SMED30014003

Overview
NameSMED30014003
Smed IDSMED30014003
Length (bp)1487
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 SMED30014003 (SMED30014003) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30014003 (SMED30014003) 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 SMED30014003 (SMED30014003) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30014003 (SMED30014003) 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



SMED30014003

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
oocyteSMED30014003 Contig15165uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30014003 Contig15165newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30014003 Contig15165uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30014003 Contig15165newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30014003 vs. Planmine SMEST
Match: SMESG000079932.1 (SMESG000079932.1)

HSP 1 Score: 259.225 bits (661), Expect = 4.148e-84
Identity = 126/149 (84.56%), Postives = 133/149 (89.26%), Query Frame = 1 
Query:  943 MWDAGFTVSQVREARSGSLQQAEDVELPFVAIKREPGRNPAREIRCQAEFFLARLEEHQRQTNEQVERERRYLANVNDDIAAGRIASTDGYAPPYNTSYNLDDERLNIRFTAINVVVPQKILPRHMRRTEKPTEEHREHPYARLAPERN 1389
            MWDAGF VSQVR AR+GSLQQA DVELPFVAIKR+PG+NPAREIR Q EF L RLEEHQRQTNEQV+  RRYLANV+DDIAAGRI STDGYAPPYNTSYNLDDERLNIR TAINVVVPQKILPRHMRRTEKP +EHREHPYA    ER+
Sbjct:    1 MWDAGFNVSQVRGARAGSLQQATDVELPFVAIKRKPGQNPAREIRGQVEFLLMRLEEHQRQTNEQVDWARRYLANVDDDIAAGRIVSTDGYAPPYNTSYNLDDERLNIRSTAINVVVPQKILPRHMRRTEKPADEHREHPYAWPVSERD 149
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BLAST of SMED30014003 vs. Planmine SMEST
Match: SMESG000039041.1 (SMESG000039041.1)

HSP 1 Score: 257.299 bits (656), Expect = 7.824e-82
Identity = 128/195 (65.64%), Postives = 150/195 (76.92%), Query Frame = 1 
Query:  838 FINWDLF**SDESWVDESRVTVRFPEHAANRCRQAMWDAGFTVSQVREARSGSLQQAEDVELPFVAIKREPGRNPAREIRCQAEFFLARLEEHQRQTNEQVERERRYLANVNDDIAAGRIASTDGYAPPYNTSYNLDDERLNIRFTAINVVVPQKILPRHMRRTEKPTEEHREHPYARLAPERNIKKHRRDHRYY 1422
            FI + L    D+SW+D SR+TVRFP HAANRCRQA+WDAGFTVSQ +E+R G  + +E+++LPFVAIKREPGRN AREIR  AEF +A LEEHQRQT+  VE  RRYLANVNDDIA GRI STDGYAP YNTS+NLDD RLN     INVVVP +ILPR+MR  ++  +EHREHPYAR+ P R+  K     RYY
Sbjct:   10 FIYFGL----DDSWIDSSRITVRFPAHAANRCRQALWDAGFTVSQAKESRFGQQRPSEEIKLPFVAIKREPGRNSAREIRGHAEFLIAPLEEHQRQTDAHVESARRYLANVNDDIAKGRILSTDGYAPSYNTSFNLDDRRLNTNSKTINVVVPWRILPRNMRTEKEQIDEHREHPYARINPRRDNHK-----RYY 195
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BLAST of SMED30014003 vs. Planmine SMEST
Match: SMESG000019398.1 (SMESG000019398.1)

HSP 1 Score: 273.478 bits (698), Expect = 1.064e-80
Identity = 127/159 (79.87%), Postives = 141/159 (88.68%), Query Frame = 1 
Query:  868 DESWVDESRVTVRFPEHAANRCRQAMWDAGFTVSQVREARSGSLQQAEDVELPFVAIKREPGRNPAREIRCQAEFFLARLEEHQRQTNEQVERERRYLANVNDDIAAGRIASTDGYAPPYNTSYNLDDERLNIRFTAINVVVPQKILPRHMRRTEKPTE 1344
            DESWV+ESRVT+RFP HAANRCRQAMWDAGFT+SQVRE+RSG+LQQ E+VELPFVAIKREPGRNPAREIR QAEF LARLEEHQRQT+ QV R R YLANVN+D AAGRIA T+GYAPPYNTS+NLDDERLN+   A+NVV+P+K LPR MRR E P E
Sbjct: 1109 DESWVNESRVTIRFPAHAANRCRQAMWDAGFTISQVRESRSGTLQQMEEVELPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQTDLQVARARLYLANVNEDKAAGRIACTEGYAPPYNTSFNLDDERLNVNAEAMNVVIPRKALPRKMRRNEGPAE 1267
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BLAST of SMED30014003 vs. Planmine SMEST
Match: SMESG000018162.1 (SMESG000018162.1)

HSP 1 Score: 241.506 bits (615), Expect = 1.606e-75
Identity = 123/177 (69.49%), Postives = 138/177 (77.97%), Query Frame = 1 
Query:  886 ESRVTVRFPEHAANRCRQAMWDAGFTVSQVREARSGSLQQAEDVELPFVAIKREPGRNPAREIRCQAEFFLARLEEHQRQTNEQVERERRYLANVNDDIAAGRIASTDGYAPPYNTSYNLDDERLNIRFTAINVVVPQKILPRHMRRTEKPTEEHREHPYARLAPERNIKKHRRDHR 1416
            ESRV +RFP  AA+R RQAMWDAGFTVSQ RE RS +L+Q +DVELPFVAIKRE GRNPAREIR  A FFLA LEEHQRQ+N QV R R YLANV +DIAAGRIASTD Y PP ++S NL +ER N R T INVVVPQK  P H RRTE+PT  +R HPYAR APE N+ +H + HR
Sbjct:  162 ESRVIIRFPAQAADRWRQAMWDAGFTVSQPREFRSDTLRQTKDVELPFVAIKRESGRNPAREIREHAVFFLAHLEEHQRQSNLQVARARLYLANVEEDIAAGRIASTDDYTPPPSSSLNLGNERSNDRPTGINVVVPQKTFPSHRRRTERPTYVYRRHPYARPAPEGNVDRHHQTHR 338
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BLAST of SMED30014003 vs. Planmine SMEST
Match: SMESG000042239.1 (SMESG000042239.1)

HSP 1 Score: 236.113 bits (601), Expect = 2.105e-75
Identity = 116/149 (77.85%), Postives = 129/149 (86.58%), Query Frame = 1 
Query:  865 SDESWVDESRVTVRFPEHAANRCRQAMWDAGFTVSQVREARSGSLQQAEDVELPFVAIKREPGRNPAREIRCQAEFFLARLEEHQRQTNEQVERERRYLANVNDDIAAGRIASTDGYAPPYNTSYNLDDERLNIRFTAINVVVPQKILP 1311
            ++ESW+DESRVTVRFP HAANRC QAM DAGFTVSQVRE+RSG+ QQ E+VEL FVAIKREPGRNPAREIR QAEF LA LEEHQRQT+ QV+R RRYLA+VN+DIAAGRIA TD YAPPYNTS+NLDDERLN +  AINVVV  +  P
Sbjct:   51 ANESWIDESRVTVRFPAHAANRCLQAMCDAGFTVSQVRESRSGTPQQMEEVELRFVAIKREPGRNPAREIRGQAEFLLASLEEHQRQTDIQVDRARRYLASVNEDIAAGRIACTDCYAPPYNTSFNLDDERLNTKAVAINVVVRGRSFP 199
The following BLAST results are available for this feature:
BLAST of SMED30014003 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 SMED30014003 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 SMED30014003 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 SMED30014003 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 SMED30014003 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 SMED30014003 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 SMED30014003 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 SMED30014003 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 SMED30014003 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 SMED30014003 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 SMED30014003 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 SMED30014003 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 SMED30014003 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 SMED30014003 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000079932.14.148e-8484.56SMESG000079932.1[more]
SMESG000039041.17.824e-8265.64SMESG000039041.1[more]
SMESG000019398.11.064e-8079.87SMESG000019398.1[more]
SMESG000018162.11.606e-7569.49SMESG000018162.1[more]
SMESG000042239.12.105e-7577.85SMESG000042239.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014003 ID=SMED30014003|Name=SMED30014003|organism=Schmidtea mediterranea sexual|type=transcript|length=1487bp
AGGACTTAGAATTATATATTTTCGTTAAACTTAAACTTTCGATGGTTTGC
AGTCATTCTCAATTTAATATCCATGTAGCATGTGGTATACACGGAACTCT
TCCCCACCAATTACTAAATTCTGGAAACCCTAGAATTGTTAAAATATCGT
TGTATGCAATATCTATAGTAAGGATATTTATTAAATGAACACTATTAAAT
ATACGGTATTTTGAAATCATATTATTATTATCGTAGTGGAAAATTAAGTA
AGAATTTAAAACAAAGTTACCTGGTTTACATAAATTTAGATCCATAGTTC
TGACCTCGGTGGAGAACTTGTTCGCCGACATCTCGTCATCGACAATTATT
TTATTAGACATTTCGGAAAATTTTTAGAAACGTTATTTTGGTTATTGATC
TGTCTATCATCCTATTTATGGAATTTAATGGTAAGTGTATGCGGTAGATA
TCACACTCGATTGCAATTTCTATCCCTCCGGTGTGCCATTGGAATAGCGT
GTTTATGCCTGACTAGTACATTACGGGCATGCGTGATCACTATCGAACAC
GACATATGAGGAAAATTTGTTTAATATCTCGAGGAATTTGCCACGTCTTT
AGAAGGATTCGTCGCTAACACTTGGGATTGAATTTCTTGAAGCCACTGGC
GTGATGTTGTTTCAGTGTAAGTCAAAGGAGAATTATGCGAACGAAATTGG
GAAACCCGCCGGGGATTGGAAGGACATCACTACAGGGGAAAATTGATACT
CACTGATCGAGGAGTTAATATGTATTCCCTCATTCTGCGGCACTATTTCG
GTTGCGGAATATTCTCCAAAAAATTTATTCAGATCATTTTATTAATTGGG
ATCTATTTTGATAGTCAGATGAGTCGTGGGTTGACGAATCCAGAGTCACC
GTCCGATTCCCCGAGCATGCTGCAAATCGTTGTCGGCAAGCTATGTGGGA
TGCGGGATTTACCGTATCCCAAGTCAGAGAGGCCAGATCCGGTAGCCTAC
AACAAGCGGAAGATGTCGAGCTCCCGTTCGTCGCGATAAAGCGGGAGCCG
GGACGAAATCCGGCCAGGGAGATCCGTTGCCAGGCTGAGTTCTTCCTCGC
GCGGCTTGAGGAACATCAGCGACAAACCAACGAACAAGTGGAGCGGGAAA
GACGCTACCTCGCCAATGTAAACGACGACATTGCCGCGGGCCGGATCGCC
AGTACAGACGGTTATGCCCCGCCGTACAATACGTCGTACAATCTGGACGA
CGAAAGGTTGAATATTCGATTTACGGCCATCAACGTGGTCGTTCCCCAGA
AGATACTGCCCCGACACATGAGAAGGACTGAGAAACCAACAGAAGAACAT
CGCGAACATCCTTACGCTAGACTGGCCCCGGAAAGAAATATCAAGAAGCA
TCGTCGAGATCATCGCTACTACTAGCAATTATCAATAGAACACATTGACT
GATCATGAACACTTAGTTAGGCGAGAGATCGGAAGAG
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protein sequence of SMED30014003-orf-1

>SMED30014003-orf-1 ID=SMED30014003-orf-1|Name=SMED30014003-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=161bp
MWDAGFTVSQVREARSGSLQQAEDVELPFVAIKREPGRNPAREIRCQAEF
FLARLEEHQRQTNEQVERERRYLANVNDDIAAGRIASTDGYAPPYNTSYN
LDDERLNIRFTAINVVVPQKILPRHMRRTEKPTEEHREHPYARLAPERNI
KKHRRDHRYY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland