SMED30002667

Overview
NameSMED30002667
Smed IDSMED30002667
Length (bp)1439
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 SMED30002667 (SMED30002667) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30002667 (SMED30002667) 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 SMED30002667 (SMED30002667) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30002667 (SMED30002667) 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



SMED30002667

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
tail regionSMED30002667SMESG000030057.1 SMESG000029964.1 SMESG000029963.1 SMESG000029961.1 SmedASXL_007930SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30002667SMESG000030057.1 SMESG000029964.1 dd_Smed_v4_74126_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30002667SMESG000076089.1 SMESG000056400.1 dd_Smed_v4_5143_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002667SMESG000076089.1 SMESG000056400.1 dd_Smed_v4_5143_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30002667SMESG000076089.1 SMESG000056400.1 dd_Smed_v4_5143_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30002667SMESG000076089.1 SMESG000056400.1 dd_Smed_v4_5143_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30002667SMESG000076089.1 SMESG000056400.1 dd_Smed_v4_5143_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30002667SMESG000076089.1 SMESG000056400.1 dd_Smed_v4_5143_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002667SMESG000076089.1 SMESG000056400.1 Contig40005uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002667SMESG000076089.1 SMESG000056400.1 Contig40005newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002667SMESG000030057.1 SMESG000029964.1 SMESG000029963.1 Contig53522newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30002667 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003501:22525..24251 -5462
v31.005165:21576..23308 +5426
v31.017379:5272..7039 -5417
v31.009438:1939..3586 -5380
v31.007755:15231..16814 -5339
v31.000147:115123..116856 +5327
v31.010781:10056..11556 +4097
Homology
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BLAST of SMED30002667 vs. Planmine SMEST
Match: SMESG000029964.1 (SMESG000029964.1)

HSP 1 Score: 464.537 bits (1194), Expect = 3.783e-164
Identity = 254/256 (99.22%), Postives = 254/256 (99.22%), Query Frame = 2 
Query:  326 MENKKTIIARVEKEMQEINGKLLEVENKIKIQTDEINKTKDTIKIFNELQGRQTDMLILFRNNKQKLQTRKSQLHKYLNPAESTNSESSDFLEEKKSPNVXXXXXXXXXXXXXXXSIDLTGTETIATDVHSVRERRIRKFPHSVSEHSESSDFLEDKEPRTSGTSKNYCKKYIKDQTGKHNLASTSYDLIGLGDSSNDLDSEETQIVDFVNLNDSREKRLRTFWLDSGIRVITMRYYQCTLYVCGTNGYLGHMKAR 1093
            MENKKTIIARVEKEMQEINGKLLE ENKIKIQTDEINKTKDTIKIFNELQGRQTDMLILFRNNKQKLQTRKSQLHKYLNPAESTNSESSDFLEEKKSPNVRIKNYKKRKYEEKKISIDLTGTETIATDVHSVRERRIRKFPHSVSEHSESSDFLEDKEPRTSGTSKNYCKKYIKDQTGKHNLASTSYDLIGLGDSS DLDSEETQIVDFVNLNDSREKRLRTFWLDSGIRVITMRYYQCTLYVCGTNGYLGHMKAR
Sbjct:    1 MENKKTIIARVEKEMQEINGKLLEAENKIKIQTDEINKTKDTIKIFNELQGRQTDMLILFRNNKQKLQTRKSQLHKYLNPAESTNSESSDFLEEKKSPNVRIKNYKKRKYEEKKISIDLTGTETIATDVHSVRERRIRKFPHSVSEHSESSDFLEDKEPRTSGTSKNYCKKYIKDQTGKHNLASTSYDLIGLGDSSTDLDSEETQIVDFVNLNDSREKRLRTFWLDSGIRVITMRYYQCTLYVCGTNGYLGHMKAR 256
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BLAST of SMED30002667 vs. Planmine SMEST
Match: SMESG000029964.1 (SMESG000029964.1)

