SMED30009134

Overview
NameSMED30009134
Smed IDSMED30009134
Length (bp)553
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 SMED30009134 (SMED30009134) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30009134 (SMED30009134) 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 SMED30009134 (SMED30009134) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30009134 (SMED30009134) 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



SMED30009134

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30009134SMESG000022478.1 SmedASXL_019246SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
neoblastSMED30009134SMESG000022478.1 dd_Smed_v4_4419_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30009134SMESG000022478.1 dd_Smed_v4_4419_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30009134SMESG000022478.1 dd_Smed_v4_4419_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
Alignments
SMED30009134 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001622:107064..107654 +2705
v31.024091:894..1484 -2687
Homology
[Close]
BLAST of SMED30009134 vs. TrEMBL
Match: A0A3P6H0A9 (Uncharacterized protein OS=Mesocestoides corti OX=53468 GN=MCOS_LOCUS6985 PE=4 SV=1)

HSP 1 Score: 73.1738 bits (178), Expect = 4.324e-13
Identity = 39/100 (39.00%), Postives = 60/100 (60.00%), Query Frame = -1 
Query:  128 KREVKVYFDKNGNPDINMEKVKDRFFRLRSGIYSHLPIPKYVRKG---RKPDWLTMENKNYVLTGKDKSFMLDNMNNEYYRSSKYYPEDPFDPYHERPGL 418
            ++E K Y+ ++G  D  ++ V DRF RLR G Y H   P+  R+    RK  W+  +   ++LT +  SF LDNM N ++R  ++YPED ++PYH R G+
Sbjct:   36 RQEAKRYWAEDGTHDPPVKVVIDRFKRLRWGAYIH---PRAGRRKHLYRKNPWVVAKRDEHILTSRALSFCLDNMLNAHWRKPRFYPEDIYEPYHRRTGV 132
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BLAST of SMED30009134 vs. TrEMBL
Match: A0A183STJ8 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=SSLN_LOCUS7546 PE=4 SV=1)

HSP 1 Score: 73.1738 bits (178), Expect = 1.115e-12
Identity = 35/96 (36.46%), Postives = 57/96 (59.38%), Query Frame = -1 
Query:  131 KREVKVYFDKNGNPDINMEKVKDRFFRLRSGIYSHLPIPKYVRKGRKPDWLTMENKNYVLTGKDKSFMLDNMNNEYYRSSKYYPEDPFDPYHERPG 418
             REVK Y+ ++G  D  ++   DRF RLR G + H    +     RK  W+  +   ++LT +  SF++DN+ N Y+R  ++YP+D ++PYH+R G
Sbjct:   58 SREVKRYWTEDGVRDPPLQDAVDRFKRLRWGAFIHARAGRRKHLYRKNPWVVAKKDEHILTNRATSFLVDNLVNRYWRRPQFYPQDIYEPYHKRTG 153
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BLAST of SMED30009134 vs. TrEMBL
Match: A0A0R3X5E9 (Uncharacterized protein OS=Hydatigena taeniaeformis OX=6205 PE=4 SV=1)

HSP 1 Score: 71.2478 bits (173), Expect = 1.315e-12
Identity = 37/97 (38.14%), Postives = 56/97 (57.73%), Query Frame = -1 
Query:  128 KREVKVYFDKNGNPDINMEKVKDRFFRLRSGIYSHLPIPKYVRKGRKPDWLTMENKNYVLTGKDKSFMLDNMNNEYYRSSKYYPEDPFDPYHERPGL 418
            ++E K Y+ ++G  D  ++ V DRF RLR G Y H    +     RK  W+  +   ++LT +  SF LDN+ N  +R  K+YPED ++PYH R G+
Sbjct:   18 RQEAKRYWAEDGTFDPPVQVVIDRFKRLRWGAYIHPRAGRRKHLYRKNPWIVAKKDEHILTSRAMSFALDNLLNAEWRRPKFYPEDIYEPYHRRTGV 114
[Close]
BLAST of SMED30009134 vs. TrEMBL
Match: A0A3P7FWT1 (Uncharacterized protein OS=Hydatigena taeniaeformis OX=6205 GN=TTAC_LOCUS8673 PE=4 SV=1)

HSP 1 Score: 71.2478 bits (173), Expect = 1.358e-12
Identity = 37/97 (38.14%), Postives = 56/97 (57.73%), Query Frame = -1 
Query:  128 KREVKVYFDKNGNPDINMEKVKDRFFRLRSGIYSHLPIPKYVRKGRKPDWLTMENKNYVLTGKDKSFMLDNMNNEYYRSSKYYPEDPFDPYHERPGL 418
            ++E K Y+ ++G  D  ++ V DRF RLR G Y H    +     RK  W+  +   ++LT +  SF LDN+ N  +R  K+YPED ++PYH R G+
Sbjct:   18 RQEAKRYWAEDGTFDPPVQVVIDRFKRLRWGAYIHPRAGRRKHLYRKNPWIVAKKDEHILTSRAMSFALDNLLNAEWRRPKFYPEDIYEPYHRRTGV 114
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BLAST of SMED30009134 vs. TrEMBL
Match: A0A0X3Q3E7 (39S ribosomal protein L35 OS=Schistocephalus solidus OX=70667 GN=RM35 PE=4 SV=1)

HSP 1 Score: 71.633 bits (174), Expect = 2.620e-12
Identity = 34/96 (35.42%), Postives = 58/96 (60.42%), Query Frame = -1 
Query:  128 REVKVYFDKNGNPDINMEKVKDRFFRLRSGIYSHLPIPKYVRKGRKPDWLTMENKNYVLTGKDKSFMLDNMNNEYYRSSKYYPEDPFDPYHERPGL 415
            REVK Y+ ++G  D  ++   DRF RLR G + H    +     RK  W+  +   ++LT +  SF+++N+ N Y+R  ++YP+D ++PYH+R G+
Sbjct:   57 REVKRYWTEDGVRDPPLQDAVDRFKRLRWGAFIHARAGRRKHLYRKNPWVVAKKDEHILTNRATSFLVNNLVNRYWRRPQFYPQDIYEPYHKRTGV 152
[Close]
BLAST of SMED30009134 vs. Ensembl Sea Lamprey
Match: mrpl35 (mitochondrial ribosomal protein L35 [Source:ZFIN;Acc:ZDB-GENE-060929-1082])

HSP 1 Score: 50.8322 bits (120), Expect = 3.405e-9
Identity = 29/95 (30.53%), Postives = 46/95 (48.42%), Query Frame = -1 
Query:  125 VYFDKNGNPDINMEKVKDRFFRLRSGIY--SHLPIPKYVRKGRKPDWLTMENKNYVLTGKDKSFMLDNMNNEYYRSSKYYPEDPFDPYHERPGLK 403
            +YF K       ++ V  RF RL  G++        K + K RKP       + +VL  K +S +LD M  ++++  K+Y  DP+  YHER   +
Sbjct:   11 IYFSKGRGKRKTVKAVVKRFLRLDCGLWLRRQAGCKKRLWKKRKPR--IRRLRQHVLCNKWQSKLLDKMVTDFWKRRKWYENDPYQLYHERTNFR 103
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BLAST of SMED30009134 vs. Planmine SMEST
Match: SMESG000022478.1 (SMESG000022478.1)

HSP 1 Score: 244.973 bits (624), Expect = 3.310e-84
Identity = 137/137 (100.00%), Postives = 137/137 (100.00%), Query Frame = -1 
Query:  104 MNFLFSYKXXXXXXXXXXXXXXSQILYLRRPLKREVKVYFDKNGNPDINMEKVKDRFFRLRSGIYSHLPIPKYVRKGRKPDWLTMENKNYVLTGKDKSFMLDNMNNEYYRSSKYYPEDPFDPYHERPGLKKTKKYHP 514
            MNFLFSYKSLLSLNIISRSISTSQILYLRRPLKREVKVYFDKNGNPDINMEKVKDRFFRLRSGIYSHLPIPKYVRKGRKPDWLTMENKNYVLTGKDKSFMLDNMNNEYYRSSKYYPEDPFDPYHERPGLKKTKKYHP
Sbjct:    1 MNFLFSYKSLLSLNIISRSISTSQILYLRRPLKREVKVYFDKNGNPDINMEKVKDRFFRLRSGIYSHLPIPKYVRKGRKPDWLTMENKNYVLTGKDKSFMLDNMNNEYYRSSKYYPEDPFDPYHERPGLKKTKKYHP 137
[Close]
BLAST of SMED30009134 vs. Planmine SMEST
Match: SMESG000022478.1 (SMESG000022478.1)

HSP 1 Score: 180.644 bits (457), Expect = 1.741e-59
Identity = 88/88 (100.00%), Postives = 88/88 (100.00%), Query Frame = -1 
Query:  104 MEKVKDRFFRLRSGIYSHLPIPKYVRKGRKPDWLTMENKNYVLTGKDKSFMLDNMNNEYYRSSKYYPEDPFDPYHERPGLKKTKKYHP 367
            MEKVKDRFFRLRSGIYSHLPIPKYVRKGRKPDWLTMENKNYVLTGKDKSFMLDNMNNEYYRSSKYYPEDPFDPYHERPGLKKTKKYHP
Sbjct:    1 MEKVKDRFFRLRSGIYSHLPIPKYVRKGRKPDWLTMENKNYVLTGKDKSFMLDNMNNEYYRSSKYYPEDPFDPYHERPGLKKTKKYHP 88
The following BLAST results are available for this feature:
BLAST of SMED30009134 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 SMED30009134 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 SMED30009134 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 SMED30009134 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 SMED30009134 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 SMED30009134 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 SMED30009134 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 SMED30009134 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A3P6H0A94.324e-1339.00Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A183STJ81.115e-1236.46Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A0R3X5E91.315e-1238.14Uncharacterized protein OS=Hydatigena taeniaeformi... [more]
A0A3P7FWT11.358e-1238.14Uncharacterized protein OS=Hydatigena taeniaeformi... [more]
A0A0X3Q3E72.620e-1235.4239S ribosomal protein L35 OS=Schistocephalus solid... [more]
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BLAST of SMED30009134 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 SMED30009134 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 1
Match NameE-valueIdentityDescription
mrpl353.405e-930.53mitochondrial ribosomal protein L35 [Source:ZFIN;A... [more]
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BLAST of SMED30009134 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 SMED30009134 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 SMED30009134 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 SMED30009134 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000022478.13.310e-84100.00SMESG000022478.1[more]
SMESG000022478.11.741e-59100.00SMESG000022478.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009134 ID=SMED30009134|Name=SMED30009134|organism=Schmidtea mediterranea sexual|type=transcript|length=553bp
TTTAATATTAATAGTTTATACATTTCCAGTTTAGTATTTGGTAAATGAAT
AAGCAATGGCATAAAAGAACATTTCATCACAAAAACTGTTAATATTGTTT
TCAGGGATGATATTTTTTAGTTTTTTTCAAACCAGGTCTTTCGTGATAAG
GGTCGAACGGATCTTCTGGATAATATTTAGAAGACCTATAATATTCATTG
TTCATGTTGTCGAGCATAAAAGATTTATCCTTTCCAGTTAAAACATAATT
TTTATTTTCCATAGTAAGCCAATCAGGTTTCCTTCCTTTCCGGACATATT
TTGGAATTGGTAAATGACTATAAATGCCAGATCTCAATCTGAAAAATCTA
TCTTTAACCTTCTCCATGTTGATATCTGGATTTCCATTCTTATCAAAATA
AACTTTAACTTCCCTTTTTAAAGGTCTCCTTAAATATAAAATTTGAGATG
TTGAAATTGATCGACTAATAATATTCAGTGATAACAAAGACTTGTAAGAA
AATAAAAAATTCATTTTTGAAATTTGCCTTTGATAATTAATTATTTAAGG
AGA
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protein sequence of SMED30009134-orf-1

>SMED30009134-orf-1 ID=SMED30009134-orf-1|Name=SMED30009134-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=138bp
MNFLFSYKSLLSLNIISRSISTSQILYLRRPLKREVKVYFDKNGNPDINM
EKVKDRFFRLRSGIYSHLPIPKYVRKGRKPDWLTMENKNYVLTGKDKSFM
LDNMNNEYYRSSKYYPEDPFDPYHERPGLKKTKKYHP*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal
PLANA:0000429neoblast
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR019338Ribosomal-L35_mit
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR019338Ribosomal protein L35, mitochondrialPANTHERPTHR1590939S RIBOSOMAL PROTEIN L35, MITOCHONDRIALcoord: 35..131