SMED30009268

Overview
NameSMED30009268
Smed IDSMED30009268
Length (bp)385
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 SMED30009268 (SMED30009268) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30009268 (SMED30009268) 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 SMED30009268 (SMED30009268) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30009268 (SMED30009268) 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



SMED30009268

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
pharynxSMED30009268 dd_Smed_v4_3354_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30009268 dd_Smed_v4_3354_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30009268 dd_Smed_v4_3354_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30009268 dd_Smed_v4_3354_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30009268 dd_Smed_v4_3354_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30009268 dd_Smed_v4_3354_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30009268 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.014661:5486..5914 -1907
v31.019097:1..376 +1435
Homology
[Close]
BLAST of SMED30009268 vs. TrEMBL
Match: A0A1I8H6V5 (Dynein light chain OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig034129g1 PE=3 SV=1)

HSP 1 Score: 53.9138 bits (128), Expect = 2.836e-6
Identity = 26/76 (34.21%), Postives = 41/76 (53.95%), Query Frame = 3 
Query:  111 VTILDGDMEEELYSEVVKVVKECSDLEKNKGILKEKIKFALDAKFSPSWAVFIIKGNFNARFSHKPGMSIVFTFGK 338
            +T++  DM  EL   ++++V++   L   +  + + IK   DAK    W V II G F   +SH+PG S +F  GK
Sbjct:   87 ITVISSDMTLELQLRIIEIVRDGQRLNSMEKDMAKYIKQQCDAKMERLWHVVIINGQFWCWYSHEPGYSFIFRLGK 162
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BLAST of SMED30009268 vs. TrEMBL
Match: A0A267F2V4 (Dynein light chain (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig034129g2 PE=3 SV=1)

HSP 1 Score: 53.9138 bits (128), Expect = 3.223e-6
Identity = 26/76 (34.21%), Postives = 41/76 (53.95%), Query Frame = 3 
Query:  111 VTILDGDMEEELYSEVVKVVKECSDLEKNKGILKEKIKFALDAKFSPSWAVFIIKGNFNARFSHKPGMSIVFTFGK 338
            +T++  DM  EL   ++++V++   L   +  + + IK   DAK    W V II G F   +SH+PG S +F  GK
Sbjct:   91 ITVISSDMTLELQLRIIEIVRDGQRLNSMEKDMAKYIKQQCDAKMERLWHVVIINGQFWCWYSHEPGYSFIFRLGK 166
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BLAST of SMED30009268 vs. TrEMBL
Match: A0A1I8GCD0 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig015343g1 PE=4 SV=1)

HSP 1 Score: 52.7582 bits (125), Expect = 9.191e-6
Identity = 30/87 (34.48%), Postives = 43/87 (49.43%), Query Frame = 3 
Query:  111 VTILDGDMEEELYSEVVKVVKECSDLEKNKGILKEKIKFALDAKFSPSWAVFIIKGNFNARFSHKPGMSIVFTFGKGDTYICVKLEC 371
            V  + GDM  E   +VV+V K+     +    + ++IK  LD  +S  W V I +G F   + H+PG S VF  GK   +I  K  C
Sbjct:   85 VIYISGDMSLEWQIKVVEVTKQALRDSQKMSDVPKRIKTTLDRMYSQLWHVVIAQGQFWCYYGHEPGYSFVFQIGK-QVFIIFKTPC 170
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BLAST of SMED30009268 vs. Planmine SMEST
Match: SMESG000065344.1 (SMESG000065344.1)

HSP 1 Score: 192.971 bits (489), Expect = 3.351e-65
Identity = 94/94 (100.00%), Postives = 94/94 (100.00%), Query Frame = 3 
Query:   90 MNEEEFKVTILDGDMEEELYSEVVKVVKECSDLEKNKGILKEKIKFALDAKFSPSWAVFIIKGNFNARFSHKPGMSIVFTFGKGDTYICVKLEC 371
            MNEEEFKVTILDGDMEEELYSEVVKVVKECSDLEKNKGILKEKIKFALDAKFSPSWAVFIIKGNFNARFSHKPGMSIVFTFGKGDTYICVKLEC
Sbjct:    1 MNEEEFKVTILDGDMEEELYSEVVKVVKECSDLEKNKGILKEKIKFALDAKFSPSWAVFIIKGNFNARFSHKPGMSIVFTFGKGDTYICVKLEC 94
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BLAST of SMED30009268 vs. Planmine SMEST
Match: SMESG000006807.1 (SMESG000006807.1)

HSP 1 Score: 43.8986 bits (102), Expect = 4.465e-6
Identity = 18/56 (32.14%), Postives = 32/56 (57.14%), Query Frame = 3 
Query:  156 VVKVVKECSDLEKNKGILKEKIKFALDAKFSPSWAVFIIKGNFNARFSHKPGMSIV 323
               +++      ++K  + E++K ALD + +  W   I+KG + A +SH+PG SIV
Sbjct:   96 TANIIRRTQSAYQDKKEIAERVKKALDKQMNELWHCVIVKGQYWAYYSHEPGCSIV 151
[Close]
BLAST of SMED30009268 vs. Planmine SMEST
Match: SMESG000006807.1 (SMESG000006807.1)

HSP 1 Score: 43.5134 bits (101), Expect = 5.039e-6
Identity = 18/56 (32.14%), Postives = 32/56 (57.14%), Query Frame = 3 
Query:  156 VVKVVKECSDLEKNKGILKEKIKFALDAKFSPSWAVFIIKGNFNARFSHKPGMSIV 323
               +++      ++K  + E++K ALD + +  W   I+KG + A +SH+PG SIV
Sbjct:   91 TANIIRRTQSAYQDKKEIAERVKKALDKQMNELWHCVIVKGQYWAYYSHEPGCSIV 146
The following BLAST results are available for this feature:
BLAST of SMED30009268 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 SMED30009268 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 SMED30009268 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 SMED30009268 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 SMED30009268 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 SMED30009268 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 SMED30009268 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 SMED30009268 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A1I8H6V52.836e-634.21Dynein light chain OS=Macrostomum lignano OX=28230... [more]
A0A267F2V43.223e-634.21Dynein light chain (Fragment) OS=Macrostomum ligna... [more]
A0A1I8GCD09.191e-634.48Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of SMED30009268 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 SMED30009268 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 SMED30009268 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 SMED30009268 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 SMED30009268 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 SMED30009268 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000065344.13.351e-65100.00SMESG000065344.1[more]
SMESG000006807.14.465e-632.14SMESG000006807.1[more]
SMESG000006807.15.039e-632.14SMESG000006807.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009268 ID=SMED30009268|Name=SMED30009268|organism=Schmidtea mediterranea sexual|type=transcript|length=385bp
AGTTAGTCGATTACCAACGCACACAAAACATTGAAATAATTAATGATCAA
CTAATTTTATCATATCTAAATACAATTTTAAAAGTAAATATGAACGAGGA
AGAATTCAAAGTGACTATTTTAGATGGAGACATGGAAGAAGAATTATATT
CAGAAGTTGTAAAAGTTGTAAAGGAATGCTCAGATTTGGAAAAGAATAAA
GGAATATTAAAAGAAAAGATAAAATTCGCACTGGACGCAAAATTTTCTCC
TTCTTGGGCAGTTTTCATCATAAAAGGAAATTTTAATGCAAGATTTTCTC
ACAAACCCGGAATGTCCATCGTTTTTACCTTTGGAAAAGGAGACACTTAT
ATTTGTGTGAAGTTAGAGTGTTAAAATAAATTTTT
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protein sequence of SMED30009268-orf-1

>SMED30009268-orf-1 ID=SMED30009268-orf-1|Name=SMED30009268-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=124bp
LVDYQRTQNIEIINDQLILSYLNTILKVNMNEEEFKVTILDGDMEEELYS
EVVKVVKECSDLEKNKGILKEKIKFALDAKFSPSWAVFIIKGNFNARFSH
KPGMSIVFTFGKGDTYICVKLEC*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR037177DLC_sf
IPR001372Dynein_light_chain_typ-1/2
Vocabulary: biological process
TermDefinition
GO:0007017microtubule-based process
Vocabulary: cellular component
TermDefinition
GO:0030286dynein complex
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001372Dynein light chain, type 1/2PFAMPF01221Dynein_lightcoord: 36..112
e-value: 1.2E-10
score: 41.5
IPR037177Dynein light chain superfamilyGENE3DG3DSA:3.30.740.10coord: 25..119
e-value: 3.3E-10
score: 41.8
IPR037177Dynein light chain superfamilySUPERFAMILYSSF54648DLCcoord: 30..112