SMED30023082

Overview
NameSMED30023082
Smed IDSMED30023082
Length (bp)856
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 SMED30023082 (SMED30023082) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023082 (SMED30023082) 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 SMED30023082 (SMED30023082) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023082 (SMED30023082) 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



SMED30023082

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
neoblastSMED30023082SMESG000021722.1 SMED30023082smed_20140614PMID:29906446
Zeng et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30023082SMESG000021722.1 dd_Smed_v4_18900_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30023082SMESG000021722.1 dd_Smed_v4_18900_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30023082SMESG000021722.1 dd_Smed_v6_18900_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30023082 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005452:16254..17154 +4232
Homology
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BLAST of SMED30023082 vs. TrEMBL
Match: A0A3S5AFZ6 (Uncharacterized protein OS=Protopolystoma xenopodis OX=117903 GN=PXEA_LOCUS16344 PE=4 SV=1)

HSP 1 Score: 69.3218 bits (168), Expect = 1.015e-10
Identity = 58/149 (38.93%), Postives = 89/149 (59.73%), Query Frame = 2 
Query:  413 ESKNKLVSSPGGNLDLSHYEFAPKDA-----SHLTNVLNMELNKNLDPDXXXXXXXXXXXXXXXXXX-------------XXXXXXNSRLEKVINFLEDRRIKEGSELYQLEDLKMPKLRKFLNIIFVAXXXXXXXXXXXXXXYSTFSE 805
            E+   LVS+PGG LDLS Y++ P+ A     S  T   +M     +  +A   L    +     +               F RPR+NS+L++VI FLED+R+K+ +++++L+DL+MP+LR+ LNIIFV  G+ FLL V+IVIIY+T ++
Sbjct:   16 EAHKLLVSAPGGALDLSQYDYKPQIAPPTITSTQTGSADMATTGLMASEAAAGLRSPTQSRGLAEDTNTDEECERKRLRRFMRPRRNSKLDRVIAFLEDKRVKDDADIHRLDDLQMPRLRRILNIIFVTLGVCFLLAVVIVIIYTTLTK 164
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BLAST of SMED30023082 vs. TrEMBL
Match: A0A183VLS9 (Uncharacterized protein OS=Trichobilharzia regenti OX=157069 GN=TRE_LOCUS1435 PE=4 SV=1)

HSP 1 Score: 67.0106 bits (162), Expect = 2.583e-9
Identity = 71/203 (34.98%), Postives = 97/203 (47.78%), Query Frame = 2 
Query:  233 PLFIIPKSYSKGKQCLFPNVENQD----SKYNETKVVDQLNDAKVFIKEIKHDNIISEAIL----KNQESKNKLV-SSPGGNLDLSHYEFAP-----KDA-----------------SHLTNVL-NMELNKNLDPDXXXXXXXXXXXXXXXXXXXXXXXXNSRLEKVINFLEDRRIKEGSELYQLEDLKMPKLRKFLNIIFVA 745
            P F IP SY KG Q    +V + +    S  + T    Q   A     EI+  +  +        K  E KN L+  SP G LDLSHY F P     KD+                 + L+N   N + N N +      L        +K++ F RPRKNS+L+++I FLED+R+K+     +LEDL+MP+LRK LNIIFV 
Sbjct:    7 PQFFIPASY-KGHQTSPTSVPSANIRPQSPSSTTYTNRQRIPASQTSNEIRPPSSTASGTTFANGKASEVKNSLLYPSPTGTLDLSHYNFVPAQTNNKDSKSNRPNGGLSSRTLVANNRLSNTPDNTDGNNNAEFVDSAQLNGGNGGKEKKRRRFRRPRKNSKLDRLIRFLEDKRVKDDGNGEELEDLQMPRLRKVLNIIFVT 208
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BLAST of SMED30023082 vs. TrEMBL
Match: A0A0R3SQZ1 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=HDID_LOCUS7533 PE=4 SV=1)

