SMED30029023

Overview
NameSMED30029023
Smed IDSMED30029023
Length (bp)608
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 SMED30029023 (SMED30029023) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30029023 (SMED30029023) 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 SMED30029023 (SMED30029023) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30029023 (SMED30029023) 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



SMED30029023

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30029023 dd_Smed_v4_17408_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30029023 dd_Smed_v4_17408_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30029023 dd_Smed_v4_17408_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
Homology
[Close]
BLAST of SMED30029023 vs. TrEMBL
Match: A0A0C2JKS9 (Uncharacterized protein OS=Thelohanellus kitauei OX=669202 GN=RF11_02307 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 5.137e-8
Identity = 37/104 (35.58%), Postives = 54/104 (51.92%), Query Frame = -2 
Query:    2 ITEEAKMFIRSKIESDVSVTLGALKLKLQASLNIICSTTTIDGAIRDLNYSFNRV*LVQERINVAANIE*RFNYAGRYLGYDEDKVIFLNEFSLSCSTRQKYGR 313
            +T+E   +I   ++ D S+TL  LK+KL     I    TTI  ++ D  YSF RV ++ +R N    I  RF+        DE K+IF++E   + S R  YGR
Sbjct:    7 LTQEQNDYILDLVDEDCSITLKELKIKLHERFGIQVCITTISKSLGDFLYSFKRVHMIPKRRNGVQTINSRFD-------IDESKIIFMDETGFNISMRSIYGR 103
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BLAST of SMED30029023 vs. TrEMBL
Match: A0A4Q9LYZ4 (Putative DDE endonuclease OS=Hamiltosporidium tvaerminnensis OX=1176355 GN=CWI38_0380p0040 PE=4 SV=1)

HSP 1 Score: 57.3806 bits (137), Expect = 1.393e-7
Identity = 38/122 (31.15%), Postives = 65/122 (53.28%), Query Frame = -2 
Query:   17 FINTGRVNAMTQRRPRESIITEEAKMFIRSKIESDVSVTLGALKLKLQASLNIICSTTTIDGAIRDLNYSFNRV*LVQERINVAANIE*RFNYAGRY----LGYDEDKVIFLNEFSLSCSTR 370
            ++ TG V        R S ++ E K  +++ ++ + + TL  L   ++ + N+  ST+TID A+R+ +Y+  RV LV ER N  + IE R NYA  +    +  D+   +FL+E   +  TR
Sbjct:  100 YLKTGLVFVEKGGGDRRSKLSLEIKESLQAYVDLECTKTLYELAEWVKCTFNVYGSTSTIDRALREFHYTLKRVTLVPERRNTLSTIELRTNYATSFRELEVDNDDKNFVFLDEVGFAVVTR 221

HSP 2 Score: 26.1794 bits (56), Expect = 1.393e-7
Identity = 15/42 (35.71%), Postives = 24/42 (57.14%), Query Frame = -1 
Query:  366 RKITDNERSLIIRKYEDQKSIQLISEELGINVKMVTSIIRLY 491
            +K++ N+R  II K  +  S+  I+    IN + V SI+R Y
Sbjct:   59 QKVSINDRERIIEKKLESYSMSAIASMYRINYQTVNSIVRRY 100
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BLAST of SMED30029023 vs. TrEMBL
Match: A0A0C2MJ68 (Uncharacterized protein OS=Thelohanellus kitauei OX=669202 GN=RF11_11236 PE=4 SV=1)

HSP 1 Score: 57.3806 bits (137), Expect = 5.473e-7
Identity = 34/122 (27.87%), Postives = 63/122 (51.64%), Query Frame = -2 
Query:    2 TGRVNAMTQRRPRESIITEEAKMFIRSKIESDVSVTLGALKLKLQASLNIICSTTTIDGAIRDLNYSFNRV*LVQERINVAANIE*RFNYAGRYLGYDEDK--VIFLNEFSLSCSTRQKYGR 361
            +G++    + R R   +    +  +   +E D S+TL  L  +   + NI  S  T+   +++ NYSF ++  + ER N+A+ I  R +Y  +YL Y      ++F++E  ++ S R+ YGR
Sbjct:   19 SGKITKAPKGRDRAKSLNNSQESILCYIVEDDCSLTLENLSDRFFNAKNIRISKNTVARYLKEYNYSFKKIKFIPERRNIASTIRERHDYVIKYLEYSASNRFILFIDETGVNVSMRRNYGR 140
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BLAST of SMED30029023 vs. TrEMBL
Match: A0A0C2JI12 (DDE_3 domain-containing protein OS=Thelohanellus kitauei OX=669202 GN=RF11_01522 PE=4 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 8.160e-7
Identity = 35/127 (27.56%), Postives = 68/127 (53.54%), Query Frame = -2 
Query:    2 FINTGRVNAMTQRRPRESIITEEAKMFIRSKIESDVSVTLGALKLKLQASLNIICSTTTIDGAIRDLNYSFNRV*LVQERINVAANIE*RFNYAGRYL----GYDEDKVIFLNEFSLSCSTRQKYGR 370
            F  +GR+++  +   +   + E+ K  I+S ++ +  + L  +  K+Q  ++I    +TID  ++  +YS+ RV ++ ER N  + +  R  YA RYL     + E + IF++E  ++ S R  +GR
Sbjct:   45 FHQSGRIDSNKRGYIQPEKLNEDQKERIKSWVDDNAGIPLRTIVTKVQEEMDISVGKSTIDRILQRFHYSWKRVSIIPERRNNESTLNIRERYATRYLELLQSFREHQFIFIDECGVNISMRTSHGR 171
[Close]
BLAST of SMED30029023 vs. TrEMBL
Match: A0A4Q9M1Z3 (DDE-like endonuclease OS=Hamiltosporidium tvaerminnensis OX=1176355 GN=CWI38_0243p0030 PE=4 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 8.531e-7
Identity = 35/96 (36.46%), Postives = 54/96 (56.25%), Query Frame = -2 
Query:    2 IESDVSVTLGALKLKLQASLNIICSTTTIDGAIRDLNYSFNRV*LVQERINVAANIE*RFNYAGRY----LGYDEDKVIFLNEFSLSCSTRQKYGR 277
            ++ + + TL  L   ++ + NI  ST+TID A+R+ +Y+  RV LV ER N+ + IE R NYA  +    +  D+   +FL+E   S  TR   GR
Sbjct:  107 VDLECTKTLYKLAEWVKCTFNIDVSTSTIDRALREFHYTLKRVTLVHERRNILSTIELRTNYATSFRELEVDNDDKNFVFLDEVGFSVVTRPSRGR 202
[Close]
BLAST of SMED30029023 vs. Planmine SMEST
Match: SMESG000045086.1 (SMESG000045086.1)

