SMED30010108

Overview
NameSMED30010108
Smed IDSMED30010108
Length (bp)1072
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 SMED30010108 (SMED30010108) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30010108 (SMED30010108) 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 SMED30010108 (SMED30010108) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30010108 (SMED30010108) 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



SMED30010108

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30010108 SmedASXL_073394SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30010108 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000314:72397..73447 +4970
Homology
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BLAST of SMED30010108 vs. Planmine SMEST
Match: SMESG000033974.1 (SMESG000033974.1)

HSP 1 Score: 201.445 bits (511), Expect = 7.099e-63
Identity = 113/184 (61.41%), Postives = 134/184 (72.83%), Query Frame = 3 
Query:  198 MKGTWCSLEATRELYKKITRISRARDDLIIENRSQRITIANQSDALRQIFTEKELQARLPGRSMNQHLNIILAHHLPVNSSNHPERKVPNIVMITLTSSTPNQKHKPXXXXXXXXXXXXXXX-LQANFSAMENVNSSRISEVTSHEPISLSDDSDLKIIYAPRLMDFSQQAPTPSQFSISIENL 746
            MKGTWCS EAT++LYKKITR+SRARDDLI++NRSQRITIA+Q   LRQIFTEKELQARLP RS+ Q LN+I   HLPVN SN  E    N+  +    S PN+KHKPNKNRRR+ +R      LQ N   +EN N  +I EVTS+E   +  +SDL+II  PRLMDF Q AP P QF+IS+ENL
Sbjct:    1 MKGTWCSPEATKKLYKKITRVSRARDDLIVKNRSQRITIADQCATLRQIFTEKELQARLPDRSITQQLNMIPVQHLPVNLSNCVEWDATNVFTLAPVPSIPNRKHKPNKNRRRKEKRRTENALLQVNLITIENPNVIKIPEVTSYESNEMPANSDLEIISPPRLMDFPQSAPIPFQFNISMENL 184

HSP 2 Score: 55.0694 bits (131), Expect = 1.842e-8
Identity = 31/54 (57.41%), Postives = 39/54 (72.22%), Query Frame = 2 
Query:  758 TNVQITISTRTYTVREEVY*NFSGRSTPQIISVTEPP-VRNNFDPAARNVARQH 916
            TN QI IS R+  +REE +   SGRSTPQIISVTEPP VRN+ +  A + +RQ+
Sbjct:  190 TNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQN 243
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BLAST of SMED30010108 vs. Planmine SMEST
Match: SMESG000032225.1 (SMESG000032225.1)

HSP 1 Score: 198.364 bits (503), Expect = 1.637e-62
Identity = 114/166 (68.67%), Postives = 126/166 (75.90%), Query Frame = 3 
Query:  186 KYAKMKGTWCSLEATRELYKKITRISRARDDLIIENRSQRITIANQSDALRQIFTEKELQARLPGRSMNQHLNIILAHHLPVNSSNHPERKVPNIVMITLTSSTPNQKHKP-XXXXXXXXXXXXXXXLQANFSAMENVNSSRISEVTSHEPISLSDDSDLKIIYAP 680
            KY KMKGTWCS EAT+ELYK ITRISRARDDLI+ENR+QRITI ++S ALRQ+FTEKELQARLPGRS  Q LNII  HHLPV SSN  ER V N VM        N+KHKP    RRRE RR  NA+LQAN +A+ENV S  ISE T +EPIS+  DSDL IIYAP
Sbjct:   29 KYEKMKGTWCSPEATKELYKNITRISRARDDLIVENRTQRITIVDKSPALRQLFTEKELQARLPGRSTAQQLNIISVHHLPVYSSNRIERDVTNAVMTRPVLPICNRKHKPNKNQRRREKRRTENALLQANLNAIENVISIGISETTPYEPISMPADSDLAIIYAP 194
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BLAST of SMED30010108 vs. Planmine SMEST
Match: SMESG000046646.1 (SMESG000046646.1)

