Hadrian

Overview
NameHadrian
Smed IDSMED30035446
Length (bp)634
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 (SMED30035446) t-SNE clustered cells

Violin plots show distribution of expression levels for Hadrian (SMED30035446) 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 (SMED30035446) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Hadrian (SMED30035446) 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



SMED30035446

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
prepharyngeal regionSMED30035446h1SMcG0002841 SmedASXL_009634SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30035446h1SMcG0002841 SmedASXL_009634SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30035446h1SMcG0002841 dd_Smed_v6_1360_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30035446h1SMcG0002841 OX_Smed_1.0.19570ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
reproductive organSMED30035446h1SMcG0002841 Contig34311uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30035446h1SMcG0002841 Contig34311newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of Hadrian vs. TrEMBL
Match: I1ZI61 (Hadrian OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 84.7297 bits (208), Expect = 5.821e-17
Identity = 45/142 (31.69%), Postives = 88/142 (61.97%), Query Frame = 1 
Query:  157 DVTEMGKKLVPHQIVFP-IFDKRFYGIVEDLHNMNATLYENPSGLN--QLVFIFPKLNISNSFQKCIVKISVRNFVITIELEHSKIQRVRHSLDSCRIIENDCFIKTLEKKYNSIFLENPAKTFIAESLLNVISMNVNIDTI 573
            ++TE+GKK++P++IV   +F+      ++ LHN+N TL  +P   N   L+  FPKL  +     C +  ++++ +I +E+    ++ V+ S+ S +I  NDC++KT+E+++N +  +  +K F+A +++N+IS  VNI  +
Sbjct:   25 ELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNIGKV 166
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BLAST of Hadrian vs. Planmine SMEST
Match: SMESG000060389.1 (SMESG000060389.1)

HSP 1 Score: 287.345 bits (734), Expect = 6.834e-100
Identity = 152/164 (92.68%), Postives = 157/164 (95.73%), Query Frame = 1 
Query:   85 MSKXXXXXXXXXXXXDGNEGARVVDVTEMGKKLVPHQIVFPIFDKRFYGIVEDLHNMNATLYENPSGLNQLVFIFPKLNISNSFQKCIVKISVRNFVITIELEHSKIQRVRHSLDSCRIIENDCFIKTLEKKYNSIFLENPAKTFIAESLLNVISMNVNIDTIR 576
            MSKLIILVLIVWAVVDGNEGARVVDVTEMGKKLVP++I+FPIF  RFYG+VE LHNMNATLYENPSGLNQLVFIFPKLNIS  FQKCIVKISVRNF ITIELEHSKIQRVRHSLDSCRIIENDCFIKTLEKKYNSIFLENP KTFIAESLLNVISMNVN+DTIR
Sbjct:    1 MSKLIILVLIVWAVVDGNEGARVVDVTEMGKKLVPYKILFPIFGTRFYGVVEGLHNMNATLYENPSGLNQLVFIFPKLNISKDFQKCIVKISVRNFAITIELEHSKIQRVRHSLDSCRIIENDCFIKTLEKKYNSIFLENPTKTFIAESLLNVISMNVNVDTIR 164
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BLAST of Hadrian vs. Planmine SMEST
Match: SMESG000060365.1 (SMESG000060365.1)

HSP 1 Score: 266.929 bits (681), Expect = 4.133e-92
Identity = 147/164 (89.63%), Postives = 149/164 (90.85%), Query Frame = 1 
Query:   85 MSKXXXXXXXXXXXXDGNEGARVVDVTEMGKKLVPHQIVFPIFDKRFYGIVEDLHNMNATLYENPSGLNQLVFIFPKLNISNSFQKCIVKISVRNFVITIELEHSKIQRVRHSLDSCRIIENDCFIKTLEKKYNSIFLENPAKTFIAESLLNVISMNVNIDTIR 576
            MSKLIILVLIVWAVVDGNEGARVVDVTEMGKKLVPHQIVFPIFDKRFYGIVEDLHNMNATLYENPSGLN              FQKCIVKISVRNFVITIELEHSKIQRVRHSLDSCRII+NDCFIKTLEKKYNS+FLENPAKTFIAESLLNVIS NVNIDTIR
Sbjct:    1 MSKLIILVLIVWAVVDGNEGARVVDVTEMGKKLVPHQIVFPIFDKRFYGIVEDLHNMNATLYENPSGLNH-------------FQKCIVKISVRNFVITIELEHSKIQRVRHSLDSCRIIQNDCFIKTLEKKYNSLFLENPAKTFIAESLLNVISKNVNIDTIR 151
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BLAST of Hadrian vs. Planmine SMEST
Match: SMESG000060343.1 (SMESG000060343.1)

HSP 1 Score: 95.5153 bits (236), Expect = 1.079e-24
Identity = 49/147 (33.33%), Postives = 90/147 (61.22%), Query Frame = 1 
Query:  136 NEGARVVDVTEMGKKLVPHQIVFPIFDKRFYGIVEDLHNMNATLYENPSGLNQLVFIFPKLNISNSFQKCIVKISVRNFVITIELEHSKIQRVRHSLDSCRIIENDCFIKTLEKKYNSIFLENPAKTFIAESLLNVISMNVNIDTIR 576
            NEG + +D+TEM KKL+ +   F + ++   G +E LHN+ AT + +    N+L F FP+L +  +   C +K+S++N  ITI L+  K++R++++L S +II+NDC  K+LE + N +     ++   A  +  ++   ++I+TI+
Sbjct:   18 NEGHKAIDLTEMSKKLIGNNTTFYMIEEGVNGKIEGLHNVTATFFVSKRKYNKLFFEFPELYVIPNLPDCNLKLSMKNLTITINLKGFKVRRIKNNLRSFQIIQNDCLKKSLEIQINKLLSTEFSEHVFASLVSTLLQSQIDIETIK 164
[Close]
BLAST of Hadrian vs. Planmine SMEST
Match: SMESG000060332.1 (SMESG000060332.1)

HSP 1 Score: 91.6633 bits (226), Expect = 3.255e-23
Identity = 52/147 (35.37%), Postives = 87/147 (59.18%), Query Frame = 1 
Query:  136 NEGARVVDVTEMGKKLVPHQIVFPIFDKRFYGIVEDLHNMNATLYENPSGLNQLVFIFPKLNISNSFQKCIVKISVRNFVITIELEHSKIQRVRHSLDSCRIIENDCFIKTLEKKYNSIFLENPAKTFIAESLLNVISMNVNIDTIR 576
            NEG +VVD+TEM KKL+ + I F I ++   G +E LHN+ AT + +    N+LVF F +L +  +   C +K+S++N  I + L+      ++++L S +II+NDC  K+LE + N +     AK   A  +  ++   V+I+TI+
Sbjct:   18 NEGHKVVDLTEMSKKLIGNSIKFYIIEEGVNGKIEGLHNVTATFFVSRRRYNKLVFEFSELYVIPNLPDCNLKLSMKNLTIAVYLKSFNELHIKNNLRSFQIIQNDCLKKSLEIQINKLLSTELAKNLFASLVSTLLQSQVDIETIK 164
[Close]
BLAST of Hadrian vs. Planmine SMEST
Match: SMESG000043821.1 (SMESG000043821.1)

HSP 1 Score: 84.7297 bits (208), Expect = 1.441e-20
Identity = 45/142 (31.69%), Postives = 88/142 (61.97%), Query Frame = 1 
Query:  157 DVTEMGKKLVPHQIVFP-IFDKRFYGIVEDLHNMNATLYENPSGLN--QLVFIFPKLNISNSFQKCIVKISVRNFVITIELEHSKIQRVRHSLDSCRIIENDCFIKTLEKKYNSIFLENPAKTFIAESLLNVISMNVNIDTI 573
            ++TE+GKK++P++IV   +F+      ++ LHN+N TL  +P   N   L+  FPKL  +     C +  ++++ +I +E+    ++ V+ S+ S +I  NDC++KT+E+++N +  +  +K F+A +++N+IS  VNI  +
Sbjct:   25 ELTELGKKILPNKIVIKHVFNSHVSVSLDGLHNLNVTLRVSPRNKNIKALLVRFPKLVFTYDQVVCKIVHTIKHLIIRVEIYGKVVRGVQASVRSAKITTNDCYLKTVEQRFNELLEKPESKQFMANAMMNLISAKVNIGKV 166
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
I1ZI615.821e-1731.69Hadrian 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
SMESG000060389.16.834e-10092.68SMESG000060389.1[more]
SMESG000060365.14.133e-9289.63SMESG000060365.1[more]
SMESG000060343.11.079e-2433.33SMESG000060343.1[more]
SMESG000060332.13.255e-2335.37SMESG000060332.1[more]
SMESG000043821.11.441e-2031.69SMESG000043821.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035446 ID=SMED30035446|Name=Hadrian|organism=Schmidtea mediterranea sexual|type=transcript|length=634bp
TAATTATTTGTCAACACAAATTTAAATTAAATCAATTACAACGGAATATA
AATTGCGTTTTGTTAGTCAATTGGATTCAAACAAATGTCTAAATTAATAA
TTTTAGTTTTAATCGTTTGGGCTGTCGTTGATGGCAATGAAGGAGCTCGA
GTCGTCGATGTGACAGAAATGGGCAAGAAACTCGTTCCACATCAAATCGT
GTTTCCCATATTCGATAAAAGATTCTATGGTATTGTTGAAGATTTACACA
ATATGAATGCTACTTTGTACGAGAATCCGTCCGGCCTCAACCAGTTAGTC
TTTATCTTCCCGAAATTGAATATTTCGAATAGCTTTCAAAAATGTATAGT
GAAAATATCAGTAAGAAACTTTGTCATTACAATTGAGTTGGAGCATTCAA
AGATACAGAGAGTTCGGCACAGTCTGGACAGTTGTAGGATTATTGAAAAC
GATTGTTTCATAAAGACCTTGGAGAAGAAATATAATTCTATTTTCTTAGA
AAATCCTGCAAAGACTTTTATAGCTGAATCTCTTTTGAATGTTATATCAA
TGAATGTTAACATTGATACAATAAGAAACGCTCTTATCAATTTTCTAGCT
TGATTTAATAATAAAATCTTAATTTACTTTTAAA
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protein sequence of SMED30035446-orf-1

>SMED30035446-orf-1 ID=SMED30035446-orf-1|Name=SMED30035446-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=173bp
MSKLIILVLIVWAVVDGNEGARVVDVTEMGKKLVPHQIVFPIFDKRFYGI
VEDLHNMNATLYENPSGLNQLVFIFPKLNISNSFQKCIVKISVRNFVITI
ELEHSKIQRVRHSLDSCRIIENDCFIKTLEKKYNSIFLENPAKTFIAESL
LNVISMNVNIDTIRNALINFLA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000420parapharyngeal region
PLANA:0002089reproductive organ