SMED30035813

Overview
NameSMED30035813
Smed IDSMED30035813
Length (bp)740
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 SMED30035813 (SMED30035813) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30035813 (SMED30035813) 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 SMED30035813 (SMED30035813) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30035813 (SMED30035813) 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



SMED30035813

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30035813h1SMcG0012269 SmedASXL_061180SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30035813h1SMcG0012269 dd_Smed_v4_7960_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30035813h1SMcG0012269 dd_Smed_v4_7960_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30035813h1SMcG0012269 dd_Smed_v6_7960_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
reproductive organSMED30035813h1SMcG0012269 Contig35015uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30035813h1SMcG0012269 Contig35015newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
epidermisSMED30035813h1SMcG0012269 dd_Smed_v4_7960_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30035813h1SMcG0012269 dd_Smed_v4_7960_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
SMED30035813 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000126:123160..124029 -3615
Homology
[Close]
BLAST of SMED30035813 vs. TrEMBL
Match: A0A4S2LB75 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_008429 PE=4 SV=1)

HSP 1 Score: 115.931 bits (289), Expect = 2.271e-28
Identity = 61/139 (43.88%), Postives = 83/139 (59.71%), Query Frame = 3 
Query:  132 TEKYVAGPQHYPTQTSLYHSRGGVSHQWKGPGFYLLYPLSRYTAPDEVWDPLLQGLD--RNALKTKAPEFEFRYPHSHQPMNQKWPMRPFFHSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMVACPTLSGLPIV 542
              +Y +G Q+  T    +H+RG VSHQW+GP +Y+  P +RY   +E  +   Q L   RN    +    E   PH+  P++  WP RP F+S  HNKWLNEH+ T IPRDARLFYNEEDW+K+K+MV    L  + + 
Sbjct:   11 VRRYTSGVQNQHTFHEHHHNRGAVSHQWRGPAYYIPGPQARYLHLEEFKNTQEQELVLYRNNHWCRYNPPEAVKPHNRDPLHLVWPRRPVFYSAHHNKWLNEHADTLIPRDARLFYNEEDWIKYKHMVETAKLPAISLT 149
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BLAST of SMED30035813 vs. TrEMBL
Match: A0A267FB16 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig001692g1 PE=4 SV=1)

HSP 1 Score: 92.0485 bits (227), Expect = 3.209e-19
Identity = 55/137 (40.15%), Postives = 74/137 (54.01%), Query Frame = 3 
Query:  126 EATEKYVAGPQHYPTQTSLYHSRGGVSHQWKGPGFYLLYPLSRYTAPDEVW-DPLLQGLDRNALKTKAPEFE--------FRYPHSHQPMNQKWPMRPFFHSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMV 509
            +A  KY++GPQ+     ++  SRG VSHQW+GPGFY      R+T P +V  DP+ QGLD+ A  +  P               H+  P  ++W  RP F S  H    NEH    +  DARLFYNE+DW K+K M+
Sbjct:   10 QARLKYLSGPQNLVIPCAVRPSRGAVSHQWRGPGFYQ-SETHRFTDPPQVTRDPVGQGLDKTAAVSGWPSAASSTTGVGCHAAEHAPAPYAERWHGRPVFFSAEHQTLSNEHPAGPVAPDARLFYNEDDWEKYKYML 145
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BLAST of SMED30035813 vs. TrEMBL
Match: A0A267GR19 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig001692g2 PE=4 SV=1)

HSP 1 Score: 92.4337 bits (228), Expect = 4.529e-19
Identity = 55/137 (40.15%), Postives = 74/137 (54.01%), Query Frame = 3 
Query:  126 EATEKYVAGPQHYPTQTSLYHSRGGVSHQWKGPGFYLLYPLSRYTAPDEVW-DPLLQGLDRNALKTKAPEFE--------FRYPHSHQPMNQKWPMRPFFHSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMV 509
            +A  KY++GPQ+     ++  SRG VSHQW+GPGFY      R+T P +V  DP+ QGLD+ A  +  P               H+  P  ++W  RP F S  H    NEH    +  DARLFYNE+DW K+K M+
Sbjct:   36 QARLKYLSGPQNLVIPCAIRPSRGAVSHQWRGPGFYQ-SETHRFTDPPQVTRDPVGQGLDKTAAVSGWPSAASSTTGVGCHAAEHAPAPYAERWRGRPVFFSAEHQTLSNEHPAGPVAPDARLFYNEDDWEKYKYML 171
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BLAST of SMED30035813 vs. TrEMBL
Match: A0A267GAX5 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig001692g3 PE=4 SV=1)

HSP 1 Score: 92.0485 bits (227), Expect = 8.065e-19
Identity = 55/137 (40.15%), Postives = 74/137 (54.01%), Query Frame = 3 
Query:  126 EATEKYVAGPQHYPTQTSLYHSRGGVSHQWKGPGFYLLYPLSRYTAPDEVW-DPLLQGLDRNALKTKAPEFEFRYP--------HSHQPMNQKWPMRPFFHSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMV 509
            +A  KY++GPQ+     ++  SRG VSHQW+GPGFY      R+T P +V  DP+ QGLD+ A  +  P               H+  P  ++W  RP F S  H    NEH    +  DARLFYNE+DW K+K M+
Sbjct:   44 QARLKYLSGPQNLVIPCAVRPSRGAVSHQWRGPGFYQ-SETHRFTDPPQVTRDPVGQGLDKTAAVSGWPSAASSTTGVGCHAAEHAPAPYAERWRGRPVFFSAEHQTLSNEHPAGPVAPDARLFYNEDDWEKYKYML 179
[Close]
BLAST of SMED30035813 vs. TrEMBL
Match: A0A504YLX6 (Uncharacterized protein OS=Fasciola gigantica OX=46835 GN=FGIG_03096 PE=4 SV=1)

HSP 1 Score: 77.0258 bits (188), Expect = 1.864e-14
Identity = 38/88 (43.18%), Postives = 49/88 (55.68%), Query Frame = 3 
Query:  372 QKWPMRPFFHSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMVACPTLSGLPIVPQSRPVIKPTGKRRIKCP------QDHDFYF 617
            ++WP  P F+S  HNKWL+EH+ T IPRDARLFYNEEDW+KFK+M        L I        +     ++ C       +D  FYF
Sbjct:    9 KEWPKHPIFYSAHHNKWLSEHADTLIPRDARLFYNEEDWIKFKHMANTAKQPNLSISDVREINCRAFSDAKLVCKKGKKPYEDMKFYF 96
[Close]
BLAST of SMED30035813 vs. Planmine SMEST
Match: SMESG000004300.1 (SMESG000004300.1)

HSP 1 Score: 364.385 bits (934), Expect = 7.130e-130
Identity = 172/173 (99.42%), Postives = 172/173 (99.42%), Query Frame = 3 
Query:   99 MESDYQCRNEATEKYVAGPQHYPTQTSLYHSRGGVSHQWKGPGFYLLYPLSRYTAPDEVWDPLLQGLDRNALKTKAPEFEFRYPHSHQPMNQKWPMRPFFHSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMVACPTLSGLPIVPQSRPVIKPTGKRRIKCPQDHDFYF 617
            MESDYQCRNEATEKYVAGPQHYPTQTSLYHSRGGVSHQWKGPGFYLLYPLSRYTAPDEVWDPLLQGLDRNALKTKAPEFEFRYPHSHQPMNQKWPMRPFFHSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMVACPTL GLPIVPQSRPVIKPTGKRRIKCPQDHDFYF
Sbjct:    1 MESDYQCRNEATEKYVAGPQHYPTQTSLYHSRGGVSHQWKGPGFYLLYPLSRYTAPDEVWDPLLQGLDRNALKTKAPEFEFRYPHSHQPMNQKWPMRPFFHSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMVACPTLPGLPIVPQSRPVIKPTGKRRIKCPQDHDFYF 173
The following BLAST results are available for this feature:
BLAST of SMED30035813 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 SMED30035813 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 SMED30035813 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 SMED30035813 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 SMED30035813 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 SMED30035813 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 SMED30035813 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 SMED30035813 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4S2LB752.271e-2843.88Uncharacterized protein OS=Opisthorchis felineus O... [more]
A0A267FB163.209e-1940.15Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267GR194.529e-1940.15Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A267GAX58.065e-1940.15Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A504YLX61.864e-1443.18Uncharacterized protein OS=Fasciola gigantica OX=4... [more]
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BLAST of SMED30035813 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 SMED30035813 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 SMED30035813 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 SMED30035813 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 SMED30035813 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 SMED30035813 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000004300.17.130e-13099.42SMESG000004300.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035813 ID=SMED30035813|Name=SMED30035813|organism=Schmidtea mediterranea sexual|type=transcript|length=740bp
GTTGTGTTATAAACTTATATTGTTAAAATTATTTTAATCGAAATCTAATA
TTATAAGTTGCCAATTCGTGTTTAAATATTCATTATTTATTGGTTGTTAT
GGAAAGTGATTATCAATGTCGAAACGAAGCTACCGAGAAGTATGTAGCTG
GGCCTCAGCATTATCCAACACAGACATCACTTTATCATAGTCGTGGTGGT
GTATCTCACCAATGGAAAGGTCCTGGATTTTACCTTTTATATCCACTTTC
TCGATATACGGCTCCCGATGAAGTGTGGGATCCATTATTGCAAGGTCTCG
ACCGAAACGCATTGAAGACTAAAGCTCCAGAATTTGAATTTAGATATCCA
CATTCTCATCAACCAATGAATCAAAAATGGCCAATGAGGCCATTTTTTCA
TTCAGTGTCGCATAACAAGTGGCTAAATGAACATTCTCGTACAGCAATTC
CACGAGATGCTCGCTTATTTTACAACGAGGAAGATTGGATGAAATTCAAA
AATATGGTCGCATGTCCAACATTATCGGGATTGCCTATTGTACCTCAATC
TCGCCCTGTAATAAAACCAACAGGTAAAAGACGAATTAAATGCCCACAAG
ATCACGATTTTTATTTCTAATAATCAAATTCTACCAGTAGAAACTGATAA
ATTATATTCCATAGTTACCAATGGGATATATTTAAATAAATAAATTGACA
ATTTTGATTTATTTGTTTTATAAATAAATTGCTTATTGTC
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protein sequence of SMED30035813-orf-1

>SMED30035813-orf-1 ID=SMED30035813-orf-1|Name=SMED30035813-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=174bp
MESDYQCRNEATEKYVAGPQHYPTQTSLYHSRGGVSHQWKGPGFYLLYPL
SRYTAPDEVWDPLLQGLDRNALKTKAPEFEFRYPHSHQPMNQKWPMRPFF
HSVSHNKWLNEHSRTAIPRDARLFYNEEDWMKFKNMVACPTLSGLPIVPQ
SRPVIKPTGKRRIKCPQDHDFYF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000106ciliated epithelial cell
PLANA:0000418head
PLANA:0002089reproductive organ