HSP 1 Score: 177.178 bits (448), Expect = 1.501e-55
Identity = 103/207 (49.76%), Postives = 135/207 (65.22%), Query Frame = 3 
Query:  126 VVVATQHLANLENKHRILKEKYAKMKGTWCSLEATRELYKKITRISRARDDLIIENRSQRITIANQSDALRQIFTEKELQARLPGRSMNQHLNIILAHHLPVNSSNHPERKVPNI-VMITLTSSTPNQKHKPXXXXXXXXXXXXXXXLQANFSAMENVNSSRISEVTSHEPISLSDDSDLKIIYAPRLMDFSQQAPTPSQFSISIEN 743
             V   Q+L  LE ++  L+EKY ++K TWCS E TRE YKKI R+SRARDDLIIENRSQRI I+ +  A RQIFTEKE QARLP R+M Q L+II  HHLP N  N  +    N+   +T  S+   +       RRR+ R+A NA+LQ+N    EN +   I+E+   +PI+L+D  DL +I APR  DFSQ AP P+Q +I+++N
Sbjct:   15 AVAEAQYLEKLERENFTLREKYNRLKVTWCSPEITRERYKKINRLSRARDDLIIENRSQRIMISYECAAFRQIFTEKEKQARLPSRNMTQRLDIIPVHHLPTNPKNQRDNNNKNVPTKLTTPSTVNQRHRPNRNRRRRQRRKAENALLQSNLGVRENASLESITELFWPQPIALNDGEDLGVIDAPRQPDFSQPAPIPAQINITMDN 221

HSP 2 Score: 53.5286 bits (127), Expect = 1.501e-55
Identity = 34/83 (40.96%), Postives = 49/83 (59.04%), Query Frame = 2 
Query:  731 LDRKPSRTPTNVQITISTRTYTVREEVY*NFSGRSTPQIISVTEPPVRNNFDPAARNVARQHPDPTPRRPKKRYFPVDIDTEE 979
            +D   +    N+QI+I++RT   R+ +    SGRS+PQIISV EP +  N    + N+ R     T R PK++Y PVDID E+
Sbjct:  219 MDNYSAEMLINMQISIASRTTPDRDAIS---SGRSSPQIISVIEPTI--NRSQRSDNLPRAPSSSTTRPPKRKYLPVDIDEED 296

HSP 3 Score: 26.1794 bits (56), Expect = 1.501e-55
Identity = 10/15 (66.67%), Postives = 14/15 (93.33%), Query Frame = 1 
Query:   85 MHLPKISKITPAPSS 129
            M+LP+I KI+PAPS+
Sbjct:    1 MNLPRIPKISPAPSA 15
[Close]
BLAST of SMED30010108 vs. Planmine SMEST
Match: SMESG000021652.1 (SMESG000021652.1)

HSP 1 Score: 176.792 bits (447), Expect = 8.234e-55
Identity = 92/123 (74.80%), Postives = 100/123 (81.30%), Query Frame = 3 
Query:  123 VVVVATQHLANLENKHRILKEKYAKMKGTWCSLEATRELYKKITRISRARDDLIIENRSQRITIANQSDALRQIFTEKELQARLPGRSMNQHLNIILAHHLPVNSSNHPERKVPNIVMITLTS 491
            +VV A QHL NLEN+ RILKEKYAKMKG W S EAT ELYKKITRISRA DDLIIENRSQRITIA+QS ALRQ FTEKELQARLPGR+  Q LN I A+HL V+SSN+ E +V NIV  T TS
Sbjct:   14 LVVTAAQHLPNLENEQRILKEKYAKMKGIWLSKEATSELYKKITRISRAHDDLIIENRSQRITIADQSAALRQTFTEKELQARLPGRNTAQPLNSIPAYHLLVDSSNYAEHEVSNIVTTTPTS 136
[Close]
BLAST of SMED30010108 vs. Planmine SMEST
Match: SMESG000037309.1 (SMESG000037309.1)

