SMED30018499

Overview
NameSMED30018499
Smed IDSMED30018499
Length (bp)532
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 SMED30018499 (SMED30018499) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30018499 (SMED30018499) 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 SMED30018499 (SMED30018499) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30018499 (SMED30018499) 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




SMED30018499

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30018499h1SMcG0000021 SmedASXL_005896SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30018499h1SMcG0000021 dd_Smed_v4_18268_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30018499h1SMcG0000021 dd_Smed_v4_18268_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30018499h1SMcG0000021 dd_Smed_v6_18268_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
reproductive organSMED30018499h1SMcG0000021 Contig16772uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30018499h1SMcG0000021 Contig16772newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30018499 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002988:42830..49319 +2613
Homology
BLAST of SMED30018499 vs. TrEMBL
Match: A0A1I8HAV3 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 1.518e-6
Identity = 24/44 (54.55%), Postives = 34/44 (77.27%), Query Frame = 1
Query:  289 KNRRMTRLVMAIGIVLLVMSVILVGITLSLSEHIDKMVKETHQK 420
            K +R+ R+VMA+  VLL M VILVG+TLS+S+HID +V++   K
Sbjct:   82 KQKRIARVVMAVAFVLLAMCVILVGVTLSMSDHIDDLVRKAQLK 125          
BLAST of SMED30018499 vs. Planmine SMEST
Match: SMESG000029677.1 (SMESG000029677.1)

HSP 1 Score: 246.514 bits (628), Expect = 5.708e-85
Identity = 122/123 (99.19%), Postives = 122/123 (99.19%), Query Frame = 1
Query:   91 MENKESEKTDNIISKPSENHDVIPNLNQAVPESVTMETLLAYTAEAAKYRSDSRRSSYQNELARNLKNRRMTRLVMAIGIVLLVMSVILVGITLSLSEHIDKMVKETHQKSVKSEDSVSGKSN 459
            MENKESEKTDNIISKPSENHDVIPNLNQ VPESVTMETLLAYTAEAAKYRSDSRRSSYQNELARNLKNRRMTRLVMAIGIVLLVMSVILVGITLSLSEHIDKMVKETHQKSVKSEDSVSGKSN
Sbjct:    1 MENKESEKTDNIISKPSENHDVIPNLNQTVPESVTMETLLAYTAEAAKYRSDSRRSSYQNELARNLKNRRMTRLVMAIGIVLLVMSVILVGITLSLSEHIDKMVKETHQKSVKSEDSVSGKSN 123          
BLAST of SMED30018499 vs. Planmine SMEST
Match: SMESG000026902.1 (SMESG000026902.1)

HSP 1 Score: 66.6254 bits (161), Expect = 6.836e-14
Identity = 34/82 (41.46%), Postives = 62/82 (75.61%), Query Frame = 1
Query:  175 AVPESVTMETLLAYTAEAAKYRSDSRRSSYQNELARNLKNRRMTRLVMAIGIVLLVMSVILVGITLSLSEHIDKMVKETHQK 420
            A+P+S T E +LA++ +++++    +R   Q+ L  NL+++R T++V+ +G +LL+MS++L+ ++LSLSEHID+MV+E H K
Sbjct:   75 AMPDSKTYEDILAFSHQSSRHLWTLKR---QDTL--NLRDKRTTKVVVVVGTMLLIMSLVLIAVSLSLSEHIDRMVREHHLK 151          
BLAST of SMED30018499 vs. Planmine SMEST
Match: SMESG000016957.1 (SMESG000016957.1)

HSP 1 Score: 64.3142 bits (155), Expect = 1.154e-12
Identity = 29/62 (46.77%), Postives = 45/62 (72.58%), Query Frame = 1
Query:  235 YRSDSRRSSYQNELARNLKNRRMTRLVMAIGIVLLVMSVILVGITLSLSEHIDKMVKETHQK 420
            ++++   S Y  +  ++ K +R+ R+VM + I+LL M VILVG+TLS+S++ID MVKE HQK
Sbjct:  143 FKNNVSSSMYDIQETQSPKEKRIARIVMVVAILLLTMCVILVGVTLSMSDYIDTMVKELHQK 204          
BLAST of SMED30018499 vs. Planmine SMEST
Match: SMESG000027325.1 (SMESG000027325.1)

HSP 1 Score: 54.299 bits (129), Expect = 2.261e-9
Identity = 33/82 (40.24%), Postives = 61/82 (74.39%), Query Frame = 1
Query:  175 AVPESVTMETLLAYTAEAAKYRSDSRRSSYQNELARNLKNRRMTRLVMAIGIVLLVMSVILVGITLSLSEHIDKMVKETHQK 420
            ++PES   E +L +T+++ K+  +     ++N+   NL+++R T++V+ +GI+LL+MS+IL+ ++LSLSEHI+K+VKE  +K
Sbjct:   79 SIPESKHYEYVLDFTSQSTKHLCN-----FKNQETLNLRDKRTTKIVLIVGIILLLMSLILIAVSLSLSEHINKLVKEQFKK 155          
The following BLAST results are available for this feature:
BLAST of SMED30018499 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 SMED30018499 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 SMED30018499 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 SMED30018499 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 SMED30018499 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 SMED30018499 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 SMED30018499 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 SMED30018499 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A1I8HAV31.518e-654.55Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of SMED30018499 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 SMED30018499 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 SMED30018499 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 SMED30018499 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 SMED30018499 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 SMED30018499 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000029677.15.708e-8599.19SMESG000029677.1[more]
SMESG000026902.16.836e-1441.46SMESG000026902.1[more]
SMESG000016957.11.154e-1246.77SMESG000016957.1[more]
SMESG000027325.12.261e-940.24SMESG000027325.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018499 ID=SMED30018499|Name=SMED30018499|organism=Schmidtea mediterranea sexual|type=transcript|length=532bp
TATATACCTTGCATTATTCCCTTGGAAAAGAAAATCATTGAAAGAATATT
TATTCATGAAAAAATGTTGAATTGGATCTTGCAATAGAAAATGGAAAATA
AAGAAAGCGAGAAAACTGACAATATCATATCGAAACCCTCCGAAAATCAT
GACGTGATTCCCAATCTGAACCAGGCGGTGCCTGAATCCGTAACGATGGA
AACATTATTGGCATATACTGCTGAAGCAGCAAAATATCGCAGCGATTCCA
GGAGGTCCTCGTATCAGAATGAGTTGGCGAGAAACTTGAAAAATCGCAGA
ATGACGAGACTCGTCATGGCAATCGGAATTGTACTTTTAGTTATGAGTGT
CATTCTCGTTGGGATTACGTTGTCACTGTCAGAGCACATTGATAAAATGG
TAAAAGAAACTCATCAAAAAAGTGTGAAATCGGAGGATTCAGTGAGCGGT
AAAAGTAATATTACGACGTCAACTTTCTAGATTTGATATTTTTTCAAGTA
AATTTACAATATATTTTTGATTGTTGATTACT
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protein sequence of SMED30018499-orf-1

>SMED30018499-orf-1 ID=SMED30018499-orf-1|Name=SMED30018499-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=130bp
MENKESEKTDNIISKPSENHDVIPNLNQAVPESVTMETLLAYTAEAAKYR
SDSRRSSYQNELARNLKNRRMTRLVMAIGIVLLVMSVILVGITLSLSEHI
DKMVKETHQKSVKSEDSVSGKSNITTSTF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..29
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 107..129
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..15
NoneNo IPR availableTMHMMTMhelixcoord: 74..96