hadrian

Overview
Namehadrian (AFJ24715.1)
Smed IDSMED30003738
Length (bp)651
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 hadrian (SMED30003738) t-SNE clustered cells

Violin plots show distribution of expression levels for hadrian (SMED30003738) 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 hadrian (SMED30003738) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for hadrian (SMED30003738) 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




SMED30003738

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30003738SMESG000043826.1 SMESG000043821.1 SmedASXL_002439SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30003738SMESG000043826.1 SMESG000043821.1 dd_Smed_v4_3606_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30003738SMESG000043826.1 SMESG000043821.1 dd_Smed_v4_3606_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30003738SMESG000043826.1 SMESG000043821.1 dd_Smed_v6_3606_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30003738SMESG000043826.1 SMESG000043821.1 dd_Smed_v4_3606_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
non-ciliated epidermisSMED30003738SMESG000043826.1 SMESG000043821.1 dd_Smed_v4_3606_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30003738SMESG000043826.1 SMESG000043821.1 dd_Smed_v4_3606_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of hadrian vs. TrEMBL
Match: I1ZI61 (Hadrian OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 312.383 bits (799), Expect = 3.289e-106
Identity = 171/171 (100.00%), Postives = 171/171 (100.00%), Query Frame = 3
Query:   93 MIKXXXXXXXXXXXXXXHGEKTSKELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNIGKVVRDNL 605
            MIKFTILLLIVAFVLLAHGEKTSKELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNIGKVVRDNL
Sbjct:    1 MIKFTILLLIVAFVLLAHGEKTSKELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNIGKVVRDNL 171          
BLAST of hadrian vs. Planmine SMEST
Match: SMESG000043821.1 (SMESG000043821.1)

HSP 1 Score: 312.768 bits (800), Expect = 7.109e-110
Identity = 170/171 (99.42%), Postives = 170/171 (99.42%), Query Frame = 3
Query:   93 MIKXXXXXXXXXXXXXXHGEKTSKELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNIGKVVRDNL 605
            MIKFTILLLIVAFVL AHGEKTSKELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNIGKVVRDNL
Sbjct:    1 MIKFTILLLIVAFVLQAHGEKTSKELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNIGKVVRDNL 171          
BLAST of hadrian vs. Planmine SMEST
Match: SMESG000043826.1 (SMESG000043826.1)

HSP 1 Score: 312.383 bits (799), Expect = 9.148e-110
Identity = 171/171 (100.00%), Postives = 171/171 (100.00%), Query Frame = 3
Query:   93 MIKXXXXXXXXXXXXXXHGEKTSKELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNIGKVVRDNL 605
            MIKFTILLLIVAFVLLAHGEKTSKELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNIGKVVRDNL
Sbjct:    1 MIKFTILLLIVAFVLLAHGEKTSKELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNIGKVVRDNL 171          
BLAST of hadrian vs. Planmine SMEST
Match: SMESG000060389.1 (SMESG000060389.1)

HSP 1 Score: 87.8113 bits (216), Expect = 1.436e-21
Identity = 46/142 (32.39%), Postives = 88/142 (61.97%), Query Frame = 3
Query:  165 ELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNIGKV 590
            ++TE+GKK++P KI+   +F +     ++GLHN+N TL  +P   N   L+  FPKL  + D   C +  ++++  I +E+    ++ V+ S+ S +I  NDC++KT+E+++N +  +  +K F+A +++N+IS  VN+  +
Sbjct:   25 DVTEMGKKLVPYKILFP-IFGTRFYGVVEGLHNMNATLYENPSGLN--QLVFIFPKLNISKDFQKCIVKISVRNFAITIELEHSKIQRVRHSLDSCRIIENDCFIKTLEKKYNSIFLENPTKTFIAESLLNVISMNVNVDTI 163          
BLAST of hadrian vs. Planmine SMEST
Match: SMESG000060365.1 (SMESG000060365.1)

HSP 1 Score: 77.0258 bits (188), Expect = 1.298e-17
Identity = 43/142 (30.28%), Postives = 83/142 (58.45%), Query Frame = 3
Query:  165 ELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNIGKV 590
            ++TE+GKK++P++IV   +F+      ++ LHN+N TL  +P   N       F K         C +  ++++ +I +E+    ++ V+ S+ S +I  NDC++KT+E+++N L  +  +K F+A +++N+IS  VNI  +
Sbjct:   25 DVTEMGKKLVPHQIVFP-IFDKRFYGIVEDLHNMNATLYENPSGLN------HFQK---------CIVKISVRNFVITIELEHSKIQRVRHSLDSCRIIQNDCFIKTLEKKYNSLFLENPAKTFIAESLLNVISKNVNIDTI 150          
BLAST of hadrian vs. Planmine SMEST
Match: SMESG000060343.1 (SMESG000060343.1)

HSP 1 Score: 67.3958 bits (163), Expect = 6.660e-14
Identity = 42/139 (30.22%), Postives = 77/139 (55.40%), Query Frame = 3
Query:  165 ELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNI 581
            +LTE+ KK++ N     ++    V+  ++GLHN+  T  VS R  N   L   FP+L    +   C +  ++K+L I + + G  VR ++ ++RS +I  NDC  K++E + N+LL    S+   A+ +  L+ ++++I
Sbjct:   25 DLTEMSKKLIGNNTTF-YMIEEGVNGKIEGLHNVTATFFVSKRKYN--KLFFEFPELYVIPNLPDCNLKLSMKNLTITINLKGFKVRRIKNNLRSFQIIQNDCLKKSLEIQINKLLSTEFSEHVFASLVSTLLQSQIDI 160          
The following BLAST results are available for this feature:
BLAST of hadrian 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 hadrian 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 hadrian 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 hadrian 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 hadrian 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 hadrian 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 hadrian 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 hadrian vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZI613.289e-106100.00Hadrian OS=Schmidtea mediterranea OX=79327 PE=2 SV... [more]
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BLAST of hadrian 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 hadrian 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 hadrian 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 hadrian 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 hadrian 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 hadrian vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000043821.17.109e-11099.42SMESG000043821.1[more]
SMESG000043826.19.148e-110100.00SMESG000043826.1[more]
SMESG000060389.11.436e-2132.39SMESG000060389.1[more]
SMESG000060365.11.298e-1730.28SMESG000060365.1[more]
SMESG000060343.16.660e-1430.22SMESG000060343.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30003738
GenBankAFJ24715.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003738 ID=SMED30003738|Name=hadrian|organism=Schmidtea mediterranea sexual|type=transcript|length=651bp
AATCTATATAAATCTTATATGCATTTAGCGGCCAATTCAAGAAAAATTCA
AGTATAAATTCAGCTGGTTTTCTCAGATAAAATCATATCAAAATGATTAA
ATTTACAATTTTACTCTTAATTGTCGCGTTTGTTTTACTAGCACATGGCG
AAAAAACCTCAAAAGAATTGACTGAACTCGGAAAGAAAATTCTCCCAAAC
AAAATAGTCATAAAGCATGTATTCAATTCCCATGTAAGTGTAAGTCTGGA
CGGGCTGCACAATCTCAATGTCACGCTGCGAGTCAGTCCTCGAAATAAGA
ACATCAAAGCTCTATTAGTCCGATTTCCAAAATTGGTGTTTACCTATGAC
CAAGTGGTTTGCAAGATCGTCCACACAATTAAGCACTTGATAATCCGAGT
GGAGATTTATGGAAAAGTCGTAAGAGGCGTTCAAGCTTCCGTTAGAAGTG
CCAAAATAACAACAAATGATTGTTACTTGAAAACCGTGGAACAGAGATTC
AATGAGCTCTTGGAAAAGCCTGAATCGAAACAATTCATGGCCAATGCTAT
GATGAACCTTATTTCTGCCAAGGTTAATATTGGAAAAGTGGTTCGAGATA
ATTTATAAATGATTGTTTTTTGTTTTAAATAAAATTTCAATTAGTTTAAA
A
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protein sequence of SMED30003738-orf-1

>SMED30003738-orf-1 ID=SMED30003738-orf-1|Name=SMED30003738-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=172bp
MIKFTILLLIVAFVLLAHGEKTSKELTELGKKILPNKIVIKHVFNSHVSV
SLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLI
IRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMA
NAMMNLISAKVNIGKVVRDNL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000106ciliated epithelial cell
PLANA:0000418head
PLANA:0002032epidermal cell
PLANA:0002063non-ciliated epidermis
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..19
score: 0.913