HSP 1 Score: 166.392 bits (420), Expect = 2.311e-50
Identity = 91/134 (67.91%), Postives = 99/134 (73.88%), Query Frame = 3 
Query:  117 SSVVVVATQHLANLENKHRILKEKYAKMKGTWCSLEATRELYKKITRISRARDDLIIENRSQRITIANQSDALRQIFTEKELQARLPGRSMNQHLNIILAHHLPVNSSNHPERKVPNIVMITLTSSTPNQKHKP 518
            +  V+ A QHLANLEN+HRILKEKY KMKGTW S EATRELYK ITRISRARDDLI ENRSQRITIA+QS ALRQIFTEK  +    G  +    NII  HHLPVNSSNH    V N+V I  T S  N+KHKP
Sbjct:   12 APAVIAAVQHLANLENEHRILKEKYDKMKGTWRSPEATRELYKNITRISRARDDLIFENRSQRITIADQSAALRQIFTEKSCRC---GYRVEVWPNIIPTHHLPVNSSNH----VTNVVTIEPTPSILNRKHKP 138
The following BLAST results are available for this feature:
BLAST of SMED30010108 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 SMED30010108 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 SMED30010108 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 SMED30010108 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 SMED30010108 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 SMED30010108 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 SMED30010108 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 SMED30010108 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 SMED30010108 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 SMED30010108 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 SMED30010108 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 SMED30010108 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 SMED30010108 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 SMED30010108 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000033974.17.099e-6361.41SMESG000033974.1[more]
SMESG000032225.11.637e-6268.67SMESG000032225.1[more]
SMESG000046646.11.501e-5549.76SMESG000046646.1[more]
SMESG000021652.18.234e-5574.80SMESG000021652.1[more]
SMESG000037309.12.311e-5067.91SMESG000037309.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010108 ID=SMED30010108|Name=SMED30010108|organism=Schmidtea mediterranea sexual|type=transcript|length=1072bp
TGTTTACAAGATCTTGAAGAAGAGACCGAATTTTCAAACAGACCAAAATG
TCTCCGATCAAAAACCAAATCTAGCTCAAAAATTATGCATCTGCCAAAAA
TCTCGAAGATTACTCCAGCTCCGTCGTCGTCGTCGCCACTCAGCATTTGG
CAAATCTAGAAAACAAACACCGCATTCTCAAAGAAAAATATGCTAAAATG
AAAGGGACATGGTGTTCCCTAGAGGCTACGAGAGAGTTATATAAGAAGAT
AACTCGAATTTCTCGAGCTCGTGACGATCTAATAATTGAAAACAGAAGCC
AAAGAATCACTATTGCGAATCAAAGTGACGCACTGAGGCAAATTTTTACA
GAAAAAGAGCTGCAGGCGCGGCTACCGGGTCGAAGTATGAACCAACATCT
CAATATCATTCTGGCGCATCATCTGCCGGTCAATTCGTCAAATCACCCCG
AACGTAAAGTCCCTAATATAGTCATGATAACGCTAACTTCGTCGACCCCA
AATCAAAAACATAAGCCCAATAAGAACCGTCGGAGAGAAAATCGAAGGGC
CGTGAATGCCGTATTACAGGCGAATTTTAGCGCCATGGAAAATGTCAATT
CGAGTAGGATATCTGAAGTAACTTCGCACGAGCCTATTTCCCTTTCCGAC
GACTCCGATCTAAAGATAATTTACGCACCCAGATTGATGGATTTTTCCCA
GCAAGCTCCGACACCTTCACAATTTAGTATCTCGATCGAAAACCTTCGCG
GACACCAACCAATGTGCAAATAACGATATCTACTAGAACATATACTGTCA
GGGAAGAAGTATACTAAAATTTCAGCGGAAGATCCACCCCGCAAATTATT
TCGGTTACCGAACCACCGGTACGTAATAATTTCGACCCGGCAGCTAGAAA
TGTTGCTCGACAACATCCAGACCCAACTCCACGCAGACCTAAGAAGCGAT
ATTTTCCGGTGGACATCGATACCGAAGAGGACTGATGGAAAAGTCTGATT
TGACGATATTGCTTTTTTTTGTCGTGATTAAACGGAAGTTTTAGCTTTTC
TTAATCTAAATAGAATTTTTGT
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protein sequence of SMED30010108-orf-1

>SMED30010108-orf-1 ID=SMED30010108-orf-1|Name=SMED30010108-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=192bp
MKGTWCSLEATRELYKKITRISRARDDLIIENRSQRITIANQSDALRQIF
TEKELQARLPGRSMNQHLNIILAHHLPVNSSNHPERKVPNIVMITLTSST
PNQKHKPNKNRRRENRRAVNAVLQANFSAMENVNSSRISEVTSHEPISLS
DDSDLKIIYAPRLMDFSQQAPTPSQFSISIENLRGHQPMCK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell