SMED30020715

Overview
NameSMED30020715
Smed IDSMED30020715
Length (bp)935
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 SMED30020715 (SMED30020715) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020715 (SMED30020715) 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 SMED30020715 (SMED30020715) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30020715 (SMED30020715) 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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Alignments
SMED30020715 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003380:23092..24077 -4641
Homology
BLAST of SMED30020715 vs. TrEMBL
Match: A0A1I8HAV3 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 66.6254 bits (161), Expect = 9.887e-10
Identity = 30/48 (62.50%), Postives = 38/48 (79.17%), Query Frame = 3
Query:  669 KEKRIARIVMVVAILLLTMCVILVGVTLSMSDYIDTMVKELHQKRNAN 812
            K+KRIAR+VM VA +LL MCVILVGVTLSMSD+ID +V++   K   +
Sbjct:   82 KQKRIARVVMAVAFVLLAMCVILVGVTLSMSDHIDDLVRKAQLKDKGD 129          
BLAST of SMED30020715 vs. TrEMBL
Match: A0A1I8I650 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 66.6254 bits (161), Expect = 1.390e-8
Identity = 30/44 (68.18%), Postives = 37/44 (84.09%), Query Frame = 3
Query:  669 KEKRIARIVMVVAILLLTMCVILVGVTLSMSDYIDTMVKELHQK 800
            K+KRIAR+VM VA +LL MCVILVGVTLSMSD+ID +V++   K
Sbjct:   82 KQKRIARVVMAVAFVLLAMCVILVGVTLSMSDHIDDLVRKAQLK 125          
BLAST of SMED30020715 vs. TrEMBL
Match: A0A1I8HI58 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 62.3882 bits (150), Expect = 5.839e-8
Identity = 27/40 (67.50%), Postives = 33/40 (82.50%), Query Frame = 3
Query:  669 KEKRIARIVMVVAILLLTMCVILVGVTLSMSDYIDTMVKE 788
            K++R+ARIVM VA  LL MCVIL+GVTLSMSD +D M K+
Sbjct:  114 KQRRVARIVMAVAFALLAMCVILIGVTLSMSDRVDEMDKQ 153          
BLAST of SMED30020715 vs. TrEMBL
Match: A0A1I8J7J7 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 2.645e-7
Identity = 25/42 (59.52%), Postives = 36/42 (85.71%), Query Frame = 3
Query:  663 SPKEKRIARIVMVVAILLLTMCVILVGVTLSMSDYIDTMVKE 788
            + K+KR+AR+VM VA +LL+MC +L+ VTLSMSD+ID MV++
Sbjct:   96 TAKQKRVARVVMAVAFILLSMCFVLIVVTLSMSDHIDRMVRK 137          
BLAST of SMED30020715 vs. TrEMBL
Match: A0A448WRF2 (Uncharacterized protein OS=Protopolystoma xenopodis OX=117903 GN=PXEA_LOCUS11811 PE=4 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 1.096e-6
Identity = 26/41 (63.41%), Postives = 32/41 (78.05%), Query Frame = 3
Query:  651 QETQSPKEKRIARIVMVVAILLLTMCVILVGVTLSMSDYID 773
            +E Q+P+E+RIARIVMVVA  L  MC +LV V L MSD+ID
Sbjct:  151 EENQTPRERRIARIVMVVAFFLFMMCFLLVAVNLMMSDHID 191          
BLAST of SMED30020715 vs. Planmine SMEST
Match: SMESG000016957.1 (SMESG000016957.1)

HSP 1 Score: 486.493 bits (1251), Expect = 5.404e-176
Identity = 236/237 (99.58%), Postives = 236/237 (99.58%), Query Frame = 3
Query:  189 MFTDEIGLQPLKVKKEFRRFSIDEIDLQKEQLSFVDHCQFNFQPNTNLSEPNNPSIALTQSLCFIDSPSQIPLPNSMSSALYIKPCCLSAKPSFSAENEKEILHLLYDEPYSNLMPLTIADENGIRYATLPHGKVIDISSLYFKNNVSSSMYDIQETQSPKEKRIARIVMVVAILLLTMCVILVGVTLSMSDYIDTMVKELHQKRNANPIVLPKSNNTSRNLALYSYLINTTGKTGA 899
            MFTDEIGLQPLKVKKEFRRFSIDEIDLQKEQLSFVDHCQFNFQPNTNLSEPNNPSIALTQSLCFIDSPSQIPLPNSMSSALYIKPCCLSAKPSFS ENEKEILHLLYDEPYSNLMPLTIADENGIRYATLPHGKVIDISSLYFKNNVSSSMYDIQETQSPKEKRIARIVMVVAILLLTMCVILVGVTLSMSDYIDTMVKELHQKRNANPIVLPKSNNTSRNLALYSYLINTTGKTGA
Sbjct:    1 MFTDEIGLQPLKVKKEFRRFSIDEIDLQKEQLSFVDHCQFNFQPNTNLSEPNNPSIALTQSLCFIDSPSQIPLPNSMSSALYIKPCCLSAKPSFSTENEKEILHLLYDEPYSNLMPLTIADENGIRYATLPHGKVIDISSLYFKNNVSSSMYDIQETQSPKEKRIARIVMVVAILLLTMCVILVGVTLSMSDYIDTMVKELHQKRNANPIVLPKSNNTSRNLALYSYLINTTGKTGA 237          
BLAST of SMED30020715 vs. Planmine SMEST
Match: SMESG000029677.1 (SMESG000029677.1)

HSP 1 Score: 65.0846 bits (157), Expect = 6.832e-13
Identity = 29/62 (46.77%), Postives = 45/62 (72.58%), Query Frame = 3
Query:  615 FKNNVSSSMYDIQETQSPKEKRIARIVMVVAILLLTMCVILVGVTLSMSDYIDTMVKELHQK 800
            ++++   S Y  +  ++ K +R+ R+VM + I+LL M VILVG+TLS+S++ID MVKE HQK
Sbjct:   49 YRSDSRRSSYQNELARNLKNRRMTRLVMAIGIVLLVMSVILVGITLSLSEHIDKMVKETHQK 110          
BLAST of SMED30020715 vs. Planmine SMEST
Match: SMESG000026902.1 (SMESG000026902.1)

HSP 1 Score: 46.2098 bits (108), Expect = 7.160e-6
Identity = 25/66 (37.88%), Postives = 45/66 (68.18%), Query Frame = 3
Query:  609 LYFKNNVSSSMYDI--QETQSPKEKRIARIVMVVAILLLTMCVILVGVTLSMSDYIDTMVKELHQK 800
            L F +  S  ++ +  Q+T + ++KR  ++V+VV  +LL M ++L+ V+LS+S++ID MV+E H K
Sbjct:   86 LAFSHQSSRHLWTLKRQDTLNLRDKRTTKVVVVVGTMLLIMSLVLIAVSLSLSEHIDRMVREHHLK 151          
The following BLAST results are available for this feature:
BLAST of SMED30020715 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 SMED30020715 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 SMED30020715 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 SMED30020715 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 SMED30020715 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 SMED30020715 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 SMED30020715 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 SMED30020715 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1I8HAV39.887e-1062.50Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8I6501.390e-868.18Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8HI585.839e-867.50Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8J7J72.645e-759.52Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A448WRF21.096e-663.41Uncharacterized protein OS=Protopolystoma xenopodi... [more]
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BLAST of SMED30020715 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 SMED30020715 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 SMED30020715 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 SMED30020715 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 SMED30020715 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 SMED30020715 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000016957.15.404e-17699.58SMESG000016957.1[more]
SMESG000029677.16.832e-1346.77SMESG000029677.1[more]
SMESG000026902.17.160e-637.88SMESG000026902.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020715 ID=SMED30020715|Name=SMED30020715|organism=Schmidtea mediterranea sexual|type=transcript|length=935bp
GGAGTTTGCAATAATAATTCTGTCCAATAATACCTATTATTTTATTTTCT
CTCATTTTTCTTTTATATGGGAGTTAATTTTTTCAAACTGGTGGAATATC
AGAGGAAAAAAAATTTACAGAATATTTAAAAAATTCTTCGTTCGAATATC
TCGTCGTTTTGGTTTTGGTTTGGGTTTCAAAATCGGAAATGTTTACGGAT
GAAATCGGCTTGCAACCGCTAAAAGTCAAAAAGGAATTTCGTAGATTTTC
AATTGACGAAATTGACTTGCAAAAAGAACAGTTGTCATTTGTAGATCATT
GTCAGTTCAATTTCCAACCGAACACCAATCTGTCAGAACCGAATAATCCT
TCGATTGCTTTAACACAATCTCTGTGTTTTATTGACTCTCCATCACAGAT
CCCTTTACCGAATTCGATGTCTTCAGCACTCTATATCAAACCTTGCTGTT
TGTCAGCGAAGCCATCATTCAGTGCGGAAAATGAAAAAGAGATTCTTCAT
TTATTATACGATGAGCCGTACTCAAATTTAATGCCGTTGACAATAGCCGA
TGAAAATGGAATTCGTTATGCAACTTTACCCCACGGAAAAGTCATTGATA
TTTCGTCGTTGTATTTCAAAAATAATGTCTCCTCTTCTATGTATGATATA
CAAGAAACTCAGAGTCCCAAGGAGAAACGTATCGCGAGAATCGTAATGGT
TGTGGCAATATTATTATTGACAATGTGTGTGATTCTGGTTGGAGTTACTC
TATCTATGTCCGACTACATCGACACAATGGTCAAAGAACTGCATCAGAAA
CGCAATGCCAATCCGATTGTGCTGCCAAAGTCTAACAATACATCAAGAAA
TCTAGCTTTGTATTCATATCTCATAAACACCACAGGTAAAACGGGAGCAT
GATTTCATATTTGCCGCTCCAGAATCTCAAATGGG
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protein sequence of SMED30020715-orf-1

>SMED30020715-orf-1 ID=SMED30020715-orf-1|Name=SMED30020715-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=238bp
MFTDEIGLQPLKVKKEFRRFSIDEIDLQKEQLSFVDHCQFNFQPNTNLSE
PNNPSIALTQSLCFIDSPSQIPLPNSMSSALYIKPCCLSAKPSFSAENEK
EILHLLYDEPYSNLMPLTIADENGIRYATLPHGKVIDISSLYFKNNVSSS
MYDIQETQSPKEKRIARIVMVVAILLLTMCVILVGVTLSMSDYIDTMVKE
LHQKRNANPIVLPKSNNTSRNLALYSYLINTTGKTGA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000017photoreceptor neuron
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0000418head
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 168..190