SMED30001640

Overview
NameSMED30001640
Smed IDSMED30001640
Length (bp)544
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 SMED30001640 (SMED30001640) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30001640 (SMED30001640) 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 SMED30001640 (SMED30001640) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30001640 (SMED30001640) 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



SMED30001640

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30001640SMESG000007247.1 SmedASXL_007496SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30001640SMESG000007247.1 dd_Smed_v4_4472_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30001640SMESG000007247.1 dd_Smed_v4_4472_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30001640SMESG000007247.1 dd_Smed_v4_4472_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
cilated neuronSMED30001640SMESG000007247.1 dd_Smed_v4_4472_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30001640SMESG000007247.1 Contig35296newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30001640SMESG000007247.1 Contig35296uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30001640SMESG000007247.1 dd_Smed_v6_4472_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30001640SMESG000007247.1 OX_Smed_1.0.12176ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
GABAergic neuronSMED30001640SMESG000031270.1 SMESG000031234.1 SMESG000007247.1 dd_Smed_v6_4472_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30001640 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001571:37892..38477 +2459
v31.000232:14476..15071 -2328
v31.001676:28172..28767 -2321
v31.000150:165650..166180 +1612
Homology
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BLAST of SMED30001640 vs. TrEMBL
Match: A0A2H1CCY5 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_004900 PE=4 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 3.251e-6
Identity = 41/116 (35.34%), Postives = 54/116 (46.55%), Query Frame = 2 
Query:  203 LLFFVIAITDLQLGHAQLINCYVCIGCPNPF--VISGAMTSPNCSSCMT------TTALTVISKTCITGTCVTISGIAGTSN-----TCCSTNLCNTGSEFKVPIAVVIGLPVLAS 511
            LL+F   I D Q      I CY C+ CP PF  + +G     +C  C T      T ALT   +TC+T T   I+ + GT+       CC  N CN GS  K P  V+  + VL +
Sbjct:   19 LLYFCALIVDAQ------ITCYECMNCPRPFSTIGTGVSLKKDCKYCRTEDMYNKTGALTSSKRTCVTNTDSCINSLNGTNEGVTEIGCCRWNACNMGSRMK-PTMVIASVLVLGA 127
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BLAST of SMED30001640 vs. Planmine SMEST
Match: SMESG000031270.1 (SMESG000031270.1)

HSP 1 Score: 154.836 bits (390), Expect = 6.205e-49
Identity = 83/114 (72.81%), Postives = 93/114 (81.58%), Query Frame = 2 
Query:  188 MISKLLLFFVIAITDLQLGHAQLINCYVCIGCPNPFVISGAMTS-PNCSSCMTTTALTVISKTCITGTCVTISGIAGTSNTCCSTNLCNTGSEFKVPIAVVIGLPVLASLLRAY 526
            MISKLLLFFVIAITDLQLGH QLINCY C+GC NPFVIS A+T+    S   TT+AL +++KTC + TC TI+   G +N CCSTNLCNTGSEFKVPIAVVIGLPVLASL RAY
Sbjct:    1 MISKLLLFFVIAITDLQLGHTQLINCYACVGCSNPFVISSALTATNCSSCTTTTSALNIVTKTCASITCNTITSYIGATNICCSTNLCNTGSEFKVPIAVVIGLPVLASLFRAY 114
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BLAST of SMED30001640 vs. Planmine SMEST
Match: SMESG000007247.1 (SMESG000007247.1)

HSP 1 Score: 127.872 bits (320), Expect = 6.582e-39
Identity = 64/67 (95.52%), Postives = 65/67 (97.01%), Query Frame = 2 
Query:  188 MISKLLLFFVIAITDLQLGHAQLINCYVCIGCPNPFVISGAMTSPNCSSCMTTTALTVISKTCITGT 388
            MISKLLLFFVIAITDLQLGHAQLINCYVC GCPNPF+ISGAMTS NCSSCMTTTALTVISKTCITGT
Sbjct:    1 MISKLLLFFVIAITDLQLGHAQLINCYVCAGCPNPFIISGAMTSTNCSSCMTTTALTVISKTCITGT 67
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BLAST of SMED30001640 vs. Planmine SMEST
Match: SMESG000031234.1 (SMESG000031234.1)

HSP 1 Score: 129.028 bits (323), Expect = 7.299e-39
Identity = 74/101 (73.27%), Postives = 85/101 (84.16%), Query Frame = 2 
Query:  227 TDLQLGHAQLINCYVCIGCPNPFVISGAMTSPNCSSCMTTT-ALTVISKTCITGTCVTISGIAGTSNTCCSTNLCNTGSEFKVPIAVVIGLPVLASLLRAY 526
            +DLQLGH+QLINCY C+GC NPFVIS A+T+ NCSSC TTT AL +++KTC + TC TI+   G +N CCSTNLCNTGSEFKVPIAVVIGLPVLASL RAY
Sbjct:   12 SDLQLGHSQLINCYACVGCSNPFVISSALTATNCSSCTTTTSALNIVTKTCASITCNTITSFIGPTNICCSTNLCNTGSEFKVPIAVVIGLPVLASLFRAY 112
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BLAST of SMED30001640 vs. Planmine SMEST
Match: SMESG000007344.1 (SMESG000007344.1)

HSP 1 Score: 88.1965 bits (217), Expect = 8.714e-23
Identity = 46/107 (42.99%), Postives = 59/107 (55.14%), Query Frame = 2 
Query:  188 MISKLLLFFVIAITDLQLGHAQLINCYVCIGCPNPFVISGAMTSPNCSSCMTTTALTVISKTCITGTCVTISGIAGTSNTCCSTNLCNTGSEFKVPIAVVIGLPVLA 508
            M  K L     AI   Q   AQ I+CY C GCP PFV +G  T  NC+SC+  T L +++K+C  G C     I G S +CC+TNLCN G  F V  A ++   +LA
Sbjct:    1 MAFKFLFLLAFAIAHFQQNSAQTISCYTCFGCPVPFVTAGITTFSNCTSCLKMTTLNIVTKSCNPGACGANIDITGVSTSCCNTNLCNVGQRFTVQRAGIVIAMMLA 107
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BLAST of SMED30001640 vs. Planmine SMEST
Match: SMESG000028039.1 (SMESG000028039.1)

HSP 1 Score: 75.8702 bits (185), Expect = 3.999e-18
Identity = 40/109 (36.70%), Postives = 60/109 (55.05%), Query Frame = 2 
Query:  188 MISKLLLFFVIAITDLQLGHAQLINCYVCIGCPNPFVISGAMTSPNCSSCMTTTALTVISKTCITGTCVTISGIAGTSNTCCSTNLCNTGSEFKVPIAVVIGLPVLASL 514
            M  K +    IA+  +   + Q INCY C+GCPNPFV S A+   NC+SC TTT  ++I+KT  +    + + + G S  CC+TNLCN G          I + ++ ++
Sbjct:    1 MTIKFIFLLTIALASIHQNYGQTINCYTCVGCPNPFVASSAIVITNCTSCYTTTLYSIITKT-CSLASCSSASVLGASVACCNTNLCNKGHWLTASTGGFISVALMVTM 108
The following BLAST results are available for this feature:
BLAST of SMED30001640 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 SMED30001640 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 SMED30001640 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 SMED30001640 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 SMED30001640 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 SMED30001640 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 SMED30001640 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 SMED30001640 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A2H1CCY53.251e-635.34Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
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BLAST of SMED30001640 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 SMED30001640 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 SMED30001640 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 SMED30001640 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 SMED30001640 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 SMED30001640 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000031270.16.205e-4972.81SMESG000031270.1[more]
SMESG000007247.16.582e-3995.52SMESG000007247.1[more]
SMESG000031234.17.299e-3973.27SMESG000031234.1[more]
SMESG000007344.18.714e-2342.99SMESG000007344.1[more]
SMESG000028039.13.999e-1836.70SMESG000028039.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001640 ID=SMED30001640|Name=SMED30001640|organism=Schmidtea mediterranea sexual|type=transcript|length=544bp
CCTGGAAACGCTGGGAAATGCGATGGGGAAGCGTACCCATTGGAAACTGT
AAGCATGAGTCATTGAATGATAAATATTTATTTAATGGAATTGTTCTTTG
TCAGAGTTGAATGAGAAGAAACATATTTTATTTGTTTGTAATTTTTAGCT
TTATAAAACACAATCACAAAATATTATTAACATAAATATGATTTCAAAGT
TGCTGTTGTTTTTTGTGATTGCAATAACTGATCTTCAACTTGGTCATGCT
CAATTGATTAATTGTTATGTTTGCATTGGATGCCCAAATCCGTTTGTCAT
TTCCGGTGCTATGACTTCCCCCAATTGTTCATCATGCATGACAACGACAG
CTCTGACTGTCATCTCAAAAACATGCATCACTGGAACTTGTGTTACAATC
TCAGGAATAGCTGGAACATCCAATACGTGCTGCTCTACAAATCTCTGCAA
CACCGGAAGTGAATTCAAAGTTCCAATAGCAGTTGTGATAGGATTGCCGG
TCTTGGCGAGTTTATTACGTGCATATTGATGATATGTCAGTTGT
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protein sequence of SMED30001640-orf-1

>SMED30001640-orf-1 ID=SMED30001640-orf-1|Name=SMED30001640-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=114bp
MISKLLLFFVIAITDLQLGHAQLINCYVCIGCPNPFVISGAMTSPNCSSC
MTTTALTVISKTCITGTCVTISGIAGTSNTCCSTNLCNTGSEFKVPIAVV
IGLPVLASLLRAY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
PLANA:0000464GABAergic neuron
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..21
score: 0.836