SMED30005181

Overview
NameSMED30005181
Smed IDSMED30005181
Length (bp)2295
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 SMED30005181 (SMED30005181) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30005181 (SMED30005181) 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 SMED30005181 (SMED30005181) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30005181 (SMED30005181) 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



SMED30005181

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
X1 cellSMED30005181 SmedASXL_062809SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30005181 SmedASXL_062809SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30005181 SmedASXL_077364SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30005181 SmedASXL_077364SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30005181 SmedASXL_072951SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30005181 SmedASXL_072951SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
epidermisSMED30005181 dd_Smed_v4_14193_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30005181 vs. Planmine SMEST
Match: SMESG000039041.1 (SMESG000039041.1)

HSP 1 Score: 184.496 bits (467), Expect = 3.464e-72
Identity = 88/120 (73.33%), Postives = 100/120 (83.33%), Query Frame = -1 
Query:  976 KSEPGRNPAREIRGQAEFLLARLEEHQRQTNAQVERARRYLSSVNEDITAGRIPSTDGYAPPYNTSFNLDDSRLNARSTAIDVVVPRRILPRDMRMERDQTDEHREHPYARTTPKRDNYR 1335
            K EPGRN AREIRG AEFL+A LEEHQRQT+A VE ARRYL++VN+DI  GRI STDGYAP YNTSFNLDD RLN  S  I+VVVP RILPR+MR E++Q DEHREHPYAR  P+RDN++
Sbjct:   73 KREPGRNSAREIRGHAEFLIAPLEEHQRQTDAHVESARRYLANVNDDIAKGRILSTDGYAPSYNTSFNLDDRRLNTNSKTINVVVPWRILPRNMRTEKEQIDEHREHPYARINPRRDNHK 192

HSP 2 Score: 108.227 bits (269), Expect = 3.464e-72
Identity = 48/64 (75.00%), Postives = 56/64 (87.50%), Query Frame = -2 
Query: 1329 IFFLLDNSWIDASWITTRFPAHAANRCRQAMWDAGFTVSQVKESRFSTQQQSKEVELPFVAINR 1520
            I+F LD+SWID+S IT RFPAHAANRCRQA+WDAGFTVSQ KESRF  Q+ S+E++LPFVAI R
Sbjct:   11 IYFGLDDSWIDSSRITVRFPAHAANRCRQALWDAGFTVSQAKESRFGQQRPSEEIKLPFVAIKR 74
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BLAST of SMED30005181 vs. Planmine SMEST
Match: SMESG000000026.1 (SMESG000000026.1)

HSP 1 Score: 233.417 bits (594), Expect = 6.795e-72
Identity = 113/176 (64.20%), Postives = 138/176 (78.41%), Query Frame = -1 
Query:  976 QFVDRCIMDHDTLPRTCGKSMSSSHVGCGIHRLPGEGIEIQHPTAVQGGRASVCRYKSEPGRNPAREIRGQAEFLLARLEEHQRQTNAQVERARRYLSSVNEDITAGRIPSTDGYAPPYNTSFNLDDSRLNARSTAIDVVVPRRILPRDMRMERDQTDEHREHPYARTTPKRDNYR 1503
            +F+DR I+DH  LPRT GKS+S   VGCGIHR P +G++++  T + G R  VCR+K+   RNPAREIRG AEFLLARLEEHQ QT+AQ+E ARRYL++VN+DI   RI STDG AP YNTSFNLDD RLN  S AI+VVVPRRILP +M  E++Q DEHREHPYAR  P+R++Y+
Sbjct:   16 RFMDRLILDHGALPRTRGKSVSPGPVGCGIHRTPSQGVKVRTTTTIGGDRTPVCRHKTGARRNPAREIRGHAEFLLARLEEHQLQTDAQMESARRYLANVNDDIAKRRILSTDGNAPSYNTSFNLDDRRLNTNSKAINVVVPRRILPPNMMTEKEQIDEHREHPYARINPRRESYK 191
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BLAST of SMED30005181 vs. Planmine SMEST
Match: SMESG000019398.1 (SMESG000019398.1)

HSP 1 Score: 153.68 bits (387), Expect = 9.669e-62
Identity = 72/95 (75.79%), Postives = 81/95 (85.26%), Query Frame = -1 
Query: 1051 KSEPGRNPAREIRGQAEFLLARLEEHQRQTNAQVERARRYLSSVNEDITAGRIPSTDGYAPPYNTSFNLDDSRLNARSTAIDVVVPRRILPRDMR 1335
            K EPGRNPAREIRGQAEFLLARLEEHQRQT+ QV RAR YL++VNED  AGRI  T+GYAPPYNTSFNLDD RLN  + A++VV+PR+ LPR MR
Sbjct: 1166 KREPGRNPAREIRGQAEFLLARLEEHQRQTDLQVARARLYLANVNEDKAAGRIACTEGYAPPYNTSFNLDDERLNVNAEAMNVVIPRKALPRKMR 1260

HSP 2 Score: 103.99 bits (258), Expect = 9.669e-62
Identity = 48/68 (70.59%), Postives = 55/68 (80.88%), Query Frame = -2 
Query: 1329 LTIEIFFLLDNSWIDASWITTRFPAHAANRCRQAMWDAGFTVSQVKESRFSTQQQSKEVELPFVAINR 1532
            L I+I  L D SW++ S +T RFPAHAANRCRQAMWDAGFT+SQV+ESR  T QQ +EVELPFVAI R
Sbjct: 1100 LYIDINNLYDESWVNESRVTIRFPAHAANRCRQAMWDAGFTISQVRESRSGTLQQMEEVELPFVAIKR 1167
[Close]
BLAST of SMED30005181 vs. Planmine SMEST
Match: SMESG000011208.1 (SMESG000011208.1)

HSP 1 Score: 147.517 bits (371), Expect = 3.566e-58
Identity = 71/92 (77.17%), Postives = 80/92 (86.96%), Query Frame = -1 
Query: 1060 KSEPGRNPAREIRGQAEFLLARLEEHQRQTNAQVERARRYLSSVNEDITAGRIPSTDGYAPPYNTSFNLDDSRLNARSTAIDVVVPRRILPR 1335
            K +PG NPAR IR QAEFLLARLEEHQRQT+  V++ARRYL +VN+DI AGRI STDGY+PPYNTSFNL D RLN+RSTAI+VVVP RILPR
Sbjct:  124 KRKPGHNPARGIRSQAEFLLARLEEHQRQTDIHVDQARRYLDNVNDDIAAGRIASTDGYSPPYNTSFNLHDERLNSRSTAINVVVPWRILPR 215

HSP 2 Score: 98.2117 bits (243), Expect = 3.566e-58
Identity = 47/58 (81.03%), Postives = 49/58 (84.48%), Query Frame = -2 
Query: 1329 NSWIDASWITTRFPAHAANRCRQAMWDAGFTVSQVKESRFSTQQQSKEVELPFVAINR 1502
            +SWID S IT RFP HAANRCRQAM DAGFTVSQVKESRF T QQ+KEVEL FVAI R
Sbjct:   68 DSWIDESRITVRFPPHAANRCRQAMLDAGFTVSQVKESRFGTLQQTKEVELLFVAIKR 125

HSP 3 Score: 65.855 bits (159), Expect = 6.859e-11
Identity = 33/57 (57.89%), Postives = 40/57 (70.18%), Query Frame = -1 
Query:  538 INEGSTANQGYLGRAEEGQNALPENDSSTEGLD*GETVQPEPENTDKRPRGSSVGLS 708
            +++G   NQ YL RAEEG NALP+++S TEGL  GET QPEPE+TDK      V LS
Sbjct:  216 VDKGGATNQSYLDRAEEGTNALPKDNSGTEGLVRGETTQPEPEDTDKGSGSGGVCLS 272
[Close]
BLAST of SMED30005181 vs. Planmine SMEST
Match: SMESG000032540.1 (SMESG000032540.1)

HSP 1 Score: 155.606 bits (392), Expect = 1.785e-57
Identity = 78/119 (65.55%), Postives = 92/119 (77.31%), Query Frame = -1 
Query:  982 KSEPGRNPAREIRGQAEFLLARLEEHQRQTNAQVERARRYLSSVNEDITAGRIPSTDGYAPPYNTSFNLDDSRLNARSTAIDVVVPRRILPRDMRMERDQTDEHREHPYARTTP-KRDN 1335
            K EPGRNPAREIRGQAE+LLARLEEH+RQT+ +V++ARR+L  +N DI AG IPSTDGYAPPYNT FNLDD RLN  S+A+ VVVPR  L R      +  +EH +HPYAR  P +RDN
Sbjct:   63 KREPGRNPAREIRGQAEYLLARLEEHKRQTDHEVDKARRHLEEINWDIAAGIIPSTDGYAPPYNTPFNLDDPRLNRSSSAMKVVVPRETLIRGWGEANEPANEHHDHPYARERPSRRDN 181

HSP 2 Score: 88.1965 bits (217), Expect = 1.785e-57
Identity = 38/61 (62.30%), Postives = 49/61 (80.33%), Query Frame = -2 
Query: 1329 LLDNSWIDASWITTRFPAHAANRCRQAMWDAGFTVSQVKESRFSTQQQSKEVELPFVAINR 1511
             L+NSWI AS +T RFPAH+A RCRQAMWDAGF++S V+ESR  ++  + +V+LPFVAI R
Sbjct:    4 FLENSWIYASRVTLRFPAHSAVRCRQAMWDAGFSISPVRESRMGSRSNTDDVDLPFVAIKR 64
The following BLAST results are available for this feature:
BLAST of SMED30005181 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 SMED30005181 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 SMED30005181 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 SMED30005181 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 SMED30005181 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 SMED30005181 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 SMED30005181 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 SMED30005181 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 SMED30005181 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 SMED30005181 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 SMED30005181 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 SMED30005181 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 SMED30005181 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 SMED30005181 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000039041.13.464e-7273.33SMESG000039041.1[more]
SMESG000000026.16.795e-7264.20SMESG000000026.1[more]
SMESG000019398.19.669e-6275.79SMESG000019398.1[more]
SMESG000011208.13.566e-5877.17SMESG000011208.1[more]
SMESG000032540.11.785e-5765.55SMESG000032540.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005181 ID=SMED30005181|Name=SMED30005181|organism=Schmidtea mediterranea sexual|type=transcript|length=2295bp
TTTAGGTAAAATCATATATACTAGAATACCTTCTAAATCCTTGATTTTGT
GGGGTTTATGGTCTGGATATCCTCGACCCCAGATGAAAATATTTTCTTAC
CCCCAATGGCTACCCGTCGCTAAGCAACGTTGGGAATGCAACCATTGGTT
TTGGAGATCGCCAAAGGTGAGCGCCATCTAGGAACTGCTCTGGCCCTAGC
TCAAACTGGGTTCAACGCACTGCCGTTAGAAGGCCTGCGTGCGCTTTATT
CGTTCTGATCCCCTTCTTGTATCTTCAATCTTGTTCATTCTATAAACTAA
ATCTTTCACCCTTACTAATTATTCTAGTTCGTCCTGACGTCAAACTTATT
ACACAAAACAATAGATCAAAAGAAACATTTATTTAATAATAATCATCAAC
AAATTTTATTCGGGGTGTAGAGCGGCACGATGCTTGGCGCGCTCGTTTCT
TCCTGGGCGACGCCTGCTTGTTTTGGGACGGTCTTCGAAGTAACTGCCGC
ATCCCTGTAGGCCAGCTGTGCAGGGGCGAAGATCACTTGACAGGCCGACA
CTGCTACCTCTAGGCCTTTTATCTGTGTTTTCAGGTTCTGGTTGAACTGT
TTCTCCTCAGTCCAACCCTTCTGTGCTGCTGTCATTTTCTGGTAGAGCGT
TTTGACCTTCTTCGGCTCTACCCAGGTAGCCTTGATTTGCTGTACTTCCT
TCGTTAATTGCAAAATCTGTTCGTACAATTTCTTATTCGCCTTGCGCGCA
TTGTATAATTCGCGCTGCAGGATTTGGCTTGATTCCATATCTACAAAAGA
ATGATTATTAGGCCACACAATTCCACTTCAATGTTATTTAACAAAAAAAA
ATCCCTCAATCGTGGAATTTTTATAGATACAATCGTTAAAGTTTTAGATT
GGAAAAGAAAACTCAACTAAGAACTAGGATATTTTATTTTTTAACAATTA
TTTACAATTCGGTTCGCGATGGTGTCCTATAGTTATCTCGCTTTGGAGTT
GTCCGAGCATAAGGGTGCTCGCGGTGTTCATCGGTTTGATCTCTCTCCAT
CCTCATGTCACGGGGAAGGATCCTCCGTGGGACCACCACATCGATGGCCG
TGGATCTCGCATTCAATCTGCTGTCATCGAGGTTAAAAGATGTGTTGTAC
GGAGGAGCGTATCCGTCCGTACTGGGAATTCTCCCTGCTGTTATGTCTTC
GTTAACACTGGACAGATAACGTCTAGCCCTCTCTACTTGAGCGTTGGTTT
GCCGCTGATGTTCTTCAAGGCGAGCGAGGAGGAACTCAGCTTGACCCCGG
ATTTCTCGTGCCGGGTTGCGTCCTGGTTCCGATTTATAGCGACAAACGGA
AGCTCGACCTCCTTGGACTGCTGTTGGGTGCTGAATCTCGATTCCTTCAC
CTGGGAGACGGTGAATCCCGCATCCCACATGGCTTGACGACATCGATTTG
CCGCATGTGCGGGGAAGCGTGTCGTGATCCATGATGCATCGATCCACGAA
TTGTCTAAAAGGAAGAAAATTTCAATAGTTAATCGGTTCACCTTAATCGG
AACCACTTAGTCGTGAGTCACCGAAATGGTTGTAGTGAAACTCGTCGGTC
GATTATCGCATATTATTTTGTCTAACTCTTTTCGGTGGTCACTCGCTCCT
TGAAGCGGTCAATTCGATACCTTGATTTTATCTTTTTCAACTTCCCTTTA
AATCGTTCTCTTTGCGAACTTCAGTCATTCAGGATTCGTCTGCCCTTCCT
TTATGTAATGCGTGCTGGGTTGGTCGTGGATTTAGAAGGACTACCTCCTA
AGGCGTGTAATTATCATATTGTATTCAAGACATTAATGATCATGGCTCTG
TAACGGGTTACTCCTTAACGAATTTGGATCCCATAGGAAACGTTCGTCGG
AAAAATGTCATAATGGCGATTTCAACCATCTTGACCTACCTGTAATGAGA
AAGGAATCCGAGACTGGTTGATTCCAAAAATTAAATAACATAAAATTATT
TGTTCTAATAAAAATAAGTTATTCACTTCCCTTCACCTTACACTGCGTGG
ATGAACAGGGCATTTTATTTAAAATTATTAAAATTAATCAGCCATGCAAA
TAAAATATTCCAATAAAAATAATCCATTCCTTTCTCTTTACTCTACAACC
GCGCGAATAAAGCAAATAAAAATGACATTTCATTTAAAATACTAAAATTA
ACCATTTATATAAACTGATTGTTCTAATAATACTGATTTATTCGTTTCTT
TACTTTATACTACACTAATAAAAATGACATTTTATTTAAATTATT
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protein sequence of SMED30005181-orf-1

>SMED30005181-orf-1 ID=SMED30005181-orf-1|Name=SMED30005181-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=131bp
MESSQILQRELYNARKANKKLYEQILQLTKEVQQIKATWVEPKKVKTLYQ
KMTAAQKGWTEEKQFNQNLKTQIKGLEVAVSACQVIFAPAQLAYRDAAVT
SKTVPKQAGVAQEETSAPSIVPLYTPNKIC*
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protein sequence of SMED30005181-orf-2

>SMED30005181-orf-2 ID=SMED30005181-orf-2|Name=SMED30005181-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=177bp
MDHDTLPRTCGKSMSSSHVGCGIHRLPGEGIEIQHPTAVQGGRASVCRYK
SEPGRNPAREIRGQAEFLLARLEEHQRQTNAQVERARRYLSSVNEDITAG
RIPSTDGYAPPYNTSFNLDDSRLNARSTAIDVVVPRRILPRDMRMERDQT
DEHREHPYARTTPKRDNYRTPSRTEL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell