SMED30008973

Overview
NameSMED30008973
Smed IDSMED30008973
Length (bp)1831
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 SMED30008973 (SMED30008973) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30008973 (SMED30008973) 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 SMED30008973 (SMED30008973) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008973 (SMED30008973) 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



SMED30008973

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30008973SMESG000017122.1 SmedASXL_010802SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30008973SMESG000017122.1 dd_Smed_v4_13867_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30008973SMESG000017122.1 dd_Smed_v4_13867_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30008973SMESG000017122.1 dd_Smed_v4_13867_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30008973SMESG000017122.1 dd_Smed_v6_13867_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
enteric muscle cellSMED30008973SMESG000017122.1 dd_Smed_v4_13867_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
dorsal ventral margin of the whole animalSMED30008973SMESG000017122.1 dd_Smed_v4_13867_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
Alignments
SMED30008973 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.008217:16223..21972 -7071
Homology
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BLAST of SMED30008973 vs. Planmine SMEST
Match: SMESG000017122.1 (SMESG000017122.1)

HSP 1 Score: 841.262 bits (2172), Expect = 0.000e+0
Identity = 425/427 (99.53%), Postives = 426/427 (99.77%), Query Frame = 1 
Query:  133 MFNFNDQLRNKIFQILFFVIRTRVCSLNIPSVSIFSYNISENKMGLHCTVSTHIKSFNDINKIHLFCPFLDGSSCYINCDNQCLYGVGPCRKVFTSCNYVSNNESTINLYYQLDMRFVNVTGQWICQYDEQKSLPIEISKYVQPMETSTATQKITQKYEXXXXXXXXXXXXXXXXPNFDLKMAIFVIISLGFSVIFNLILIGVVCITRKKFQRSRRRTKKKEISRDITETNSMLTRSSTHQQMLNRSNCSRTPSLDSPSFRESIATYLPDGSTIISANILPRESSSYYVDHCGRIIGILQPLNNYHLDTTDLMSRHSSGESASAFISAIHTNSMMPQKVSTHPSNNANWSHGTPQHQDSYSSTRACSSKQQVYGDSNDESGLGSQSLNHSIKQKHGSFCAGSDKVDLILDCDPSINNISRPPLNIQS 1413
            MFNFNDQLRNKIFQILFFVIRTRVCSLNIPSVSIFSYNISENKMGLHC+VSTHIKSFNDINKIHLFCPFLDGSSCYINCDNQCLYGVGPCRKVFTSCNYVSNNESTINLYYQLDMRFVNVTGQWICQYDEQKSLPIEISKYVQPMETSTATQKITQKYESSTVTSMFSTTVLSFFPNFDLKMAIFVIISLGFSVIFNLILIGVVCITRKKFQRSRRRTKKKEISRDITETNSMLTRSSTHQQMLNRSN SRTPSLDSPSFRESIATYLPDGSTIISANILPRESSSYYVDHCGRIIGILQPLNNYHLDTTDLMSRHSSGESASAFISAIHTNSMMPQKVSTHPSNNANWSHGTPQHQDSYSSTRACSSKQQVYGDSNDESGLGSQSLNHSIKQKHGSFCAGSDKVDLILDCDPSINNISRPPLNIQS
Sbjct:    1 MFNFNDQLRNKIFQILFFVIRTRVCSLNIPSVSIFSYNISENKMGLHCSVSTHIKSFNDINKIHLFCPFLDGSSCYINCDNQCLYGVGPCRKVFTSCNYVSNNESTINLYYQLDMRFVNVTGQWICQYDEQKSLPIEISKYVQPMETSTATQKITQKYESSTVTSMFSTTVLSFFPNFDLKMAIFVIISLGFSVIFNLILIGVVCITRKKFQRSRRRTKKKEISRDITETNSMLTRSSTHQQMLNRSNYSRTPSLDSPSFRESIATYLPDGSTIISANILPRESSSYYVDHCGRIIGILQPLNNYHLDTTDLMSRHSSGESASAFISAIHTNSMMPQKVSTHPSNNANWSHGTPQHQDSYSSTRACSSKQQVYGDSNDESGLGSQSLNHSIKQKHGSFCAGSDKVDLILDCDPSINNISRPPLNIQS 427
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BLAST of SMED30008973 vs. Planmine SMEST
Match: SMESG000057504.1 (SMESG000057504.1)

HSP 1 Score: 59.3066 bits (142), Expect = 2.701e-9
Identity = 37/113 (32.74%), Postives = 59/113 (52.21%), Query Frame = 1 
Query:  250 SENKMGLHCTVST-HIK-------SFNDINKIHLFCPFLDGSSCYINCDNQCLYGVGPCRKVFTSCNYVSNNESTINLYYQLDMRFVNVTGQWICQYDEQKSLPIEISKYVQP 564
            +E+K+ ++ T S+ HIK          +  +IHL CPF D   C+ +C           +++ T C+ +S  + T ++ YQ+++  V VTG W C Y   KS+ I ISKY  P
Sbjct:   20 AEDKLLINATYSSAHIKLTCSTKIGTGERFQIHLKCPFTDSEICFTDCSGNLTTDGNSLKQMITKCDIISTYD-TYSVTYQINIAQVTVTGDWYCIYRGNKSIRIPISKYEIP 131

HSP 2 Score: 57.3806 bits (137), Expect = 1.016e-8
Identity = 39/113 (34.51%), Postives = 57/113 (50.44%), Query Frame = 1 
Query:  250 SENKMGLHCTVST-HIK-------SFNDINKIHLFCPFLDGSSCYINCDNQCLYGVGPCRKVFTSCNYVSNNESTINLYYQLDMRFVNVTGQWICQYDEQKSLPIEISKYVQP 564
            +ENK+ +  T S+ HIK          +  +IHL CPF D   C+ +CD          +++ T C   S+   T ++ YQ+++  V VTG W C Y   KS+ I ISKY  P
Sbjct:  168 AENKLLITSTYSSAHIKLTCSTKIETGERFQIHLKCPFTDSEMCFTDCDAT---DGNSLKQIITKCEK-SSTYDTFSITYQINIAQVTVTGDWYCIYRGNKSIRIPISKYEIP 276
[Close]
BLAST of SMED30008973 vs. Planmine SMEST
Match: SMESG000074733.1 (SMESG000074733.1)

HSP 1 Score: 59.3066 bits (142), Expect = 4.840e-9
Identity = 38/108 (35.19%), Postives = 55/108 (50.93%), Query Frame = 1 
Query:  235 FSYNISENKMGLHCTVSTHIKSFNDINKIHLFCPFLDGSSCYINCDNQCLYGVGPCRKVFTSCNYVSNNESTINLYYQLDMRFVNVTGQWICQYDEQKSLPIEISKYV 558
            F+   S  K+ L C V   IK  N+ + + L CPF D   CY++CD  C      C  + +SC+    N +TI L + +D+  VN TG W C Y    S P ++ +YV
Sbjct:   32 FTVTYSYVKIVLECDVKYDIKD-NNFSTV-LKCPFTDNHLCYLDCDALCY--AENCLPMISSCSKNQTN-TTIKLTWIIDITKVNKTGDWSCSYGSHGSKPAKVERYV 134
The following BLAST results are available for this feature:
BLAST of SMED30008973 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 SMED30008973 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 SMED30008973 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 SMED30008973 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 SMED30008973 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 SMED30008973 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 SMED30008973 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 SMED30008973 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 SMED30008973 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 SMED30008973 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 SMED30008973 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 SMED30008973 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 SMED30008973 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 SMED30008973 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000017122.10.000e+099.53SMESG000017122.1[more]
SMESG000057504.12.701e-932.74SMESG000057504.1[more]
SMESG000074733.14.840e-935.19SMESG000074733.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008973 ID=SMED30008973|Name=SMED30008973|organism=Schmidtea mediterranea sexual|type=transcript|length=1831bp
AAATATATCAATGATGCAAATATAAAAAGCATTTATTTTGTATGAATAGA
AAAAGTATAATTCACTATAAAGGACCTCCCTGTTTCAGTCGGTTTCGGTT
TATATTTTGGAATTAATTTGGGGGAAAAAAATATGTTCAATTTTAACGAT
CAACTTCGGAATAAAATTTTCCAAATTTTATTTTTTGTGATAAGGACAAG
GGTTTGCAGTCTGAATATCCCGTCAGTTTCAATCTTCTCATACAATATAT
CTGAAAATAAAATGGGCTTGCACTGTACCGTATCTACACATATCAAATCC
TTCAATGATATCAACAAAATTCATTTGTTTTGCCCATTTCTAGATGGCAG
TAGCTGCTACATAAACTGTGACAATCAGTGCCTATATGGTGTTGGACCAT
GCAGAAAGGTCTTCACCAGTTGCAATTACGTATCTAACAACGAAAGCACT
ATCAATCTCTATTATCAGTTGGACATGAGATTCGTGAACGTCACGGGTCA
GTGGATCTGCCAATATGATGAACAGAAATCGCTCCCGATAGAGATCAGTA
AATATGTGCAACCTATGGAGACTTCGACAGCAACTCAAAAAATTACCCAG
AAATATGAGAGCTCAACCGTAACTTCCATGTTTTCTACAACCGTTCTGAG
TTTTTTCCCTAATTTTGATCTGAAAATGGCAATCTTTGTCATAATTAGTT
TGGGTTTTTCTGTAATTTTCAACTTAATTCTTATTGGAGTCGTCTGCATA
ACTCGAAAAAAATTTCAAAGATCAAGAAGAAGAACTAAGAAAAAAGAAAT
CTCAAGAGATATAACTGAAACCAACTCAATGCTTACAAGAAGCTCGACTC
ATCAGCAGATGCTCAACCGTTCGAACTGCAGCCGAACTCCAAGTCTCGAT
AGTCCAAGTTTCAGAGAATCCATTGCCACCTATTTACCAGACGGTTCAAC
AATTATTTCAGCAAACATTCTTCCTAGAGAATCTTCTTCGTATTATGTAG
ACCATTGTGGTCGCATCATTGGTATTTTACAACCACTCAATAACTATCAT
CTTGATACCACGGATCTGATGTCTCGCCACAGCAGCGGTGAATCAGCCTC
CGCCTTCATATCGGCCATCCATACTAATTCAATGATGCCTCAAAAAGTCT
CAACTCACCCCTCCAATAATGCCAACTGGTCTCATGGGACTCCTCAACAC
CAAGATTCATATTCTAGCACACGTGCTTGCAGTAGCAAACAACAAGTATA
TGGCGATTCCAACGACGAATCCGGACTCGGATCACAGTCGCTGAACCACT
CGATCAAACAGAAACACGGATCGTTTTGTGCTGGAAGCGATAAAGTCGAT
TTGATTTTGGATTGCGATCCAAGTATAAATAATATATCTCGACCACCTCT
CAATATACAATCGTGAATATTCTTGGTGCAGCTGACAAAATGTTCACAAG
ATACAAAATAGCTCTTACATTTTTGGTGCATTTTTCATTAGAATTTTCAG
TTAATAAAGGTGCTCAGCTCGAATAGCGAATCTCATGCTCATTTCTGTTA
CATCTCAGGCTCAACTCATAGAAGTTACAAAATTTCTCTCTTAAAAAAAT
CACGTAAAACAATAAAGAAAATAAAAAAAAATTGTAACAAGTCTCAGTTG
TATGTAACATTGTTGAGAGATGTATAAAACTTCACTTTTGCATATGTTTG
TTATTGATGGTCATTTTGTTCTGGAATCGATTTGGCACAGTGAAACTGTA
ATAATAATTGATTGATTGATAATTTGATTTTTTAATTGATTGACTTGAGA
TGGATTTGAGTTGCAGAGGTTTTGCAGCTTC
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protein sequence of SMED30008973-orf-1

>SMED30008973-orf-1 ID=SMED30008973-orf-1|Name=SMED30008973-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=428bp
MFNFNDQLRNKIFQILFFVIRTRVCSLNIPSVSIFSYNISENKMGLHCTV
STHIKSFNDINKIHLFCPFLDGSSCYINCDNQCLYGVGPCRKVFTSCNYV
SNNESTINLYYQLDMRFVNVTGQWICQYDEQKSLPIEISKYVQPMETSTA
TQKITQKYESSTVTSMFSTTVLSFFPNFDLKMAIFVIISLGFSVIFNLIL
IGVVCITRKKFQRSRRRTKKKEISRDITETNSMLTRSSTHQQMLNRSNCS
RTPSLDSPSFRESIATYLPDGSTIISANILPRESSSYYVDHCGRIIGILQ
PLNNYHLDTTDLMSRHSSGESASAFISAIHTNSMMPQKVSTHPSNNANWS
HGTPQHQDSYSSTRACSSKQQVYGDSNDESGLGSQSLNHSIKQKHGSFCA
GSDKVDLILDCDPSINNISRPPLNIQS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000043dorsal ventral margin of the whole animal
PLANA:0000101muscle cell
PLANA:0000418head
PLANA:0002032epidermal cell
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: 228..257
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 217..257
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 336..381
NoneNo IPR availableTMHMMTMhelixcoord: 184..206