SMED30008381

Overview
NameSMED30008381
Smed IDSMED30008381
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 SMED30008381 (SMED30008381) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30008381 (SMED30008381) 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 SMED30008381 (SMED30008381) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008381 (SMED30008381) 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.
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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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Homology
BLAST of SMED30008381 vs. TrEMBL
Match: A0A0L8GX06 (GIY-YIG domain-containing protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22026335mg PE=4 SV=1)

HSP 1 Score: 41.9726 bits (97), Expect = 1.232e-6
Identity = 47/172 (27.33%), Postives = 72/172 (41.86%), Query Frame = 1
Query:  211 KNEKQSIANRCTKGKENYEQQLQFDKVLRRNRYHKENIERMDSKPKIPMDRTQKKDT---FI*RSHLS--VTRSTSRSGKSSITLAFQFVYHTSLGY*GKHWQTTQKKRTFA*WKIARHQRKCASEKTLQKC---------------IM*NACKEIYIGSTLRNLHQRIKEH 666
            +NE   I  +C+K ++       F  +L+ NRY +  + ++   P+ P  RT +K +   F+   H S  +TRS  R+ +    L  Q   H+     G                +A+ Q K +S+ TL  C               I  N C + Y+GST R LH  IKEH
Sbjct:   62 RNELAHIQGKCSKTEDKVTHTTCFLDILKTNRYPRSIVNQL-KYPRRPTHRTHRKPSNTCFLKIPHFSKRITRSIRRAIRRE-GLDIQLA-HSGPSLRG---------------HLAKKQAKDSSQCTLANCPIRDTDLCQRVNVYRIQCNKCNKFYVGSTTRPLHVHIKEH 215          

HSP 2 Score: 40.0466 bits (92), Expect = 1.232e-6
Identity = 22/56 (39.29%), Postives = 35/56 (62.50%), Query Frame = 2
Query:   35 DIKFEIEYPDENGSLNLLDLRIKIDVDTPT-*GFYKKSARKEIFMHQKLLLPIYSK 199
            +IKF +EY    GSL+LLDL++ I  +      FY+K+A K++F+     LP+ +K
Sbjct:    2 NIKFTLEYSSITGSLSLLDLKLNITEEGEIHIEFYRKAASKDMFVQYNSALPLGAK 57          
BLAST of SMED30008381 vs. TrEMBL
Match: A0A0L8GYC4 (GIY-YIG domain-containing protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22026335mg PE=4 SV=1)

HSP 1 Score: 41.5874 bits (96), Expect = 1.428e-6
Identity = 47/172 (27.33%), Postives = 72/172 (41.86%), Query Frame = 1
Query:  211 KNEKQSIANRCTKGKENYEQQLQFDKVLRRNRYHKENIERMDSKPKIPMDRTQKKDT---FI*RSHLS--VTRSTSRSGKSSITLAFQFVYHTSLGY*GKHWQTTQKKRTFA*WKIARHQRKCASEKTLQKC---------------IM*NACKEIYIGSTLRNLHQRIKEH 666
            +NE   I  +C+K ++       F  +L+ NRY +  + ++   P+ P  RT +K +   F+   H S  +TRS  R+ +    L  Q   H+     G                +A+ Q K +S+ TL  C               I  N C + Y+GST R LH  IKEH
Sbjct:   62 RNELAHIQGKCSKTEDKVTHTTCFLDILKTNRYPRSIVNQL-KYPRRPTHRTHRKPSNTCFLKIPHFSKRITRSIRRAIRRE-GLDIQLA-HSGPSLRG---------------HLAKKQAKDSSQCTLANCPIRDTDLCQRVNVYRIQCNKCNKFYVGSTTRPLHVHIKEH 215          

HSP 2 Score: 40.0466 bits (92), Expect = 1.428e-6
Identity = 22/56 (39.29%), Postives = 35/56 (62.50%), Query Frame = 2
Query:   35 DIKFEIEYPDENGSLNLLDLRIKIDVDTPT-*GFYKKSARKEIFMHQKLLLPIYSK 199
            +IKF +EY    GSL+LLDL++ I  +      FY+K+A K++F+     LP+ +K
Sbjct:    2 NIKFTLEYSSITGSLSLLDLKLNITEEGEIHIEFYRKAASKDMFVQYNSALPLGAK 57          
BLAST of SMED30008381 vs. TrEMBL
Match: A0A3M6TYW2 (GIY-YIG domain-containing protein OS=Pocillopora damicornis OX=46731 GN=pdam_00017828 PE=4 SV=1)

HSP 1 Score: 50.447 bits (119), Expect = 4.674e-6
Identity = 28/75 (37.33%), Postives = 41/75 (54.67%), Query Frame = 3
Query:  360 QNTKKRYFYLKIPFIGYTLDFKIGKELNHTGFPIRVSHKSWILRQALANNTKKENICIMENCQTSK-KMCFRKNV 581
            Q   K + YLKIP I   L+ KI         P+R++HKS+ +RQAL++NT  E  C   NC  +   +C ++N 
Sbjct:  414 QTQTKEWHYLKIPCISDQLNRKITGIFKRGNIPVRIAHKSYTMRQALSHNT-TERKCNRPNCPIADTNLCLQRNT 487          

HSP 2 Score: 29.6462 bits (65), Expect = 4.674e-6
Identity = 13/21 (61.90%), Postives = 14/21 (66.67%), Query Frame = 1
Query:  604 ACKEIYIGSTLRNLHQRIKEH 666
            AC E YIGS  + LH R KEH
Sbjct:  495 ACGEYYIGSMTQFLHDRTKEH 515          
BLAST of SMED30008381 vs. Planmine SMEST
Match: SMESG000069853.1 (SMESG000069853.1)

HSP 1 Score: 110.923 bits (276), Expect = 7.803e-28
Identity = 75/149 (50.34%), Postives = 88/149 (59.06%), Query Frame = 2
Query:    2 EIFHIFNVAHPDIKFEIEYPDENGSLNLLDLRIKIDVDTPT*GFYKKSARKEIFMHQKLLLPIYSKGML*RTRSR--A*PIGVLKEKRIMNNNYNSIKS---YAETDTTRRTSKEWIQNQKYLWTEHKKKILLSKDPIYRLHARLQDRE 433
            EIFHI N AHP+IKFEIEYPDENGSLNLLDLRIKIDVDTPT  FYK SA +EIFMHQ+  LP   K  + R   +  A     +K+      N+N + S   Y   D     SK      +   T+ K++ILLSK PI   H R  D E
Sbjct:  162 EIFHISNAAHPNIKFEIEYPDENGSLNLLDLRIKIDVDTPTFEFYKISAHEEIFMHQRSSLPYLQKVYVIRNEKQRIANRCTEVKDNYKQQLNFNVVLSKNGYHNEDIETMNSKPKTPIDR---TQKKEEILLSKHPI---HQRDSDLE 304          
BLAST of SMED30008381 vs. Planmine SMEST
Match: SMESG000049225.1 (SMESG000049225.1)

