SMED30005995

Overview
NameSMED30005995
Smed IDSMED30005995
Length (bp)875
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 SMED30005995 (SMED30005995) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30005995 (SMED30005995) 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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Anatomical Expression

PAGE et. al., 2020



SMED30005995

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
nervous systemSMED30005995SMESG000018616.1 dd_Smed_v4_24171_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30005995SMESG000018616.1 dd_Smed_v4_24171_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30005995SMESG000018616.1 dd_Smed_v4_24171_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30005995SMESG000018616.1 dd_Smed_v6_24171_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30005995SMESG000018616.1 dd_Smed_v4_24171_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30005995SMESG000018616.1 dd_Smed_v4_24171_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
Homology
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BLAST of SMED30005995 vs. TrEMBL
Match: A0A1I8HZW2 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 67.781 bits (164), Expect = 4.257e-9
Identity = 44/158 (27.85%), Postives = 71/158 (44.94%), Query Frame = 1 
Query:  364 IFF--QTKPIPLDPQEVWCGFSNNIYFDPIKINCAPFKTKSIEIKAPPLNNCSIKLQEILINSRLNPER-LINKMNKDEEMSERCRNIRNQDQISRQKKLFESYKQNAPAKLDWNKLKDTASSFNQ------------------QMYWKSNATGSLKF 774
            +F+  Q +P P+ P + W G+  N+YF P++I  + F     ++  P L  CS +LQ++L +SRLN E  L+ +   D    +R    R    +  Q     S  Q    +LD   L   A+S  Q                   +Y  ++ATG+L+F
Sbjct:   99 VFYIRQKRPRPMTPLKAWAGYHGNVYFSPLRIRRSEFAHPDSQLSLPSLPACSGRLQQVLESSRLNAEHLLLLRARSDAAAMKRRPPPRRAAMVGGQ-----SSGQQPLVQLDRAYLASRAASRQQGPDGPETAGGTMSVSRDVHLYRSAHATGTLQF 251
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BLAST of SMED30005995 vs. TrEMBL
Match: A0A267E7Z0 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig013622g3 PE=4 SV=1)

HSP 1 Score: 67.3958 bits (163), Expect = 7.540e-9
Identity = 42/145 (28.97%), Postives = 67/145 (46.21%), Query Frame = 1 
Query:  364 IFF--QTKPIPLDPQEVWCGFSNNIYFDPIKINCAPFKTKSIEIKAPPLNNCSIKLQEILINSRLNPERLIN-KMNKDEEMSERCRNIRNQDQISRQKKLFESYKQNAPAKLDWNKLKDTASSFNQQMYWKSNATGSLKFICDIK 789
            +F+  Q +P P+ P + W G+  N+YF P++I  + F     ++  P L  CS +LQ++L +SRLN E L++ +   D    +R    R    +  Q     S  Q    +LD   L   A+S  Q       A GS+    D+ 
Sbjct:  228 VFYIRQKRPRPMTPLKAWAGYHGNVYFSPLRIRRSEFAHPDSQLSLPSLPACSGRLQQVLESSRLNAEHLLHLRARLDAAAMKRRLPPRRAAVLGGQ-----SSGQQPLVQLDRAYLASRAASRQQGPDGPETAGGSMSVSRDVH 367
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BLAST of SMED30005995 vs. TrEMBL
Match: A0A267EBB2 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig013622g1 PE=4 SV=1)

HSP 1 Score: 67.0106 bits (162), Expect = 8.775e-9
Identity = 44/158 (27.85%), Postives = 71/158 (44.94%), Query Frame = 1 
Query:  364 IFF--QTKPIPLDPQEVWCGFSNNIYFDPIKINCAPFKTKSIEIKAPPLNNCSIKLQEILINSRLNPER-LINKMNKDEEMSERCRNIRNQDQISRQKKLFESYKQNAPAKLDWNKLKDTASSFNQ------------------QMYWKSNATGSLKF 774
            +F+  Q +P P+ P + W G+  N+YF P++I  + F     ++  P L  CS +LQ++L +SRLN E  L+ +   D    +R    R    +  Q     S  Q    +LD   L   A+S  Q                   +Y  ++ATG+L+F
Sbjct:  206 VFYIRQKRPRPMTPLKAWAGYHGNVYFSPLRIRRSEFAHPDSQLSLPSLPACSGRLQQVLESSRLNAEHLLLLRARSDAAAMKRRPPPRRAAMVGGQ-----SSGQQPLVQLDRAYLASRAASRQQGPDGPETAGGTMSVSRDVHLYRSAHATGTLQF 358
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BLAST of SMED30005995 vs. Planmine SMEST
Match: SMESG000018616.1 (SMESG000018616.1)

HSP 1 Score: 427.943 bits (1099), Expect = 1.888e-153
Identity = 220/223 (98.65%), Postives = 221/223 (99.10%), Query Frame = 1 
Query:  121 MNISQLYFDSQKNSFVSKLNNIPANTPVSNFTRDNSISRKKKTWVEEKLPKIIKMKNNNSGKATLIYVSEPKXXXXXXLKAIFFQTKPIPLDPQEVWCGFSNNIYFDPIKINCAPFKTKSIEIKAPPLNNCSIKLQEILINSRLNPERLINKMNKDEEMSERCRNIRNQDQISRQKKLFESYKQNAPAKLDWNKLKDTASSFNQQMYWKSNATGSLKFICDIK 789
            MNISQLYFDSQKNSFVSKLNNIPANTPVSNFTRDNSI+RKKK WVEEKLPKIIKMKNNNSGKATLIYVSEPKSSSNSSLKAIFFQTKPIPLDP EVWCGFSNNIYFDPIKINCAPFKTKSIEIKAPPLNNCSIKLQEILINSRLNPERLINKMNKDEEMSERCRNIRNQDQISRQKKLFESYKQNAPAKLDWNKLKDTASSFNQQMYWKSNATGSLKFICDIK
Sbjct:    1 MNISQLYFDSQKNSFVSKLNNIPANTPVSNFTRDNSITRKKKIWVEEKLPKIIKMKNNNSGKATLIYVSEPKSSSNSSLKAIFFQTKPIPLDPLEVWCGFSNNIYFDPIKINCAPFKTKSIEIKAPPLNNCSIKLQEILINSRLNPERLINKMNKDEEMSERCRNIRNQDQISRQKKLFESYKQNAPAKLDWNKLKDTASSFNQQMYWKSNATGSLKFICDIK 223
The following BLAST results are available for this feature:
BLAST of SMED30005995 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 SMED30005995 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 SMED30005995 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 SMED30005995 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 SMED30005995 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 SMED30005995 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 SMED30005995 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 SMED30005995 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A1I8HZW24.257e-927.85Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267E7Z07.540e-928.97Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A267EBB28.775e-927.85Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of SMED30005995 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 SMED30005995 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 SMED30005995 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 SMED30005995 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 SMED30005995 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 SMED30005995 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000018616.11.888e-15398.65SMESG000018616.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005995 ID=SMED30005995|Name=SMED30005995|organism=Schmidtea mediterranea sexual|type=transcript|length=875bp
CTTCATTGAGATGTGTATGGTTTAATAATTATTTTTTAATTGAAAGTGTG
TTACTAAGCAAATATTTATGATATTGTACCAAAATTGAAAAATTTGAAGA
TCTTTTACTTGGACTTTCAAATGAATATTAGTCAATTATATTTTGATTCT
CAAAAAAATTCCTTCGTCTCAAAGCTGAACAATATTCCTGCAAATACACC
AGTTTCCAATTTTACGAGAGATAATTCGATCTCGAGGAAAAAAAAGACTT
GGGTTGAAGAAAAACTTCCGAAAATAATCAAAATGAAAAACAATAATTCA
GGGAAAGCAACTCTCATCTATGTATCAGAACCTAAGTCATCCTCCAATTC
TTCCCTGAAAGCTATATTTTTCCAAACTAAACCGATTCCTCTAGATCCAC
AAGAGGTTTGGTGCGGATTTAGCAACAATATTTATTTTGATCCAATTAAA
ATCAATTGCGCTCCATTTAAAACAAAAAGCATCGAAATTAAAGCACCGCC
GTTGAATAATTGCAGCATCAAATTACAAGAAATTCTGATTAATTCGAGAC
TTAATCCGGAAAGGCTTATTAATAAAATGAATAAAGACGAAGAAATGAGT
GAGAGATGTAGAAATATTAGAAATCAAGATCAAATATCTCGACAAAAAAA
ACTGTTTGAATCGTACAAGCAAAATGCACCTGCCAAACTAGACTGGAATA
AACTCAAAGATACTGCTTCTTCCTTTAATCAGCAGATGTACTGGAAGTCT
AATGCAACAGGTTCTTTGAAGTTCATTTGCGACATTAAATAATGCCGTTT
TTGAATAGCTGTCATGCTTTAGATGACTGGATGTCACTCTTGAAAAATAA
GCTTCAAAATGCTTGTAAATTTTAT
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protein sequence of SMED30005995-orf-1

>SMED30005995-orf-1 ID=SMED30005995-orf-1|Name=SMED30005995-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=224bp
MNISQLYFDSQKNSFVSKLNNIPANTPVSNFTRDNSISRKKKTWVEEKLP
KIIKMKNNNSGKATLIYVSEPKSSSNSSLKAIFFQTKPIPLDPQEVWCGF
SNNIYFDPIKINCAPFKTKSIEIKAPPLNNCSIKLQEILINSRLNPERLI
NKMNKDEEMSERCRNIRNQDQISRQKKLFESYKQNAPAKLDWNKLKDTAS
SFNQQMYWKSNATGSLKFICDIK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000096ventral epidermis
PLANA:0000418head