SMED30007857

Overview
NameSMED30007857
Smed IDSMED30007857
Length (bp)2627
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 SMED30007857 (SMED30007857) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30007857 (SMED30007857) 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 SMED30007857 (SMED30007857) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30007857 (SMED30007857) 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




SMED30007857

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30007857h1SMcG0022147 SmedASXL_000639SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30007857h1SMcG0022147 dd_28465dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult fluorescence in situ hybridization evidence
neuronSMED30007857h1SMcG0022147 dd_28465dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult fluorescence in situ hybridization evidence
head marginSMED30007857h1SMcG0022147 dd_28465dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult fluorescence in situ hybridization evidence
nervous systemSMED30007857h1SMcG0022147 dd_Smed_v4_28465_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30007857h1SMcG0022147 dd_Smed_v4_28465_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30007857h1SMcG0022147 dd_Smed_v4_28465_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30007857h1SMcG0022147 dd_Smed_v4_28465_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30007857h1SMcG0022147 dd_Smed_v6_28465_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
SMED30007857 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001816:54730..58165 +12688
Homology
BLAST of SMED30007857 vs. Planmine SMEST
Match: SMESG000022810.1 (SMESG000022810.1)

HSP 1 Score: 234.572 bits (597), Expect = 1.477e-70
Identity = 113/125 (90.40%), Postives = 117/125 (93.60%), Query Frame = 2
Query: 1136 WLEFTILQIVSSNSQLKISDAEIVCSSFNMELPIFQDESDYLDFKMALNQASLNRVWINMTVAKPIDYKGFTRPPIIYWFNNISTYYPNILWDCTSDNCMAFDLPSNSFKSDKCTSTLNYLCMSS 1510
            +L    L I+ +  QLKISDAEIVCSSFNMELPIFQDESDYLDFKMALNQASLNRVWINMTVAKPIDYKGFTRPPIIYWFNNISTYYPNILWDCTSDNCMAFDLPSNSFKSDKCTSTLNYLCMS+
Sbjct:  128 YLCLLTLLIIHTKCQLKISDAEIVCSSFNMELPIFQDESDYLDFKMALNQASLNRVWINMTVAKPIDYKGFTRPPIIYWFNNISTYYPNILWDCTSDNCMAFDLPSNSFKSDKCTSTLNYLCMSN 252          

HSP 2 Score: 105.916 bits (263), Expect = 5.863e-25
Identity = 54/134 (40.30%), Postives = 77/134 (57.46%), Query Frame = 2
Query: 1166 SSNSQLKISDAEIVCSSFNMELPIFQDESDYLDFKMALNQASLNRVWINMTVAKPIDYKGFTRPPIIYWFNNISTYYPNILWDCTSDNCMAFDLPSNSFKSDKCTSTLNYLCMSSK**RYLLQSLNLTVLYTIC 1567
            S  + ++   A   C +  +ELP+F + +DYL+ K  +  A L+RVWINMTV +P    G   P  I W  N S YY +I WDC  +NCM ++L S+SFK  KCTS++NYLC+           L L +++T C
Sbjct:   19 SLGAAVQFPQAATACLNQQLELPMFFNNNDYLNLKTQMTTAKLDRVWINMTVLQPTAVTGKVPPQTIIWALNASQYYGSISWDCNQENCMTYELSSDSFKDYKCTSSMNYLCL-----------LTLLIIHTKC 141          
The following BLAST results are available for this feature:
BLAST of SMED30007857 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 SMED30007857 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 SMED30007857 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 SMED30007857 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 SMED30007857 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 SMED30007857 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 SMED30007857 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 SMED30007857 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 SMED30007857 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 SMED30007857 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 SMED30007857 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 SMED30007857 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 SMED30007857 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 SMED30007857 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000022810.11.477e-7090.40SMESG000022810.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007857 ID=SMED30007857|Name=SMED30007857|organism=Schmidtea mediterranea sexual|type=transcript|length=2627bp
ATGCATACATAAATCACACCTTTGTCATTCAGACATACATTACATAATCA
TCAGTCATACAAATTCAACAAACACATACATATATATTATATATATTATA
TTATTTAGAATATCTATTATTTAATGTTATCCTACAGTGTGTAAATAGAA
CTCTAACATAGACAGATAGAAAAGGTAAGTGAGAGAAGAGAAATAAATAA
CTGCACACAAGCATGGTGTACTTTAAATATTAATTGTATACATTGTTGAT
GGTGGCTGAGTTTTTAGTCTTTGGAGGTCTTACAATTACAATTTAATACA
AATTTGAAACACTAAAAGGTAAAATCAAATGTTTCTTGGTATACAAAAAG
TAAAGAAAAATAAAAATTCATTTATTAGCATTGACAGCCTTGAAATTAGG
TCATCGGTAGAGGAAAAATTAATTGGTTGAAGTGTCACTAATTCCAGGTA
CAAACCAATAAAATAATAGTGACAGAGTTAAAAAAATATAATACAAATAT
CAATGTAATTCGCTATTTGTAAGTAAAAACCTTTCGTTCTAACAATAAAT
TGACATCCGTACGTGGTGAACTCGCTCAAAGCAATTAATAGCGAATTGGC
ATGTTATTTTAATATAACTTGTTGGTAGAACACCCAACCTAGCTAAGAGC
AAACAACGTGCAATGCACGACACATCGACTTTGGTACAGATTGTTGTCGA
CGTGCATAGCACGTCATTTCAGCATAAATGAATAAAAAGAATGAAAAGAT
GATAAAAGAATTTACTTATATATCAGAGCATTAAATCTATTAATAAAATG
GCACAATGTTTCCCAAACCAAATAGAAAGAAACGAAGAATGTTATTACTA
TCTCGAAACTTTACATAACACTGAAATTGTGCTAAGCCTGCAGTAATTTG
AAGAACCTTTATGTCAGTTATTATCTGATATAATAACCCCCCCTCCTCCT
TAACCTCATTCAAAATTACACGTACTGCATTGGCAAATGAAATGATTGCT
ATCATCTGTCTGAAAGAGAATTCCATATAATAATTTCCCAAGAGTATTTT
CAACATAAATATATATTAAAATGACATCAAGTTGGTAAAGTTATTCCGAA
AATTCACAATCTTCATGATAAAATTAATTTTCATTTGGTTAGAATTTACA
ATTTTGCAAATAGTTTCTTCTAACAGCCAACTGAAAATTTCTGACGCTGA
GATAGTTTGCTCTTCTTTTAATATGGAGTTGCCCATTTTCCAGGATGAAT
CCGATTATCTCGATTTCAAAATGGCTCTTAATCAAGCAAGTTTAAATCGA
GTTTGGATCAACATGACAGTTGCTAAACCAATAGATTATAAAGGATTTAC
TCGACCTCCAATTATTTACTGGTTCAACAATATTTCCACGTATTATCCGA
ACATCCTTTGGGATTGTACGTCCGATAATTGTATGGCATTTGACTTGCCA
AGTAATTCTTTCAAAAGTGATAAATGTACATCTACATTGAATTACCTCTG
CATGTCAAGTAAGTAATAAAGGTATCTTTTGCAATCACTAAATCTCACTG
TTTTATACACAATTTGTTTCAATTATGAGGATTGGGATGTTCTTTATACT
TTCACTTAATTTTACCCACAGAAAGATTCTATAACCAGGAATCTAAAAAC
CTTTCTACCGTATTGGAAATGTTTAGACTTACCTAGGAAAATTGAGAAAA
GTTTAACCCATGAAACAAACTACCAAAATTCTTCAAATATTGAAAAGATG
TTACTTATTCTTTATTCTGTAGAGAAAAAATTAACAGAATTAAAATTACA
AATAATAAATGAAGAAAAGAGAACTTGAAAAAAATCAATGATGATAAAAA
CAAAATATTTTACTCAGAGATGAGAATTATATAAAATAATGTATTAAAAA
ATGTACAGAAGACCGTTTAATTTAAAATATCGTGAAAAAAATGCATTTTA
ATAATTATTTAATAAGCTTCAACACTGCATAGCATTTTTTACAATATTCT
TACAAAAGCAATATTAACTATATTTAACCCAGTTTTCAGTTGAATTTTGT
CTATCTAAGTACCTAAGACTAATTATTTCACATATGCAACAGCAGTTACA
ATTTAATATTCTACATTCATTTTTAACAACCACTTAGAAAGGTTTGTTTT
TTGTGAAGTTTTATGTCAGTCGTATTTTAATTATGTTTGGAGTGTTAATC
CCATCAAGCAGGTATTTTTTCTGCTTCTACTATTGGCTATTATACGAATA
TATTGTTTGGATATATTTTTAATCACTAAAAGAGTTTCATTTTATGTGCC
TGCTACTGCAAAAGCCAAGAAATTATAAAATATATTTTTATCACATACTT
TAACTAAGATATATCTGTTGTGAAATTATTTCCTCATACCTAAAAGGGTA
AAGATGACTTTTCAATAGAAATGCTTGATTTTCCCATTTCATGTGATTCA
AAATAAATGAAATTTACAACAGTATTTAAAACATTTATTTCAACATATGT
GCAAATAAAGTGACTGGCAATTTAATTAAACATTTCATATTTCTTTTATT
CACAATCCAGATGCAATTCACGCAAAATGAACGAAATCTTTCCTTATCAT
AAAAAATAACTAATATTCTGAAACAGC
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protein sequence of SMED30007857-orf-1

>SMED30007857-orf-1 ID=SMED30007857-orf-1|Name=SMED30007857-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=134bp
MIKLIFIWLEFTILQIVSSNSQLKISDAEIVCSSFNMELPIFQDESDYLD
FKMALNQASLNRVWINMTVAKPIDYKGFTRPPIIYWFNNISTYYPNILWD
CTSDNCMAFDLPSNSFKSDKCTSTLNYLCMSSK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000418head
PLANA:0000420parapharyngeal region
PLANA:0007561head margin
Vocabulary: INTERPRO
TermDefinition
IPR016186C-type_lectin-like/link_sf
IPR016187CTDL_fold
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR016186C-type lectin-like/link domain superfamilyGENE3DG3DSA:3.10.100.10coord: 8..133
e-value: 3.7E-7
score: 32.1
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..19
score: 0.694
IPR016187C-type lectin foldSUPERFAMILYSSF56436C-type lectin-likecoord: 20..129