HSP 1 Score: 436.417 bits (1121), Expect = 2.339e-153
Identity = 240/242 (99.17%), Postives = 240/242 (99.17%), Query Frame = 2 
Query:  368 MQEINGKLLEVENKIKIQTDEINKTKDTIKIFNELQGRQTDMLILFRNNKQKLQTRKSQLHKYLNPAESTNSESSDFLEEKKSPNVXXXXXXXXXXXXXXXSIDLTGTETIATDVHSVRERRIRKFPHSVSEHSESSDFLEDKEPRTSGTSKNYCKKYIKDQTGKHNLASTSYDLIGLGDSSNDLDSEETQIVDFVNLNDSREKRLRTFWLDSGIRVITMRYYQCTLYVCGTNGYLGHMKAR 1093
            MQEINGKLLE ENKIKIQTDEINKTKDTIKIFNELQGRQTDMLILFRNNKQKLQTRKSQLHKYLNPAESTNSESSDFLEEKKSPNVRIKNYKKRKYEEKKISIDLTGTETIATDVHSVRERRIRKFPHSVSEHSESSDFLEDKEPRTSGTSKNYCKKYIKDQTGKHNLASTSYDLIGLGDSS DLDSEETQIVDFVNLNDSREKRLRTFWLDSGIRVITMRYYQCTLYVCGTNGYLGHMKAR
Sbjct:    1 MQEINGKLLEAENKIKIQTDEINKTKDTIKIFNELQGRQTDMLILFRNNKQKLQTRKSQLHKYLNPAESTNSESSDFLEEKKSPNVRIKNYKKRKYEEKKISIDLTGTETIATDVHSVRERRIRKFPHSVSEHSESSDFLEDKEPRTSGTSKNYCKKYIKDQTGKHNLASTSYDLIGLGDSSTDLDSEETQIVDFVNLNDSREKRLRTFWLDSGIRVITMRYYQCTLYVCGTNGYLGHMKAR 242
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BLAST of SMED30002667 vs. Planmine SMEST
Match: SMESG000029963.1 (SMESG000029963.1)

HSP 1 Score: 431.024 bits (1107), Expect = 9.816e-152
Identity = 206/209 (98.56%), Postives = 207/209 (99.04%), Query Frame = 2 
Query:  803 RTSGTSKNYCKKYIKDQTGKHNLASTSYDLIGLGDSSNDLDSEETQIVDFVNLNDSREKRLRTFWLDSGIRVITMRYYQCTLYVCGTNGYLGHMKARNLRTLQLNTTEDVINVIGLKHYVYAFTHNEMIIFDKSKNTLLQSFVFNGLFRPILVANRELIIIPLENGEIWKFNCITNRRRIMFQTSSTLKGFVINDGNFMFFLNTVKMIS 1429
            RTSGTSKNYCKKYIKDQTGKHNLASTSYDLIGLGDSS DLDSE TQIVDFVNLNDSREKRLRTFWLDSGIRVITMRYYQCTLYVCGTNGYLGHMKARNLRTLQLNTTEDVI+VIGLKHYVYAFTHNEMIIFDKSKNTLLQSFVFNGLFRPILVANRELIIIPLENGEIWKFNCITNRRRIMFQTSSTLKGFVINDGNFMFFLNTVKMIS
Sbjct:    9 RTSGTSKNYCKKYIKDQTGKHNLASTSYDLIGLGDSSTDLDSEATQIVDFVNLNDSREKRLRTFWLDSGIRVITMRYYQCTLYVCGTNGYLGHMKARNLRTLQLNTTEDVIDVIGLKHYVYAFTHNEMIIFDKSKNTLLQSFVFNGLFRPILVANRELIIIPLENGEIWKFNCITNRRRIMFQTSSTLKGFVINDGNFMFFLNTVKMIS 217
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BLAST of SMED30002667 vs. Planmine SMEST
Match: SMESG000030057.1 (SMESG000030057.1)

HSP 1 Score: 417.542 bits (1072), Expect = 7.829e-145
Identity = 199/204 (97.55%), Postives = 201/204 (98.53%), Query Frame = 2 
Query:  803 RTSGTSKNYCKKYIKDQTGKHNLASTSYDLIGLGDSSNDLDSEETQIVDFVNLNDSREKRLRTFWLDSGIRVITMRYYQCTLYVCGTNGYLGHMKARNLRTLQLNTTEDVINVIGLKHYVYAFTHNEMIIFDKSKNTLLQSFVFNGLFRPILVANRELIIIPLENGEIWKFNCITNRRRIMFQTSSTLKGFVINDGNFMFFLNT 1414
            RTSGTSKNYCKKYIKDQTGKHNLASTSYDLIGLGDSS DLDSE TQIVDFVNLNDSREKRLRTFWLDSGIRVITMRYYQCTLYVCGTNGYLGHMKARNLRTLQLNTTEDVI+VIGLKHYVYAFTHNEMIIFDKSKNTLLQSFVFN LFRPILVANR+LIIIPLENGEIWKFNCITNRRRIMFQTSSTLKGFVINDGNFMFFLNT
Sbjct:    9 RTSGTSKNYCKKYIKDQTGKHNLASTSYDLIGLGDSSTDLDSEATQIVDFVNLNDSREKRLRTFWLDSGIRVITMRYYQCTLYVCGTNGYLGHMKARNLRTLQLNTTEDVIDVIGLKHYVYAFTHNEMIIFDKSKNTLLQSFVFNELFRPILVANRDLIIIPLENGEIWKFNCITNRRRIMFQTSSTLKGFVINDGNFMFFLNT 212
[Close]
BLAST of SMED30002667 vs. Planmine SMEST
Match: SMESG000030057.1 (SMESG000030057.1)

HSP 1 Score: 270.396 bits (690), Expect = 2.064e-88
Identity = 127/130 (97.69%), Postives = 129/130 (99.23%), Query Frame = 2 
Query: 1025 MRYYQCTLYVCGTNGYLGHMKARNLRTLQLNTTEDVINVIGLKHYVYAFTHNEMIIFDKSKNTLLQSFVFNGLFRPILVANRELIIIPLENGEIWKFNCITNRRRIMFQTSSTLKGFVINDGNFMFFLNT 1414
            MRYYQCTLYVCGTNGYLGHMKARNLRTLQLNTTEDVI+VIGLKHYVYAFTHNEMIIFDKSKNTLLQSFVFN LFRPILVANR+LIIIPLENGEIWKFNCITNRRRIMFQTSSTLKGFVINDGNFMFFLNT
Sbjct:    1 MRYYQCTLYVCGTNGYLGHMKARNLRTLQLNTTEDVIDVIGLKHYVYAFTHNEMIIFDKSKNTLLQSFVFNELFRPILVANRDLIIIPLENGEIWKFNCITNRRRIMFQTSSTLKGFVINDGNFMFFLNT 130
The following BLAST results are available for this feature:
BLAST of SMED30002667 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 SMED30002667 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 SMED30002667 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 SMED30002667 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 SMED30002667 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 SMED30002667 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 SMED30002667 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 SMED30002667 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 SMED30002667 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 SMED30002667 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 SMED30002667 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 SMED30002667 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 SMED30002667 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 SMED30002667 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000029964.13.783e-16499.22SMESG000029964.1[more]
SMESG000029964.12.339e-15399.17SMESG000029964.1[more]
SMESG000029963.19.816e-15298.56SMESG000029963.1[more]
SMESG000030057.17.829e-14597.55SMESG000030057.1[more]
SMESG000030057.12.064e-8897.69SMESG000030057.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002667 ID=SMED30002667|Name=SMED30002667|organism=Schmidtea mediterranea sexual|type=transcript|length=1439bp
GAGAAATGATTCTCATGACGCTCATCGATGTCTGCAATATTCGACACAAA
TTTTATTTCTTTCTCAATTCGTTCTGTTGTCGTCATAGATGAAAATTCAT
TGGAATATGGGATTAAATTAGACGTGGCTGAGTAGAGACATTTATGAGAT
TGTGTGTCAGTCTGAATCCAATCAACTTTATTCTCATTTTTACGAACCAA
GATCGGAAATTGATTTTGCTTTTTCAATTCCAAATGCAACCACAAACTGT
ATTTGGGATTATTTATTGAATTTAGTCTCAACCATACATTTGGACCAAAA
GTTAGAGAATTGATTTTCGAGGAAAATGGAAAATAAAAAAACTATTATTG
CGAGAGTTGAGAAGGAAATGCAGGAAATTAATGGGAAACTATTAGAAGTG
GAAAATAAAATAAAGATACAAACTGACGAAATCAATAAAACAAAAGACAC
AATAAAGATATTTAATGAACTGCAAGGCCGACAGACTGACATGCTCATTC
TGTTTAGAAACAACAAACAGAAACTCCAAACGAGGAAATCTCAATTGCAC
AAGTATTTGAACCCGGCCGAAAGCACCAATTCAGAATCCAGCGACTTTCT
AGAAGAAAAAAAATCGCCAAATGTGAGAATAAAGAATTACAAGAAAAGAA
AATACGAGGAAAAGAAAATTTCCATTGATCTCACCGGCACAGAAACAATT
GCCACCGATGTGCATAGCGTCAGGGAAAGGAGAATCCGCAAGTTTCCACA
CTCAGTAAGTGAGCACTCTGAGTCGAGTGACTTTTTAGAAGATAAGGAAC
CGCGAACTTCTGGAACATCGAAAAATTACTGTAAAAAGTATATAAAAGAT
CAAACTGGAAAACATAATTTAGCATCCACTTCCTATGACCTCATAGGCCT
AGGCGATTCTTCCAACGATTTGGACTCAGAGGAGACTCAAATTGTTGATT
TCGTCAATCTGAATGATTCAAGGGAAAAAAGACTTCGGACGTTCTGGTTA
GATAGCGGAATTAGAGTAATTACGATGCGATATTATCAGTGTACTCTCTA
TGTTTGTGGAACTAACGGATACCTTGGCCATATGAAAGCTAGAAATTTGA
GAACTTTGCAGCTGAATACGACGGAAGATGTCATCAACGTTATCGGCCTC
AAGCATTATGTTTACGCGTTCACTCACAATGAAATGATAATATTTGACAA
ATCAAAGAATACACTGTTACAAAGTTTCGTGTTTAATGGACTTTTCAGGC
CCATTCTAGTGGCAAATAGAGAGTTGATCATTATCCCGCTTGAGAATGGA
GAGATTTGGAAATTTAATTGCATTACAAACAGGAGAAGAATAATGTTTCA
AACCTCCAGCACGTTGAAAGGATTTGTGATTAATGATGGAAATTTTATGT
TCTTTCTGAATACGGTAAAAATGATTTCATAGTGACCGC
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protein sequence of SMED30002667-orf-1

>SMED30002667-orf-1 ID=SMED30002667-orf-1|Name=SMED30002667-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=369bp
MENKKTIIARVEKEMQEINGKLLEVENKIKIQTDEINKTKDTIKIFNELQ
GRQTDMLILFRNNKQKLQTRKSQLHKYLNPAESTNSESSDFLEEKKSPNV
RIKNYKKRKYEEKKISIDLTGTETIATDVHSVRERRIRKFPHSVSEHSES
SDFLEDKEPRTSGTSKNYCKKYIKDQTGKHNLASTSYDLIGLGDSSNDLD
SEETQIVDFVNLNDSREKRLRTFWLDSGIRVITMRYYQCTLYVCGTNGYL
GHMKARNLRTLQLNTTEDVINVIGLKHYVYAFTHNEMIIFDKSKNTLLQS
FVFNGLFRPILVANRELIIIPLENGEIWKFNCITNRRRIMFQTSSTLKGF
VINDGNFMFFLNTVKMIS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal
PLANA:0000421tail
PLANA:0003116parenchymal cell