SMESG000036779.1 SMESG000024821.1 SMESG000024754.1 SMESG000005117.1 SMESG000003422.1 SMESG000000687.1 Contig20277newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30000746SMESG000075824.1 SMESG000072099.1 SMESG000064652.1 SMESG000061492.1 SMESG000042033.1 SMESG000038610.1 SMESG000036779.1 SMESG000024821.1 SMESG000024754.1 SMESG000005117.1 SMESG000003422.1 SMESG000000687.1 Contig20277uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30000746SMESG000024821.1 SMESG000024754.1 Contig50426newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30000746SMESG000024821.1 SMESG000024754.1 Contig50426uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30000746SMESG000024821.1 SMESG000024754.1 dd_Smed_v6_306_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30000746SMESG000024821.1 SMESG000024754.1 OX_Smed_1.0.09211ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30000746SMESG000024821.1 SMESG000024754.1 dd_Smed_v4_306_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Category 4 cellSMED30000746SMESG000024821.1 SMESG000024754.1 dd_Smed_v4_306_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
SMED30000746 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006583:11637..12184 -2440
v31.020245:4350..4897 +2431
v31.034604:531..1078 +2413
Homology
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BLAST of SMED30000746 vs. TrEMBL
Match: I1ZI82 (Uncharacterized protein (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 98.2117 bits (243), Expect = 3.024e-23
Identity = 51/118 (43.22%), Postives = 72/118 (61.02%), Query Frame = 2 
Query:   44 IQIGLLVVLALINVECVSK---SKKAFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKVDSYCDKRYNVLDTHCDGLY 388
            I    +++ +++ V C S     KK F C  +L +ID ECD +Y  LD  CD SY  +H+ CDIKY +LSGRC+ KL+  CI++YG LD  CL +   +   C ++YN +D HCD LY
Sbjct:    1 ILFAAVLIQSMLVVHCASVKAVEKKGF-CSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALY 117
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BLAST of SMED30000746 vs. Planmine SMEST
Match: SMESG000024754.1 (SMESG000024754.1)

HSP 1 Score: 249.98 bits (637), Expect = 1.682e-86
Identity = 128/129 (99.22%), Postives = 128/129 (99.22%), Query Frame = 2 
Query:   32 MKLMIQIGLLVVLALINVECVSKSKKAFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKVDSYCDKRYNVLDTHCDGLYKLQEKCENNS 418
            MKLMIQIGLLVVLALINVECVSKSKKAFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCL AYDKVDSYCDKRYNVLDTHCDGLYKLQEKCENNS
Sbjct:    1 MKLMIQIGLLVVLALINVECVSKSKKAFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLRAYDKVDSYCDKRYNVLDTHCDGLYKLQEKCENNS 129
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BLAST of SMED30000746 vs. Planmine SMEST
Match: SMESG000024821.1 (SMESG000024821.1)

HSP 1 Score: 203.756 bits (517), Expect = 1.594e-68
Identity = 103/103 (100.00%), Postives = 103/103 (100.00%), Query Frame = 2 
Query:  110 AFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKVDSYCDKRYNVLDTHCDGLYKLQEKCENNS 418
            AFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKVDSYCDKRYNVLDTHCDGLYKLQEKCENNS
Sbjct:    6 AFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKVDSYCDKRYNVLDTHCDGLYKLQEKCENNS 108
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BLAST of SMED30000746 vs. Planmine SMEST
Match: SMESG000072142.1 (SMESG000072142.1)

HSP 1 Score: 204.142 bits (518), Expect = 2.212e-68
Identity = 99/129 (76.74%), Postives = 111/129 (86.05%), Query Frame = 2 
Query:   32 MKLMIQIGLLVVLALINVECVSKSKKAFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKVDSYCDKRYNVLDTHCDGLYKLQEKCENNS 418
            MKLMIQIG  + LAL+NVECVSKSK + DCLTMLDKID ECD++YLVLD HCD  YA LHK CDI YD LSGRCK  +SMRCI KYG+LD KCLGAYD+VD++CDKRYNVLDTHCD LYK+QEKCE+NS
Sbjct:    1 MKLMIQIGFFMTLALLNVECVSKSKNSADCLTMLDKIDRECDRKYLVLDNHCDSRYAHLHKTCDINYDKLSGRCKNNMSMRCILKYGRLDRKCLGAYDRVDTFCDKRYNVLDTHCDELYKIQEKCEDNS 129
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BLAST of SMED30000746 vs. Planmine SMEST
Match: SMESG000072142.1 (SMESG000072142.1)

HSP 1 Score: 198.749 bits (504), Expect = 2.868e-66
Identity = 96/126 (76.19%), Postives = 108/126 (85.71%), Query Frame = 2 
Query:   41 MIQIGLLVVLALINVECVSKSKKAFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKVDSYCDKRYNVLDTHCDGLYKLQEKCENNS 418
            MIQIG  + LAL+NVECVSKSK + DCLTMLDKID ECD++YLVLD HCD  YA LHK CDI YD LSGRCK  +SMRCI KYG+LD KCLGAYD+VD++CDKRYNVLDTHCD LYK+QEKCE+NS
Sbjct:    1 MIQIGFFMTLALLNVECVSKSKNSADCLTMLDKIDRECDRKYLVLDNHCDSRYAHLHKTCDINYDKLSGRCKNNMSMRCILKYGRLDRKCLGAYDRVDTFCDKRYNVLDTHCDELYKIQEKCEDNS 126
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BLAST of SMED30000746 vs. Planmine SMEST
Match: SMESG000021388.1 (SMESG000021388.1)

HSP 1 Score: 114.39 bits (285), Expect = 6.853e-33
Identity = 62/136 (45.59%), Postives = 79/136 (58.09%), Query Frame = 2 
Query:   38 LMIQIGLLVVLALINVECVSKSK------------KAFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKVDSYCDKRYNVLDTHCDGLYKLQEKCE 409
            L I     V LA++ V C+   K            K   C   LDK+D ECDK+Y +LD  C+ SY  L+K CD+ Y  LSGRC+ +LS  CI+KYGKLD  C+ AY ++D  CDKRY  LD +CD LY  +E CE
Sbjct:    2 LRIIYAFSVTLAVLRVNCLESPKVFKDEIVNNYEKKWMKCTKFLDKVDAECDKKYDLLDNDCNGSYKQLYKTCDVNYLKLSGRCQMRLSKNCIKKYGKLDRHCIKAYGEIDESCDKRYAKLDPYCDALYTKEENCE 137
The following BLAST results are available for this feature:
BLAST of SMED30000746 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 SMED30000746 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 SMED30000746 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 SMED30000746 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 SMED30000746 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 SMED30000746 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 SMED30000746 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 SMED30000746 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZI823.024e-2343.22Uncharacterized protein (Fragment) OS=Schmidtea me... [more]
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BLAST of SMED30000746 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 SMED30000746 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 SMED30000746 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 SMED30000746 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 SMED30000746 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 SMED30000746 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000024754.11.682e-8699.22SMESG000024754.1[more]
SMESG000024821.11.594e-68100.00SMESG000024821.1[more]
SMESG000072142.12.212e-6876.74SMESG000072142.1[more]
SMESG000072142.12.868e-6676.19SMESG000072142.1[more]
SMESG000021388.16.853e-3345.59SMESG000021388.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000746 ID=SMED30000746|Name=SMED30000746|organism=Schmidtea mediterranea sexual|type=transcript|length=506bp
TGGATAGACAATTCAATAACAAATATCAACCATGAAATTGATGATTCAGA
TCGGACTTCTCGTGGTGTTGGCATTGATCAATGTCGAATGCGTGAGCAAG
TCAAAGAAAGCTTTTGATTGCCTGACGATGTTGGATAAGATTGACAATGA
ATGTGACAAGAGATATTTGGTACTCGATGGCCACTGTGACAGAAGTTACG
CCGACTTACACAAGAATTGCGATATTAAATACGACCTATTAAGTGGTCGT
TGCAAAGGGAAATTATCAATGCGTTGCATCAGAAAGTACGGCAAACTCGA
TGGAAAATGCTTGGGAGCTTATGACAAGGTTGATTCCTACTGTGACAAAA
GATATAATGTCTTGGACACTCATTGCGATGGCTTGTATAAGCTGCAGGAG
AAATGTGAAAATAATAGTTAGAAAAAGTTATGAATAATTCAACTGCTTGA
AGACTTGCGATAATTTTTGTATTTGAATACAATTTTCTTTTAGGTCAAAA
AAAAAG
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protein sequence of SMED30000746-orf-1

>SMED30000746-orf-1 ID=SMED30000746-orf-1|Name=SMED30000746-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=130bp
MKLMIQIGLLVVLALINVECVSKSKKAFDCLTMLDKIDNECDKRYLVLDG
HCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKV
DSYCDKRYNVLDTHCDGLYKLQEKCENNS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000034epidermis
PLANA:0000035Category 3 cell
PLANA:0000418head
PLANA:0002032epidermal cell
PLANA:0002142parenchyma
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..20
score: 0.702