SMED30008230

Overview
NameSMED30008230
Smed IDSMED30008230
Length (bp)522
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 SMED30008230 (SMED30008230) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30008230 (SMED30008230) 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 SMED30008230 (SMED30008230) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008230 (SMED30008230) 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



SMED30008230

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30008230SMESG000067801.1 SmedASXL_045186SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30008230 vs. TrEMBL
Match: Q5DHG6 (SJCHGC02465 protein OS=Schistosoma japonicum OX=6182 GN=EWB00_005500 PE=2 SV=1)

HSP 1 Score: 70.4774 bits (171), Expect = 2.036e-12
Identity = 35/97 (36.08%), Postives = 58/97 (59.79%), Query Frame = 2 
Query:   95 NDNVNKPLLYSANFKHTKSINIEFNPFDQRCESIRFFTKVISVPKWTKTNQSLAIKNVVKSVSCEPTIYLTFNTGLDLEIKTEHLSCAEIFKILVAY 385
            +  V+K ++   NFK  K I   FNP  ++ ESIR F  ++S PKW  +N +L +K  V S +  P + +T++ G  L +KTEHLS  E+ ++++ +
Sbjct:   24 DSKVSKKIIKQLNFKPIKRIACRFNPLLEKTESIRRFCLILSEPKWRTSNANLLVKTNVLSENSPPEVEITYDNGQVLLVKTEHLSLREVMEVVILH 120
[Close]
BLAST of SMED30008230 vs. TrEMBL
Match: G4VMR4 (Putative mitochondrial ribosomal protein L53 OS=Schistosoma mansoni OX=6183 GN=Smp_010900 PE=4 SV=1)

HSP 1 Score: 65.855 bits (159), Expect = 1.149e-10
Identity = 36/97 (37.11%), Postives = 57/97 (58.76%), Query Frame = 2 
Query:   95 NDNVNKPLLYSANFKHTKSINIEFNPFDQRCESIRFFTKVISVPKWTKTNQSLAIKNVVKSVSCEPTIYLTFNTGLDLEIKTEHLSCAEIFKILVAY 385
            +  ++K +L   NFK    ++  FNP  Q+ ESIR F  +IS PKW  +N +L IK  V S +  P I ++++ G  L +KTE+LS  E  +I++ +
Sbjct:   24 DSRISKAILKQLNFKPVIKMSFRFNPLLQKTESIRQFCSIISDPKWRTSNTNLIIKINVLSDNSPPEIEVSYDNGRILILKTENLSLRETIEIIITH 120
[Close]
BLAST of SMED30008230 vs. TrEMBL
Match: A0A074ZR56 (Uncharacterized protein OS=Opisthorchis viverrini OX=6198 GN=T265_04829 PE=4 SV=1)

HSP 1 Score: 65.0846 bits (157), Expect = 2.262e-10
Identity = 40/103 (38.83%), Postives = 57/103 (55.34%), Query Frame = 2 
Query:   74 RNLKGKPNDNVNKPLLYSANFKHTKSINIEFNPFDQRCESIRFFTKVISVPKWTKTNQSLAIKNVVKSVSCEPTIYLTFNTGLDLEIKTEHLSCAEIFKILVA 382
            R L+      V+K +L   +FK  KSI   FNPF  R ESIR   +++S P+W  TN +L  K  V S +  P I + ++ G  + IKT++LS  EI  I+ A
Sbjct:   17 RPLRAVDESVVSKDILKKLDFKPVKSICFSFNPFVGRTESIREACRILSNPRWRSTNTNLVFKARVLSDNHAPVIEVVYSNGNIVLIKTDNLSIREIIDIIYA 119
[Close]
BLAST of SMED30008230 vs. TrEMBL
Match: A0A430QDQ4 (Large subunit ribosomal protein L53 OS=Schistosoma bovis OX=6184 GN=DC041_0001466 PE=4 SV=1)

HSP 1 Score: 65.0846 bits (157), Expect = 2.855e-10
Identity = 34/97 (35.05%), Postives = 57/97 (58.76%), Query Frame = 2 
Query:   95 NDNVNKPLLYSANFKHTKSINIEFNPFDQRCESIRFFTKVISVPKWTKTNQSLAIKNVVKSVSCEPTIYLTFNTGLDLEIKTEHLSCAEIFKILVAY 385
            +  V+K +L   NFK    I+  FNP  Q+ ESIR    ++S P+W  +N ++ +K  V S S  P + ++++ G  L +KTE+LS  E  +I++A+
Sbjct:   24 DSRVSKTILKQLNFKPVIKISFRFNPLLQKTESIRHLCSILSEPRWRASNTNMLVKINVLSDSNPPEVEISYDNGHILILKTENLSLRETVEIIIAH 120
[Close]
BLAST of SMED30008230 vs. TrEMBL
Match: A0A183KQL8 (Uncharacterized protein OS=Schistosoma curassoni OX=6186 GN=SCUD_LOCUS17353 PE=4 SV=1)

HSP 1 Score: 65.0846 bits (157), Expect = 2.855e-10
Identity = 34/97 (35.05%), Postives = 57/97 (58.76%), Query Frame = 2 
Query:   95 NDNVNKPLLYSANFKHTKSINIEFNPFDQRCESIRFFTKVISVPKWTKTNQSLAIKNVVKSVSCEPTIYLTFNTGLDLEIKTEHLSCAEIFKILVAY 385
            +  V+K +L   NFK    I+  FNP  Q+ ESIR    ++S P+W  +N ++ +K  V S S  P + ++++ G  L +KTE+LS  E  +I++A+
Sbjct:   24 DSRVSKTILKQLNFKPVIKISFRFNPLLQKTESIRHLCSILSEPRWRASNTNMLVKINVLSDSNPPEVEISYDNGHILILKTENLSLRETVEIIIAH 120
[Close]
BLAST of SMED30008230 vs. Planmine SMEST
Match: SMESG000067801.1 (SMESG000067801.1)

HSP 1 Score: 244.588 bits (623), Expect = 3.643e-84
Identity = 119/121 (98.35%), Postives = 119/121 (98.35%), Query Frame = 2 
Query:   74 RNLKGKPNDNVNKPLLYSANFKHTKSINIEFNPFDQRCESIRFFTKVISVPKWTKTNQSLAIKNVVKSVSCEPTIYLTFNTGLDLEIKTEHLSCAEIFKILVAYYRKYHEKLDSTNVISYE 436
            RNLKGKPNDNVNKPLLYSANFKHTKSINIEFNPFDQRCESIRFFTKVISVPKWTKTNQSL IKNVVKSVSCEPTIYLTFNTGLDLEIKTEHLSCAEIFKILVAYYRKYHE LDSTNVISYE
Sbjct:   18 RNLKGKPNDNVNKPLLYSANFKHTKSINIEFNPFDQRCESIRFFTKVISVPKWTKTNQSLVIKNVVKSVSCEPTIYLTFNTGLDLEIKTEHLSCAEIFKILVAYYRKYHENLDSTNVISYE 138
The following BLAST results are available for this feature:
BLAST of SMED30008230 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 SMED30008230 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 SMED30008230 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 SMED30008230 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 SMED30008230 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 SMED30008230 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 SMED30008230 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 SMED30008230 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
Q5DHG62.036e-1236.08SJCHGC02465 protein OS=Schistosoma japonicum OX=61... [more]
G4VMR41.149e-1037.11Putative mitochondrial ribosomal protein L53 OS=Sc... [more]
A0A074ZR562.262e-1038.83Uncharacterized protein OS=Opisthorchis viverrini ... [more]
A0A430QDQ42.855e-1035.05Large subunit ribosomal protein L53 OS=Schistosoma... [more]
A0A183KQL82.855e-1035.05Uncharacterized protein OS=Schistosoma curassoni O... [more]
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BLAST of SMED30008230 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 SMED30008230 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 SMED30008230 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 SMED30008230 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 SMED30008230 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 SMED30008230 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000067801.13.643e-8498.35SMESG000067801.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008230 ID=SMED30008230|Name=SMED30008230|organism=Schmidtea mediterranea sexual|type=transcript|length=522bp
CTAATATACGTTTTTAATTTAAATGTCTATCTTTATTAAACCTGTGAAAC
CAAAGCCTTTTATTAAATATTTCCGAAATTTAAAAGGAAAACCAAATGAT
AATGTAAATAAACCACTGCTTTATTCTGCAAATTTTAAACACACCAAATC
AATTAATATTGAATTTAATCCTTTTGATCAACGATGTGAATCTATTAGGT
TTTTTACTAAGGTAATTTCTGTTCCAAAATGGACTAAAACTAATCAGTCC
TTAGCAATAAAAAATGTTGTTAAATCAGTTTCATGTGAACCAACAATATA
TTTAACATTCAACACGGGTCTAGATCTTGAAATTAAAACTGAGCATCTTT
CATGTGCTGAAATATTCAAGATTTTAGTCGCTTATTATAGAAAGTATCAC
GAGAAGCTTGATTCAACTAATGTCATTAGTTATGAATAAATTGCGTTTCT
TAAAATTAACAAAATAAATTATTTATTATGAATATTAATATAATTATTAG
ATAAATCTGATTGATAGCGAAG
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protein sequence of SMED30008230-orf-1

>SMED30008230-orf-1 ID=SMED30008230-orf-1|Name=SMED30008230-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=139bp
MSIFIKPVKPKPFIKYFRNLKGKPNDNVNKPLLYSANFKHTKSINIEFNP
FDQRCESIRFFTKVISVPKWTKTNQSLAIKNVVKSVSCEPTIYLTFNTGL
DLEIKTEHLSCAEIFKILVAYYRKYHEKLDSTNVISYE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR036249Thioredoxin-like_sf
IPR019716Ribosomal_L53_mit
Vocabulary: cellular component
TermDefinition
GO:0005840ribosome
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR019716Ribosomal protein L53, mitochondrialPFAMPF10780MRP_L53coord: 48..97
e-value: 1.5E-6
score: 28.3
IPR036249Thioredoxin-like superfamilyGENE3DG3DSA:3.40.30.10coord: 32..135
e-value: 8.5E-21
score: 75.5