SMED30020243

Overview
NameSMED30020243
Smed IDSMED30020243
Length (bp)2949
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 SMED30020243 (SMED30020243) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020243 (SMED30020243) 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 SMED30020243 (SMED30020243) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30020243 (SMED30020243) 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



SMED30020243

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30020243SMESG000073042.1 SMESG000067639.1 SMESG000056479.1 dd_Smed_v4_1152_2_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30020243SMESG000073042.1 SMESG000067639.1 SMESG000056479.1 dd_Smed_v4_1152_2_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30020243SMESG000073042.1 SMESG000067639.1 SMESG000056479.1 dd_Smed_v4_1152_2_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30020243SMESG000073042.1 SMESG000067639.1 SMESG000056479.1 dd_Smed_v4_1152_2_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30020243SMESG000073042.1 SMESG000067639.1 SMESG000056479.1 dd_Smed_v4_1152_2_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30020243SMESG000073042.1 SMESG000067639.1 SMESG000056479.1 dd_Smed_v4_1152_2_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020243SMESG000073042.1 SMESG000025866.1 Contig34865uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020243SMESG000073042.1 SMESG000025866.1 Contig34865newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30020243SMESG000073042.1 SMESG000067639.1 SMESG000056479.1 dd_Smed_v4_1152_2_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 SMED30020243 vs. Planmine SMEST
Match: SMESG000003594.1 (SMESG000003594.1)

HSP 1 Score: 281.567 bits (719), Expect = 1.938e-87
Identity = 133/145 (91.72%), Postives = 137/145 (94.48%), Query Frame = 1 
Query: 1387 MQPGYKIPKLTSQRSEKSNPSILNNDDKSHQECRRKYDRLVVEHERTLGTWFAPKAVKALHKQIHRLTRCREDLIAENRAQRIIINNQSAVLVASFNEAELTKRLAGRDLAIKLNIIPANHIPEKATTGPPQTPKTSKKHNPSKN 1821
            MQPGYKIPKLTSQRSEKSN SILNNDDKSHQECRRKYD+LVVEHERTL TWFAP+AVKALHKQIHRLTRCREDLIAENRAQRI+INNQSAVL ASFNE EL KRLAGRDLAIKLNIIPA H+PE ATTGPPQ PKTSKKHNPSKN
Sbjct:    1 MQPGYKIPKLTSQRSEKSNLSILNNDDKSHQECRRKYDQLVVEHERTLSTWFAPEAVKALHKQIHRLTRCREDLIAENRAQRIVINNQSAVLTASFNETELKKRLAGRDLAIKLNIIPAEHVPETATTGPPQMPKTSKKHNPSKN 145
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BLAST of SMED30020243 vs. Planmine SMEST
Match: SMESG000036778.1 (SMESG000036778.1)

HSP 1 Score: 249.595 bits (636), Expect = 6.898e-70
Identity = 118/133 (88.72%), Postives = 124/133 (93.23%), Query Frame = 1 
Query: 1423 QRSEKSNPSILNNDDKSHQECRRKYDRLVVEHERTLGTWFAPKAVKALHKQIHRLTRCREDLIAENRAQRIIINNQSAVLVASFNEAELTKRLAGRDLAIKLNIIPANHIPEKATTGPPQTPKTSKKHNPSKN 1821
            + SEKS PSILNNDDKSHQECRRKY++LVVEHERTLGTWFAP+AVKALHKQIHRLTRCREDLIAENRAQRI+INNQSAVL ASFNE EL KRLAGRDLAIKLNIIPA H+PE ATTGPPQ PK SKKHNPSKN
Sbjct:  576 KESEKSKPSILNNDDKSHQECRRKYEQLVVEHERTLGTWFAPEAVKALHKQIHRLTRCREDLIAENRAQRIVINNQSAVLTASFNETELKKRLAGRDLAIKLNIIPAEHVPETATTGPPQMPKISKKHNPSKN 708
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BLAST of SMED30020243 vs. Planmine SMEST
Match: SMESG000036854.1 (SMESG000036854.1)

