SMED30014759

Overview
NameSMED30014759
Smed IDSMED30014759
Length (bp)2093
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 SMED30014759 (SMED30014759) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30014759 (SMED30014759) 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 SMED30014759 (SMED30014759) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30014759 (SMED30014759) 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



SMED30014759

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
neoblastSMED30014759SMESG000009721.1 dd_Smed_v4_14933_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
enteric muscle cellSMED30014759SMESG000009721.1 dd_Smed_v4_14933_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30014759 vs. Planmine SMEST
Match: SMESG000053271.1 (SMESG000053271.1)

HSP 1 Score: 212.231 bits (539), Expect = 2.480e-65
Identity = 106/135 (78.52%), Postives = 118/135 (87.41%), Query Frame = -1 
Query:  282 MEPHRILQGELDKAQRLNREMNQQIVQLTTETQHIKSSWVEPKKVKALYEKMTVTQRGWAEEKQLNQSKKTQIRGLEVALSACQEVNAVTYLLVFAPVKLAYKEPTSNTKPANKPPRHRPGRNERAKRRVTQPAE 686
            ME H+ILQ EL KAQRLNRE++QQIVQLTTE Q IKSSWVEPKKVK LY+KMT  QRGWAEEKQLNQ++KTQIRGLEVALSACQE NAVTY L FAP +LAY+E TSN+KPA+KPP  RPGRNERAKR+  QPA+
Sbjct:    1 MESHKILQEELVKAQRLNRELHQQIVQLTTEIQRIKSSWVEPKKVKILYQKMTAAQRGWAEEKQLNQNQKTQIRGLEVALSACQEGNAVTYPLAFAPAQLAYQEATSNSKPASKPP--RPGRNERAKRQAAQPAD 133
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BLAST of SMED30014759 vs. Planmine SMEST
Match: SMESG000023390.1 (SMESG000023390.1)

HSP 1 Score: 199.519 bits (506), Expect = 9.713e-56
Identity = 95/112 (84.82%), Postives = 103/112 (91.96%), Query Frame = -3 
Query:  889 REPGHNPAREIRGQAEFLLARLEEHQRQTNKQVDRARRHLAEINKAIETGSIPSTDGYAPPYNVSFNLNDPNLEEESEAMNVVVPRRILTREMRDEDRRPHRDQEHPYAREI 1224
            REPG NPAREIRGQAEFLLARLEEHQRQT +QV+RARRHLAEINKAI TG IPSTD YAPPYNVSFNL+DPNL  E+EAMNVVVPRRILTREM+D+DRR ++DQEH YAREI
Sbjct:  417 REPGRNPAREIRGQAEFLLARLEEHQRQTKRQVNRARRHLAEINKAIATGDIPSTDRYAPPYNVSFNLDDPNLAGEAEAMNVVVPRRILTREMKDKDRRSNQDQEHSYAREI 528

HSP 2 Score: 107.071 bits (266), Expect = 5.688e-24
Identity = 57/92 (61.96%), Postives = 63/92 (68.48%), Query Frame = -2 
Query: 1121 DHSWIDASRVTVRFHARSTARCRQALWDAGFSVSPVRESREGAQRDDGEADLPFVAIKRARPQSSPRDPRASGVLTSTLGGASAPDKQTSRQ 1396
            DHSWIDASRVTVRF ARS ARCRQ LWDAGFSVSPVRESR   +RDD + DLPFVAIKR   ++  R+ R  G     L       +QT RQ
Sbjct:  359 DHSWIDASRVTVRFPARSVARCRQVLWDAGFSVSPVRESRTATRRDDEKVDLPFVAIKREPGRNPAREIR--GQAEFLLARLEEHQRQTKRQ 448
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BLAST of SMED30014759 vs. Planmine SMEST
Match: SMESG000032540.1 (SMESG000032540.1)

HSP 1 Score: 145.206 bits (365), Expect = 2.880e-54
Identity = 72/111 (64.86%), Postives = 82/111 (73.87%), Query Frame = -3 
Query:  892 REPGHNPAREIRGQAEFLLARLEEHQRQTNKQVDRARRHLAEINKAIETGSIPSTDGYAPPYNVSFNLNDPNLEEESEAMNVVVPRRILTREMRDEDRRPHRDQEHPYARE 1224
            REPG NPAREIRGQAE+LLARLEEH+RQT+ +VD+ARRHL EIN  I  G IPSTDGYAPPYN  FNL+DP L   S AM VVVPR  L R   + +   +   +HPYARE
Sbjct:   64 REPGRNPAREIRGQAEYLLARLEEHKRQTDHEVDKARRHLEEINWDIAAGIIPSTDGYAPPYNTPFNLDDPRLNRSSSAMKVVVPRETLIRGWGEANEPANEHHDHPYARE 174

