SMED30016664

Overview
NameSMED30016664
Smed IDSMED30016664
Length (bp)354
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 SMED30016664 (SMED30016664) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016664 (SMED30016664) 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 SMED30016664 (SMED30016664) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30016664 (SMED30016664) 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




SMED30016664

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



PAGE Curations: 18

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30016664SMESG000011618.1 SmedASXL_005370SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30016664SMESG000011618.1 dd_Smed_v4_2370_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30016664SMESG000011618.1 dd_Smed_v4_2370_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30016664SMESG000011618.1 dd_Smed_v4_2370_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult fluorescence in situ hybridization evidence
muscle cellSMED30016664SMESG000011618.1 dd_Smed_v4_2370_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30016664SMESG000011618.1 dd_Smed_v4_2370_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30016664SMESG000011618.1 dd_Smed_v4_2370_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30016664SMESG000011618.1 dd_Smed_v4_2370_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30016664SMESG000011618.1 dd_Smed_v6_2370_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30016664SMESG000011618.1 OX_Smed_1.0.09465ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30016664SMESG000011618.1 BK007009smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism asexual adult colorimetric in situ hybridization evidence
cephalic gangliaSMED30016664SMESG000011618.1 BK007009smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism asexual adult colorimetric in situ hybridization evidence
ventral nerve cordSMED30016664SMESG000011618.1 BK007009smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30016664SMESG000011618.1 BK007009smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism asexual adult colorimetric in situ hybridization evidence
reproductive organSMED30016664SMESG000011618.1 Contig52940newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30016664SMESG000011618.1 Contig52940uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
nervous systemSMED30016664SMESG000011618.1 DAA33898smed_ncbi_20200123PMID:25356635
Cowles et al., 2014
whole organism asexual adult colorimetric in situ hybridization evidence
neuronSMED30016664SMESG000011618.1 DAA33898smed_ncbi_20200123PMID:25356635
Cowles et al., 2014
whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30016664 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.008338:12557..12924 +974
Homology
BLAST of SMED30016664 vs. TrEMBL
Match: E3CTI4 (Neuropeptide Y prohormone-3 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 152.14 bits (383), Expect = 7.504e-46
Identity = 73/74 (98.65%), Postives = 74/74 (100.00%), Query Frame = -2
Query:  114 STKEFTFCFLMICALFCQIVQISANKDELDILFKKRNNNQLDDPDIQQYLQDLNNFYQFYGRPRFGKRQKFHRD 335
            STKEFTFCF+MICALFCQIVQISANKDELDILFKKRNNNQLDDPDIQQYLQDLNNFYQFYGRPRFGKRQKFHRD
Sbjct:    2 STKEFTFCFVMICALFCQIVQISANKDELDILFKKRNNNQLDDPDIQQYLQDLNNFYQFYGRPRFGKRQKFHRD 75          
BLAST of SMED30016664 vs. Planmine SMEST
Match: SMESG000011618.1 (SMESG000011618.1)

HSP 1 Score: 152.14 bits (383), Expect = 2.087e-49
Identity = 73/74 (98.65%), Postives = 74/74 (100.00%), Query Frame = -2
Query:  114 STKEFTFCFLMICALFCQIVQISANKDELDILFKKRNNNQLDDPDIQQYLQDLNNFYQFYGRPRFGKRQKFHRD 335
            STKEFTFCF+MICALFCQIVQISANKDELDILFKKRNNNQLDDPDIQQYLQDLNNFYQFYGRPRFGKRQKFHRD
Sbjct:    2 STKEFTFCFVMICALFCQIVQISANKDELDILFKKRNNNQLDDPDIQQYLQDLNNFYQFYGRPRFGKRQKFHRD 75          
BLAST of SMED30016664 vs. Planmine SMEST
Match: SMESG000030037.1 (SMESG000030037.1)

HSP 1 Score: 46.9802 bits (110), Expect = 8.767e-8
Identity = 20/60 (33.33%), Postives = 36/60 (60.00%), Query Frame = -2
Query:  129 LMICALFCQIVQISANKDELDILFKKRNNNQLDDPDIQQYLQDLNNFYQFYGRPRFGKRQ 308
            ++  A+F   + ++A + +  +++ K  N+   D D + YL+ +  + Q YGRPRFGKRQ
Sbjct:   25 VLFLAVFIFGISLTAKEVKRKVVYLKSRNHFRSDEDYESYLRKVQKYIQLYGRPRFGKRQ 84          
BLAST of SMED30016664 vs. Planmine SMEST
Match: SMESG000076421.1 (SMESG000076421.1)

HSP 1 Score: 43.5134 bits (101), Expect = 1.768e-6
Identity = 19/60 (31.67%), Postives = 36/60 (60.00%), Query Frame = -2
Query:  129 LMICALFCQIVQISANKDELDILFKKRNNNQLDDPDIQQYLQDLNNFYQFYGRPRFGKRQ 308
            ++  A+F   + ++A + +  +++ K  ++   D D + YL+ +  + Q YGRPRFGKRQ
Sbjct:   25 VIFLAVFIFGISLTAMEVKRKVVYLKTRDHFRSDEDYESYLRKVQKYIQLYGRPRFGKRQ 84          
The following BLAST results are available for this feature:
BLAST of SMED30016664 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 SMED30016664 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 SMED30016664 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 SMED30016664 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 SMED30016664 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 SMED30016664 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 SMED30016664 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 SMED30016664 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
E3CTI47.504e-4698.65Neuropeptide Y prohormone-3 OS=Schmidtea mediterra... [more]
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BLAST of SMED30016664 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 SMED30016664 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 SMED30016664 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 SMED30016664 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 SMED30016664 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 SMED30016664 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000011618.12.087e-4998.65SMESG000011618.1[more]
SMESG000030037.18.767e-833.33SMESG000030037.1[more]
SMESG000076421.11.768e-631.67SMESG000076421.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016664 ID=SMED30016664|Name=SMED30016664|organism=Schmidtea mediterranea sexual|type=transcript|length=354bp
TTTTTTTCAAAAATNNNNTTTAATGGATAAAGTAATATCATTTATTTAAA
TATCTTTAAGACAATAAATAAACTAAATTCCAGATATAATACATAGTAAG
AATTGAATCTTCAGTCTCGGTGGAATTTCTGACGTTTTCCAAATCTTGGC
CTCCCATAAAATTGGTAGAAATTGTTCAAATCTTGAAGATATTGCTGAAT
GTCTGGATCGTCCAGTTGATTATTGTTTCGTTTTTTAAACAGAATGTCAA
GCTCGTCTTTGTTTGCAGAAATCTGAACGATTTGGCAAAATAATGCACAG
ATCATTAAAAAGCAAAATGTAAACTCTTTGGTTGACANNNTCGGAAGAGC
GGTT
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Aliases
The feature 'SMED30016664' has the following synonyms
Synonym
npy-3
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000025nervous system
PLANA:0000044cephalic ganglia
PLANA:0000097ventral nerve cord
PLANA:0000099neuron
PLANA:0000418head
PLANA:0000420parapharyngeal region
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR001955Pancreatic_hormone-like
Vocabulary: cellular component
TermDefinition
GO:0005576extracellular region
Vocabulary: molecular function
TermDefinition
GO:0005179hormone activity
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001955Pancreatic hormone-likePROSITEPS50276PANCREATIC_HORMONE_2coord: 45..65
score: 8.622
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..24
score: 0.719
NoneNo IPR availableTMHMMTMhelixcoord: 5..24