SMED30027106

Overview
NameSMED30027106
Smed IDSMED30027106
Length (bp)870
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 SMED30027106 (SMED30027106) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30027106 (SMED30027106) 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 SMED30027106 (SMED30027106) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30027106 (SMED30027106) 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




SMED30027106

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



PAGE Curations: 24

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043.1smed_ncbi_20200123PMID:20707997
Gurley et al., 2010
whole organism asexual adult fluorescence in situ hybridization evidence
cephalic gangliaSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043.1smed_ncbi_20200123PMID:20707997
Gurley et al., 2010
whole organism asexual adult fluorescence in situ hybridization evidence
ventral nerve cordSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043.1smed_ncbi_20200123PMID:20707997
Gurley et al., 2010
whole organism asexual adult fluorescence in situ hybridization evidence
nervous systemSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043.1smed_ncbi_20200123PMID:25558068
Reuter et al., 2015
whole organism asexual adult fluorescence in situ hybridization evidence
X1 cellSMED30027106SMESG000008069.1 SmedASXL_007365SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30027106SMESG000008069.1 SmedASXL_007365SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043.1smed_ncbi_20200123PMID:29557542
Han et al., 2019
whole organism asexual adult colorimetric in situ hybridization evidence
Smed sexual biotypeSMED30027106SMESG000008070.1 SMESG000008069.1 Contig45128newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30027106SMESG000008070.1 SMESG000008069.1 Contig45128uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043.1smed_ncbi_20200123PMID:21566185
Wagner et al., 2011
whole organism asexual adult fluorescence in situ hybridization evidence
nervous systemSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043smed_ncbi_20200123PMID:21566185
Wagner et al., 2011
whole organism asexual adult fluorescence in situ hybridization evidence
embryonic pharynx neuronSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043.1smed_ncbi_20200123PMID:28072387
Davies et al., 2017
whole organism Stage 4 colorimetric in situ hybridization evidence
embryonic pharynx neuronSMED30027106SMESG000008070.1 SMESG000008069.1 DAA33932.1smed_ncbi_20200123PMID:28072387
Davies et al., 2017
whole organism Stage 4 colorimetric in situ hybridization evidence
head regionSMED30027106SMESG000008070.1 SMESG000008069.1 OX_Smed_1.0.20218ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
photoreceptor neuronSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
cephalic gangliaSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
ventral nerve cordSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
central nervous systemSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
copulatory apparatusSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
submuscular nerve plexusSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
zeta neoblastSMED30027106SMESG000008069.1 dd_Smed_v4_17071_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
central nervous systemSMED30027106SMESG000008070.1 SMESG000008069.1 BK007043.1smed_ncbi_20200123PMID:21566195
Petersen et al., 2011
whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30027106 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000098:125976..127955 +4126
Homology
BLAST of SMED30027106 vs. Planmine SMEST
Match: SMESG000008069.1 (SMESG000008069.1)

HSP 1 Score: 286.96 bits (733), Expect = 5.469e-99
Identity = 146/153 (95.42%), Postives = 146/153 (95.42%), Query Frame = 2
Query:   65 MVDNDSTTSNSDRKNIKISLHTCTICAKSFLLKNSLQVHYKSHYKEITKNNDTIIRKNDKENLKVSSGHSKSPIQKKLTAYYQKSSASNTIKFTCYICPLDFTDKNNLYKHLLCHILNEVKAGYQLKQHNKLELSAKESSNKTFTQGSSTAHD 523
            MVDNDSTTSNSDRKNIKISLHTCTICAKSFLLKNSLQVHYKSHYKEITK       KNDKENLKVSSGHSKSPIQKKLTAYYQKSSASNTIKFTCYICPLDFTDKNNLYKHLLCHILNEVKAGYQLKQHNKLELSAKESSNKTFTQGSSTAHD
Sbjct:    1 MVDNDSTTSNSDRKNIKISLHTCTICAKSFLLKNSLQVHYKSHYKEITK-------KNDKENLKVSSGHSKSPIQKKLTAYYQKSSASNTIKFTCYICPLDFTDKNNLYKHLLCHILNEVKAGYQLKQHNKLELSAKESSNKTFTQGSSTAHD 146          
The following BLAST results are available for this feature:
BLAST of SMED30027106 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 SMED30027106 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 SMED30027106 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 SMED30027106 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 SMED30027106 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 SMED30027106 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 SMED30027106 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 SMED30027106 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 SMED30027106 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 SMED30027106 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 SMED30027106 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 SMED30027106 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 SMED30027106 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 SMED30027106 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000008069.15.469e-9995.42SMESG000008069.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027106 ID=SMED30027106|Name=SMED30027106|organism=Schmidtea mediterranea sexual|type=transcript|length=870bp
CGATCTTGAACCAACATTGTTTAAACTTGAACTTTAGCTTTATTAAAATT
TAACATTAAAGGCTATGGTTGACAATGATTCCACAACAAGCAATTCTGAT
AGGAAAAATATAAAAATTTCGTTGCACACCTGTACCATATGTGCAAAATC
ATTTTTACTTAAAAATAGTTTGCAAGTTCATTACAAATCTCATTACAAAG
AAATTACCAAAAATAATGATACAATCATTAGAAAAAATGATAAAGAAAAT
CTGAAGGTTTCTAGTGGACATTCTAAAAGTCCGATTCAGAAAAAACTAAC
GGCTTACTATCAGAAAAGTAGCGCATCAAATACAATAAAATTTACCTGTT
ATATCTGTCCCTTAGATTTCACTGACAAGAATAATCTCTACAAACATTTG
TTATGTCATATTCTTAATGAAGTTAAAGCCGGCTATCAACTGAAACAACA
CAATAAACTTGAATTAAGCGCCAAAGAGAGCAGCAACAAGACTTTTACAC
AAGGAAGTAGTACGGCGCACGATTAGGATTTTATTCACAATTTAATCAAT
AAGTTTTAAAGATTTTAAGTCCTTTTGAATTTCCTTGAATTTTGTAGCGA
TTTTGGAATATGTTTATGATAATGTTTGTAATAAACTTGACTTTTTTAAT
TGGATGCTCCGTAACCGTTGGCAATTTGTCATTGAAATTAACCTCCTCAC
ACCCTGGGCACATTATAATGAACGATATTTTCTTTTGAAGCCGTTTTCAA
TCTTTTTTTACTATGTATTGATTGAGTCGTTCTTTTGCACATTGAAATGT
AGAGGCTGTAATCTCTAAAAATGAAGTTTTCAAAATACCAAAATAAAAAG
TCAGGATTGAGGAGGTTAAG
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protein sequence of SMED30027106-orf-1

>SMED30027106-orf-1 ID=SMED30027106-orf-1|Name=SMED30027106-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=154bp
MVDNDSTTSNSDRKNIKISLHTCTICAKSFLLKNSLQVHYKSHYKEITKN
NDTIIRKNDKENLKVSSGHSKSPIQKKLTAYYQKSSASNTIKFTCYICPL
DFTDKNNLYKHLLCHILNEVKAGYQLKQHNKLELSAKESSNKTFTQGSST
AHD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000016pharynx
PLANA:0000017photoreceptor neuron
PLANA:0000025nervous system
PLANA:0000044cephalic ganglia
PLANA:0000097ventral nerve cord
PLANA:0000103central nervous system
PLANA:0000208testis
PLANA:0000232copulatory apparatus
PLANA:0000418head
PLANA:0000467submuscular nerve plexus
PLANA:0002109X1 cell
PLANA:0002111X2 cell
PLANA:0004519embryonic pharynx neuron
Vocabulary: INTERPRO
TermDefinition
IPR036236Znf_C2H2_sf
IPR015880Znf_C2H2-like
IPR013087Znf_C2H2_type
IPR007087Znf_C2H2
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0046872metal ion binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR013087Zinc finger C2H2-typeSMARTSM00355c2h2final6coord: 21..43
e-value: 0.023
score: 23.9
coord: 93..115
e-value: 0.54
score: 19.3
IPR013087Zinc finger C2H2-typePROSITEPS00028ZINC_FINGER_C2H2_1coord: 23..43
IPR013087Zinc finger C2H2-typePROSITEPS00028ZINC_FINGER_C2H2_1coord: 95..115
IPR013087Zinc finger C2H2-typePROSITEPS50157ZINC_FINGER_C2H2_2coord: 21..48
score: 10.783
IPR013087Zinc finger C2H2-typePROSITEPS50157ZINC_FINGER_C2H2_2coord: 93..115
score: 8.517
NoneNo IPR availableGENE3DG3DSA:3.30.160.60coord: 19..115
e-value: 1.8E-7
score: 33.4
IPR036236Zinc finger C2H2 superfamilySUPERFAMILYSSF57667beta-beta-alpha zinc fingerscoord: 21..115