SMED30021344

Overview
NameSMED30021344
Smed IDSMED30021344
Length (bp)1031
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30021344 (SMED30021344) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021344 (SMED30021344) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30021344

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30021344h1SMcG0022571 SmedASXL_018799SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30021344h1SMcG0022571 SmedASXL_018799SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30021344h1SMcG0022571 dd_Smed_v4_1043_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30021344h1SMcG0022571 dd_Smed_v4_1043_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30021344h1SMcG0022570 dd_Smed_v4_3515_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30021344h1SMcG0022570 dd_Smed_v4_3515_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30021344h1SMcG0022570 dd_Smed_v4_3515_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30021344 dd_Smed_v4_3946_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30021344 dd_Smed_v4_3946_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30021344h1SMcG0022571 dd_Smed_v6_1043_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30021344h1SMcG0000684 OX_Smed_1.0.21649ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
head regionSMED30021344h1SMcG0022571 OX_Smed_1.0.21649ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30021344 dd_Smed_v4_3946_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
Alignments
SMED30021344 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000144:30679..31762 +5091
Homology
[Close]
BLAST of SMED30021344 vs. Planmine SMEST
Match: SMESG000016307.1 (SMESG000016307.1)

HSP 1 Score: 504.982 bits (1299), Expect = 0.000e+0
Identity = 262/263 (99.62%), Postives = 262/263 (99.62%), Query Frame = 3 
Query:  225 MSGAPVDSPLYVYKDLKVSHGPQKINRCFFYF*CINRLDCLWNLLANMINTITFALLLSQIFNINAESKSDLNIREITGETCSRNNMNSIFDVLLRKFATEHKQVALPNATAAGVSILSPILYNTSSIFRSCNIXXXXXXXXXXXDVRICFNITNAIILTDLKVDLYVKKMGTLMKVALKNAIINARLTIPLKSKGPMVLKNSTLISLDDVHVENAGFIAKFDSFLNAMLKNKIRETLSRLVSEEIPPIVNEHFRKHPFSLLE 1013
            MSGAPVDSPLYVYKDLKVSHGPQKINRCFFYF CINRLDCLWNLLANMINTITFALLLSQIFNINAESKSDLNIREITGETCSRNNMNSIFDVLLRKFATEHKQVALPNATAAGVSILSPILYNTSSIFRSCNITSNLNSTTNNLDVRICFNITNAIILTDLKVDLYVKKMGTLMKVALKNAIINARLTIPLKSKGPMVLKNSTLISLDDVHVENAGFIAKFDSFLNAMLKNKIRETLSRLVSEEIPPIVNEHFRKHPFSLLE
Sbjct:    1 MSGAPVDSPLYVYKDLKVSHGPQKINRCFFYFKCINRLDCLWNLLANMINTITFALLLSQIFNINAESKSDLNIREITGETCSRNNMNSIFDVLLRKFATEHKQVALPNATAAGVSILSPILYNTSSIFRSCNITSNLNSTTNNLDVRICFNITNAIILTDLKVDLYVKKMGTLMKVALKNAIINARLTIPLKSKGPMVLKNSTLISLDDVHVENAGFIAKFDSFLNAMLKNKIRETLSRLVSEEIPPIVNEHFRKHPFSLLE 263
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BLAST of SMED30021344 vs. Planmine SMEST
Match: SMESG000016306.1 (SMESG000016306.1)

HSP 1 Score: 110.923 bits (276), Expect = 8.566e-29
Identity = 53/178 (29.78%), Postives = 104/178 (58.43%), Query Frame = 3 
Query:  468 CSRNNMNSIFDVLLRKFATEHKQVALPNATAAGVSILSPILYNTSSIFRSCNIXXXXXXXXXXXDVRICFNITNAIILTDLKVDLYVKKMGTLMKVALKNAIINARLTIPLKSKGPMVLKNSTLISLDDVHVENAGFIAKFDSFLNAMLKNKIRETLSRLVSEEIPPIVNEHFRKHPF 1001
            CSR  ++ I D+++ + A +   + +PN T  G+ + SP L    SI RSC+I     + T ++ V+ C ++    + + +KVDL V K   ++K+ L N +I    T+P ++ G +V+    ++ + ++ +E  G I+ FDS +N M+K K++E + +LVS+++P ++N   +++P 
Sbjct:   26 CSRT-LDIISDLMISRMALKIDYIVIPNVTTGGIQMFSPTLIGLGSIKRSCSIDMKFINETKDMAVKACVSVDEVELNSGVKVDLIVGKFSNIVKLTLDNIVIEITATVPWETGGAVVINKVNVVQIKNIKIEARGIISGFDSVINVMMKTKMKEAILKLVSKQLPAVINAKLKQYPI 202
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BLAST of SMED30021344 vs. Planmine SMEST
Match: SMESG000016301.1 (SMESG000016301.1)

HSP 1 Score: 104.76 bits (260), Expect = 1.911e-26
Identity = 54/178 (30.34%), Postives = 105/178 (58.99%), Query Frame = 3 
Query:  462 ETCSRNNMNSIFDVLLRKFATEHKQVALPNATAAGVSILSPILYNTSSIFRSCNIXXXXXXXXXXXDVRICFNITNAIILTDLKVDLYVKKMGTLMKVALKNAIINARLTIPLKSKGPMVLKNSTLISLDDVHVENAGFIAKFDSFLNAMLKNKIRETLSRLVSEEIPPIVNEHFRKH 995
            ET      +S+ D+L+ +++   + + LPN + +G+S+ S IL   SSI RSC IT  ++  T N+ + IC       +LT LK++ ++K   +  +V + + II+ +  IP+K  GP+V+K   ++ + ++H +N G +  FD+ LN MLK+++++ L  + + ++ P +NE  + +
Sbjct:   35 ETTCTKLFDSVVDILIERYSPSMENMKLPNISQSGISMNSTILGGLSSIKRSCQITFEVDPKTKNISIGICLTAKETTLLTFLKIESWIKNFYSFTRVIVTDIIISVKAIIPIKVGGPVVVKKLFIVDIGNIHFDNTGILGSFDTALNLMLKSRLKDMLIDMANNKLTPTINELLKTY 212
[Close]
BLAST of SMED30021344 vs. Planmine SMEST
Match: SMESG000016304.1 (SMESG000016304.1)

HSP 1 Score: 85.1149 bits (209), Expect = 1.117e-19
Identity = 48/182 (26.37%), Postives = 96/182 (52.75%), Query Frame = 3 
Query:  456 TGETCSRNNMNSIFDVLLRKFATEHKQVALPNATAAGVSILSPILYNTSSIFRSCNIXXXXXXXXXXXDVRICFNITNAIILTDLKVDLYVKKMGTLMKVALKNAIINARLTIPLKSKGPMVLKNSTLISLDDVHVENAGFIAKFDSFLNAMLKNKIRETLSRLVSEEIPPIVNEHFRKHPF 1001
            +G  C+ N +NSI DVL+ K+      + LP+  A    + +P +   SS++RSCNI   L+  + NL +  C  +                   + MK+ + +  ++  +T  LK+ GP+V+    L ++  V+++N+GF+   D  +N M+K ++++ +  ++++++P I+NE   K+P 
Sbjct:    6 SGGECTPN-LNSIIDVLIGKYIRMFDPLHLPDINATDTFMFAPNVTGLSSLYRSCNIVVVLDPISKNLTLSFCLAVNET----------------SYMKIIISDLTVHINVTAQLKTGGPIVINKIGLATIGKVNIDNSGFLGIMDPLVNVMMKTRVKDAVVNIINKKLPNIINETLSKYPL 170
[Close]
BLAST of SMED30021344 vs. Planmine SMEST
Match: SMESG000016304.1 (SMESG000016304.1)

HSP 1 Score: 85.1149 bits (209), Expect = 1.592e-19
Identity = 48/182 (26.37%), Postives = 96/182 (52.75%), Query Frame = 3 
Query:  456 TGETCSRNNMNSIFDVLLRKFATEHKQVALPNATAAGVSILSPILYNTSSIFRSCNIXXXXXXXXXXXDVRICFNITNAIILTDLKVDLYVKKMGTLMKVALKNAIINARLTIPLKSKGPMVLKNSTLISLDDVHVENAGFIAKFDSFLNAMLKNKIRETLSRLVSEEIPPIVNEHFRKHPF 1001
            +G  C+ N +NSI DVL+ K+      + LP+  A    + +P +   SS++RSCNI   L+  + NL +  C  +                   + MK+ + +  ++  +T  LK+ GP+V+    L ++  V+++N+GF+   D  +N M+K ++++ +  ++++++P I+NE   K+P 
Sbjct:   20 SGGECTPN-LNSIIDVLIGKYIRMFDPLHLPDINATDTFMFAPNVTGLSSLYRSCNIVVVLDPISKNLTLSFCLAVNET----------------SYMKIIISDLTVHINVTAQLKTGGPIVINKIGLATIGKVNIDNSGFLGIMDPLVNVMMKTRVKDAVVNIINKKLPNIINETLSKYPL 184
The following BLAST results are available for this feature:
BLAST of SMED30021344 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 SMED30021344 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 SMED30021344 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 SMED30021344 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 SMED30021344 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 SMED30021344 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 SMED30021344 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 SMED30021344 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 SMED30021344 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 SMED30021344 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 SMED30021344 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 SMED30021344 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 SMED30021344 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 SMED30021344 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000016307.10.000e+099.62SMESG000016307.1[more]
SMESG000016306.18.566e-2929.78SMESG000016306.1[more]
SMESG000016301.11.911e-2630.34SMESG000016301.1[more]
SMESG000016304.11.117e-1926.37SMESG000016304.1[more]
SMESG000016304.11.592e-1926.37SMESG000016304.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021344 ID=SMED30021344|Name=SMED30021344|organism=Schmidtea mediterranea sexual|type=transcript|length=1031bp
ATTTTGGATCATAATTCCGCAACGTTTTGTATATTTTTGAAGATATTGAA
GGAGATTGGATCCGTTTCTTAGCTTATTTAACTTGAACTGTTCTTATAGA
TTTAAACAAACAATTAAATAAATATACTGTCAATTTTAAATTATTTATTT
ATTGTTTCTGATTGTATTATTATTTCCCCAGAAAATTTAATAAATCACAT
GTCACTTGTTTGCCTATTGAAAACATGTCGGGCGCCCCTGTTGACAGTCC
GTTGTATGTTTATAAAGATTTAAAAGTTTCCCACGGGCCTCAAAAAATCA
ACAGGTGTTTCTTTTATTTTTAATGTATAAATAGATTGGACTGTTTATGG
AATTTATTGGCAAATATGATAAACACGATTACATTTGCGTTATTGCTGAG
TCAAATCTTCAACATAAATGCTGAGTCTAAATCCGATCTCAACATTCGGG
AAATTACTGGAGAGACTTGTTCGAGAAACAATATGAATTCGATATTCGAT
GTGCTGCTAAGGAAATTTGCAACGGAGCATAAACAAGTGGCTCTCCCAAA
TGCCACGGCGGCTGGAGTCTCAATACTCTCTCCAATTCTGTACAATACCT
CCTCAATATTCCGAAGTTGTAACATCACCTCGAATTTGAACTCCACGACA
AATAATCTGGATGTCAGGATTTGTTTCAACATAACAAATGCAATAATACT
AACCGATCTTAAAGTCGATCTCTACGTGAAAAAGATGGGAACATTGATGA
AGGTTGCGCTGAAAAATGCAATAATAAACGCCAGACTTACCATACCCTTG
AAATCTAAAGGCCCGATGGTCTTAAAGAATTCGACTCTTATCAGTTTGGA
CGATGTTCACGTGGAAAATGCCGGATTTATCGCAAAATTTGATTCTTTCC
TCAATGCGATGTTAAAAAACAAAATCCGAGAAACATTGTCCAGATTGGTT
TCTGAGGAAATCCCGCCCATTGTCAATGAACATTTTAGAAAGCACCCTTT
TTCTCTGCTTGAATAAATATTGAAATTTGTC
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protein sequence of SMED30021344-orf-1

>SMED30021344-orf-1 ID=SMED30021344-orf-1|Name=SMED30021344-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=217bp
MINTITFALLLSQIFNINAESKSDLNIREITGETCSRNNMNSIFDVLLRK
FATEHKQVALPNATAAGVSILSPILYNTSSIFRSCNITSNLNSTTNNLDV
RICFNITNAIILTDLKVDLYVKKMGTLMKVALKNAIINARLTIPLKSKGP
MVLKNSTLISLDDVHVENAGFIAKFDSFLNAMLKNKIRETLSRLVSEEIP
PIVNEHFRKHPFSLLE*
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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:0002032epidermal cell