SMED30023339

Overview
NameSMED30023339
Smed IDSMED30023339
Length (bp)991
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 SMED30023339 (SMED30023339) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023339 (SMED30023339) 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 SMED30023339 (SMED30023339) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023339 (SMED30023339) 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



SMED30023339

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30023339SMESG000045132.1 dd_Smed_v4_182_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023339SMESG000045132.1 dd_Smed_v4_182_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30023339SMESG000045132.1 dd_Smed_v6_182_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
goblet cellSMED30023339SMESG000045132.1 dd_Smed_v6_182_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
reproductive organSMED30023339SMESG000045132.1 Contig48438newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30023339SMESG000045132.1 Contig48438uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30023339 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011435:19127..20117 -4946
Homology
[Close]
BLAST of SMED30023339 vs. TrEMBL
Match: A0A419PHI1 (Uncharacterized protein OS=Clonorchis sinensis OX=79923 GN=CSKR_1389s PE=4 SV=1)

HSP 1 Score: 99.7525 bits (247), Expect = 1.516e-19
Identity = 45/97 (46.39%), Postives = 62/97 (63.92%), Query Frame = 2 
Query:  680 QLDIPMIEYTFYVTDIEICRRPLIDKRVDSIVANCNCLLKIHGQPICSSFANQQTRKVFYKGNPVIPVTIKSYSMSSLRKCIGRLDLQFPYFNVKAF 970
            Q ++  IEYTFY+ D E  +RP  D+RV++I     C + +H  P          + V+YKG  V+PVTI S +M SL++CI RLD+Q+PYFNVKAF
Sbjct:  366 QQNLSRIEYTFYINDTEAYQRPFYDRRVEAIARASQCSISLHKPPPGH-------KPVYYKGIRVLPVTISSRTMVSLKRCIARLDMQYPYFNVKAF 455
[Close]
BLAST of SMED30023339 vs. TrEMBL
Match: A0A074ZW82 (Uncharacterized protein (Fragment) OS=Opisthorchis viverrini OX=6198 GN=T265_12942 PE=4 SV=1)

HSP 1 Score: 99.7525 bits (247), Expect = 1.620e-19
Identity = 45/97 (46.39%), Postives = 62/97 (63.92%), Query Frame = 2 
Query:  680 QLDIPMIEYTFYVTDIEICRRPLIDKRVDSIVANCNCLLKIHGQPICSSFANQQTRKVFYKGNPVIPVTIKSYSMSSLRKCIGRLDLQFPYFNVKAF 970
            Q ++  IEYTFY+ D E  +RP  D+RV++I     C + +H  P          + V+YKG  V+PVTI S +M SL++CI RLD+Q+PYFNVKAF
Sbjct:  369 QQNLSRIEYTFYINDTEAYQRPFYDRRVEAIARASQCSISLHKPPPGH-------KPVYYKGIRVLPVTISSRTMVSLKRCIARLDMQYPYFNVKAF 458
[Close]
BLAST of SMED30023339 vs. TrEMBL
Match: A0A4V6RGN9 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_010519 PE=4 SV=1)

HSP 1 Score: 99.3673 bits (246), Expect = 1.818e-19
Identity = 45/97 (46.39%), Postives = 62/97 (63.92%), Query Frame = 2 
Query:  680 QLDIPMIEYTFYVTDIEICRRPLIDKRVDSIVANCNCLLKIHGQPICSSFANQQTRKVFYKGNPVIPVTIKSYSMSSLRKCIGRLDLQFPYFNVKAF 970
            Q ++  IEYTFY+ D E  +RP  D+RV++I     C + +H  P          + V+YKG  V+PVTI S +M SL++CI RLD+Q+PYFNVKAF
Sbjct:  369 QQNLSRIEYTFYINDTEAYQRPFYDRRVEAIARASQCSISLHKPPPGH-------KPVYYKGIRVLPVTISSRTMVSLKRCIARLDMQYPYFNVKAF 458
[Close]
BLAST of SMED30023339 vs. TrEMBL
Match: A0A183AG47 (Uncharacterized protein OS=Echinostoma caproni OX=27848 GN=ECPE_LOCUS5932 PE=4 SV=1)

