Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A)

Overview
NameSerine-rich adhesin for platelets (Staphylococcus aureus surface protein A)
Smed IDSMED30035908
Length (bp)380
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 Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) (SMED30035908) t-SNE clustered cells

Violin plots show distribution of expression levels for Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) (SMED30035908) 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 Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) (SMED30035908) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) (SMED30035908) 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.
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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




SMED30035908

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30035908 SmedASXL_006843SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30035908h1SMcG0007930 Contig4586newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30035908 dd_Smed_v4_3220_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30035908 dd_Smed_v4_3220_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30035908 dd_Smed_v4_3220_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30035908 dd_Smed_v4_3220_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30035908 dd_Smed_v4_3220_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30035908 dd_Smed_v4_3220_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
parenchymaSMED30035908 dd_Smed_v4_3220_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30035908 dd_Smed_v4_3220_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30035908 dd_Smed_v6_3220_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) vs. TrEMBL
Match: A0A267EK15 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig022973g1 PE=4 SV=1)

HSP 1 Score: 105.531 bits (262), Expect = 3.993e-27
Identity = 44/90 (48.89%), Postives = 67/90 (74.44%), Query Frame = 3
Query:   51 MSIKNGRNKEPYTAYIKDDLIEFY-EPKTMFHTTRTGMECRRYFCGTCGELHSSNTCRSLRDVEWVTGTTMADALFRAREAMIIDEKLQE 317
            M+ K GR+ EPYT +++D  +EFY  PK++F+TT +GM+C+RY+C TCG LH    C S R +E++ GTT+ DAL+++R+A  IDE +Q+
Sbjct:    1 MAKKTGRDTEPYTGFVEDPQLEFYGPPKSLFYTTSSGMQCKRYYCSTCGPLHRVQQCSSQRTMEYMNGTTLPDALWKSRQAYRIDEAVQQ 90          
BLAST of Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) vs. TrEMBL
Match: A0A0X3PVA1 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=SSLN_LOCUS11355 PE=4 SV=1)

HSP 1 Score: 92.4337 bits (228), Expect = 8.393e-22
Identity = 41/88 (46.59%), Postives = 53/88 (60.23%), Query Frame = 3
Query:   51 MSIKNGRNKEPYTAYIKDDLIEFYEPKTMFHTTRTGMECRRYFCGTCGELHSSNTCRSLRDVEWVTGTTMADALFRAREAMIIDEKLQ 314
            M+ +   N EPY AY+    +   +P+  F+ T +G  C+RYFCGTCG  H  N C S R  EWVTGTT+ D+LF   EA +IDE  Q
Sbjct:    1 MARRVNVNSEPYNAYLSQKQVPQLKPENSFYNTDSGATCKRYFCGTCGPCHPVNNCPSKRVTEWVTGTTLPDSLFHVSEAYVIDEFTQ 88          
BLAST of Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) vs. TrEMBL
Match: A0A068WBM8 (Expressed conserved protein OS=Echinococcus granulosus OX=6210 GN=EgrG_001025400 PE=4 SV=1)

HSP 1 Score: 89.7373 bits (221), Expect = 1.599e-20
Identity = 38/81 (46.91%), Postives = 55/81 (67.90%), Query Frame = 3
Query:   72 NKEPYTAYIKDDLIEFYEPKTMFHTTRTGMECRRYFCGTCGELHSSNTCRSLRDVEWVTGTTMADALFRAREAMIIDEKLQ 314
            N EPY+AY+    ++  EP+  F+TT  G  C R++CG CGE HS+N C S+R +E VTGT++ DA F A EA +I++ +Q
Sbjct:    8 NSEPYSAYLSPRQVDQLEPENAFYTTEVGNRCERHYCGACGECHSTNICASMRLLEHVTGTSLPDAAFHASEAYVINDYVQ 88          
BLAST of Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) vs. TrEMBL
Match: A0A0R3WE48 (Uncharacterized protein OS=Taenia asiatica OX=60517 GN=TASK_LOCUS9076 PE=4 SV=1)

HSP 1 Score: 86.2705 bits (212), Expect = 3.245e-19
Identity = 39/88 (44.32%), Postives = 56/88 (63.64%), Query Frame = 3
Query:   51 MSIKNGRNKEPYTAYIKDDLIEFYEPKTMFHTTRTGMECRRYFCGTCGELHSSNTCRSLRDVEWVTGTTMADALFRAREAMIIDEKLQ 314
            M+ +   N EPY AY+    I+  +P+  F+TT  G  C R++CG CGE H+ N C S R +E+VTGT++ DA F A EA +ID+ +Q
Sbjct:    1 MTRRWNANSEPYNAYLSPRQIDQLKPENAFYTTEFGDRCERHYCGACGECHAMNACTSTRLLEYVTGTSLPDAAFHASEAYVIDDYVQ 88          
BLAST of Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) vs. TrEMBL
Match: A0A267F1N8 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig022973g2 PE=4 SV=1)

