SMED30020948

Overview
NameSMED30020948
Smed IDSMED30020948
Length (bp)470
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 SMED30020948 (SMED30020948) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020948 (SMED30020948) 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 SMED30020948 (SMED30020948) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30020948 (SMED30020948) 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



SMED30020948

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



PAGE Curations: 16

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30020948SMESG000024857.1 dd_Smed_v4_409_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30020948SMESG000024857.1 dd_Smed_v4_409_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30020948SMESG000024857.1 dd_Smed_v4_409_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30020948SMESG000024857.1 dd_Smed_v4_409_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30020948SMESG000024857.1 dd_Smed_v4_409_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30020948SMESG000024857.1 dd_Smed_v4_409_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30020948SMESG000024857.1 dd_Smed_v4_409_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020948SMESG000024857.1 Contig46856newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020948SMESG000024857.1 Contig46856uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020948SMESG000024857.1 Contig13785newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020948SMESG000024857.1 Contig13785uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30020948SMESG000024857.1 dd_Smed_v6_409_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 2 cellSMED30020948SMESG000024857.1 dd_Smed_v6_409_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30020948SMESG000024857.1 dd_Smed_v6_409_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30020948SMESG000024857.1 dd_Smed_v6_409_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30020948SMESG000024857.1 dd_Smed_v4_409_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
SMED30020948 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004738:54203..54764 -2271
v31.018125:1126..1686 -2227
Homology
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BLAST of SMED30020948 vs. TrEMBL
Match: A0A0V0QKC5 (Dynein light chain OS=Pseudocohnilembus persalinus OX=266149 GN=PPERSA_01834 PE=3 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 2.533e-7
Identity = 30/94 (31.91%), Postives = 49/94 (52.13%), Query Frame = 1 
Query:  121 IAKSKMAEFHVRLSHFENDKAKEERILEIFRSVFQETEELKDRAQQIKKELDAKEEGMWHVTIGKHYTSYVSCAEESFFQATFGDLLIQVYCCG 402
            I +S   EF ++ +  +ND  ++ +  EI +   Q+    KD A  IK   D K E +WHV +GK + SYV+   + +    +G+L I +Y  G
Sbjct:   14 IGESDKPEFEIKSADMQNDMIEDAK--EIIKRAVQKYSIEKDIAMYIKNTFDNKYESIWHVIVGKSFASYVTHYSKHYLYIYYGELTILIYKFG 105
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BLAST of SMED30020948 vs. TrEMBL
Match: V6M5F0 (Dynein light chain OS=Spironucleus salmonicida OX=348837 GN=SS50377_11200 PE=3 SV=1)

HSP 1 Score: 53.1434 bits (126), Expect = 3.120e-6
Identity = 28/87 (32.18%), Postives = 47/87 (54.02%), Query Frame = 1 
Query:  142 EFHVRLSHFENDKAKEERILEIFRSVFQETEELKDRAQQIKKELDAKEEGMWHVTIGKHYTSYVSCAEESFFQATFGDLLIQVYCCG 402
            +F V ++  +  +  E  I+ I ++  Q     KD A  IKKE+D + +  WHV +G++++SYV+  +  F     G L  QV+ CG
Sbjct:    9 DFKVVINTNDVPEDTERFIVNISKNALQRFNLEKDIAAFIKKEVDKEYKSTWHVYVGRNFSSYVTHDKNRFIDFNIGQLAFQVFQCG 95
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BLAST of SMED30020948 vs. Ensembl Yeast
Match: DYN2 (Cytoplasmic light chain dynein, microtubule motor protein; required for intracellular transport and cell division; involved in mitotic spindle positioning; forms complex with dynein intermediate chain Pac11p that promotes Dyn1p homodimerization, potentiates motor processivity; Dyn2p-Pac11p complex important for interaction of dynein motor complex with dynactin complex; acts as molecular glue to dimerize, stabilize Nup82-Nsp1-Nup159 complex module of cytoplasmic pore filaments [Source:SGD;Acc:S000002832])

