SMED30016988

Overview
NameSMED30016988
Smed IDSMED30016988
Length (bp)959
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 SMED30016988 (SMED30016988) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016988 (SMED30016988) 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 SMED30016988 (SMED30016988) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30016988 (SMED30016988) 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




SMED30016988

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
headSMED30016988SMESG000005116.1 SmedASXL_080379SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
epidermal cellSMED30016988SMESG000005116.1 dd_Smed_v4_4867_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
headSMED30016988SMESG000005116.1 dd_Smed_v6_4867_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30016988SMESG000005116.1 dd_Smed_v4_4867_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30016988SMESG000005116.1 dd_Smed_v4_4867_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30016988SMESG000005116.1 dd_Smed_v4_4867_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
SMED30016988 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007670:22126..23086 +4669
Homology
BLAST of SMED30016988 vs. Planmine SMEST
Match: SMESG000005116.1 (SMESG000005116.1)

HSP 1 Score: 218.394 bits (555), Expect = 3.583e-71
Identity = 158/163 (96.93%), Postives = 159/163 (97.55%), Query Frame = 2
Query:  401 MIRVCIVDLVKSKQICTSTITCTNYCCSISPVTCCNDYTRRVLQSNYYDSSSTSAIVGGVISGTIFVIFLIAIIVSICCGCICRSRTGIQRRYVGRQARVTAVETNVHGQIIYPQGHXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLTNPAYADNTKY 889
            MI  CIVDLVKSKQICTSTITCTNYCCSISPVTCCNDYTRRVLQSNYY SSSTSAIVGGVISGTIFVIFLIAIIVSICCGCICRSRTGIQRRYVGRQARVTAVETNVHGQIIYPQGHNVYPVAPYPA QPTTTVPPPYPGNYNGQ+PPPYNLTNPAYADNTKY
Sbjct:    1 MICACIVDLVKSKQICTSTITCTNYCCSISPVTCCNDYTRRVLQSNYYYSSSTSAIVGGVISGTIFVIFLIAIIVSICCGCICRSRTGIQRRYVGRQARVTAVETNVHGQIIYPQGHNVYPVAPYPAAQPTTTVPPPYPGNYNGQLPPPYNLTNPAYADNTKY 163          
BLAST of SMED30016988 vs. Planmine SMEST
Match: SMESG000001878.1 (SMESG000001878.1)

HSP 1 Score: 77.7962 bits (190), Expect = 7.127e-17
Identity = 55/133 (41.35%), Postives = 79/133 (59.40%), Query Frame = 2
Query:  371 MILFKIFLGLMIRVCIVDLVKSKQICTSTITCTNYCCSIS-PVTCCNDYTRRVLQSNYYDSSSTSAIVGGVISGTIFVIFLIAIIVSICCGCICRSRTGIQRRYVGR-----QARVTAVETNVHGQIIYPQGH 751
            MI    F  L+I +   DLV   + C S   C++YCCS + P  CC+  +  V+ S YY ++++   + G I  TI  I ++++++SICCGCIC +RTGIQRR  GR     Q  VT V +N  GQ++YPQG 
Sbjct:    1 MIFLNFFASLIILIYATDLVSCGEYCNSMFYCSDYCCSSTFPYRCCSSCSLSVISSCYYSTNTSVGAIIGGIISTIIFIIVVSLLISICCGCICSTRTGIQRR--GRILQTGQTTVTVVSSNQQGQVVYPQGQ 131          
BLAST of SMED30016988 vs. Planmine SMEST
Match: SMESG000001789.1 (SMESG000001789.1)

HSP 1 Score: 55.0694 bits (131), Expect = 6.569e-9
Identity = 45/131 (34.35%), Postives = 69/131 (52.67%), Query Frame = 2
Query:  392 LGLMIRVCIVDLVKSKQICTSTIT--CTNYCCSI--SPVTCCNDYTRRVLQSNYYDSSSTSAIVGGVISGTIFVIFLIAIIVSICCGCICRSRTGIQRR-YVGRQAR--VTAVETNVHG----QIIYPQGH 751
            L  +I   I+ L ++ + C+ST +  C +YCC        CC+  +  +     +      +IVGG+I   +FVI +I++IV+ CCGCIC +RTGI++R +V   A   VT +  N  G    Q  YPQ  
Sbjct:    2 LQFVILFSILALCQAGEFCSSTASYYCPDYCCGYYNGVPKCCSTCSFSIKS---HPECGFGSIVGGIIGFILFVI-IISLIVTCCCGCICSNRTGIRKRGWVVSPATNLVTVINPNSTGYFPAQYNYPQAQ 128          
BLAST of SMED30016988 vs. Planmine SMEST
Match: SMESG000001790.1 (SMESG000001790.1)

HSP 1 Score: 53.9138 bits (128), Expect = 1.514e-8
Identity = 47/137 (34.31%), Postives = 71/137 (51.82%), Query Frame = 2
Query:  371 MILFKIFLGLMIRVCIVDLVKSKQICTSTIT--CTNYCCSISP---VTCCNDYTRRVLQSNYYDSSSTSAIVGGVISGTIFVIFLIAIIVSICCGCICRSRTGIQRR-YVGRQA--RVTAVETN----VHGQIIYPQ 745
            M++F I         I+ L ++ + C+  ++  C +YCC  +     +CC   +  +      D  S   IVGG+I    FVI ++++IV+ CCGCIC SRTGIQRR +V   A   VT +++N       Q  YPQ
Sbjct:    1 MLIFAILFS------ILALCQAGEFCSGILSPYCPSYCCRYNTGGIESCCTTCSFSIRNHPECDVGS---IVGGIIGFIAFVI-IVSLIVACCCGCICSSRTGIQRRGWVVSPATTTVTVIDSNQTAYSPAQYNYPQ 127          
BLAST of SMED30016988 vs. Planmine SMEST
Match: SMESG000001793.1 (SMESG000001793.1)

