SMED30034202

Overview
NameSMED30034202
Smed IDSMED30034202
Length (bp)506
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 SMED30034202 (SMED30034202) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30034202 (SMED30034202) 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



SMED30034202

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30034202h1SMcG0008317 SmedASXL_005396SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30034202h1SMcG0008317 Contig45549uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30034202h1SMcG0008317 Contig45549newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30034202h1SMcG0008317 dd_Smed_v4_1917_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30034202h1SMcG0008317 dd_Smed_v4_1917_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30034202h1SMcG0008317 dd_Smed_v4_1917_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30034202h1SMcG0008317 dd_Smed_v4_1917_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30034202h1SMcG0008317 dd_Smed_v4_1917_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30034202h1SMcG0008317 dd_Smed_v4_1917_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
cilated neuronSMED30034202h1SMcG0008317 dd_Smed_v4_1917_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30034202h1SMcG0008317 dd_Smed_v6_1917_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30034202h1SMcG0008317 dd_Smed_v4_1917_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30034202h1SMcG0008317 dd_Smed_v4_1917_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
SMED30034202 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002899:23620..27692 -2464
Homology
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BLAST of SMED30034202 vs. Ensembl Xenopus
Match: RSPH14 (radial spoke head 14 homolog (Chlamydomonas) [Source:NCBI gene;Acc:594888])

HSP 1 Score: 47.3654 bits (111), Expect = 3.279e-6
Identity = 22/39 (56.41%), Postives = 28/39 (71.79%), Query Frame = -2 
Query:   53 AHGKYAAINFGALPHLLPLINDPNSEVRVNSIKVVIFLS 169
              GKYAAIN GA+P LL L++D  S VR+NS+K +  LS
Sbjct:  260 TQGKYAAINSGAIPKLLALVSDGYSRVRLNSLKALTTLS 298
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BLAST of SMED30034202 vs. Planmine SMEST
Match: SMESG000057359.1 (SMESG000057359.1)

HSP 1 Score: 89.7373 bits (221), Expect = 3.100e-23
Identity = 44/67 (65.67%), Postives = 54/67 (80.60%), Query Frame = 3 
Query:  201 KSQIRVLEVAIAASQEESAVTYPLVFAPVQVAYQEQNQPKNITGKLNIHTRPGKAERERRKLQKRAN 401
            K QIR LE+A+AASQE SAVTYPLVFAP QV Y+EQ+ PKN  GK   HTRPG+A+RER K+Q++ +
Sbjct:   82 KIQIRGLEIAVAASQEGSAVTYPLVFAPTQVTYKEQHGPKNPKGKPKTHTRPGRAKRERTKVQQQKD 148
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BLAST of SMED30034202 vs. Planmine SMEST
Match: SMESG000077061.1 (SMESG000077061.1)

HSP 1 Score: 79.337 bits (194), Expect = 8.067e-18
Identity = 41/55 (74.55%), Postives = 41/55 (74.55%), Query Frame = -2 
Query:    2 HGKYAAINFGALPHLLPLINDPNSEVRVNSIKVVIFLSIYS*LQC*ALTCIAETP 166
            HGKYAAINFGALPHLLPLINDPNSEVRVNSIK              ALTCIAETP
Sbjct:  261 HGKYAAINFGALPHLLPLINDPNSEVRVNSIK--------------ALTCIAETP 301
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BLAST of SMED30034202 vs. Planmine SMEST
Match: SMESG000013207.1 (SMESG000013207.1)

HSP 1 Score: 73.559 bits (179), Expect = 4.827e-17
Identity = 41/84 (48.81%), Postives = 55/84 (65.48%), Query Frame = 3 
Query:  141 KLIAAYFPWAGKRKRL*IRPKSQIRVLEVAIAASQEESAVTYPLVFAPVQVAYQEQNQPKNITGKLNIHTRPGKAERERRKLQK 392
            +L AA   W  + K+L    K+QIR LEVA++ASQE +A TYPLVFAPVQ+AY++      +   L    RPGKAER +R+ Q+
Sbjct:   51 RLTAAQRGWT-EEKQLAQNQKTQIRSLEVALSASQESNAGTYPLVFAPVQIAYRDAISTTKLVASLRSQRRPGKAERVKRRAQQ 133
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BLAST of SMED30034202 vs. Planmine SMEST
Match: SMESG000068632.1 (SMESG000068632.1)

HSP 1 Score: 77.411 bits (189), Expect = 6.917e-17
Identity = 44/87 (50.57%), Postives = 58/87 (66.67%), Query Frame = 3 
Query:  141 KLIAAYFPWAGKRKRL*IRPKSQIRVLEVAIAASQEESAVTYPLVFAPVQVAYQEQNQPKNITGKLNIHTRPGKAERERRKLQKRAN 401
            ++ AA   WA +R+ L    K+QI+ LE A++ASQE +AVTYPLVFAP Q+AY++Q  P     K N H RPGKAER + +  K AN
Sbjct: 1110 RMEAAQKGWASERQ-LTQNLKTQIKGLETALSASQERAAVTYPLVFAPAQLAYRDQMSPATPKDKPNRH-RPGKAERAKLRRLKVAN 1194
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BLAST of SMED30034202 vs. Planmine SMEST
Match: SMESG000031748.1 (SMESG000031748.1)

HSP 1 Score: 76.6406 bits (187), Expect = 1.134e-16
Identity = 44/87 (50.57%), Postives = 58/87 (66.67%), Query Frame = 3 
Query:  141 KLIAAYFPWAGKRKRL*IRPKSQIRVLEVAIAASQEESAVTYPLVFAPVQVAYQEQNQPKNITGKLNIHTRPGKAERERRKLQKRAN 401
            +L AA   WAG+R+ L    ++QI+ LE A++ SQE +AVTYPLVFAP Q+AY++   P     K N H RPGKAER +R+  K AN
Sbjct: 1307 RLEAAQKGWAGERQ-LVQNLRTQIKGLETALSVSQEGAAVTYPLVFAPAQLAYRDTLDPSTSKDKPNRH-RPGKAERAKRRRLKEAN 1391
The following BLAST results are available for this feature:
BLAST of SMED30034202 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 SMED30034202 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 SMED30034202 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 SMED30034202 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 SMED30034202 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
RSPH143.279e-656.41radial spoke head 14 homolog (Chlamydomonas) [Sour... [more]
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BLAST of SMED30034202 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 SMED30034202 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 SMED30034202 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 SMED30034202 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 SMED30034202 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 SMED30034202 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 SMED30034202 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 SMED30034202 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 SMED30034202 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000057359.13.100e-2365.67SMESG000057359.1[more]
SMESG000077061.18.067e-1874.55SMESG000077061.1[more]
SMESG000013207.14.827e-1748.81SMESG000013207.1[more]
SMESG000068632.16.917e-1750.57SMESG000068632.1[more]
SMESG000031748.11.134e-1650.57SMESG000031748.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034202 ID=SMED30034202|Name=SMED30034202|organism=Schmidtea mediterranea sexual|type=transcript|length=506bp
CCGGTGTCTCAGCAATGCATGTCAACGCCTAGCATTGCAATTACGAATAA
ATACTCAGAAATATAACTACTTTGATGGAATTGACTCTCACTTCGCTGTT
CGGATCATTTATCAAAGGCAACAAATGAGGCAGAGCACCAAAATTGATAG
CGGCATACTTTCCATGGGCTGGCAAGAGGAAAAGGCTTTAAATCAGGCCC
AAAAGTCAAATTCGCGTATTGGAAGTTGCCATTGCGGCCAGCCAAGAGGA
GAGTGCGGTCACTTACCCCTTGGTATTTGCGCCAGTGCAAGTGGCCTACC
AAGAGCAGAATCAACCCAAGAATATAACCGGTAAGCTGAATATCCACACG
AGGCCTGGAAAAGCCGAGCGAGAGCGCAGAAAGCTCCAAAAACGAGCCAA
CTGAACGTGATTGACTTTATGATGAATGTCATTATTAGTTTCGCGCATAA
GTAGAAAGTTGTGTTTTTTTGATACCAGAATAAATGTTTTATGTTTTAAA
AAAAAA
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protein sequence of SMED30034202-orf-1

>SMED30034202-orf-1 ID=SMED30034202-orf-1|Name=SMED30034202-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=111bp
RCLSNACQRLALQLRINTQKYNYFDGIDSHFAVRIIYQRQQMRQSTKIDS
GILSMGWQEEKALNQAQKSNSRIGSCHCGQPRGECGHLPLGICASASGLP
RAESTQEYNR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000106ciliated epithelial cell
PLANA:0000418head
PLANA:0002032epidermal cell