SMED30034379

Overview
NameSMED30034379
Smed IDSMED30034379
Length (bp)2436
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 SMED30034379 (SMED30034379) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30034379 (SMED30034379) 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



SMED30034379

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30034379SMESG000002573.1 dd_Smed_v4_95036_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30034379SMESG000002573.1 dd_Smed_v4_95036_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30034379SMESG000002573.1 dd_Smed_v4_95036_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30034379SMESG000070650.1 Contig4691GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30034379SMESG000002573.1 Contig4691GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
reproductive organSMED30034379SMESG000002573.1 Contig34429newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30034379SMESG000002573.1 Contig34429uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
testis primordiumSMED30034379SMESG000002573.1 Contig4691_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism juvenile cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30034379 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000165:13569..30965 -11888
Homology
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BLAST of SMED30034379 vs. Planmine SMEST
Match: SMESG000002573.1 (SMESG000002573.1)

HSP 1 Score: 1433.31 bits (3709), Expect = 0.000e+0
Identity = 720/720 (100.00%), Postives = 720/720 (100.00%), Query Frame = 1 
Query:   94 MVVDARSFNEIDKELSRIMRNIRFRYKNEVKLQLVNAQTMTEIKLHIYHQTAPYNRFVFLVNIPKNYPLSPLCVEPIDISDEMRKQFDRDQFKFQRMKYLIEGVLDFCNMYKEKQRKRSVIKLTRNSSNSKSGVPAHQDQMLSFAECINSTHSRSLSRMNLMKKYSEKIICYSKSVGYQKYQHLLDLISQGPYQTDRKRPFIKPQSVVKSLNEYYYQDFXXXXXXXXXXINTKIPTAQQSSENFINCLELNSYLENTIEYVFLHKNIDIHSGSRDCRDLNHLLRKQYLISSIVANPEIVSTRPMISNNYLESFLSISDKDVGEISTDDNIMELGENCQVYMKLVYEDLTIKITENRSVYSVNDVNNSPRFYWPVLEIQKFPLKYSTKSIEIQTSSDNSTEINSRIFLSLQTISDILFFSVDEMILDFLNKSVIRYEHNNLKYFGDCNNPLGQRFNVVEEDYLIIYDSDMEYLKELNLSSVYSQPFESMHITNYQLNSHNCGKCELNFQEKISIKSLGEISKIKALSSSFPLIEIYKTCLRSFRFPVNKSNNILNEIEFTLELNLKNKEERRVLKFLNIPMTNNPVETLEFFIPLINHKEETVILIKDESLSGQKDKENCILIHKVMKNSSLHKFFQDKYRIDNYINETNKKVYFSPSSETPFWMLKNFLEFFSIIRLKNNLKLLRDSIKKDFNLSKIVLNRIYFYNESFEFLKSLSKSVA 2253
            MVVDARSFNEIDKELSRIMRNIRFRYKNEVKLQLVNAQTMTEIKLHIYHQTAPYNRFVFLVNIPKNYPLSPLCVEPIDISDEMRKQFDRDQFKFQRMKYLIEGVLDFCNMYKEKQRKRSVIKLTRNSSNSKSGVPAHQDQMLSFAECINSTHSRSLSRMNLMKKYSEKIICYSKSVGYQKYQHLLDLISQGPYQTDRKRPFIKPQSVVKSLNEYYYQDFRRQLPRRRRRINTKIPTAQQSSENFINCLELNSYLENTIEYVFLHKNIDIHSGSRDCRDLNHLLRKQYLISSIVANPEIVSTRPMISNNYLESFLSISDKDVGEISTDDNIMELGENCQVYMKLVYEDLTIKITENRSVYSVNDVNNSPRFYWPVLEIQKFPLKYSTKSIEIQTSSDNSTEINSRIFLSLQTISDILFFSVDEMILDFLNKSVIRYEHNNLKYFGDCNNPLGQRFNVVEEDYLIIYDSDMEYLKELNLSSVYSQPFESMHITNYQLNSHNCGKCELNFQEKISIKSLGEISKIKALSSSFPLIEIYKTCLRSFRFPVNKSNNILNEIEFTLELNLKNKEERRVLKFLNIPMTNNPVETLEFFIPLINHKEETVILIKDESLSGQKDKENCILIHKVMKNSSLHKFFQDKYRIDNYINETNKKVYFSPSSETPFWMLKNFLEFFSIIRLKNNLKLLRDSIKKDFNLSKIVLNRIYFYNESFEFLKSLSKSVA
Sbjct:    1 MVVDARSFNEIDKELSRIMRNIRFRYKNEVKLQLVNAQTMTEIKLHIYHQTAPYNRFVFLVNIPKNYPLSPLCVEPIDISDEMRKQFDRDQFKFQRMKYLIEGVLDFCNMYKEKQRKRSVIKLTRNSSNSKSGVPAHQDQMLSFAECINSTHSRSLSRMNLMKKYSEKIICYSKSVGYQKYQHLLDLISQGPYQTDRKRPFIKPQSVVKSLNEYYYQDFRRQLPRRRRRINTKIPTAQQSSENFINCLELNSYLENTIEYVFLHKNIDIHSGSRDCRDLNHLLRKQYLISSIVANPEIVSTRPMISNNYLESFLSISDKDVGEISTDDNIMELGENCQVYMKLVYEDLTIKITENRSVYSVNDVNNSPRFYWPVLEIQKFPLKYSTKSIEIQTSSDNSTEINSRIFLSLQTISDILFFSVDEMILDFLNKSVIRYEHNNLKYFGDCNNPLGQRFNVVEEDYLIIYDSDMEYLKELNLSSVYSQPFESMHITNYQLNSHNCGKCELNFQEKISIKSLGEISKIKALSSSFPLIEIYKTCLRSFRFPVNKSNNILNEIEFTLELNLKNKEERRVLKFLNIPMTNNPVETLEFFIPLINHKEETVILIKDESLSGQKDKENCILIHKVMKNSSLHKFFQDKYRIDNYINETNKKVYFSPSSETPFWMLKNFLEFFSIIRLKNNLKLLRDSIKKDFNLSKIVLNRIYFYNESFEFLKSLSKSVA 720
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BLAST of SMED30034379 vs. Planmine SMEST
Match: SMESG000080402.1 (SMESG000080402.1)