HSP 1 Score: 103.605 bits (257), Expect = 1.100e-24
Identity = 62/118 (52.54%), Postives = 74/118 (62.71%), Query Frame = 2
Query:    2 EIFHIFNVAHPDIKFEIEYPDENGSLNLLDLRIKIDVDTPT*GFYKKSARKEIFMHQKLLLPIYSK-GML*RTRSRA*PIGVLKEKRIMNNN-YNSIKSYAETDTTRRTSKEWIQNQK 349
            EIFHIFN  HP+IKFEIEYPD NGSLNLLDLRIKIDVDTPT    KKSA +EIFMHQ+  LP   K   +   + R     +  +K+   N  YNS  + A ++     S+E I  QK
Sbjct:  170 EIFHIFNEDHPEIKFEIEYPDINGSLNLLDLRIKIDVDTPTYELCKKSAGEEIFMHQRSALPNLQKVNFIKNDKQRIANRSLFDQKKFNRNAMYNSYTNLATSNKMEAFSREDILKQK 287          
The following BLAST results are available for this feature:
BLAST of SMED30008381 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 SMED30008381 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 SMED30008381 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 SMED30008381 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 SMED30008381 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 SMED30008381 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 SMED30008381 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 SMED30008381 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A0L8GX061.232e-627.33GIY-YIG domain-containing protein OS=Octopus bimac... [more]
A0A0L8GYC41.428e-627.33GIY-YIG domain-containing protein OS=Octopus bimac... [more]
A0A3M6TYW24.674e-637.33GIY-YIG domain-containing protein OS=Pocillopora d... [more]
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BLAST of SMED30008381 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 SMED30008381 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 SMED30008381 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 SMED30008381 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 SMED30008381 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 SMED30008381 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000069853.17.803e-2850.34SMESG000069853.1[more]
SMESG000049225.11.100e-2452.54SMESG000049225.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008381 ID=SMED30008381|Name=SMED30008381|organism=Schmidtea mediterranea sexual|type=transcript|length=959bp
AGAAATATTTCATATATTCAATGTAGCGCATCCGGATATAAAGTTCGAAA
TAGAATATCCGGACGAAAATGGATCCCTCAATCTACTAGATTTAAGAATA
AAAATAGATGTAGACACACCAACCTAAGGATTCTACAAGAAATCAGCTCG
CAAAGAAATATTTATGCACCAAAAATTATTACTTCCGATTTACAGCAAAG
GAATGTTATAAAGAACGAGAAGCAGAGCATAGCCAATCGGTGTACTAAAG
GAAAAGAGAATTATGAACAACAATTACAATTCGATAAAGTCCTACGCAGA
AACAGATACCACAAGGAGAACATCGAAAGAATGGATTCAAAACCAAAAAT
ACCTATGGACAGAACACAAAAAAAAGATACTTTTATCTAAAGATCCCATT
TATCGGTTACACGCTCGACTTCAAGATCGGGAAAGAGCTCAATCACACTG
GCTTTCCAATTCGTGTATCACACAAGTCTTGGATACTGAGGCAAGCACTG
GCAAACAACACAAAAAAAGAGAACATTTGCATAATGGAAAATTGCCAGAC
ATCAAAGAAAATGTGCTTCAGAAAAAACGTTACAAAAATGCATCATGTGA
AATGCATGCAAAGAAATATACATTGGAAGTACACTCAGGAACCTACACCA
AAGAATTAAAGAACACCCGGATCCTGTAGACATTTTTAACAATGCCAACC
AATGAAGGAAAGTTAAAGTATTTCAATCAAAATCTTGGTCAAAATAATCT
TAAGAGCAATTCTAATCTAAGATAAATATCCAACAATTAACACGAAAAAA
GAAGTCAGTGAAATCGTCAGTTTGATCTGTTGTTGAGTTTGATAAAAGGA
TAAAAATTCAAAAGAAAACTTATAATCAGATATAATTTATTTAAGAAAAA
AGAAAACATGCAAAAGGTTTTAGGAACTCTTTTCAGTAAAAATCAAAGTT
TTATAGAGG
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protein sequence of SMED30008381-orf-1

>SMED30008381-orf-1 ID=SMED30008381-orf-1|Name=SMED30008381-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=139bp
MNNNYNSIKSYAETDTTRRTSKEWIQNQKYLWTEHKKKILLSKDPIYRLH
ARLQDRERAQSHWLSNSCITQVLDTEASTGKQHKKREHLHNGKLPDIKEN
VLQKKRYKNASCEMHAKKYTLEVHSGTYTKELKNTRIL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell