SMED30003978

Overview
NameSMED30003978
Smed IDSMED30003978
Length (bp)706
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 SMED30003978 (SMED30003978) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30003978 (SMED30003978) 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 SMED30003978 (SMED30003978) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30003978 (SMED30003978) 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




SMED30003978

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30003978h1SMcG0015416 SmedASXL_004201SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30003978h1SMcG0015416 dd_Smed_v4_10608_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30003978h1SMcG0015416 dd_Smed_v4_10608_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30003978h1SMcG0015416 dd_Smed_v6_10608_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30003978h1SMcG0015416 dd_Smed_v4_10608_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
SMED30003978 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003428:9004..9700 -3467
Homology
BLAST of SMED30003978 vs. TrEMBL
Match: A0A1I8IDA1 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 87.0409 bits (214), Expect = 6.772e-16
Identity = 60/174 (34.48%), Postives = 91/174 (52.30%), Query Frame = 2
Query:  164 TGLPDDIIEGISDAFDLLYDPENMCHLSKEERIKLYAQRDLRIAKEYKTIMKYFGNLRSVIELLGTNSGRKRIITVS------GSIESDSGSVFPKRMDCSQVPRANPDPYKIVLPPIVDYRSMMISKVNYK------EIKDMDIKVDVVKFLSAK-PDLTSMEHRQLQKLKQN 646
            TG+ D+++EG++DAF+LLYDP    HL  EE+IK +  RDL  AK YKT +K FGN R V E L  ++GRKR+          G     S S  PK    S+   A+P  +      + D  +  +S+          + +D++   DV ++L  K   L+SME   L K++++
Sbjct:   46 TGVSDEVLEGLTDAFELLYDPNYFGHLEFEEQIKKFKSRDLLEAKLYKTALKAFGNQRFVRERLTKDNGRKRVFVAQPLSELRGFDSFSSVSCLPKISSDSR--NADPSEFDATTSELEDPAAKEMSRYQQWLKKRQVQHRDLERMGDVERYLRGKGGQLSSMERATLHKIEES 217          
BLAST of SMED30003978 vs. TrEMBL
Match: A0A267DH14 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig005600g2 PE=4 SV=1)

HSP 1 Score: 84.7297 bits (208), Expect = 4.786e-15
Identity = 59/175 (33.71%), Postives = 91/175 (52.00%), Query Frame = 2
Query:  164 TGLPDDIIEGISDAFDLLYDPENMCHLSKEERIKLYAQRDLRIAKEYKTIMKYFGNLRSVIELLGTNSGRKRIITVS------GSIESDSGSVFPK------RMDCSQVPRANPDPYKIVLPPIVDYRSMMISK-VNYKEIKDMDIKVDVVKFLSAK-PDLTSMEHRQLQKLKQN 646
            TG+ D+++EG++DAF+LLY+P    HL  EE+IK +  RDL  AK YKT +K FGN R V E L  ++GRKR+          G     S S  PK        D S+   A  +        +  Y+  +  + V +++++ M    DV ++L  K   L+SME   L K++++
Sbjct:   53 TGVSDEVLEGLTDAFELLYNPNYFGHLEFEEQIKKFKSRDLLEAKLYKTALKAFGNQRFVRERLAKDNGRKRVFVAQPLSELRGFDSFSSVSCLPKISSDSRNADSSESDAATAELEDPAAQEMSRYQQWLKKRQVQHRDLERMG---DVERYLRGKGGQLSSMERATLHKIEES 224          
BLAST of SMED30003978 vs. TrEMBL
Match: A0A267F6W9 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig011107g1 PE=4 SV=1)

HSP 1 Score: 81.6481 bits (200), Expect = 4.503e-14
Identity = 60/174 (34.48%), Postives = 95/174 (54.60%), Query Frame = 2
Query:  164 TGLPDDIIEGISDAFDLLYDPENMCHLSKEERIKLYAQRDLRIAKEYKTIMKYFGNLRSVIELLGTNSGRKRIIT------VSGSIESDSGSVFPKRMDCSQVPRANPDPYKIVLPPIVDYRSMMISK----VNYKEIKDMDIKV--DVVKFLSAK-PDLTSMEHRQLQKLKQN 646
            TG+ D+++EG++DAF+LLYDP    HL  EE+IK +  RDL  AK YKT +K FGN R V E L  ++GRKR+        + G     S S  PK    S+   A+P  +      + D  +  +S+    +  ++++  D++   DV ++L  K   L+SME   L K++++
Sbjct:   54 TGVSDEVLEGLTDAFELLYDPNYFGHLEFEEQIKKFKSRDLLEAKLYKTALKAFGNQRFVRERLTKDNGRKRVFVAQPLSELRGFDSFSSVSCLPKISSDSR--NADPSEFDATTSELEDPAAKEMSRYQQWLKKRQVQHRDLERMGDVERYLRGKGGQLSSMERATLHKIEES 225          
BLAST of SMED30003978 vs. TrEMBL
Match: A0A1I8GDW8 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 79.7221 bits (195), Expect = 2.317e-13
Identity = 59/174 (33.91%), Postives = 90/174 (51.72%), Query Frame = 2
Query:  164 TGLPDDIIEGISDAFDLLYDPENMCHLSKEERIKLYAQRDLRIAKEYKTIMKYFGNLRSVIELLGTNSGRKRIIT------VSGSIESDSGSVFPK------RMDCSQVPRANPDPYKIVLPPIVDYRSMMISKVNYKEIKDMDIKVDVVKFLSAK-PDLTSMEHRQLQKLKQN 646
            TG+ D+++EG++DAF+LLY+P    HL  EE+IK +  RDL  AK YKT +K FGN R V E L  ++GRKR+        + G     S S  PK        D S+   A  +        +  Y+  +  K    + +D++   DV ++L  K   L+SME   L K++++
Sbjct:   46 TGVSDEVLEGLTDAFELLYNPNYFGHLEFEEQIKKFKSRDLLEAKLYKTALKAFGNQRFVRERLAKDNGRKRVFVAQPLSELRGFDSFSSVSCLPKISSDSRNADSSESDAATAELEDPAAQEMSRYQQWL--KKRQVQHRDLERMGDVERYLRGKGGQLSSMERATLHKIEES 217          
BLAST of SMED30003978 vs. TrEMBL
Match: A0A267FNF7 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig011107g2 PE=4 SV=1)

HSP 1 Score: 78.9518 bits (193), Expect = 4.175e-13
Identity = 59/174 (33.91%), Postives = 90/174 (51.72%), Query Frame = 2
Query:  164 TGLPDDIIEGISDAFDLLYDPENMCHLSKEERIKLYAQRDLRIAKEYKTIMKYFGNLRSVIELLGTNSGRKRIIT------VSGSIESDSGSVFPK------RMDCSQVPRANPDPYKIVLPPIVDYRSMMISKVNYKEIKDMDIKVDVVKFLSAK-PDLTSMEHRQLQKLKQN 646
            TG+ D+++EG++DAF+LLY+P    HL  EE+IK +  RDL  AK YKT +K FGN R V E L  ++GRKR+        + G     S S  PK        D S+   A  +        +  Y+  +  K    + +D++   DV ++L  K   L+SME   L K++++
Sbjct:   55 TGVSDEVLEGLTDAFELLYNPNYFGHLEFEEQIKKFKSRDLLEAKLYKTALKAFGNQRFVRERLAKDNGRKRVFVAQPLSELRGFDSFSSVSCLPKISSDSRNADSSESDAATAELEDPAAQEMSRYQQWL--KKRQVQHRDLERMGDVERYLRGKGGQLSSMERATLHKIEES 226          
BLAST of SMED30003978 vs. Planmine SMEST
Match: SMESG000052391.1 (SMESG000052391.1)

HSP 1 Score: 288.115 bits (736), Expect = 2.324e-100
Identity = 140/142 (98.59%), Postives = 141/142 (99.30%), Query Frame = 2
Query:  233 MCHLSKEERIKLYAQRDLRIAKEYKTIMKYFGNLRSVIELLGTNSGRKRIITVSGSIESDSGSVFPKRMDCSQVPRANPDPYKIVLPPIVDYRSMMISKVNYKEIKDMDIKVDVVKFLSAKPDLTSMEHRQLQKLKQNLNHN 658
            MCHLSKEERIKLYAQRDLRIAKEYKTIMKYFGNLRSVIELLGTNSGRKRIITVSGSIESDSGSVFPKRMDCSQVPRANPDPYKIVLPPIVDYRSMMISKVNYKEIKDMDI+VDVVKFLSAKPDLTSMEHRQLQKLKQ LNHN
Sbjct:    1 MCHLSKEERIKLYAQRDLRIAKEYKTIMKYFGNLRSVIELLGTNSGRKRIITVSGSIESDSGSVFPKRMDCSQVPRANPDPYKIVLPPIVDYRSMMISKVNYKEIKDMDIEVDVVKFLSAKPDLTSMEHRQLQKLKQKLNHN 142          
The following BLAST results are available for this feature:
BLAST of SMED30003978 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 SMED30003978 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 SMED30003978 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 SMED30003978 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 SMED30003978 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 SMED30003978 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 SMED30003978 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 SMED30003978 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1I8IDA16.772e-1634.48Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267DH144.786e-1533.71Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A267F6W94.503e-1434.48Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A1I8GDW82.317e-1333.91Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267FNF74.175e-1333.91Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
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BLAST of SMED30003978 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 SMED30003978 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 SMED30003978 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 SMED30003978 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 SMED30003978 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 SMED30003978 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000052391.12.324e-10098.59SMESG000052391.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003978 ID=SMED30003978|Name=SMED30003978|organism=Schmidtea mediterranea sexual|type=transcript|length=706bp
TCTAATTAAAATCTGTTATTCAATAGAAATATTTTTATAATACTCATATA
AACAATTATTTTATTGAAATTAATTAAAACTGGCTTTCCAAAAGAGACGA
TTATCTCATTTCTTAACTCCTATAAAGATTTCAAATATTAAAAAAGAAAA
AAAGGCAGATAAAACCGGTTTGCCAGATGATATTATAGAAGGAATCTCTG
ATGCTTTTGATCTCCTATATGATCCTGAAAACATGTGTCATCTATCGAAA
GAAGAAAGAATTAAATTATATGCTCAGCGAGATCTAAGAATCGCAAAAGA
ATATAAAACAATAATGAAATATTTTGGTAATCTCAGGTCTGTCATTGAAT
TATTGGGTACAAATTCTGGTAGGAAACGAATTATTACTGTGTCTGGCTCA
ATTGAATCTGACAGTGGATCTGTGTTCCCAAAACGAATGGACTGTTCACA
GGTACCAAGAGCAAATCCAGATCCCTATAAAATCGTTCTACCTCCAATAG
TGGATTATCGCTCCATGATGATATCGAAGGTCAATTACAAGGAAATTAAA
GACATGGATATCAAAGTTGATGTTGTAAAATTTTTATCAGCCAAGCCCGA
TCTCACGTCAATGGAACATCGGCAACTGCAGAAATTAAAACAAAACTTAA
ATCATAATTAAGAATCAAACTGTTATAATTTGATTCCAGAATTTCATAGA
TCGGAA
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protein sequence of SMED30003978-orf-1

>SMED30003978-orf-1 ID=SMED30003978-orf-1|Name=SMED30003978-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=143bp
MCHLSKEERIKLYAQRDLRIAKEYKTIMKYFGNLRSVIELLGTNSGRKRI
ITVSGSIESDSGSVFPKRMDCSQVPRANPDPYKIVLPPIVDYRSMMISKV
NYKEIKDMDIKVDVVKFLSAKPDLTSMEHRQLQKLKQNLNHN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 129..142