HSP 1 Score: 52.373 bits (124), Expect = 4.394e-8
Identity = 42/111 (37.84%), Postives = 59/111 (53.15%), Query Frame = 2
Query:  455 TITCTNYCC-SISPVTCCNDYTRRV-LQSNYYDSSST-SAIVGGVISGTIFVIFLIAIIVSICCGCICRSRTGIQRRYVGR-----QARVTAVETN----VHGQIIYPQGH 751
            +ITC  YCC +   + CC    + +      Y +S T   I+GG+ S  IFVI ++++I+++CCG IC SRTGIQRR  G+     +A VT    N    V     YP G 
Sbjct:    9 SITCDYYCCGTFDNMRCCKSCVQSLNFHPECYTTSITVGPIIGGIASFIIFVI-IVSLIIALCCGYICSSRTGIQRR--GQIIQTGEATVTVTNPNGTSFVQNPSAYPPGQ 116          
The following BLAST results are available for this feature:
BLAST of SMED30016988 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 SMED30016988 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 SMED30016988 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 SMED30016988 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 SMED30016988 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 SMED30016988 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 SMED30016988 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 SMED30016988 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30016988 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 SMED30016988 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 SMED30016988 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 SMED30016988 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 SMED30016988 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 SMED30016988 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000005116.13.583e-7196.93SMESG000005116.1[more]
SMESG000001878.17.127e-1741.35SMESG000001878.1[more]
SMESG000001789.16.569e-934.35SMESG000001789.1[more]
SMESG000001790.11.514e-834.31SMESG000001790.1[more]
SMESG000001793.14.394e-837.84SMESG000001793.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016988 ID=SMED30016988|Name=SMED30016988|organism=Schmidtea mediterranea sexual|type=transcript|length=959bp
GGATTTTTTATTTATTCCAGGATGTCAACTAGTTTTCTTCAGTCATCAAA
ATTTGGAAAATCTTCAAGGTAATTACATTATTTGTTTTAATACCGTCAAA
TTCAAACTGATTATCTATGAAAACTTGGAGAATTTTTAAATAGTCCAAAA
ATATTTAAAAATAAAAGATAAGAAGGTTTGAATGGGATGGTTGATCAACG
TGAAGACAACTGAATGTTATCATCCATTGTCCACCTACGGTACATTGAGT
GTGCGCATCGCAATTGTAATCTGATTGGCTAGAATTACTGACACGCCGAC
ATTTATGTCTTTTATTTCTGAATTTAATGCTCAATTAATTCTGTTTTTAA
ACACTATCAAGACGAATTTAATGATTTTATTCAAGATCTTCCTTGGATTA
ATGATCCGCGTATGTATTGTGGACCTCGTGAAGAGTAAACAAATTTGCAC
AAGTACAATCACCTGCACTAATTATTGTTGCAGCATCTCGCCCGTTACGT
GCTGTAACGATTACACCAGAAGGGTATTACAGTCAAATTATTATGATTCA
TCATCCACCTCGGCCATTGTTGGTGGAGTTATTTCCGGGACTATATTTGT
TATTTTCCTCATAGCTATAATCGTTTCTATATGCTGTGGCTGCATATGTA
GAAGTAGAACCGGGATTCAAAGACGGTACGTAGGCAGACAGGCTCGAGTT
ACTGCTGTAGAAACCAATGTACATGGGCAGATTATCTATCCCCAAGGTCA
CAATGTATATCCAGTTGCGCCGTATCCTGCTGTGCAACCGACTACCACCG
TTCCTCCTCCGTATCCAGGAAATTACAATGGTCAAGTACCTCCACCTTAT
AATCTCACCAATCCAGCTTATGCTGATAATACTAAATACTAGTGCTCATG
CCTGTCGGACCCTTCACTTGTGAAACACTTGATTATTTGATTATATTTTG
TTTGATTTT
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protein sequence of SMED30016988-orf-1

>SMED30016988-orf-1 ID=SMED30016988-orf-1|Name=SMED30016988-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=196bp
MSFISEFNAQLILFLNTIKTNLMILFKIFLGLMIRVCIVDLVKSKQICTS
TITCTNYCCSISPVTCCNDYTRRVLQSNYYDSSSTSAIVGGVISGTIFVI
FLIAIIVSICCGCICRSRTGIQRRYVGRQARVTAVETNVHGQIIYPQGHN
VYPVAPYPAVQPTTTVPPPYPGNYNGQVPPPYNLTNPAYADNTKY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000096ventral epidermis
PLANA:0000418head
PLANA:0002032epidermal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availablePRODOMPD588499coord: 32..116
e-value: 0.01
score: 89.0
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..22
score: 0.863
NoneNo IPR availableTMHMMTMhelixcoord: 65..87