HSP 1 Score: 221.476 bits (563), Expect = 2.906e-65
Identity = 105/122 (86.07%), Postives = 113/122 (92.62%), Query Frame = 1 
Query: 1456 NNDDKSHQECRRKYDRLVVEHERTLGTWFAPKAVKALHKQIHRLTRCREDLIAENRAQRIIINNQSAVLVASFNEAELTKRLAGRDLAIKLNIIPANHIPEKATTGPPQTPKTSKKHNPSKN 1821
            NN+D +HQEC+RKY +LV EHERTLGTWFAP+AVKALH QIHRLTRCREDLIAE+RAQRIIINNQSAVLVASFNE ELTKRLA RDLAIKLN+IPANHI  K TTGPPQTPKT+KKHNPSKN
Sbjct:  142 NNNDNTHQECQRKYAQLVAEHERTLGTWFAPEAVKALHNQIHRLTRCREDLIAESRAQRIIINNQSAVLVASFNEDELTKRLASRDLAIKLNLIPANHITGKGTTGPPQTPKTNKKHNPSKN 263
[Close]
BLAST of SMED30020243 vs. Planmine SMEST
Match: SMESG000077490.1 (SMESG000077490.1)

HSP 1 Score: 214.542 bits (545), Expect = 4.858e-64
Identity = 102/146 (69.86%), Postives = 120/146 (82.19%), Query Frame = 1 
Query: 1387 MQPGYKIPKLTSQRSEKSNPSILNNDDKSHQECRRKYDRLVVEHERTLGTWFAPKAVKALHKQIHRLTRCREDLIAENRAQRIIINNQSAVLVASFNEAELTKRLAGRDLAIKLNIIPANHIPEKATTGPPQTPKTSKKHNPSKNR 1824
            MQ GYKIPKL+  + + S      N+   H  C+++Y++L+ EHERTLGTWFAP+ VKALHKQIHRLTRCREDLIAENRAQRI+IN+QSAVL+ASF E ELTKRLA RDLA+KLN+IPAN +PE+   GP QTPKTSKKHNPSKNR
Sbjct:    1 MQSGYKIPKLSPAKPKLSTQPNTQNEQLDHIPCQQRYNKLLAEHERTLGTWFAPEVVKALHKQIHRLTRCREDLIAENRAQRIVINDQSAVLIASFTETELTKRLASRDLAVKLNLIPANDLPERNQIGPAQTPKTSKKHNPSKNR 146
[Close]
BLAST of SMED30020243 vs. Planmine SMEST
Match: SMESG000028417.1 (SMESG000028417.1)

HSP 1 Score: 209.92 bits (533), Expect = 3.099e-61
Identity = 100/145 (68.97%), Postives = 117/145 (80.69%), Query Frame = 1 
Query: 1387 MQPGYKIPKLTSQRSEKSNPSILNNDDKSHQECRRKYDRLVVEHERTLGTWFAPKAVKALHKQIHRLTRCREDLIAENRAQRIIINNQSAVLVASFNEAELTKRLAGRDLAIKLNIIPANHIPEKATTGPPQTPKTSKKHNPSKN 1821
            MQPGYKIPKL+S+      PS +N     H  C++KY++L  EHERTLGTWFAP+AVK L  +IHRL+RCREDLIAENRAQRIIIN+QSA LVASF E ELTKRLAGRDL +KLN+IP NH+PE+   GP QTP+TSKKH+PSKN
Sbjct:    1 MQPGYKIPKLSSK------PSAINTQ-MDHSSCQQKYNKLFAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSADLVASFTEVELTKRLAGRDLVVKLNLIPVNHLPEETQAGPAQTPRTSKKHHPSKN 138
The following BLAST results are available for this feature:
BLAST of SMED30020243 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 SMED30020243 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 SMED30020243 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 SMED30020243 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 SMED30020243 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 SMED30020243 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 SMED30020243 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 SMED30020243 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30020243 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 SMED30020243 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 SMED30020243 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 SMED30020243 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 SMED30020243 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 SMED30020243 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000003594.11.938e-8791.72SMESG000003594.1[more]
SMESG000036778.16.898e-7088.72SMESG000036778.1[more]
SMESG000036854.12.906e-6586.07SMESG000036854.1[more]
SMESG000077490.14.858e-6469.86SMESG000077490.1[more]
SMESG000028417.13.099e-6168.97SMESG000028417.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020243 ID=SMED30020243|Name=SMED30020243|organism=Schmidtea mediterranea sexual|type=transcript|length=2949bp
TCAATATGGCTGCTGTAACATAAGCACGTACCGCAAGCAGAAATCAAAAA
TAAAATAAAACAAAATAAAAACATAACAAAATTAAATAAAACAAATATTA
ATTAAAATCATTGAAAAGCCTACAGATGCAGAAAGAAACACAAAACCAAA
ATATAAAACCTCCAAAACCTTGCAAAAGAAGGTTTAGAAAATACATAGGC
GGAAGCGGCGACCAAAAATTTAAATATCAAAGGGTAAAAAGAGAAACAAT
CAAAAAGAATGGTTAAACGATAAAAAATAAAAATTTACGAAATATTGAGA
AAATAATATCAAAAAATAGAGAAAAATAAGGAGAAAAATAAAATATTTAA
AATAAAATTAAAGCAATAAAACCCCCCGAAAAATAGCCGAAAAAGGCTCA
AAATACTCTGATTGGTCGCACCCAGGCATGAAAACACTATATATACAGCA
GTCATTTTCATAATTTTTAGACATTTGGTGAACATGTTGTAGACACAAAA
TTTTAAGACAGTTGTTGAGAAAATTTTTATGCCAACGTATGACAATTTTT
CAAATTTGGATGCTTGACTGACAAACTTGTCGATCGTAAGTATTGTTTTT
TGTAGAAATATATTTTTCTAAGTTAATGTTTTGTTTAATTTAACTTATTC
TGGATGGCCGCAATGTCTTTTGGCATTGCTTGGCAGGTTCCCCCTAACTT
ATTTATATTCATTTTATATACATGTTAATTGTGGAGAATGGCAGGGCAAC
ATTCAATTCCGGCCGTTAAATTGGCAGGACGTTGACGTGTTGCTTTGTCA
CAATCCACCCTTCGGTGTCTGCTTAGTCTGGTCAGGCCTTGTTGCACTGA
TCACGGGGTAGGACACCGTCGTAATTCACCGAGGCGGCCATTTTCAATGT
TGGTCGGAGCGGTATGAGTAAAATGCGGGTAGATCGCCATACCTAGGGGG
TTGACATTTGTAAGATGTCTAAGTAGGGATATAATATTTTTTTTTAAGAT
GCCTGTCGAGAAATCGATTATAACAAAGGGGACGACTAGGGTTAAGTATA
GGAATAAATGCATAACACAATAAACCGAAACGAATTCAACAAAACGAAAA
GATGGAAAAATATTTTAACGTGAATCGCAGTGAACGGAGCATCAATATTT
TTCATTTTTCTTTTGTACAGAATTATTGTCAGCAGATCAACAATAGATAT
TTACACGAAAACCGGCATCGTAAAAATTAATATTAAATATGAGTTTGGTG
TAGGAATGTGTGATGTGACTTTCTAATTAATTATTCTCTTTTATTATCCT
TATTGTTAAATTGATAAAAATTTTCTTTTTACTGAATTATTCCCCCTCAT
GTTTGTTTATAAATTTTCTTTAAGATCTTCGACAACATGCAGCCAGGATA
TAAAATCCCGAAATTAACGTCGCAGAGATCGGAAAAATCTAATCCATCAA
TTCTCAACAACGACGACAAATCCCACCAAGAATGCCGAAGAAAATATGAT
CGGTTGGTCGTAGAACACGAACGTACGCTCGGTACGTGGTTCGCCCCCAA
GGCTGTGAAAGCCCTCCACAAGCAAATTCACCGGCTAACTAGGTGCCGCG
AAGACCTTATTGCTGAGAATCGAGCGCAGCGAATTATTATCAATAACCAG
AGTGCCGTCCTAGTAGCCTCTTTTAATGAAGCCGAATTGACGAAGCGATT
AGCCGGCCGTGATTTGGCGATAAAGTTGAATATAATTCCCGCCAATCACA
TACCCGAAAAAGCCACAACTGGTCCTCCACAAACTCCGAAAACCAGTAAG
AAACACAATCCCAGCAAAAACCGACGTGATAGCATCGTTTTGGGACTTGT
GTATACTTTTTAAAATGTTGTAAAACACTGCTCTATATTAAAATTTTAAA
TACATATAATAATTAACAGTTTATTTAGCTAACATATAAACAACCTCCTG
ACTCGCTGCCGAACCTCTTGGATCACCAAAAATAATTTTGAATATATTTT
ATTAAGTTTCAAATTCATCAAAATAACTTGCAATATTTTTAAAATTTAAC
AATTTTGATGAAGTGACATCTGACAAATAAAGATCCAAAATTTTTATCAT
TGGACCTTTTGAGATTTTATTATAAACTAAATCACATGCATCTATTTATT
CATTTACATCCGGTAATTCAATCGAACCATATTCAAGTGAATTTTTTAAT
TAATAATATTTGATTAAAGCTCCCGACCATCAATAATTAAGATCTACAAA
TGAACAAGTGAACCGTCACGTCATACATATATAGTAGTGAGTTGTGAGCC
CGCAAGAACAAGCGAATTTCTTACATAGAAATGCTGTGTGTAATCTATTT
CTTATAAATTTTTCATTTTTTATCTTTCACTTCTCAAAAAGAAAGAAAAC
AAAATCTCTATAGTAAAATATTTACAATAAACATCAGAAATCAATAAAAA
ATGGAAATTAGCAATTCGTATAGAAGTGATTGTCAGGCTTTATTATTGTT
AAATTATTTTTTTAATTATTCATTTTTGATATTTTCTACAATTCTCACTT
CACTATAGTCATTTCAATTTTTTTTATTTAATGAAGTTTATGAAGATCAT
GCATCAAAATAAAAACCTTCGGCGAGCTATTCGCCATAAATACATTATTT
GATTTAGTCGCAAGCGGCAAAAGCTTTAGAGAATTAAATATTAAATAAAA
TACAACTTCAGAACATAATAGTTTAGCAATCAAATGAACAAATATGGCGA
TTATTTAGAAAGAAATCAAATTATGATAAAAGCTATAAATTTTATAACAT
AAGACATGCCAATAATTTTATCCCAAGAAAGCACAGTCCAAACACACGTT
TCGACAGTTTTCCCGACATCATCAGATGGTATAGAAAAAACTTTACAAAT
TTTATTATTTTAAAATAATTTAAGTAATAAGTTATTTTTTAATCTTTTT
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protein sequence of SMED30020243-orf-1

>SMED30020243-orf-1 ID=SMED30020243-orf-1|Name=SMED30020243-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=159bp
MQPGYKIPKLTSQRSEKSNPSILNNDDKSHQECRRKYDRLVVEHERTLGT
WFAPKAVKALHKQIHRLTRCREDLIAENRAQRIIINNQSAVLVASFNEAE
LTKRLAGRDLAIKLNIIPANHIPEKATTGPPQTPKTSKKHNPSKNRRDSI
VLGLVYTF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000099neuron