HSP 1 Score: 97.8265 bits (242), Expect = 5.816e-19
Identity = 44/103 (42.72%), Postives = 66/103 (64.08%), Query Frame = 2 
Query:  674 SDQLDIP----MIEYTFYVTDIEICRRPLIDKRVDSIVANCNCLLKIHGQPICSSFANQQTRKVFYKGNPVIPVTIKSYSMSSLRKCIGRLDLQFPYFNVKAF 970
            +D+ D P     IEYTFY+ D E  +RP  D+RV++I     C + +H  P       +  + ++YKGN V+PVTI + +M +L++C+ RLD+Q+PYFNVKAF
Sbjct:  370 TDRPDKPPCLSRIEYTFYIHDTEAYQRPFFDRRVEAIARASQCNICLHKPP-------RGQKPIYYKGNRVLPVTISARTMVTLKRCMARLDMQYPYFNVKAF 465
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BLAST of SMED30023339 vs. TrEMBL
Match: A0A183WG92 (Uncharacterized protein OS=Trichobilharzia regenti OX=157069 GN=TRE_LOCUS11145 PE=4 SV=1)

HSP 1 Score: 97.4413 bits (241), Expect = 1.224e-18
Identity = 44/92 (47.83%), Postives = 62/92 (67.39%), Query Frame = 2 
Query:  698 IEYTFYVTDIEICRRPLIDKRVDSIVANCNCLLKIH-GQPICSSFANQQTRKVFYKGNPVIPVTIKSYSMSSLRKCIGRLDLQFPYFNVKAF 970
            IEYTFY+ D E C+RP  D+RV++I     C + +H  QP         ++ +FYKG  V+PVTI + +M SL++C+ RLD+Q+PYFNVKAF
Sbjct:  413 IEYTFYINDTESCQRPFYDRRVEAIARASQCSICLHRPQP--------GSKPIFYKGIRVLPVTIFARTMISLKRCLARLDMQYPYFNVKAF 496
[Close]
BLAST of SMED30023339 vs. Planmine SMEST
Match: SMESG000045132.1 (SMESG000045132.1)

HSP 1 Score: 567.77 bits (1462), Expect = 0.000e+0
Identity = 308/309 (99.68%), Postives = 309/309 (100.00%), Query Frame = 2 
Query:   53 MGNCLLCRLRLLESKSNTRCVQTIAAPLINSKLKSNEKKSGDCKKSANINFRCCSSNHLSTQSESINNSVASYNKTYKELFNENQEKDIDRNNNRHVSHASSKYTDISLFNNASSHSNSKKLSTAIPKSINLKRKKRTINNKHVFCDSSLETESNSNDSTQCEISQKSLTKYPRQQSNHLFHXXXXXXXXXXXXXXKVELSDLKLVKSDQLDIPMIEYTFYVTDIEICRRPLIDKRVDSIVANCNCLLKIHGQPICSSFANQQTRKVFYKGNPVIPVTIKSYSMSSLRKCIGRLDLQFPYFNVKAFLNS 979
            MGNCLLCRLRLLESKSNTRCVQTIAAPLINSKLKSNEKKSG+CKKSANINFRCCSSNHLSTQSESINNSVASYNKTYKELFNENQEKDIDRNNNRHVSHASSKYTDISLFNNASSHSNSKKLSTAIPKSINLKRKKRTINNKHVFCDSSLETESNSNDSTQCEISQKSLTKYPRQQSNHLFHISRIPPPSPVPSRRKVELSDLKLVKSDQLDIPMIEYTFYVTDIEICRRPLIDKRVDSIVANCNCLLKIHGQPICSSFANQQTRKVFYKGNPVIPVTIKSYSMSSLRKCIGRLDLQFPYFNVKAFLNS
Sbjct:    1 MGNCLLCRLRLLESKSNTRCVQTIAAPLINSKLKSNEKKSGECKKSANINFRCCSSNHLSTQSESINNSVASYNKTYKELFNENQEKDIDRNNNRHVSHASSKYTDISLFNNASSHSNSKKLSTAIPKSINLKRKKRTINNKHVFCDSSLETESNSNDSTQCEISQKSLTKYPRQQSNHLFHISRIPPPSPVPSRRKVELSDLKLVKSDQLDIPMIEYTFYVTDIEICRRPLIDKRVDSIVANCNCLLKIHGQPICSSFANQQTRKVFYKGNPVIPVTIKSYSMSSLRKCIGRLDLQFPYFNVKAFLNS 309
[Close]
BLAST of SMED30023339 vs. Planmine SMEST
Match: SMESG000070717.1 (SMESG000070717.1)

HSP 1 Score: 97.0561 bits (240), Expect = 1.215e-22
Identity = 42/92 (45.65%), Postives = 60/92 (65.22%), Query Frame = 2 
Query:  698 IEYTFYVTDIEICRRPLIDKRVDSIVANCNCLLKIHGQPICSSFANQQTRKVFYKGNPVIPVTIKSYSMSSLRKCIGRLDLQFPYFNVKAFL 973
            I+YTFYV D +IC +P  D+R+ +I   C C +  H +      A++  + ++YKG PV PVTI S  M+ L++C+G +D QFPYFN KAFL
Sbjct:  265 IQYTFYVDDNDICTKPFYDRRMVAIAKTCRCRIYFHAK------ADEAEKPLYYKGKPVRPVTITSPDMACLKRCLGSIDSQFPYFNCKAFL 350
The following BLAST results are available for this feature:
BLAST of SMED30023339 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 SMED30023339 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 SMED30023339 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 SMED30023339 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 SMED30023339 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 SMED30023339 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 SMED30023339 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 SMED30023339 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A419PHI11.516e-1946.39Uncharacterized protein OS=Clonorchis sinensis OX=... [more]
A0A074ZW821.620e-1946.39Uncharacterized protein (Fragment) OS=Opisthorchis... [more]
A0A4V6RGN91.818e-1946.39Uncharacterized protein OS=Opisthorchis felineus O... [more]
A0A183AG475.816e-1942.72Uncharacterized protein OS=Echinostoma caproni OX=... [more]
A0A183WG921.224e-1847.83Uncharacterized protein OS=Trichobilharzia regenti... [more]
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BLAST of SMED30023339 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 SMED30023339 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 SMED30023339 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 SMED30023339 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 SMED30023339 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 SMED30023339 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000045132.10.000e+099.68SMESG000045132.1[more]
SMESG000070717.11.215e-2245.65SMESG000070717.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023339 ID=SMED30023339|Name=SMED30023339|organism=Schmidtea mediterranea sexual|type=transcript|length=991bp
ACATTAAGCATTGGATAAATGATATTAATCAATTGGATCAATTAATTAGA
CTATGGGAAATTGTCTACTATGCAGATTGAGATTATTGGAATCAAAATCA
AACACTCGTTGTGTGCAAACAATTGCAGCTCCGTTAATAAATTCTAAACT
AAAATCGAATGAAAAGAAAAGTGGCGACTGTAAAAAATCTGCCAACATAA
ATTTCCGCTGTTGTTCATCAAATCATCTATCAACTCAAAGTGAATCAATA
AACAATTCTGTCGCTTCATATAATAAAACATACAAAGAATTATTTAATGA
AAATCAAGAAAAAGACATCGACAGAAACAATAACCGGCACGTATCTCACG
CCAGCAGCAAATACACCGATATCAGTTTATTTAACAACGCATCATCCCAT
TCAAACTCGAAAAAATTGTCGACTGCCATTCCAAAAAGTATTAACTTAAA
ACGAAAAAAACGTACGATTAATAACAAACACGTGTTTTGTGATTCGTCTT
TGGAAACCGAATCAAACAGCAACGACAGTACACAATGCGAAATCTCACAA
AAATCCTTGACAAAATATCCTCGTCAACAAAGCAATCATTTGTTTCACAT
CAGCCGAATCCCGCCGCCATCGCCGGTTCCGTCAAGGAGAAAAGTCGAAT
TGTCGGATTTGAAACTTGTGAAATCGGATCAATTGGACATTCCAATGATT
GAATACACATTCTATGTCACCGATATAGAAATATGCCGCAGGCCGCTTAT
TGACAAACGAGTTGATTCGATTGTGGCCAATTGCAATTGCTTGCTTAAAA
TCCACGGACAACCGATATGCAGCAGCTTTGCCAATCAACAAACTCGGAAG
GTGTTCTACAAAGGAAACCCTGTGATACCTGTCACCATTAAGTCATATAG
CATGTCTTCATTGAGAAAATGTATCGGCAGGCTTGACCTTCAATTTCCAT
ATTTCAATGTTAAAGCCTTTCTTAATAGTTGATACAATAGC
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protein sequence of SMED30023339-orf-1

>SMED30023339-orf-1 ID=SMED30023339-orf-1|Name=SMED30023339-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=310bp
MGNCLLCRLRLLESKSNTRCVQTIAAPLINSKLKSNEKKSGDCKKSANIN
FRCCSSNHLSTQSESINNSVASYNKTYKELFNENQEKDIDRNNNRHVSHA
SSKYTDISLFNNASSHSNSKKLSTAIPKSINLKRKKRTINNKHVFCDSSL
ETESNSNDSTQCEISQKSLTKYPRQQSNHLFHISRIPPPSPVPSRRKVEL
SDLKLVKSDQLDIPMIEYTFYVTDIEICRRPLIDKRVDSIVANCNCLLKI
HGQPICSSFANQQTRKVFYKGNPVIPVTIKSYSMSSLRKCIGRLDLQFPY
FNVKAFLNS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000067goblet cell
PLANA:0000420parapharyngeal region
PLANA:0002089reproductive organ