SMED30013899

Overview
NameSMED30013899
Smed IDSMED30013899
Length (bp)489
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 SMED30013899 (SMED30013899) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30013899 (SMED30013899) 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 SMED30013899 (SMED30013899) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30013899 (SMED30013899) 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



SMED30013899

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 regionSMED30013899SMESG000020109.1 SmedASXL_061746SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30013899SMESG000020109.1 dd_Smed_v4_19073_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30013899SMESG000020109.1 dd_Smed_v4_19073_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30013899SMESG000020109.1 dd_Smed_v4_19073_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
non-ciliated neuronSMED30013899SMESG000020109.1 dd_Smed_v4_19073_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30013899SMESG000020109.1 dd_Smed_v4_19073_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30013899SMESG000020109.1 dd_Smed_v6_19073_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30013899 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000776:123381..128450 +2363
Homology
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BLAST of SMED30013899 vs. TrEMBL
Match: A0A177B6C2 (DNA-directed RNA polymerase subunit OS=Intoshia linei OX=1819745 GN=A3Q56_02397 PE=3 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 3.461e-7
Identity = 36/98 (36.73%), Postives = 42/98 (42.86%), Query Frame = 3 
Query:   87 NLSCYECSADNSYLNNPSALPNTNNCIYGVSLNRRRCFPQHNGCFITWIYTLNQYTSIARGCQTNCNAGCSLTGYQIVKNTCTTCCQTLACNNGTFLN 380
            +L CYEC+ D     + +  P  NN  Y    N R+C    N C I      N    I RGC   C  GC L GY I    C  CCQ   CN G+  N
Sbjct:   31 DLWCYECTGDYVKKYDFNQSPCRNNVTY---FNIRQCSTNDNYCKIEKHQLYNYIMYIDRGCVEKCGYGCRLNGYGIPLKRCKYCCQWSGCNFGSGSN 125
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BLAST of SMED30013899 vs. TrEMBL
Match: R7UTY5 (Uncharacterized protein OS=Capitella teleta OX=283909 GN=CAPTEDRAFT_193274 PE=4 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 1.262e-6
Identity = 38/104 (36.54%), Postives = 49/104 (47.12%), Query Frame = 3 
Query:   87 NLSCYECSADNSYLNNPSALPNTNNCIYGVSLNRRRCFPQHNGCFITWI--YTLNQYTSIARGCQTNCNAGCSLTGYQIVKNTCTTCCQTLACNNGTFLNGNII 392
            +L CYECS   S   +P+  P  NN + GV    R+C      C +  +  Y  +   SIARGC   C  GC   G  I    C++CC TLACN  +  N   I
Sbjct:   36 DLWCYECSESYSRTYDPADSPCRNN-LTGVIT--RQCAKSEIYCRVERLDLYRFDTMLSIARGCTNKCEYGCRFNGLAITYRRCSSCCTTLACNTDSRTNDRSI 136
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BLAST of SMED30013899 vs. TrEMBL
Match: A0A1S3K4L9 (uncharacterized protein LOC106178789 OS=Lingula unguis OX=7574 GN=LOC106178789 PE=4 SV=1)

HSP 1 Score: 53.9138 bits (128), Expect = 6.030e-6
Identity = 36/116 (31.03%), Postives = 54/116 (46.55%), Query Frame = 3 
Query:   45 IFSIVFSQRNNRTTNLSCYECSADNSYLNNPSALPNTNNCIYGVS-LNRRRCFPQHNGCFITWIYTLNQYTSIARGCQTNCNAGCSLTGYQIVKNTCTTCCQTLACNNGTFLNGNI 389
            + S+V +     + NLSCYECS   ++ +N  +      C   +  ++ R C  +   C +       Q  +I RGC   C  GC  TG+ I   TCT+CCQ   CN G    G++
Sbjct:   23 VISMVVTGMGTFSYNLSCYECS--EAFTDNLKSYEPFTPCQTNLEEVDVRPCGSRDLYCKVERKSFKGQTVTIERGCTQRCLHGCKFTGWGITLMTCTSCCQEHVCNTGNRAPGSL 136
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BLAST of SMED30013899 vs. Planmine SMEST
Match: SMESG000020109.1 (SMESG000020109.1)

HSP 1 Score: 295.819 bits (756), Expect = 1.569e-104
Identity = 147/148 (99.32%), Postives = 147/148 (99.32%), Query Frame = 3 
Query:   24 MIWLFWFIFSIVFSQRNNRTTNLSCYECSADNSYLNNPSALPNTNNCIYGVSLNRRRCFPQHNGCFITWIYTLNQYTSIARGCQTNCNAGCSLTGYQIVKNTCTTCCQTLACNNGTFLNGNIIIMPFTILNYFFSFSLTSFAMYFLHY 467
            MIWLFWFIFSIVFSQRNNRTTNLSCYECSADNSYLNNPSALPNTNNCIYGVSLNRRRCFPQHNGCFITWIYTLNQYTSIARGCQTNCNAGCSLTGYQIVKNTCTTCCQTL CNNGTFLNGNIIIMPFTILNYFFSFSLTSFAMYFLHY
Sbjct:    1 MIWLFWFIFSIVFSQRNNRTTNLSCYECSADNSYLNNPSALPNTNNCIYGVSLNRRRCFPQHNGCFITWIYTLNQYTSIARGCQTNCNAGCSLTGYQIVKNTCTTCCQTLGCNNGTFLNGNIIIMPFTILNYFFSFSLTSFAMYFLHY 148
[Close]
BLAST of SMED30013899 vs. Planmine SMEST
Match: SMESG000020114.1 (SMESG000020114.1)

HSP 1 Score: 73.559 bits (179), Expect = 2.328e-17
Identity = 39/99 (39.39%), Postives = 55/99 (55.56%), Query Frame = 3 
Query:   96 CYECSADNSYLNNPSALPNTN-NCIYGVSLNRRRCFPQHNGCFITWIYTLNQYTSIARGCQTNCNAGCSLTGYQIVKNTCTTCCQTLACNNGTFLNGNI 389
            C+ECSA +    N +   N N NC+ G++L+ R C  +H  C+   IY  +Q  +I RGC+T+C + C   G+ IV   CT CC    CN+ T  NG I
Sbjct:    2 CFECSAKDLNSENDAMKRNENRNCLTGLNLSPRYCLRRHTHCYEKSIYIGSQIKTIERGCRTSCESSCFRKGFHIVTQMCTKCCVKSKCNHKTIGNGGI 100
The following BLAST results are available for this feature:
BLAST of SMED30013899 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 SMED30013899 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 SMED30013899 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 SMED30013899 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 SMED30013899 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 SMED30013899 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 SMED30013899 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 SMED30013899 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A177B6C23.461e-736.73DNA-directed RNA polymerase subunit OS=Intoshia li... [more]
R7UTY51.262e-636.54Uncharacterized protein OS=Capitella teleta OX=283... [more]
A0A1S3K4L96.030e-631.03uncharacterized protein LOC106178789 OS=Lingula un... [more]
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BLAST of SMED30013899 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 SMED30013899 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 SMED30013899 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 SMED30013899 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 SMED30013899 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 SMED30013899 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000020109.11.569e-10499.32SMESG000020109.1[more]
SMESG000020114.12.328e-1739.39SMESG000020114.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013899 ID=SMED30013899|Name=SMED30013899|organism=Schmidtea mediterranea sexual|type=transcript|length=489bp
TTATATGCCATAATATTGGATAGATGATTTGGTTATTTTGGTTTATATTT
TCAATTGTATTTTCACAAAGAAATAACAGAACAACAAATCTCTCATGCTA
CGAATGCAGTGCAGATAATTCATACTTAAATAATCCCTCGGCCCTTCCCA
ATACTAATAACTGTATATACGGTGTCTCCTTAAATAGGAGGAGATGCTTT
CCTCAGCACAATGGTTGTTTTATAACGTGGATTTATACGCTTAATCAGTA
CACATCTATAGCTCGGGGGTGTCAAACAAATTGTAATGCCGGGTGCTCTT
TGACTGGCTATCAGATAGTCAAAAATACCTGTACCACCTGCTGCCAAACG
CTGGCCTGTAATAACGGGACTTTTCTCAACGGAAATATTATTATTATGCC
ATTTACAATATTAAATTACTTTTTCTCATTTTCACTAACTTCTTTCGCGA
TGTATTTTCTTCATTATTAAATTAATAATTTATGTAGAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
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..14
score: 0.71
NoneNo IPR availableTMHMMTMhelixcoord: 124..146