SMED30015077

Overview
NameSMED30015077
Smed IDSMED30015077
Length (bp)1416
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 SMED30015077 (SMED30015077) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30015077 (SMED30015077) 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 SMED30015077 (SMED30015077) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30015077 (SMED30015077) 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.
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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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Alignments
SMED30015077 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000084:250410..251673 +5297
Homology
BLAST of SMED30015077 vs. Planmine SMEST
Match: SMESG000063966.1 (SMESG000063966.1)

HSP 1 Score: 97.4413 bits (241), Expect = 2.812e-35
Identity = 52/81 (64.20%), Postives = 58/81 (71.60%), Query Frame = 1
Query:  400 GRQPILKFASKYSVSVKMGRMKTTQKSVRRCSC*RPAE*RTKKHYM*WQLFVITWSKILHITS-TMQLQIRSRKTHSKIAS 639
            G   +LKFASKYSV+ KMG M   QKS+RR SC RPAE   +KHYM WQLFV+T SKIL  T+  MQLQIRSR  H KI S
Sbjct:  105 GTSTMLKFASKYSVNAKMGMMTIKQKSLRRYSCRRPAEKHARKHYMRWQLFVVTLSKILQNTTIIMQLQIRSRNKHPKIES 185          

HSP 2 Score: 70.8626 bits (172), Expect = 2.812e-35
Identity = 31/38 (81.58%), Postives = 33/38 (86.84%), Query Frame = 3
Query:  297 DVLPIPAVTAKLGEAVKQEDFEAFAGCNNEVACRGTST 410
            DVLPIPAVTA+LGEAV Q DFEA   C+NEVACRGTST
Sbjct:   71 DVLPIPAVTAELGEAVTQNDFEALVDCDNEVACRGTST 108          
BLAST of SMED30015077 vs. Planmine SMEST
Match: SMESG000036624.1 (SMESG000036624.1)

HSP 1 Score: 77.7962 bits (190), Expect = 1.202e-25
Identity = 37/62 (59.68%), Postives = 47/62 (75.81%), Query Frame = 3
Query:  294 DDVLPIPAVTAKLGEAVKQEDFEAFAGCNNEVACRGTSTNSEICEQVQRKRQNGADENDTEE 479
            DD+L IPAVT +LGEA  QE    F  C+N+V+C  TST++EICEQV+R RQN  D+NDTE+
Sbjct:  134 DDLLQIPAVTVELGEAATQE---TFVDCDNKVSCHDTSTDAEICEQVRRNRQNWDDDNDTED 192          

HSP 2 Score: 58.151 bits (139), Expect = 1.202e-25
Identity = 33/40 (82.50%), Postives = 33/40 (82.50%), Query Frame = 2
Query:  488 DAVVEGPQSNAQRSITCDGNCSSLLGAKSY-ILRVLCSCR 604
            DAVV G QSNAQ SITC GNCSSLLGAKSY I RVLCS R
Sbjct:  192 DAVVRGLQSNAQISITCAGNCSSLLGAKSYRIQRVLCSGR 231          
BLAST of SMED30015077 vs. Planmine SMEST
Match: SMESG000013207.1 (SMESG000013207.1)

HSP 1 Score: 67.3958 bits (163), Expect = 1.089e-18
Identity = 33/59 (55.93%), Postives = 40/59 (67.80%), Query Frame = 1
Query: 1138 KNIYQKLNET*RWFCEERQLVQALRTQIRSLETALLLSQEDNAVTYPVIFTQVQFAYRE 1314
            K  YQ+L    R + EE+QL Q  +TQIRSLE AL  SQE NA TYP++F  VQ AYR+
Sbjct:   46 KTTYQRLTAAQRGWTEEKQLAQNQKTQIRSLEVALSASQESNAGTYPLVFAPVQIAYRD 104          

HSP 2 Score: 45.0542 bits (105), Expect = 1.089e-18
Identity = 22/42 (52.38%), Postives = 31/42 (73.81%), Query Frame = 2
Query: 1013 METICSISQELTKLCQTNTELHSQLLQMSKRCQAIKST*IEP 1138
            ME++ ++S++L K  + NTELHSQL QMS+  Q I+ST  EP
Sbjct:    1 MESLRTLSRKLVKSRKENTELHSQLFQMSREIQKIRSTSGEP 42          
BLAST of SMED30015077 vs. Planmine SMEST
Match: SMESG000049741.1 (SMESG000049741.1)

HSP 1 Score: 68.9366 bits (167), Expect = 4.448e-17
Identity = 35/70 (50.00%), Postives = 42/70 (60.00%), Query Frame = 1
Query: 1138 KNIYQKLNET*RWFCEERQLVQALRTQIRSLETALLLSQEDNAVTYPVIFTQVQFAYREREEASQATKTS 1347
            K +Y KL    + + EERQLV +L+TQIR LE AL  SQE  AVTYP++F   Q AYRE      A  T 
Sbjct:   65 KPLYLKLAAAQKGWAEERQLVTSLKTQIRGLEVALSASQEGAAVTYPLVFAPAQLAYRESNPTPSAMPTP 134          

HSP 2 Score: 38.1206 bits (87), Expect = 4.448e-17
Identity = 18/48 (37.50%), Postives = 27/48 (56.25%), Query Frame = 2
Query:  995 IRIFSGMETICSISQELTKLCQTNTELHSQLLQMSKRCQAIKST*IEP 1138
            IR    M+ I  +  ELT+  Q N +LH QLL + +  Q +K+T + P
Sbjct:   14 IRTILDMDPIKLLQNELTRTQQANNDLHDQLLHLVREMQQLKATWVNP 61          
BLAST of SMED30015077 vs. Planmine SMEST
Match: SMESG000031748.1 (SMESG000031748.1)

HSP 1 Score: 70.8626 bits (172), Expect = 1.078e-16
Identity = 37/74 (50.00%), Postives = 49/74 (66.22%), Query Frame = 1
Query: 1135 TKNIYQKLNET*RWFCEERQLVQALRTQIRSLETALLLSQEDNAVTYPVIFTQVQFAYREREEASQA-TKTSRH 1353
             K +YQ+L    + +  ERQLVQ LRTQI+ LETAL +SQE  AVTYP++F   Q AYR+  + S +  K +RH
Sbjct: 1301 VKVVYQRLEAAQKGWAGERQLVQNLRTQIKGLETALSVSQEGAAVTYPLVFAPAQLAYRDTLDPSTSKDKPNRH 1374          

HSP 2 Score: 35.039 bits (79), Expect = 1.078e-16
Identity = 16/38 (42.11%), Postives = 25/38 (65.79%), Query Frame = 2
Query: 1028 SISQELTKLCQTNTELHSQLLQMSKRCQAIKST*IEPR 1141
            ++ +EL K   TN +LH QLLQ+++    IK T +EP+
Sbjct: 1262 ALQRELDKAHATNRDLHHQLLQLTREIPQIKGTWMEPK 1299          
The following BLAST results are available for this feature:
BLAST of SMED30015077 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 SMED30015077 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 SMED30015077 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 SMED30015077 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 SMED30015077 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 SMED30015077 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 SMED30015077 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 SMED30015077 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 SMED30015077 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 SMED30015077 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 SMED30015077 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 SMED30015077 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 SMED30015077 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 SMED30015077 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000063966.12.812e-3564.20SMESG000063966.1[more]
SMESG000036624.11.202e-2559.68SMESG000036624.1[more]
SMESG000013207.11.089e-1855.93SMESG000013207.1[more]
SMESG000049741.14.448e-1750.00SMESG000049741.1[more]
SMESG000031748.11.078e-1650.00SMESG000031748.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015077 ID=SMED30015077|Name=SMED30015077|organism=Schmidtea mediterranea sexual|type=transcript|length=1416bp
AATTCAAATTTACAGTTGTACAGAAATATATTTAAATTTATTTGTTTGGT
TCTATTTAATATAAGAATTTGAAAACTTTCTTTGAAGAAGGATTTTGCCC
TCATTTAATGGCGAACGTTAAGGAATCCAATATATCAAATGAAATTTCTG
ATGAGCCAGTTGTTAGAGAATTCAGAAAGAGCAGTTCAGTAGGTAGAAGA
TTGGCTTTAGCAAGTCTGGATGTCCCATCTCGTGTGATGCACAAAGTTTC
AAATGAATTAATAAAACAACTAGATAATACGGAACCAATAAACGATGATG
TTCTGCCAATTCCAGCAGTGACTGCTAAGCTAGGAGAAGCTGTCAAGCAA
GAAGATTTTGAAGCTTTTGCAGGCTGCAATAACGAAGTCGCATGCCGTGG
GACGTCAACCAATTCTGAAATTTGCGAGCAAGTACAGCGTAAGCGTCAAA
ATGGGGCGGATGAAAACGACACAGAAGAGCGTGAGGAGATGCAGTTGTTG
AAGGCCCGCAGAGTAACGCACAAAGAAGCATTACATGTGATGGCAACTGT
TCGTCATTACTTGGAGCAAAATCTTACATATTACGAGTACTATGCAGTTG
CAGATAAGATCGAGAAAAACGCATTCAAAAATCGCATCCAGACTTTTTTA
AATAATAAGAGTATAATTATGAGTATTATTCAATAGGAAATGATTTAGAG
ATTAAATAATTTCAAACCAAATAAAGTTGTACAGTTTGATTAAATTGAAA
CGTCGTTGCAAAACTGAATATAAAGTGGTCGATAAATATAACTTTGTGAC
TTTATTTGAAGTCAATCGAAAGCGTAGATCCTGAAAATTAATAAATAGAT
CTAAATAAAATAATCAATAAAATAGTCAAATCAGCGCGACCTTGGAATTC
ATCACAAAAAGAGAAAGAGACTATTGGGACTCATATAAATAGGATAATTT
TTGAGCACATAAAACTTTCGTAAAATTAATGCTATGGATATAAAATTCGC
ATATTTTCAGGCATGGAAACTATTTGCTCCATTAGTCAGGAGTTGACTAA
ACTGTGTCAAACCAACACCGAGCTACACAGTCAACTATTACAGATGAGCA
AAAGGTGTCAGGCGATTAAATCCACCTAGATTGAACCAAGAATATTTACC
AGAAACTTAACGAGACTTAACGGTGGTTTTGCGAGGAGAGACAGCTGGTG
CAGGCTTTACGCACCCAGATCCGCAGTTTAGAAACCGCACTCTTACTCAG
TCAGGAAGATAATGCTGTTACCTACCCTGTGATATTCACCCAGGTACAGT
TTGCTTACCGAGAACGAGAAGAAGCGTCTCAAGCAACCAAGACTAGTCGA
CACATTCAAGTCCAGGGAGATCAGAGCTGATGCGACGACGTTTGCAAACC
GCAGAGGAATTCGGAG
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protein sequence of SMED30015077-orf-1

>SMED30015077-orf-1 ID=SMED30015077-orf-1|Name=SMED30015077-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=193bp
MANVKESNISNEISDEPVVREFRKSSSVGRRLALASLDVPSRVMHKVSNE
LIKQLDNTEPINDDVLPIPAVTAKLGEAVKQEDFEAFAGCNNEVACRGTS
TNSEICEQVQRKRQNGADENDTEEREEMQLLKARRVTHKEALHVMATVRH
YLEQNLTYYEYYAVADKIEKNAFKNRIQTFLNNKSIIMSIIQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland