SMED30009905

Overview
NameSMED30009905
Smed IDSMED30009905
Length (bp)883
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30009905 (SMED30009905) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30009905 (SMED30009905) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30009905

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



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30009905h1SMcG0000104 SmedASXL_015250SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30009905h1SMcG0000104 SmedASXL_015250SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30009905h1SMcG0000104 SmedASXL_015251SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30009905h1SMcG0000104 SmedASXL_015251SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30009905h1SMcG0000104 dd_Smed_v4_10941_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30009905h1SMcG0000104 dd_Smed_v4_10941_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30009905h1SMcG0000104 dd_Smed_v4_10941_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30009905h1SMcG0000104 dd_Smed_v4_10941_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30009905h1SMcG0000104 dd_Smed_v4_10941_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30009905h1SMcG0000104 dd_Smed_v4_10941_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30009905h1SMcG0000104 dd_Smed_v4_10941_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30009905h1SMcG0000104 dd_Smed_v4_10941_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30009905h1SMcG0000104 dd_Smed_v6_10941_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
zeta neoblastSMED30009905h1SMcG0000104 dd_Smed_v4_10941_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30009905 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002944:37864..38893 -4375
Homology
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BLAST of SMED30009905 vs. Planmine SMEST
Match: SMESG000000384.1 (SMESG000000384.1)

HSP 1 Score: 362.844 bits (930), Expect = 1.990e-119
Identity = 176/195 (90.26%), Postives = 176/195 (90.26%), Query Frame = 2 
Query:  299 RSKPKYEEIRAWLQHNQIIKSFKLHLKAEKPQFAEIRIISPSTPFHFTNQSGTNYQKSITGLLEPYKDRKFYVVFHPTNSSYHMAHIVVTLEDKRFKVI*XXXXXRWSLILITQQMYLFGYAEAARVELLHFQPSSNPQNPAKLLLIRDFVNDNRSKKIQLFNSGAHTGFVSFYSHQQQVRFQPRSFLMVSKTTK 883
             SKPKYEEIRAWLQHNQIIKSFKLHLKAEKPQFAEIRIISPSTPFHFTNQSGTNYQKSITGLLEPYKDRKFYVVFHPTNSSYHMAHIVVTLEDKRFK                  MYLFGYAEAARVELLHFQPSSNPQNPAKLLLIRDFVNDNRSKKIQLFNSGAHTGFVSFYSHQQQVRFQPRSFLMVSKTTK
Sbjct:  287 ESKPKYEEIRAWLQHNQIIKSFKLHLKAEKPQFAEIRIISPSTPFHFTNQSGTNYQKSITGLLEPYKDRKFYVVFHPTNSSYHMAHIVVTLEDKRFK------------------MYLFGYAEAARVELLHFQPSSNPQNPAKLLLIRDFVNDNRSKKIQLFNSGAHTGFVSFYSHQQQVRFQPRSFLMVSKTTK 463
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BLAST of SMED30009905 vs. Planmine SMEST
Match: SMESG000000384.1 (SMESG000000384.1)

HSP 1 Score: 327.02 bits (837), Expect = 8.699e-106
Identity = 160/181 (88.40%), Postives = 160/181 (88.40%), Query Frame = 2 
Query:  341 HNQIIKSFKLHLKAEKPQFAEIRIISPSTPFHFTNQSGTNYQKSITGLLEPYKDRKFYVVFHPTNSSYHMAHIVVTLEDKRFKVI*XXXXXRWSLILITQQMYLFGYAEAARVELLHFQPSSNPQNPAKLLLIRDFVNDNRSKKIQLFNSGAHTGFVSFYSHQQQVRFQPRSFLMVSKTTK 883
             N  IKSFKLHLKAEKPQFAEIRIISPSTPFHFTNQSGTNYQKSITGLLEPYKDRKFYVVFHPTNSSYHMAHIVVTLEDKRFK                  MYLFGYAEAARVELLHFQPSSNPQNPAKLLLIRDFVNDNRSKKIQLFNSGAHTGFVSFYSHQQQVRFQPRSFLMVSKTTK
Sbjct:  284 QNNDIKSFKLHLKAEKPQFAEIRIISPSTPFHFTNQSGTNYQKSITGLLEPYKDRKFYVVFHPTNSSYHMAHIVVTLEDKRFK------------------MYLFGYAEAARVELLHFQPSSNPQNPAKLLLIRDFVNDNRSKKIQLFNSGAHTGFVSFYSHQQQVRFQPRSFLMVSKTTK 446
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BLAST of SMED30009905 vs. Planmine SMEST
Match: SMESG000072635.1 (SMESG000072635.1)

HSP 1 Score: 55.0694 bits (131), Expect = 2.537e-8
Identity = 41/139 (29.50%), Postives = 61/139 (43.88%), Query Frame = 2 
Query:  452 GTNYQKSITGLLEPYKDRKFYVVFHPTNSSYHMAHIVVTLEDKRFKVI*XXXXXRWSLILITQQMYLFGYAEAARVELLHFQPSSNPQNPAKLLLIRDFVNDNRSKKIQLFNSGAHTGFVSFYS-HQQQVRFQPRSFLM 865
            G     +I   L P  + +  VVF PT+  Y   +IVV  + K+FKV                  +LFGYA  A++           Q P +LL   +    NRS ++ L N    T F+ FY  ++  + F+PR FL+
Sbjct:  177 GRKLSSAIDVSLLPKVENRITVVFLPTDHWYCSGNIVVECQSKKFKV------------------HLFGYACPAKIVF---------QEPKRLLYNSENEESNRSVEMSLTNVSPRTAFIYFYDVYKSGITFRPRKFLV 288
The following BLAST results are available for this feature:
BLAST of SMED30009905 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 SMED30009905 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 SMED30009905 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 SMED30009905 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 SMED30009905 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 SMED30009905 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 SMED30009905 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 SMED30009905 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 SMED30009905 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 SMED30009905 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 SMED30009905 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 SMED30009905 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 SMED30009905 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 SMED30009905 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000000384.11.990e-11990.26SMESG000000384.1[more]
SMESG000000384.18.699e-10688.40SMESG000000384.1[more]
SMESG000072635.12.537e-829.50SMESG000072635.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009905 ID=SMED30009905|Name=SMED30009905|organism=Schmidtea mediterranea sexual|type=transcript|length=883bp
AGACCTAATAAAGGAGACCTAATAGAGGAGAGCTAATATAGGAGACTTAT
CAAAAAAACATTTATCTTTACAGATTCATAGTCAAATATTTCTAATATAA
AAAAGTCATTTGAAAGCAAAACTTTTGTTTATATGTTAATCTTGATTTTT
CGATGGTTAATTCAAGTTTGAACCTTGAGCTAGTATATCAATGGGAGGAG
GGGGCAGAGTAGGTGAGAGGGGACGATGCATTAGTAGTGATGAGAATTGG
GAGTTAATTATTATCAATCTCCAAGGTTTAGTGTTGTCATTTGTTACTAG
ATCAAAACCCAAATATGAGGAAATCCGTGCTTGGTTGCAACACAATCAAA
TCATTAAATCTTTCAAACTCCACCTGAAAGCCGAGAAACCACAATTTGCT
GAGATTCGAATTATTTCGCCGTCCACCCCTTTCCATTTCACCAATCAGTC
AGGAACCAATTACCAAAAGTCGATAACGGGTTTACTTGAGCCATATAAAG
ATAGAAAGTTCTACGTCGTATTTCACCCGACGAATTCCTCGTATCACATG
GCGCATATTGTGGTGACCTTGGAGGATAAACGGTTCAAAGTAATATAGAT
ATAGATATAGATAAGGTGGAGTTTGATTCTAATTACTCAACAGATGTATC
TGTTTGGCTATGCAGAAGCCGCTAGAGTTGAATTGCTTCATTTCCAACCG
AGTTCCAATCCCCAAAATCCCGCTAAATTATTATTGATACGGGATTTCGT
CAATGATAATCGTAGCAAAAAAATCCAGTTGTTTAATTCTGGAGCTCATA
CTGGCTTTGTTTCTTTCTATTCTCACCAGCAACAGGTCCGATTCCAACCG
AGATCCTTCTTAATGGTCTCGAAAACGACAAAA
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protein sequence of SMED30009905-orf-1

>SMED30009905-orf-1 ID=SMED30009905-orf-1|Name=SMED30009905-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=136bp
MGGGGRVGERGRCISSDENWELIIINLQGLVLSFVTRSKPKYEEIRAWLQ
HNQIIKSFKLHLKAEKPQFAEIRIISPSTPFHFTNQSGTNYQKSITGLLE
PYKDRKFYVVFHPTNSSYHMAHIVVTLEDKRFKVI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000026gut
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000420parapharyngeal region
PLANA:0002032epidermal cell
PLANA:0002109X1 cell
PLANA:0002111X2 cell