HSP 1 Score: 77.411 bits (189), Expect = 6.000e-18
Identity = 42/111 (37.84%), Postives = 66/111 (59.46%), Query Frame = -2 
Query:   38 FINTGRVNAMTQRRPRESIITEEAKMFIRSKIESDVSVTLGALKLKLQASLNIICSTTTIDGAIRDLNYSFNRV*LVQERINVAANIE*RFNYAGRYLGYDEDKVIFLNEF 370
            FI TGR++A+T R P+   I+E+    I++KI+ DVS+TL +L+  L     ++ S +TI   I+  N+S   V LV    N   NI+ RF Y   YL  +E++ IF+++F
Sbjct:   50 FIKTGRIDAITNRLPKIKKISEDIDRVIKTKIDEDVSITLKSLQRCLSLEKGLVVSVSTIKRTIKSFNFSLKGVVLVPVARNSEVNIKKRFGYTNDYLLLNEERCIFVDDF 160
The following BLAST results are available for this feature:
BLAST of SMED30029023 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 SMED30029023 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 SMED30029023 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 SMED30029023 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 SMED30029023 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 SMED30029023 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 SMED30029023 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 SMED30029023 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0C2JKS95.137e-835.58Uncharacterized protein OS=Thelohanellus kitauei O... [more]
A0A4Q9LYZ41.393e-731.15Putative DDE endonuclease OS=Hamiltosporidium tvae... [more]
A0A0C2MJ685.473e-727.87Uncharacterized protein OS=Thelohanellus kitauei O... [more]
A0A0C2JI128.160e-727.56DDE_3 domain-containing protein OS=Thelohanellus k... [more]
A0A4Q9M1Z38.531e-736.46DDE-like endonuclease OS=Hamiltosporidium tvaermin... [more]
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BLAST of SMED30029023 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 SMED30029023 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 SMED30029023 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 SMED30029023 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 SMED30029023 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 SMED30029023 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000045086.16.000e-1837.84SMESG000045086.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029023 ID=SMED30029023|Name=SMED30029023|organism=Schmidtea mediterranea sexual|type=transcript|length=608bp
TTCGGCCATATTTTTGCCGGGTTGAACAGCTCAGACTAAATTCATTAAGG
AAAATTACTTTATCTTCATCATATCCAAGATATCTACCGGCATAATTAAA
TCGCTACTCTATATTTGCAGCAACATTTATTCTCTCTTGTACAAGTTAGA
CACGATTAAAAGAGTAATTCAAATCTCTTATTGCACCGTCGATAGTGGTT
GTTGAGCATATGATATTTAAGCTTGCCTGAAGTTTCAATTTTAACGCTCC
TAAAGTTACGGAAACATCACTTTCAATTTTGGACCTGATAAACATCTTTG
CCTCTTCTGTTATTATACTTTCCCGTGGTCGTCTTTGTGTCATCGCATTT
ACTCTCCCAGTGTTTATAAAGTCTTATTATAGAAGTGACCATTTTAACGT
TTATGCCGAGTTCTTCAGAAATAAGTTGAATGCTTTTCTGATCTTCATAT
TTACGGATAATAAGTGACCTTTCGTTGTCTGTAATTTTCCTATGTAAATT
GGCTTCTGCTGTCTGCATATGTAATTTTGGGATTAAAATATATTTGGAAT
TGATTGGAATGAATTTTGAATTGATTGAAATATGTTTGCAAAGGATTGAA
TTAATAGG
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protein sequence of SMED30029023-orf-1

>SMED30029023-orf-1 ID=SMED30029023-orf-1|Name=SMED30029023-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=112bp
PINSILCKHISINSKFIPINSKYILIPKLHMQTAEANLHRKITDNERSLI
IRKYEDQKSIQLISEELGINVKMVTSIIRLYKHWESKCDDTKTTTGKYNN
RRGKDVYQVQN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
Vocabulary: INTERPRO
TermDefinition
IPR021036Ribosomal_S35_mit