SMED30027913

Overview
NameSMED30027913
Smed IDSMED30027913
Length (bp)1368
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 SMED30027913 (SMED30027913) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30027913 (SMED30027913) 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 SMED30027913 (SMED30027913) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30027913 (SMED30027913) 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




SMED30027913

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30027913h1SMcG0019592 dd_Smed_v4_3390_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30027913h1SMcG0019592 dd_Smed_v4_3390_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
reproductive organSMED30027913h1SMcG0019592 Contig12746newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30027913h1SMcG0019592 Contig12746uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30027913 vs. Planmine SMEST
Match: SMESG000014912.1 (SMESG000014912.1)

HSP 1 Score: 226.483 bits (576), Expect = 5.310e-71
Identity = 134/134 (100.00%), Postives = 134/134 (100.00%), Query Frame = 1
Query:   28 MFLLIYFYMLFNPVCSENQLSKCLGTHPFRQSDSTCSSFEEVCMKKDNEECANFMNTCKQCPPSNYTILMLSGMLAVSKSQQKSTNSTLVKLESMTNEIEAXXXXXXXXXXXMIQDEIEAXXXXXXXXXXXMIQ 429
            MFLLIYFYMLFNPVCSENQLSKCLGTHPFRQSDSTCSSFEEVCMKKDNEECANFMNTCKQCPPSNYTILMLSGMLAVSKSQQKSTNSTLVKLESMTNEIEALKNLSKNLNLSMIQDEIEALKNLSKNLNLSMIQ
Sbjct:    1 MFLLIYFYMLFNPVCSENQLSKCLGTHPFRQSDSTCSSFEEVCMKKDNEECANFMNTCKQCPPSNYTILMLSGMLAVSKSQQKSTNSTLVKLESMTNEIEALKNLSKNLNLSMIQDEIEALKNLSKNLNLSMIQ 134          

HSP 2 Score: 174.481 bits (441), Expect = 4.398e-51
Identity = 98/124 (79.03%), Postives = 99/124 (79.84%), Query Frame = 1
Query:  745 DPRFHIIERIFGKPSTKNPNPHNSRNPTDSELTPLNPTDSSGEMSTLMNTKFENLERIVXXXXXXXXX---------------------XXIKMDEIIEKTLPETVTANVPETVTVNASVMENC 1053
            DPRFHIIERIFGKPSTKNPNPHNSRNPTDSELTPLNPTDSSGEMSTLMNTKFENLERIVSSLS  +                       LNIKMDEIIEKTLPETVTANVPETVTVNASVMENC
Sbjct:  154 DPRFHIIERIFGKPSTKNPNPHNSRNPTDSELTPLNPTDSSGEMSTLMNTKFENLERIVSSLSDLIGTINTKCGNIETIVSSLSGSLSNLNIKMDEIIEKTLPETVTANVPETVTVNASVMENC 277          
BLAST of SMED30027913 vs. Planmine SMEST
Match: SMESG000014912.1 (SMESG000014912.1)

HSP 1 Score: 207.994 bits (528), Expect = 4.815e-64
Identity = 126/126 (100.00%), Postives = 126/126 (100.00%), Query Frame = 1
Query:   52 MLFNPVCSENQLSKCLGTHPFRQSDSTCSSFEEVCMKKDNEECANFMNTCKQCPPSNYTILMLSGMLAVSKSQQKSTNSTLVKLESMTNEIEAXXXXXXXXXXXMIQDEIEAXXXXXXXXXXXMIQ 429
            MLFNPVCSENQLSKCLGTHPFRQSDSTCSSFEEVCMKKDNEECANFMNTCKQCPPSNYTILMLSGMLAVSKSQQKSTNSTLVKLESMTNEIEALKNLSKNLNLSMIQDEIEALKNLSKNLNLSMIQ
Sbjct:    1 MLFNPVCSENQLSKCLGTHPFRQSDSTCSSFEEVCMKKDNEECANFMNTCKQCPPSNYTILMLSGMLAVSKSQQKSTNSTLVKLESMTNEIEALKNLSKNLNLSMIQDEIEALKNLSKNLNLSMIQ 126          

HSP 2 Score: 174.866 bits (442), Expect = 2.841e-51
Identity = 98/124 (79.03%), Postives = 99/124 (79.84%), Query Frame = 1
Query:  745 DPRFHIIERIFGKPSTKNPNPHNSRNPTDSELTPLNPTDSSGEMSTLMNTKFENLERIVXXXXXXXXX---------------------XXIKMDEIIEKTLPETVTANVPETVTVNASVMENC 1053
            DPRFHIIERIFGKPSTKNPNPHNSRNPTDSELTPLNPTDSSGEMSTLMNTKFENLERIVSSLS  +                       LNIKMDEIIEKTLPETVTANVPETVTVNASVMENC
Sbjct:  146 DPRFHIIERIFGKPSTKNPNPHNSRNPTDSELTPLNPTDSSGEMSTLMNTKFENLERIVSSLSDLIGTINTKCGNIETIVSSLSGSLSNLNIKMDEIIEKTLPETVTANVPETVTVNASVMENC 269          
BLAST of SMED30027913 vs. Planmine SMEST
Match: SMESG000074956.1 (SMESG000074956.1)

HSP 1 Score: 75.0998 bits (183), Expect = 4.371e-14
Identity = 27/67 (40.30%), Postives = 45/67 (67.16%), Query Frame = 1
Query:   94 CLGTHPFRQSDSTCSSFEEVCMKKDNEECANFMNTCKQCPPSNYTILMLSGMLAVSKSQQKSTNSTL 294
            C+  +PFR+ D +C +FE++C+K D++ C NF++ CKQCPP+NYT++M   +L +      + N  L
Sbjct:   25 CIIDYPFRKDDFSCDNFEKICVKTDDDVCKNFLSACKQCPPTNYTVIMYQDLLKIKDEILIAKNEIL 91          
BLAST of SMED30027913 vs. Planmine SMEST
Match: SMESG000074945.1 (SMESG000074945.1)

HSP 1 Score: 70.0922 bits (170), Expect = 6.168e-13
Identity = 32/89 (35.96%), Postives = 55/89 (61.80%), Query Frame = 1
Query:   37 LIYFYMLFNPVCSENQLSKCLGTHP--FRQSDSTCSSFEEVCMKKDNEECANFMNTCKQCPPSNYTILMLSGM------LAVSKSQQKS 279
            LI+ ++L   +C+  +  + +  +P  FR +D++C+ + +VC+K  + +CANF   C QCPPSNY+I+M   M      + +SKSQ K+
Sbjct:    4 LIFIFLLSGVICAGGEKPRFICQNPKSFRTNDNSCADYNDVCIKTGDPDCANFQTACNQCPPSNYSIMMYIDMMNMKNQIIISKSQMKN 92          
BLAST of SMED30027913 vs. Planmine SMEST
Match: SMESG000074409.1 (SMESG000074409.1)

HSP 1 Score: 66.2402 bits (160), Expect = 7.496e-13
Identity = 29/70 (41.43%), Postives = 45/70 (64.29%), Query Frame = 1
Query:   94 CLGTHPFRQSDSTCSSFEEVCMKKDNEECANFMNTCKQCPPSNYTILMLSGMLAVSKSQQKSTNSTLVKL 303
            C    PFR +D TC  FE++C+K+++++C   +N+CKQCPP+N TI +L   L +  S +  T S +V L
Sbjct:   25 CFEQTPFRLNDQTCGKFEDICIKREDDQCIQLLNSCKQCPPNNITITIL---LKIWNSLKSFTESQIVLL 91          
The following BLAST results are available for this feature:
BLAST of SMED30027913 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 SMED30027913 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 SMED30027913 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 SMED30027913 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 SMED30027913 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 SMED30027913 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 SMED30027913 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 SMED30027913 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 SMED30027913 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 SMED30027913 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 SMED30027913 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 SMED30027913 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 SMED30027913 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 SMED30027913 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000014912.15.310e-71100.00SMESG000014912.1[more]
SMESG000014912.14.815e-64100.00SMESG000014912.1[more]
SMESG000074956.14.371e-1440.30SMESG000074956.1[more]
SMESG000074945.16.168e-1335.96SMESG000074945.1[more]
SMESG000074409.17.496e-1341.43SMESG000074409.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027913 ID=SMED30027913|Name=SMED30027913|organism=Schmidtea mediterranea sexual|type=transcript|length=1368bp
GATATAATTTTTCAGTTGTAGATTAAAATGTTTTTGTTAATATATTTTTA
TATGTTGTTTAATCCGGTTTGTTCTGAGAATCAGTTATCCAAGTGCCTTG
GAACGCATCCATTCAGGCAGTCGGATTCGACTTGTAGCAGTTTCGAGGAA
GTCTGCATGAAGAAAGACAACGAAGAATGCGCTAATTTCATGAACACATG
CAAACAATGCCCTCCGTCAAATTACACGATATTGATGCTATCTGGCATGC
TGGCGGTAAGCAAAAGTCAGCAGAAGAGTACCAATTCAACACTCGTCAAA
TTGGAAAGCATGACAAATGAAATAGAAGCCTTAAAAAATCTATCGAAAAA
TCTCAATTTAAGCATGATACAAGATGAAATAGAAGCCTTAAAAAATCTAT
CGAAAAATCTCAATTTAAGCATGATACAAGATGAAATAGAAGCCTTAAAA
AATCTATCGAAAAATCTCAATTTAAGCATGATACAAGATTGTAAAACCCT
ACAGAAAATCCCAACTCAATCGGCATCGGAGAAGAAGAGAACAAAACAAT
CAAACAATCCGTTTCGTAAAACCCATCAACCAAACCCCCGATATCAAAAT
AGTTCAACAATAATCGATCAACTGCAACTCATCGAATCTCAACCCAAATC
AATCAACCAAGACGAAGTTCCAGGTCCAAGTCATCCAAGGATTTGCCTGG
TTATTCTATTATTATTATTCGGTTTATGCATCGTTTTGGTTTTGGATCCT
CGATTTCATATAATAGAAAGGATATTTGGTAAACCTTCAACGAAAAATCC
AAATCCACATAATTCCAGAAACCCAACTGATTCGGAACTTACTCCGCTAA
ATCCAACTGATTCAAGTGGAGAAATGTCAACTTTAATGAACACGAAGTTT
GAAAACTTAGAAAGAATTGTCTCATCTTTATCAGGAAGCTTGTCAAATTT
AAATATAAAGATGGACGAAATCATAGAGAAGACTTTACCAGAGACCGTTA
CAGCGAATGTACCAGAGACCGTTACAGTGAATGCATCGGTTATGGAGAAC
TGCTAAATCAACGAATGATATTATACAAATTTGTGCCAGTGAATAAATGG
ATTCTTAGTTGTTTTTTAAATTATTTAATTTGATATTATTAATCGGGTGA
AAAGCCAATAGGAAGAGGAGAGCCCCAGTATAAGTCCCTCAATGAGACAC
AAGGCATTACTGACGCTTTGCCATGAGGGGTCTTGGCCAAAATTGCGCAC
ACTGGTTGTTCTTTCAGAATTGCTCGCGATTGAGGGTAAAAGAAGAACCA
ACGCTCTAAAATTACTTCTTGATATTTATCTGTAAACAATTTCCTTCTTT
GATTTTACTGAACTTGTC
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protein sequence of SMED30027913-orf-1

>SMED30027913-orf-1 ID=SMED30027913-orf-1|Name=SMED30027913-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=343bp
MFLLIYFYMLFNPVCSENQLSKCLGTHPFRQSDSTCSSFEEVCMKKDNEE
CANFMNTCKQCPPSNYTILMLSGMLAVSKSQQKSTNSTLVKLESMTNEIE
ALKNLSKNLNLSMIQDEIEALKNLSKNLNLSMIQDEIEALKNLSKNLNLS
MIQDCKTLQKIPTQSASEKKRTKQSNNPFRKTHQPNPRYQNSSTIIDQLQ
LIESQPKSINQDEVPGPSHPRICLVILLLLFGLCIVLVLDPRFHIIERIF
GKPSTKNPNPHNSRNPTDSELTPLNPTDSSGEMSTLMNTKFENLERIVSS
LSGSLSNLNIKMDEIIEKTLPETVTANVPETVTVNASVMENC*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0002089reproductive organ