HSP 1 Score: 45.0542 bits (105), Expect = 1.551e-7
Identity = 26/74 (35.14%), Postives = 39/74 (52.70%), Query Frame = 1 
Query:  172 NDKAKEERILEIFRSVFQETEELKDRAQQIKKELDAKEEGMWHVTIGKHYTSYVSCAEESFFQATFGDLLIQVY 393
             DK KE+ IL I +    + +  +D A  +KK+LD K    WHV +GK++ SYV+  +  F     G L   V+
Sbjct:   17 TDKLKED-ILTISKDALDKYQLERDIAGTVKKQLDVKYGNTWHVIVGKNFGSYVTHEKGHFVYFYIGPLAFLVF 89
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BLAST of SMED30020948 vs. Planmine SMEST
Match: SMESG000024857.1 (SMESG000024857.1)

HSP 1 Score: 227.254 bits (578), Expect = 5.381e-78
Identity = 110/111 (99.10%), Postives = 110/111 (99.10%), Query Frame = 1 
Query:   70 MCARVSLYCQLLNECDLIAKSKMAEFHVRLSHFENDKAKEERILEIFRSVFQETEELKDRAQQIKKELDAKEEGMWHVTIGKHYTSYVSCAEESFFQATFGDLLIQVYCCG 402
            MCA VSLYCQLLNECDLIAKSKMAEFHVRLSHFENDKAKEERILEIFRSVFQETEELKDRAQQIKKELDAKEEGMWHVTIGKHYTSYVSCAEESFFQATFGDLLIQVYCCG
Sbjct:    1 MCAHVSLYCQLLNECDLIAKSKMAEFHVRLSHFENDKAKEERILEIFRSVFQETEELKDRAQQIKKELDAKEEGMWHVTIGKHYTSYVSCAEESFFQATFGDLLIQVYCCG 111
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BLAST of SMED30020948 vs. Planmine SMEST
Match: SMESG000009941.1 (SMESG000009941.1)

HSP 1 Score: 62.3882 bits (150), Expect = 2.061e-13
Identity = 32/70 (45.71%), Postives = 45/70 (64.29%), Query Frame = 1 
Query:  196 ILEIFRSVFQETEELKDRAQQIKKELDAKEEGMWHVTIGKHYTSYVSCAEESFFQ-ATFGDLLIQVYCCG 402
            I EI + VF+E E  KDRA++IKKELD K E  WHV IGK +T++V+  E  +      G+  +Q++ CG
Sbjct:   21 IKEIVKQVFEECESAKDRAERIKKELDDKFEQYWHVVIGKQFTTFVTYEESKYCHLVCGGNTAVQIFKCG 90
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BLAST of SMED30020948 vs. Planmine SMEST
Match: SMESG000007775.1 (SMESG000007775.1)

HSP 1 Score: 49.2914 bits (116), Expect = 1.883e-8
Identity = 27/71 (38.03%), Postives = 39/71 (54.93%), Query Frame = 1 
Query:  193 RILEIFRSVFQETEELKDRAQQIKKELDAKEEGMWHVTIGKHYTSYVSCAEESFFQATFGDLL-IQVYCCG 402
            RI EI   VFQ  E   +RA++IK +LD + EG W   +GK++ +YV+  E  F     G    +QV+  G
Sbjct:   17 RISEIVEDVFQNLESNAERAKEIKAKLDQEFEGPWQCIVGKNFATYVTHEEHKFCHVKVGSQTGVQVFKAG 87
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BLAST of SMED30020948 vs. Planmine SMEST
Match: SMESG000008798.1 (SMESG000008798.1)

HSP 1 Score: 47.7506 bits (112), Expect = 9.271e-8
Identity = 25/74 (33.78%), Postives = 43/74 (58.11%), Query Frame = 1 
Query:  184 KEERILEIFRSVFQETEELKDRAQQIKKELDAKEEGMWHVTIGKHYTSYVSCAEESFFQATF-GDLLIQVYCCG 402
            K ++++EIF   F+E +   DR   IKK++D +    WHV IGKH+ + ++  E++F       ++ +QVY  G
Sbjct:   14 KTDQMVEIFEKAFEENDLDCDRVVAIKKKVDEQFGTNWHVIIGKHFITKINYEEDNFCHCRMPNNMGVQVYKSG 87
The following BLAST results are available for this feature:
BLAST of SMED30020948 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 SMED30020948 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 SMED30020948 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 SMED30020948 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 SMED30020948 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 SMED30020948 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 SMED30020948 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 SMED30020948 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A0V0QKC52.533e-731.91Dynein light chain OS=Pseudocohnilembus persalinus... [more]
V6M5F03.120e-632.18Dynein light chain OS=Spironucleus salmonicida OX=... [more]
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BLAST of SMED30020948 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 SMED30020948 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 SMED30020948 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 1
Match NameE-valueIdentityDescription
DYN21.551e-735.14Cytoplasmic light chain dynein, microtubule motor ... [more]
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BLAST of SMED30020948 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 SMED30020948 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 SMED30020948 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000024857.15.381e-7899.10SMESG000024857.1[more]
SMESG000009941.12.061e-1345.71SMESG000009941.1[more]
SMESG000007775.11.883e-838.03SMESG000007775.1[more]
SMESG000008798.19.271e-833.78SMESG000008798.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020948 ID=SMED30020948|Name=SMED30020948|organism=Schmidtea mediterranea sexual|type=transcript|length=470bp
ATCTCAGTCAAGTGACACACAAAGAAACATCGATTTGCACACATACACAA
ATTGTAATCAATAACTCCAATGTGTGCGCGTGTGTCCCTCTATTGTCAAC
TGTTGAATGAATGCGATTTAATAGCAAAATCAAAAATGGCAGAATTTCAC
GTCAGATTATCTCATTTTGAAAACGATAAAGCGAAAGAAGAAAGAATTTT
GGAAATATTTCGAAGTGTTTTCCAAGAGACTGAAGAATTGAAAGATCGTG
CTCAACAGATCAAGAAAGAACTGGATGCGAAAGAAGAAGGAATGTGGCAT
GTTACAATTGGAAAGCATTATACAAGCTATGTCAGCTGTGCTGAGGAGAG
CTTCTTCCAAGCTACCTTTGGAGACTTGCTCATCCAAGTCTACTGTTGTG
GAAATTGAATCGACATCAAATGATTTTTCAATTTTAATATTAGGCAGTTT
TAAATATATCTTAATTTAAT
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protein sequence of SMED30020948-orf-1

>SMED30020948-orf-1 ID=SMED30020948-orf-1|Name=SMED30020948-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=113bp
MCARVSLYCQLLNECDLIAKSKMAEFHVRLSHFENDKAKEERILEIFRSV
FQETEELKDRAQQIKKELDAKEEGMWHVTIGKHYTSYVSCAEESFFQATF
GDLLIQVYCCGN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000028Category 2 cell
PLANA:0000034epidermis
PLANA:0000035Category 3 cell
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR037177DLC_sf
IPR001372Dynein_light_chain_typ-1/2
IPR001627Semap_dom
Vocabulary: cellular component
TermDefinition
GO:0030286dynein complex
Vocabulary: biological process
TermDefinition
GO:0007017microtubule-based process
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 51..74
IPR001372Dynein light chain, type 1/2SMARTSM01375Dynein_light_2coord: 23..110
e-value: 3.6E-12
score: 56.4
IPR001372Dynein light chain, type 1/2PFAMPF01221Dynein_lightcoord: 36..108
e-value: 4.1E-14
score: 52.7
IPR037177Dynein light chain superfamilyGENE3DG3DSA:3.30.740.10coord: 16..110
e-value: 7.9E-15
score: 56.6
IPR037177Dynein light chain superfamilySUPERFAMILYSSF54648DLCcoord: 21..108