SMED30005664

Overview
NameSMED30005664
Smed IDSMED30005664
Length (bp)1472
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 SMED30005664 (SMED30005664) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30005664 (SMED30005664) 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 SMED30005664 (SMED30005664) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30005664 (SMED30005664) 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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Homology
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BLAST of SMED30005664 vs. Planmine SMEST
Match: SMESG000058084.1 (SMESG000058084.1)

HSP 1 Score: 221.861 bits (564), Expect = 2.401e-89
Identity = 129/240 (53.75%), Postives = 151/240 (62.92%), Query Frame = 3 
Query:  660 NEHQEDHRRPKVTRVCNTKRPVMIFSNCSPEEWKARGFTDS*IRRSIAGRPSLT*HN*CG*IFA*INSLPP*MSIFFV*LF*YENFNLCLMTFILNNSELVTNNLISLIIAMGPIQILRKELARAQQTNKALYDQIIQLTREIHQIKATWVDPTRIKSVH*RLTAAQKGWADEKQMNQSLLTQIRGLEVALSACQERAAVTYPLVFAPSQLAYRESVXXXXXXXXXXXXXXNSYRPGRKE 1379
             E+++D +  +  RV NTKRPV IFSNCSPEEW ARGFTD                                               LC     L  S ++   L+SLI  M  +Q+LR ELA AQQ NK LYDQII+LTRE+HQ +ATWVDP +IK +H RLTAAQKGWA+EKQ+NQSL TQIRGLEVALSA QE AAVTYPLVFAP+QLAYRESVTTP +A++     T +YRPGRKE
Sbjct:  159 GENRKDSQVARTNRVRNTKRPVTIFSNCSPEEWVARGFTDI----------------------------------------------LCWY-LELTCSVIIVTLLMSLIPEMDSLQLLRTELALAQQNNKTLYDQIIELTREVHQTRATWVDPAKIKPLHQRLTAAQKGWAEEKQINQSLRTQIRGLEVALSASQEGAAVTYPLVFAPAQLAYRESVTTPASASTPVATATTNYRPGRKE 351

HSP 2 Score: 127.487 bits (319), Expect = 2.401e-89
Identity = 63/107 (58.88%), Postives = 78/107 (72.90%), Query Frame = 2 
Query:  311 IPTHVADRWRQAWRQFSQDRCPEFSRPESRQPNWQAGESNCDPWLSDQQWEEWSPAWEIREHARHLLGRLESHQRQIDVKVIRARQYLANIEEDISAGRISNIYRHP 631
            IP  + DRWR+AW+QF Q RC EFS  ESRQ + Q  + N +P  S+Q  EEW+PA EI EHAR LL  L +HQRQ+D++V+RARQ LANIE+DI  GRI+  YRHP
Sbjct:   38 IPIQLPDRWREAWKQFRQARCLEFSPLESRQISGQPEDFNRNPEASEQLLEEWNPAQEIHEHARRLLDSLLNHQRQVDLQVVRARQCLANIEDDIETGRIAAAYRHP 144
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BLAST of SMED30005664 vs. Planmine SMEST
Match: SMESG000024369.1 (SMESG000024369.1)

HSP 1 Score: 212.231 bits (539), Expect = 2.314e-69
Identity = 100/115 (86.96%), Postives = 107/115 (93.04%), Query Frame = 2 
Query:  311 IPTHVADRWRQAWRQFSQDRCPEFSRPESRQPNWQAGESNCDPWLSDQQWEEWSPAWEIREHARHLLGRLESHQRQIDVKVIRARQYLANIEEDISAGRISNIYRHPSQCKTPLK 655
            +PTHVADRWRQAWRQFSQDRCPEF RPESRQ NWQAGESNC+PWLSDQ W+EWSPAWEIREHARHLLGRLES QR++DV+VIRARQYLANIEEDISAGRI+NIYRHP Q K PL 
Sbjct:   16 VPTHVADRWRQAWRQFSQDRCPEFPRPESRQFNWQAGESNCNPWLSDQPWKEWSPAWEIREHARHLLGRLESRQRRLDVQVIRARQYLANIEEDISAGRIANIYRHPPQYKAPLN 130

HSP 2 Score: 70.4774 bits (171), Expect = 2.314e-69
Identity = 34/43 (79.07%), Postives = 36/43 (83.72%), Query Frame = 3 
Query:  654 RTNEHQEDHRRPKVTRVCNTKRPVMIFSNCSPEEWKARGFTDS 782
            RTN+HQE+  R KVTRVCNTKR VMI SNCSPEEW  RGFTDS
Sbjct:  135 RTNDHQENPNRSKVTRVCNTKRAVMISSNCSPEEWVERGFTDS 177
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BLAST of SMED30005664 vs. Planmine SMEST
Match: SMESG000014158.1 (SMESG000014158.1)

HSP 1 Score: 207.223 bits (526), Expect = 4.014e-69
Identity = 96/115 (83.48%), Postives = 107/115 (93.04%), Query Frame = 2 
Query:  311 IPTHVADRWRQAWRQFSQDRCPEFSRPESRQPNWQAGESNCDPWLSDQQWEEWSPAWEIREHARHLLGRLESHQRQIDVKVIRARQYLANIEEDISAGRISNIYRHPSQCKTPLK 655
            +P+HVADRWRQAWRQFSQDRCPE SRPESRQ +WQ+GESN +PWLSDQQWEEWSPAWEIREHARHLLGRLE+HQRQ+DV+VIR+RQYLANIEEDISAGRI+N+Y HP Q K PL 
Sbjct:  111 VPSHVADRWRQAWRQFSQDRCPELSRPESRQLSWQSGESNHNPWLSDQQWEEWSPAWEIREHARHLLGRLENHQRQVDVQVIRSRQYLANIEEDISAGRIANVYCHPPQDKAPLN 225

HSP 2 Score: 74.7146 bits (182), Expect = 4.014e-69
Identity = 35/44 (79.55%), Postives = 37/44 (84.09%), Query Frame = 3 
Query:  651 SRTNEHQEDHRRPKVTRVCNTKRPVMIFSNCSPEEWKARGFTDS 782
             +TN+HQED  RPKVTRV NTKRPVMIF NCSPEEW  RGFTDS
Sbjct:  229 GKTNDHQEDPTRPKVTRVRNTKRPVMIFFNCSPEEWVERGFTDS 272
[Close]
BLAST of SMED30005664 vs. Planmine SMEST
Match: SMESG000007882.1 (SMESG000007882.1)

HSP 1 Score: 196.438 bits (498), Expect = 6.995e-63
Identity = 93/115 (80.87%), Postives = 102/115 (88.70%), Query Frame = 2 
Query:  311 IPTHVADRWRQAWRQFSQDRCPEFSRPESRQPNWQAGESNCDPWLSDQQWEEWSPAWEIREHARHLLGRLESHQRQIDVKVIRARQYLANIEEDISAGRISNIYRHPSQCKTPLK 655
            +PTHVADRWRQAW QFSQDRCPEFSRPESRQ N Q  E N +PWLS+Q WEEWSPAWEIREHARHLLGRLESHQRQ+D++VIRARQYLANIEEDISAGRI+NIYRHP   + P+ 
Sbjct:   16 VPTHVADRWRQAWSQFSQDRCPEFSRPESRQFNRQTEEGNGNPWLSNQPWEEWSPAWEIREHARHLLGRLESHQRQVDIQVIRARQYLANIEEDISAGRIANIYRHPLHHQAPIN 130

HSP 2 Score: 64.6994 bits (156), Expect = 6.995e-63
Identity = 30/43 (69.77%), Postives = 35/43 (81.40%), Query Frame = 3 
Query:  651 SRTNEHQEDHRRPKVTRVCNTKRPVMIFSNCSPEEWKARGFTD 779
             ++N+HQED  RP VTRVCNTKRPVMI +NCSPEE   RGFT+
Sbjct:  134 GKSNDHQEDPNRPNVTRVCNTKRPVMISTNCSPEECVERGFTN 176
[Close]
BLAST of SMED30005664 vs. Planmine SMEST
Match: SMESG000006077.1 (SMESG000006077.1)

HSP 1 Score: 191.045 bits (484), Expect = 1.077e-62
Identity = 91/115 (79.13%), Postives = 100/115 (86.96%), Query Frame = 2 
Query:  311 IPTHVADRWRQAWRQFSQDRCPEFSRPESRQPNWQAGESNCDPWLSDQQWEEWSPAWEIREHARHLLGRLESHQRQIDVKVIRARQYLANIEEDISAGRISNIYRHPSQCKTPLK 655
            +P HVADRWR+AWRQFSQDR PEF R ESRQ NWQ GE N +PWLS+QQ EEWSP WEIREHARHLLGRLESHQRQ+DV+VIRARQYLANIEEDI+AGRI+NIYRHP   + PL 
Sbjct:   16 VPIHVADRWRKAWRQFSQDRDPEFVRLESRQFNWQTGEGNGNPWLSNQQCEEWSPVWEIREHARHLLGRLESHQRQVDVQVIRARQYLANIEEDIAAGRIANIYRHPLHHQAPLN 130

HSP 2 Score: 69.3218 bits (168), Expect = 1.077e-62
Identity = 32/43 (74.42%), Postives = 36/43 (83.72%), Query Frame = 3 
Query:  654 RTNEHQEDHRRPKVTRVCNTKRPVMIFSNCSPEEWKARGFTDS 782
            ++N+HQED  RP VTRV NTKRPVMI +NCSPEEW  RGFTDS
Sbjct:  135 KSNDHQEDPNRPNVTRVRNTKRPVMISTNCSPEEWVERGFTDS 177
The following BLAST results are available for this feature:
BLAST of SMED30005664 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 SMED30005664 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 SMED30005664 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 SMED30005664 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 SMED30005664 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 SMED30005664 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 SMED30005664 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 SMED30005664 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 SMED30005664 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 SMED30005664 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 SMED30005664 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 SMED30005664 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 SMED30005664 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 SMED30005664 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000058084.12.401e-8953.75SMESG000058084.1[more]
SMESG000024369.12.314e-6986.96SMESG000024369.1[more]
SMESG000014158.14.014e-6983.48SMESG000014158.1[more]
SMESG000007882.16.995e-6380.87SMESG000007882.1[more]
SMESG000006077.11.077e-6279.13SMESG000006077.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005664 ID=SMED30005664|Name=SMED30005664|organism=Schmidtea mediterranea sexual|type=transcript|length=1472bp
GATTTTTCCCAAATAGTTTCATTAAAATGAACATTTAATTTTATACACGG
ATATAGATATATACGTATATGTTAAAAATTTGTTAAAATGTTATAATTAG
TCGTTTTGGCATGTTTCGTTTTGTGAATCCAATGGTGTACCATGTAATGA
AACGATACATTTTACCAAGATATTTTTAACCCGCAGGTAAGTCGATGAGT
TGTATAAATTATCGGTTACCTATATTTTTTTTTATTATAAAAGATGCTAG
ATTTTGGAACAAATGTATAATGATAATGATGAATCTTCCTTATTCAGGAA
AATCCGGAAAATCCCTACCCACGTTGCCGATCGATGGAGGCAAGCGTGGA
GACAATTCAGTCAAGACAGATGCCCCGAATTTTCCCGACCGGAATCCCGA
CAGCCCAACTGGCAAGCAGGGGAAAGTAACTGCGACCCATGGCTGTCTGA
CCAACAATGGGAGGAGTGGAGCCCGGCTTGGGAGATCCGCGAACATGCCC
GCCACCTCCTCGGTCGCCTCGAAAGCCATCAGCGACAGATAGACGTGAAG
GTGATCAGAGCTCGTCAATACCTAGCAAACATCGAGGAGGACATTTCAGC
TGGCCGGATCTCCAACATCTACCGCCACCCATCACAATGCAAAACCCCGC
TCAAGGACCAACGAACATCAGGAGGACCACCGCAGGCCCAAGGTTACTCG
GGTTTGCAACACGAAACGACCCGTGATGATATTCTCAAACTGTTCTCCGG
AAGAATGGAAAGCGAGAGGGTTCACAGACTCCTGAATCCGTCGTTCCATA
GCCGGGCGTCCCAGTCTGACCTAACATAATTAATGTGGTTGAATTTTTGC
CTAAATAAATAGCTTGCCACCTTAAATGTCCATTTTTTTTGTTTGATTGT
TTTAATATGAGAATTTCAACTTATGTTTAATGACATTCATACTAAATAAT
TCCGAGTTAGTAACCAACAATTTAATATCCTTAATTATAGCAATGGGACC
CATTCAAATTTTGCGGAAGGAGCTGGCCCGTGCCCAGCAAACCAATAAAG
CTCTATACGACCAAATCATTCAATTGACACGGGAGATCCATCAAATAAAA
GCCACCTGGGTGGACCCGACCAGGATCAAATCAGTACATTAAAGGCTTAC
AGCGGCCCAAAAAGGATGGGCAGACGAAAAGCAGATGAATCAAAGTCTCC
TAACACAGATACGGGGGTTGGAGGTTGCCCTGTCCGCCTGTCAGGAAAGG
GCGGCCGTAACCTACCCCCTCGTCTTCGCGCCATCGCAGTTGGCCTATCG
TGAGTCGGTGACCACTCCGACAACGGCCGCATCCCTAACCCCAGCAATAA
CCAATAGCTATCGGCCGGGGCGAAAGGAGCGGGCTAGACGTAGAGCCGCT
CGATTATCGAATAAGACCCAGTTAACTTAAACGTGCTTTAACTTGTGAAT
TGTATATATTTGATTATAAATT
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protein sequence of SMED30005664-orf-1

>SMED30005664-orf-1 ID=SMED30005664-orf-1|Name=SMED30005664-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=189bp
MYNDNDESSLFRKIRKIPTHVADRWRQAWRQFSQDRCPEFSRPESRQPNW
QAGESNCDPWLSDQQWEEWSPAWEIREHARHLLGRLESHQRQIDVKVIRA
RQYLANIEEDISAGRISNIYRHPSQCKTPLKDQRTSGGPPQAQGYSGLQH
ETTRDDILKLFSGRMESERVHRLLNPSFHSRASQSDLT*
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protein sequence of SMED30005664-orf-2

>SMED30005664-orf-2 ID=SMED30005664-orf-2|Name=SMED30005664-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=116bp
MSCINYRLPIFFFIIKDARFWNKCIMIMMNLPYSGKSGKSLPTLPIDGGK
RGDNSVKTDAPNFPDRNPDSPTGKQGKVTATHGCLTNNGRSGARLGRSAN
MPATSSVASKAISDR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