HSP 1 Score: 63.1586 bits (152), Expect = 1.798e-8
Identity = 58/127 (45.67%), Postives = 78/127 (61.42%), Query Frame = 2 
Query:  428 LVSSPGGNLDLSHYEFAPKDASHLTNVLNMELNKNLDPDXXXXXXXXXXXXXXXXXXXXXXXXNSRLEKVINFLEDRRIKEGSE-LYQLEDLKMPKLRKFLNIIFVAXXXXXXXXXXXXXXYSTFSE 805
            L+  PGG LDL+ Y + P   +   N ++   +   D   I    +     S KKK F  PR+NS LE+ I  LED+RI E SE  +QLED+KMP+LRK LNIIF+  G+ FLL V+IVI+Y+TF+ 
Sbjct:   36 LIRGPGGALDLTLYNYHPTQGNSTRNSVS---DSAEDDSIIPNQRQNPSNSSTKKKRFKGPRRNSLLERFIAVLEDKRIMEDSEDAHQLEDIKMPRLRKVLNIIFITAGVCFLLAVVIVILYTTFAR 159
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BLAST of SMED30023082 vs. TrEMBL
Match: A0A183SRI2 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=SSLN_LOCUS6830 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 2.460e-7
Identity = 45/121 (37.19%), Postives = 64/121 (52.89%), Query Frame = 2 
Query:  428 LVSSPGGNLDLSHYEFAPKDASHLTNV------------LNMELNKNL----DPDXXXXXXXXXXXXXXXXXXXXXXXXNSRLEKVINFLEDRRIKEGSELYQLEDLKMPKLRKFLNIIFV 742
            +V +PGG LDLS Y + P   S                 L +EL+ N     + +              KK+ F  PR+NS+LE++I  LED+RI + ++ YQLED+KMP+LR  LNIIF+
Sbjct:   57 VVQAPGGALDLSLYGYQPVHRSTTAGSTTARRLEQGLDDLVVELDANGLEKNEQEQESTSGNTAGVTEGKKRRFHAPRRNSKLERLIRLLEDKRIIDEADAYQLEDIKMPRLRNALNIIFI 177
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BLAST of SMED30023082 vs. TrEMBL
Match: A0A183K8J8 (Uncharacterized protein OS=Schistosoma curassoni OX=6186 GN=SCUD_LOCUS11327 PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 1.840e-6
Identity = 37/62 (59.68%), Postives = 51/62 (82.26%), Query Frame = 2 
Query:  617 NSRLEKVINFLEDRRIKEGSELYQLEDLKMPKLRKFLNIIFVAXXXXXXXXXXXXXXYSTFS 802
            NS+L+++I FLED+R+K+     +LEDL+MP+LRK LNIIFV  G+ FLL VIIVI+Y+TF+
Sbjct:  174 NSKLDRLIRFLEDKRVKDDGNGEELEDLQMPRLRKVLNIIFVTLGVCFLLAVIIVILYTTFA 235
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BLAST of SMED30023082 vs. Planmine SMEST
Match: SMESG000021722.1 (SMESG000021722.1)

HSP 1 Score: 319.316 bits (817), Expect = 5.860e-111
Identity = 203/203 (100.00%), Postives = 203/203 (100.00%), Query Frame = 2 
Query:  200 MKKDSFATIETPLFIIPKSYSKGKQCLFPNVENQDSKYNETKVVDQLNDAKVFIKEIKHDNIISEAILKNQESKNKLVSSPGGNLDLSHYEFAPKDASHLTNVLNMELNKNLDPDXXXXXXXXXXXXXXXXXXXXXXXXNSRLEKVINFLEDRRIKEGSELYQLEDLKMPKLRKFLNIIFVAXXXXXXXXXXXXXXYSTFSET 808
            MKKDSFATIETPLFIIPKSYSKGKQCLFPNVENQDSKYNETKVVDQLNDAKVFIKEIKHDNIISEAILKNQESKNKLVSSPGGNLDLSHYEFAPKDASHLTNVLNMELNKNLDPDAIEALIEEKEKISRKKKIFSRPRKNSRLEKVINFLEDRRIKEGSELYQLEDLKMPKLRKFLNIIFVAFGILFLLGVIIVIIYSTFSET
Sbjct:    1 MKKDSFATIETPLFIIPKSYSKGKQCLFPNVENQDSKYNETKVVDQLNDAKVFIKEIKHDNIISEAILKNQESKNKLVSSPGGNLDLSHYEFAPKDASHLTNVLNMELNKNLDPDAIEALIEEKEKISRKKKIFSRPRKNSRLEKVINFLEDRRIKEGSELYQLEDLKMPKLRKFLNIIFVAFGILFLLGVIIVIIYSTFSET 203
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BLAST of SMED30023082 vs. Planmine SMEST
Match: SMESG000020876.1 (SMESG000020876.1)

HSP 1 Score: 65.0846 bits (157), Expect = 3.738e-13
Identity = 29/43 (67.44%), Postives = 37/43 (86.05%), Query Frame = 2 
Query:  617 NSRLEKVINFLEDRRIKEGSELYQLEDLKMPKLRKFLNIIFVA 745
            NS+LEK+I  LEDRRI +  ELYQLEDL+MP+LR+ LNI+FV+
Sbjct:   49 NSKLEKLIKILEDRRITDDCELYQLEDLQMPRLRRVLNIVFVS 91
[Close]
BLAST of SMED30023082 vs. Planmine SMEST
Match: SMESG000016739.1 (SMESG000016739.1)

HSP 1 Score: 62.003 bits (149), Expect = 4.859e-12
Identity = 28/43 (65.12%), Postives = 37/43 (86.05%), Query Frame = 2 
Query:  617 NSRLEKVINFLEDRRIKEGSELYQLEDLKMPKLRKFLNIIFVA 745
            +S+L K+I FL+D+RIKE  +LYQLEDL+MP+LRK LNI+FV 
Sbjct:   52 DSKLTKLITFLQDKRIKEEKDLYQLEDLQMPRLRKVLNIVFVV 94
The following BLAST results are available for this feature:
BLAST of SMED30023082 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 SMED30023082 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 SMED30023082 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 SMED30023082 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 SMED30023082 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 SMED30023082 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 SMED30023082 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 SMED30023082 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A3S5AFZ61.015e-1038.93Uncharacterized protein OS=Protopolystoma xenopodi... [more]
A0A183VLS92.583e-934.98Uncharacterized protein OS=Trichobilharzia regenti... [more]
A0A0R3SQZ11.798e-845.67Uncharacterized protein OS=Hymenolepis diminuta OX... [more]
A0A183SRI22.460e-737.19Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A183K8J81.840e-659.68Uncharacterized protein OS=Schistosoma curassoni O... [more]
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BLAST of SMED30023082 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 SMED30023082 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 SMED30023082 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 SMED30023082 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 SMED30023082 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 SMED30023082 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000021722.15.860e-111100.00SMESG000021722.1[more]
SMESG000020876.13.738e-1367.44SMESG000020876.1[more]
SMESG000016739.14.859e-1265.12SMESG000016739.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023082 ID=SMED30023082|Name=SMED30023082|organism=Schmidtea mediterranea sexual|type=transcript|length=856bp
GTGGATTCTAAAATCAAATCATTAGATTCGTTTTTCCTAAAAACTTAAGT
TATGCCCAATCAGCAAGTACATTAAGACTACAGTAGCATCGAATAAACTG
TGAGTAGTGTGTTTGTTTATCACTGTCAAGAAAATACAACCTAATAAGGA
GAGAAAAAATTTTCTTAGTTCTCAAATAAAAATAATTGCTACTTTGAAAA
TGAAGAAGGACTCCTTCGCCACTATTGAGACTCCTTTGTTTATTATTCCG
AAAAGTTATTCAAAGGGAAAACAATGCCTTTTTCCAAATGTCGAAAATCA
AGATTCCAAATATAACGAAACAAAGGTGGTAGACCAATTAAATGACGCTA
AAGTTTTTATCAAAGAAATTAAACATGATAATATCATATCTGAAGCTATA
TTAAAAAATCAAGAAAGTAAAAACAAGTTAGTAAGTTCTCCAGGAGGAAA
TTTGGATTTGTCTCATTATGAATTTGCACCAAAAGATGCTTCTCATTTGA
CAAATGTTTTAAATATGGAACTTAATAAAAATTTGGATCCTGATGCTATT
GAAGCATTAATTGAGGAAAAAGAAAAAATTTCTAGAAAAAAAAAAATTTT
TAGCAGACCAAGAAAAAACAGTCGTTTAGAAAAGGTAATTAATTTTCTTG
AAGATCGGAGAATCAAGGAAGGTAGTGAACTGTACCAACTCGAAGACCTT
AAAATGCCAAAACTTAGAAAATTTCTTAATATTATATTTGTAGCTTTTGG
TATACTTTTTCTATTGGGAGTTATTATAGTCATTATTTATTCAACATTCA
GTGAAACTTAAATGAATTTGCTTCCTTCAAATGCCTTTCGTGGTTGATAC
ATTATA
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protein sequence of SMED30023082-orf-1

>SMED30023082-orf-1 ID=SMED30023082-orf-1|Name=SMED30023082-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=204bp
MKKDSFATIETPLFIIPKSYSKGKQCLFPNVENQDSKYNETKVVDQLNDA
KVFIKEIKHDNIISEAILKNQESKNKLVSSPGGNLDLSHYEFAPKDASHL
TNVLNMELNKNLDPDAIEALIEEKEKISRKKKIFSRPRKNSRLEKVINFL
EDRRIKEGSELYQLEDLKMPKLRKFLNIIFVAFGILFLLGVIIVIIYSTF
SET*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
PLANA:0000429neoblast
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 175..197