HSP 2 Score: 87.4261 bits (215), Expect = 2.880e-54
Identity = 41/61 (67.21%), Postives = 50/61 (81.97%), Query Frame = -2 
Query: 1220 FSDHSWIDASRVTVRFHARSTARCRQALWDAGFSVSPVRESREGAQRDDGEADLPFVAIKR 1402
            F ++SWI ASRVT+RF A S  RCRQA+WDAGFS+SPVRESR G++ +  + DLPFVAIKR
Sbjct:    4 FLENSWIYASRVTLRFPAHSAVRCRQAMWDAGFSISPVRESRMGSRSNTDDVDLPFVAIKR 64
[Close]
BLAST of SMED30014759 vs. Planmine SMEST
Match: SMESG000058130.1 (SMESG000058130.1)

HSP 1 Score: 196.823 bits (499), Expect = 1.851e-53
Identity = 96/141 (68.09%), Postives = 108/141 (76.60%), Query Frame = -1 
Query:  282 FRF-ADMEPHRILQGELDKAQRLNREMNQQIVQLTTETQHIKSSWVEPKKVKALYEKMTVTQRGWAEEKQLNQSKKTQIRGLEVALSACQEVNAVTYLLVFAPVKLAYKEPTSNTKPANKPPRHRPGRNERAKRRVTQPAE 701
            F F  DM   +ILQ ELDKAQ+ N+ + +QI+QLT E Q I+S+W+EPKKVK LY+KM   QRGW EEK LNQS KTQIRGLEV LSACQE + VTY LVFAP +LAYKE T  TKP NKP RHRPGRNERAKRR  Q AE
Sbjct:  597 FSFIVDMHSSQILQKELDKAQKSNKNLLRQIIQLTAEVQQIRSTWIEPKKVKTLYQKMAAVQRGWTEEKHLNQSLKTQIRGLEVGLSACQEGDPVTYPLVFAPTQLAYKESTVVTKPVNKPLRHRPGRNERAKRRAAQHAE 737
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BLAST of SMED30014759 vs. Planmine SMEST
Match: SMESG000020037.1 (SMESG000020037.1)

HSP 1 Score: 175.637 bits (444), Expect = 1.444e-51
Identity = 85/139 (61.15%), Postives = 107/139 (76.98%), Query Frame = -1 
Query:  270 MEPHRILQGELDKAQRLNREMNQQIVQLTTETQHIKSSWVEPKKVKALYEKMTVTQRGWAEEKQLNQSKKTQIRGLEVALSACQEVNAVTYLLVFAPVKLAYKEPTSNTKPANKPPRHRPGRNERAKRRVTQPAE*NMF 686
            M P++I   EL+K++R N E++QQ++Q+T E   IK++WVEP KVK+LY+KMT  QRGWAEEKQL+Q++K QIR LEVALSACQE NAVTY LVFAP +LAY+E T  TKPA KP   RPG+ ERAKRR  Q  + + F
Sbjct:    1 MGPYKISSRELEKSRRENAELHQQLIQMTKEIHQIKATWVEPGKVKSLYQKMTAAQRGWAEEKQLHQTQKVQIRSLEVALSACQEGNAVTYPLVFAPAQLAYREATETTKPATKPTPRRPGKAERAKRRAAQAKDCSKF 139
The following BLAST results are available for this feature:
BLAST of SMED30014759 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 SMED30014759 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 SMED30014759 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 SMED30014759 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 SMED30014759 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 SMED30014759 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 SMED30014759 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 SMED30014759 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 SMED30014759 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 SMED30014759 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 SMED30014759 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 SMED30014759 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 SMED30014759 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 SMED30014759 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000053271.12.480e-6578.52SMESG000053271.1[more]
SMESG000023390.19.713e-5684.82SMESG000023390.1[more]
SMESG000032540.12.880e-5464.86SMESG000032540.1[more]
SMESG000058130.11.851e-5368.09SMESG000058130.1[more]
SMESG000020037.11.444e-5161.15SMESG000020037.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014759 ID=SMED30014759|Name=SMED30014759|organism=Schmidtea mediterranea sexual|type=transcript|length=2093bp
GAACTGTAACCATGGGCTTTGAGGTCGCCAAAGGTGAGCGCTATGAAAGA
ACTACTCTGGCCCGACCTCAAAGTGGGTTCAACGCACTACCGGTAGAAGG
TCTGCGTGCGCTTTTACTTATTCTTGTCCCATCTTCGTATATTGGTTTGT
ATTGTCACGTGGAATAATTCTCCTGTTAATTCATACTTATACTGTCTTAA
TCTTGGAATTACAAATCGTAATTTAGAATAAGAATATGAACAACATAATA
TTTATTGAGATAACCAAAAAAACATGTTCTATTCTGCTGGTTGAGTGACT
CGGCGCTTGGCACGCTCGTTCCGACCAGGTCGGTGTCGGGGCGGTTTGTT
CGCAGGTTTAGTGTTCGATGTGGGTTCCTTGTAGGCCAATTTGACTGGAG
CAAAAACCAGCAGATAAGTTACTGCATTGACCTCCTGGCACGCAGATAAA
GCTACTTCTAACCCGCGGATCTGTGTTTTTTTACTCTGGTTCAATTGTTT
TTCTTCGGCCCAACCCCGTTGAGTGACGGTCATCTTCTCATATAGAGCCT
TCACCTTCTTTGGCTCTACCCAGCTTGATTTGATATGCTGGGTTTCGGTT
GTCAGTTGTACAATTTGTTGGTTCATCTCTCGGTTCAATCTTTGGGCTTT
GTCCAATTCGCCTTGTAGAATTCTGTGGGGTTCCATATCTGCAAAACGGA
ATAAAACATTAAACTCTCCTTCGTTATGAAATTTCACTCATCAGGTTTCT
ATCTTATATTATTAATTTCTATTTATTAATTTTTATGAATAAGAAACAAG
AGAATTAAAATGAAATCCGATGCTTTATTTACAATTTACACTTATGTTAA
TCGTATCTCGTATGGCTTCGGCCTCTGAATTACCTTGAAATCTCGCGAGC
GTATGGGTGCTCTTGGTCACGGTGGGGACGTCTATCCTCGTCTCTCATCT
CTCTGGTCAATATTCTTCGTGGAACCACCACGTTCATTGCTTCTGATTCC
TCCTCCAAGTTCGGATCGTTGAGATTGAAGGATACGTTGTACGGAGGGGC
GTACCCATCCGTACTGGGGATGCTTCCCGTTTCTATTGCCTTGTTGATCT
CGGCCAGATGTCGCCTAGCCCTGTCTACTTGTTTGTTTGTCTGGCGCTGA
TGCTCCTCCAAGCGTGCTAGTAAGAACTCCGCTTGCCCTCGGATCTCTCG
GGCTGGATTGTGGCCGGGCTCTCTTGATGGCCACAAAAGGGAGGTCTGCT
TCTCCGTCGTCTCTTTGTGCGCCCTCGCGGGATTCCCTTACCGGCGAGAC
TGAGAATCCCGCGTCCCATAGGGCCTGTCGACATCTGGCTGTCGATCGTG
CGTGAAATCGCACGGTGACGCGGGACGCGTCGATCCAAGAGTGGTCTGAA
AATTTTTAATCATTAAAATATTTAATAAATCATGTATGTATGCTTTTTAT
TACGATTATCTTAAAATAAATTTAACGTATAGATGGCGATTGTATTTGTT
GGTAGTAAGATAACTATAGGACGACGAACAAGTGTGGGTCTGATCGTCGG
ATTCTCGGACGGATATTGGCATGAGTGCTGTTGCCAGTATCGTCACGTGA
TTAAGCTATTTCTTATCTGTTGTACTTTAGGAAAATTTTCATACGTCTTA
TTAGTAGCAGTTGTCATACATATTCGACTTTGTCGGGTACTCATGGTCCT
CATGGTTATGATTCGGAACTCGTGATGGCTTATCTTTGTCTGAGGATTTC
ATTACGCTGTCTCTACACTACTATGTCCGTTCGCTTTCACTTGGTATGGG
AGAAACGTTTGTCATCTCTGTTATTGGGAATTTCGCAGTGATTTGGTTCG
CTCTCAGTGGGTATGATGCCATCATCATCGTAATCGTTGATCTTCGGTTA
ATGCATTATACTAACTAGATGCTTAGCGAGTAGGCTGTCAATTTTCGGTC
AAGCTGGTTACTGGGCATTCGTCAGGAATTATGGGTGAACGAGTCATGAT
ATGAGCTTTCGAAAAATCATTTAGAAGTAATAAATTCATAATATTGTCGG
TATATTTTATTAGATAAACAACGAAATCATGGGATTCTACAGA
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protein sequence of SMED30014759-orf-1

>SMED30014759-orf-1 ID=SMED30014759-orf-1|Name=SMED30014759-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=136bp
MEPHRILQGELDKAQRLNREMNQQIVQLTTETQHIKSSWVEPKKVKALYE
KMTVTQRGWAEEKQLNQSKKTQIRGLEVALSACQEVNAVTYLLVFAPVKL
AYKEPTSNTKPANKPPRHRPGRNERAKRRVTQPAE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003104enteric muscle cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..27
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..43
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 29..43