HSP 1 Score: 85.1149 bits (209), Expect = 5.761e-19
Identity = 42/96 (43.75%), Postives = 61/96 (63.54%), Query Frame = 3
Query:   51 MSIKNGRNKEPYTAYIKDDLIEFY-EPKTMFHTTRTGMECRRYFCGTCGELHSSNTCRSL------RDVEWVTGTTMADALFRAREAMIIDEKLQE 317
            M+ K GR+ EPYT +++D  +EFY  PK++F+TT +GM+C+RY+C TCG LH    C S       RD         ADAL+++R+A  IDE +Q+
Sbjct:    1 MAKKTGRDTEPYTGFVEDPQLEFYGPPKSLFYTTSSGMQCKRYYCSTCGPLHRVQQCISAHHGVHERD-------HAADALWKSRQAYRIDEAVQQ 89          
BLAST of Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) vs. Planmine SMEST
Match: SMESG000025158.1 (SMESG000025158.1)

HSP 1 Score: 210.69 bits (535), Expect = 3.631e-72
Identity = 98/99 (98.99%), Postives = 99/99 (100.00%), Query Frame = 3
Query:   51 MSIKNGRNKEPYTAYIKDDLIEFYEPKTMFHTTRTGMECRRYFCGTCGELHSSNTCRSLRDVEWVTGTTMADALFRAREAMIIDEKLQEFHSNSYSTKH 347
            MSIKNGRNKEPYTAY+KDDLIEFYEPKTMFHTTRTGMECRRYFCGTCGELHSSNTCRSLRDVEWVTGTTMADALFRAREAMIIDEKLQEFHSNSYSTKH
Sbjct:    1 MSIKNGRNKEPYTAYVKDDLIEFYEPKTMFHTTRTGMECRRYFCGTCGELHSSNTCRSLRDVEWVTGTTMADALFRAREAMIIDEKLQEFHSNSYSTKH 99          
BLAST of Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) vs. Planmine SMEST
Match: SMESG000022807.1 (SMESG000022807.1)

HSP 1 Score: 112.079 bits (279), Expect = 5.638e-33
Identity = 52/102 (50.98%), Postives = 68/102 (66.67%), Query Frame = 3
Query:   51 MSIKNGRNKEPYTAYIKDDLIEFYEPKTMFHTTRTGMECRRYFCGTCGELHSSNTCRSLRDVEWVTGTTMADALFRAREAMIIDEKLQEFHSNSYSTKH*LD 356
            M+ + G N EPY AYI  DL+++Y+PK  F TTR+GM+CRRY+C  CG  H  N   S R +EWVTGTTM DAL++A+EA IID+ +Q       + K  LD
Sbjct:    1 MAKRTGLNCEPYNAYIPYDLLDYYQPKNSFFTTRSGMQCRRYYCAVCGPCHLGNCNPSHRMMEWVTGTTMPDALYKAKEAEIIDDMVQSRFQRKSNIKEVLD 102          
The following BLAST results are available for this feature:
BLAST of Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) 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 Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) 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 Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) 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 Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) 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 Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) 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 Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) 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 Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) 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 Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267EK153.993e-2748.89Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A0X3PVA18.393e-2246.59Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A068WBM81.599e-2046.91Expressed conserved protein OS=Echinococcus granul... [more]
A0A0R3WE483.245e-1944.32Uncharacterized protein OS=Taenia asiatica OX=6051... [more]
A0A267F1N85.761e-1943.75Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) 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 Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) 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 Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) 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 Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) 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 Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) 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 Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A) vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000025158.13.631e-7298.99SMESG000025158.1[more]
SMESG000022807.15.638e-3350.98SMESG000022807.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035908 ID=SMED30035908|Name=Serine-rich adhesin for platelets (Staphylococcus aureus surface protein A)|organism=Schmidtea mediterranea sexual|type=transcript|length=380bp
TTGTTTACAGTTACCAATAACAACGGAATTTGTAATAATTTAAATTTTCA
ATGTCTATTAAAAATGGTCGAAATAAAGAGCCTTACACAGCTTATATAAA
AGATGATCTCATTGAATTTTATGAACCGAAAACTATGTTTCACACAACAA
GAACCGGAATGGAGTGTCGACGATATTTTTGTGGCACATGCGGAGAACTG
CATTCGTCAAATACGTGTCGATCTTTGAGAGATGTCGAATGGGTGACGGG
AACAACAATGGCAGATGCGCTATTTAGAGCTCGAGAAGCGATGATAATTG
ACGAGAAACTCCAAGAGTTTCACAGCAATTCCTATTCAACAAAACATTGA
CTCGATATGTGATTTATTTTAAAAATTAAG
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protein sequence of SMED30035908-orf-1

>SMED30035908-orf-1 ID=SMED30035908-orf-1|Name=SMED30035908-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=100bp
MSIKNGRNKEPYTAYIKDDLIEFYEPKTMFHTTRTGMECRRYFCGTCGEL
HSSNTCRSLRDVEWVTGTTMADALFRAREAMIIDEKLQEFHSNSYSTKH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000099neuron
PLANA:0000418head
PLANA:0002032epidermal cell
Vocabulary: molecular function
TermDefinition
GO:0003743translation initiation factor activity
GO:0046982protein heterodimerization activity
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
Vocabulary: biological process
TermDefinition
GO:0006367transcription initiation from RNA polymerase II promoter
GO:0006413translational initiation