HSP 1 Score: 94.3597 bits (233), Expect = 1.174e-19
Identity = 46/103 (44.66%), Postives = 64/103 (62.14%), Query Frame = 1 
Query:  118 NEIDKELSRIMRNIRFRYKNEVKLQLVNAQTMTEIKLHIYHQTAPYNRFVFLVNIPKNYPLSPLCVEPIDISDEMRKQFDRDQFKFQRMKYLIEGVLDFCNMY 426
            NEID ELS ++R IR  Y+N++KLQ+ N   + E KL I  +   Y +F+FL+ IPK YP  PL  EPI +S EM   F    FK  +++ LI+ +L FC+ Y
Sbjct:    9 NEIDNELSAVLRIIRSYYRNDIKLQITNTNPIKEFKLQIIRKNFGYYKFLFLIKIPKEYPYEPLTAEPIIVSKEMMAHFYVQDFKCFKLRLLIDELLSFCHKY 111
The following BLAST results are available for this feature:
BLAST of SMED30034379 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 SMED30034379 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 SMED30034379 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 SMED30034379 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 SMED30034379 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 SMED30034379 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 SMED30034379 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 SMED30034379 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 SMED30034379 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 SMED30034379 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 SMED30034379 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 SMED30034379 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 SMED30034379 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 SMED30034379 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000002573.10.000e+0100.00SMESG000002573.1[more]
SMESG000080402.11.174e-1944.66SMESG000080402.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034379 ID=SMED30034379|Name=SMED30034379|organism=Schmidtea mediterranea sexual|type=transcript|length=2436bp
TTGTATTGATTTATTAAATATACTTTACTTTATTAAATAGTTTATTTAAA
TAATATACTGTCATCCAACTATTAAATTCCACAAGATATTAAAATGGTTG
TTGATGCTCGCAGTTTCAACGAGATTGATAAAGAATTGTCGAGAATCATG
AGGAACATTCGATTCAGGTATAAAAATGAAGTGAAGCTCCAACTTGTCAA
TGCACAAACGATGACAGAAATAAAGCTGCATATTTATCATCAAACAGCTC
CTTACAATCGTTTCGTGTTTCTGGTAAATATTCCCAAGAATTATCCGTTG
TCGCCTCTCTGTGTTGAACCGATTGATATTAGTGACGAAATGAGAAAGCA
ATTTGATCGGGATCAATTTAAATTTCAAAGAATGAAATACTTAATTGAAG
GCGTACTGGACTTTTGTAACATGTATAAAGAGAAGCAACGAAAACGTTCT
GTAATTAAATTGACAAGAAATTCATCAAATTCTAAATCCGGAGTTCCTGC
TCATCAGGATCAAATGTTATCCTTTGCAGAATGCATCAATTCTACACATT
CTCGATCTCTGTCCAGAATGAATTTAATGAAGAAATATTCCGAAAAAATA
ATTTGCTACAGCAAATCCGTTGGCTATCAAAAATATCAGCATTTGCTTGA
TCTAATTTCCCAAGGACCATACCAAACTGATAGAAAGCGGCCATTCATAA
AGCCTCAATCCGTTGTTAAGTCTCTAAATGAGTATTATTATCAAGACTTT
CGACGGCAGCTACCAAGACGAAGGCGACGCATCAATACAAAAATACCAAC
TGCTCAACAATCATCAGAAAACTTCATCAACTGTTTGGAATTAAATTCCT
ACCTTGAAAATACGATCGAATATGTATTTCTCCACAAGAATATCGATATC
CATTCAGGAAGTCGAGACTGTAGAGACCTCAATCATTTACTAAGAAAACA
ATATCTAATCTCATCAATAGTTGCCAATCCGGAAATAGTTTCCACTCGAC
CAATGATAAGCAATAATTACCTTGAATCGTTTCTAAGCATATCCGATAAA
GACGTAGGAGAAATATCCACTGACGACAACATAATGGAGTTAGGAGAAAA
TTGTCAAGTTTATATGAAATTGGTCTATGAGGATTTAACGATTAAAATCA
CAGAAAATCGATCAGTTTATTCCGTAAATGACGTAAATAATTCCCCGCGT
TTCTATTGGCCAGTTTTAGAAATCCAAAAGTTTCCATTAAAATACTCCAC
AAAAAGCATTGAAATCCAAACATCATCAGATAATTCTACGGAAATCAATT
CTCGAATCTTTCTTTCATTGCAAACCATTTCAGATATTTTATTTTTCTCG
GTAGACGAAATGATTTTGGACTTTTTAAACAAATCTGTTATTCGATACGA
GCACAACAATTTAAAATATTTTGGAGATTGCAACAATCCACTAGGACAAA
GATTTAATGTTGTCGAAGAAGACTACTTGATTATCTATGATTCCGATATG
GAATATCTAAAAGAATTGAATCTTTCATCGGTCTATTCTCAACCCTTCGA
ATCGATGCACATCACAAATTACCAATTGAATTCCCACAATTGTGGAAAAT
GTGAATTGAATTTCCAGGAGAAAATATCCATCAAAAGTCTCGGTGAGATT
TCTAAAATCAAAGCATTGAGTTCATCTTTTCCTCTGATTGAAATCTACAA
GACTTGTTTGAGGAGCTTTCGATTTCCGGTTAACAAATCGAACAACATAC
TCAATGAGATCGAGTTTACATTGGAATTAAACCTGAAAAACAAAGAGGAA
AGACGAGTTTTGAAGTTTCTCAATATCCCAATGACAAATAATCCCGTAGA
AACATTGGAATTTTTCATTCCCTTAATCAATCACAAAGAAGAAACTGTCA
TTTTGATTAAGGATGAATCTTTATCGGGTCAAAAAGACAAGGAAAATTGC
ATTCTAATACACAAAGTCATGAAGAACTCTTCGCTCCACAAGTTCTTCCA
AGACAAATACCGAATCGATAATTACATCAATGAAACAAATAAAAAAGTGT
ATTTTTCCCCATCATCGGAAACTCCGTTCTGGATGTTGAAGAATTTCCTG
GAATTTTTCTCTATCATTCGATTGAAGAACAACTTGAAACTCCTTCGAGA
TTCCATAAAAAAAGATTTTAATTTGTCGAAAATCGTTCTGAATCGAATTT
ACTTTTATAATGAAAGTTTTGAATTTCTAAAAAGCTTATCGAAATCAGTT
GCGTAAATTGATATAATTTTGATATAAATTCATATAATAAATTGCTTTAT
CCGTCAGAAGTCCTTATCGGTAATCGGGCTCGGTTTATTCCATTTGGATC
CATTTTTTTCTTACAGGCCTTTTGTTAAATTTTCTGCATGTTTGATTGAA
ATTTTATGAATGAGATTGTTGAACCCGATTCCAGGC
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protein sequence of SMED30034379-orf-1

>SMED30034379-orf-1 ID=SMED30034379-orf-1|Name=SMED30034379-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=721bp
MVVDARSFNEIDKELSRIMRNIRFRYKNEVKLQLVNAQTMTEIKLHIYHQ
TAPYNRFVFLVNIPKNYPLSPLCVEPIDISDEMRKQFDRDQFKFQRMKYL
IEGVLDFCNMYKEKQRKRSVIKLTRNSSNSKSGVPAHQDQMLSFAECINS
THSRSLSRMNLMKKYSEKIICYSKSVGYQKYQHLLDLISQGPYQTDRKRP
FIKPQSVVKSLNEYYYQDFRRQLPRRRRRINTKIPTAQQSSENFINCLEL
NSYLENTIEYVFLHKNIDIHSGSRDCRDLNHLLRKQYLISSIVANPEIVS
TRPMISNNYLESFLSISDKDVGEISTDDNIMELGENCQVYMKLVYEDLTI
KITENRSVYSVNDVNNSPRFYWPVLEIQKFPLKYSTKSIEIQTSSDNSTE
INSRIFLSLQTISDILFFSVDEMILDFLNKSVIRYEHNNLKYFGDCNNPL
GQRFNVVEEDYLIIYDSDMEYLKELNLSSVYSQPFESMHITNYQLNSHNC
GKCELNFQEKISIKSLGEISKIKALSSSFPLIEIYKTCLRSFRFPVNKSN
NILNEIEFTLELNLKNKEERRVLKFLNIPMTNNPVETLEFFIPLINHKEE
TVILIKDESLSGQKDKENCILIHKVMKNSSLHKFFQDKYRIDNYINETNK
KVYFSPSSETPFWMLKNFLEFFSIIRLKNNLKLLRDSIKKDFNLSKIVLN
RIYFYNESFEFLKSLSKSVA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ
PLANA:0003304testis primordium