SMED30021417

Overview
NameSMED30021417
Smed IDSMED30021417
Length (bp)1980
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 SMED30021417 (SMED30021417) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021417 (SMED30021417) 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 SMED30021417 (SMED30021417) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021417 (SMED30021417) 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



SMED30021417

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30021417h1SMcG0009693 Contig35249newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30021417h1SMcG0009693 Contig35249uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30021417 Contig18766newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30021417 Contig18766uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
reproductive organSMED30021417h1SMcG0009693 Contig47021newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30021417 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004539:34117..36155 +8966
v31.001962:67407..69590 +8051
v31.018242:3069..5569 +6305
Homology
[Close]
BLAST of SMED30021417 vs. Planmine SMEST
Match: SMESG000051915.1 (SMESG000051915.1)

HSP 1 Score: 92.4337 bits (228), Expect = 9.776e-23
Identity = 66/69 (95.65%), Postives = 66/69 (95.65%), Query Frame = 3 
Query:  171 MDCGIVELLDYGACQTVCNAGYVACLAXXXXXXXXXXXXXXXXXTVLPCSSAKEACMAACSTACAVAPV 377
            MDCGIVELLDYGACQTVCNAGYVACLASLG PAGVPSVVVGA PTVLPCSSAKEACMAACSTACAVA V
Sbjct:    1 MDCGIVELLDYGACQTVCNAGYVACLASLGSPAGVPSVVVGAPPTVLPCSSAKEACMAACSTACAVAAV 69
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BLAST of SMED30021417 vs. Planmine SMEST
Match: SMESG000051904.1 (SMESG000051904.1)

HSP 1 Score: 71.2478 bits (173), Expect = 4.216e-15
Identity = 49/72 (68.06%), Postives = 55/72 (76.39%), Query Frame = 3 
Query:  117 MLLRFTTVFFVLAGCINQMDCGIVEL-LDYGACQTVCNAGYVACLAXXXXXXXXXXXXXXXXXTVLPCSSAK 329
            MLLRFTTV FVLA C NQMDCG+V L + Y ACQ+ CNAGYVACLASLG  AG  +   GALP VL CS+A+
Sbjct:    1 MLLRFTTVVFVLADCFNQMDCGVVGLAVGYSACQSACNAGYVACLASLGLTAGALTAGAGALPAVLACSAAQ 72
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BLAST of SMED30021417 vs. Planmine SMEST
Match: SMESG000051914.1 (SMESG000051914.1)

HSP 1 Score: 60.077 bits (144), Expect = 3.326e-11
Identity = 25/44 (56.82%), Postives = 34/44 (77.27%), Query Frame = 3 
Query:  120 LLRFTTVFFVLAGCINQMDCGIVELLDYGACQTVCNAGYVACLA 251
            ++R   VF ++A   NQ++CGI+ +L YGACQ+VCNAGYVACL 
Sbjct:    1 MIRIAIVFIIVASSFNQINCGILGILGYGACQSVCNAGYVACLG 44
[Close]
BLAST of SMED30021417 vs. Planmine SMEST
Match: SMESG000051918.1 (SMESG000051918.1)

HSP 1 Score: 59.6918 bits (143), Expect = 5.688e-11
Identity = 25/42 (59.52%), Postives = 33/42 (78.57%), Query Frame = 3 
Query:  120 LLRFTTVFFVLAGCINQMDCGIVELLDYGACQTVCNAGYVAC 245
            ++R   VF +LA   NQ++CGI+ +L YGACQ+VCNAGYVAC
Sbjct:    1 MIRIAIVFIILASSFNQINCGILGILGYGACQSVCNAGYVAC 42
[Close]
BLAST of SMED30021417 vs. Planmine SMEST
Match: SMESG000051944.1 (SMESG000051944.1)

HSP 1 Score: 46.595 bits (109), Expect = 1.945e-6
Identity = 30/78 (38.46%), Postives = 42/78 (53.85%), Query Frame = 3 
Query:  126 RFTTVFFVLAGCINQMDCGIVELLDYGACQTVCNAGYVACLAXXXXXXXXXXXXXXXXXTVLPCSSAKEACMAACSTA 359
            +   V  +LAG  NQ +C  + + D+  CQT CN  Y  CL SLG  AG  +     +P ++ CSS+  AC+A C  A
Sbjct:    3 KIIFVLVILAGLFNQKNCKKIGIFDFSPCQTWCNLSYYTCLGSLGLAAGALTAGTVTIPALMVCSSSHGACVADCPVA 80
The following BLAST results are available for this feature:
BLAST of SMED30021417 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 SMED30021417 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 SMED30021417 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 SMED30021417 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 SMED30021417 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 SMED30021417 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 SMED30021417 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 SMED30021417 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 SMED30021417 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 SMED30021417 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 SMED30021417 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 SMED30021417 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 SMED30021417 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 SMED30021417 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000051915.19.776e-2395.65SMESG000051915.1[more]
SMESG000051904.14.216e-1568.06SMESG000051904.1[more]
SMESG000051914.13.326e-1156.82SMESG000051914.1[more]
SMESG000051918.15.688e-1159.52SMESG000051918.1[more]
SMESG000051944.11.945e-638.46SMESG000051944.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021417 ID=SMED30021417|Name=SMED30021417|organism=Schmidtea mediterranea sexual|type=transcript|length=1980bp
TAATAACTATTATAGAAAGCCAGTGAAATAATAGAAATAATAATTTGGAA
CAGTTTGTGAATAGTTTAAAAATTTTACTATAAAATAGAACATTTTTTTT
CATTATTTCATTGAAAATGTTACTACGATTTACAACTGTATTTTTTGTTC
TTGCAGGATGTATTAATCAAATGGATTGTGGCATAGTAGAACTTCTGGAT
TATGGCGCATGCCAGACTGTCTGCAATGCCGGATATGTCGCATGCTTAGC
GTCATTGGGACCACCCGCAGGAGTACCTAGTGTTGTAGTTGGAGCACTTC
CGACAGTTTTGCCTTGCTCCTCTGCCAAAGAAGCGTGTATGGCAGCTTGT
TCAACCGCATGTGCAGTAGCTCCTGTATAAACTATAATTTCGAAAACAAG
AAACTTTATCTATATTTTACAAAATGAGTTTTTATCATTTTATGATTGCA
AAGGTTTTCGTTAAATAAAAGCTGACTTACTCATTTTTGTTACCACTCTG
TAATAAGTTTCTCCAGAACTTATTACGGAAATGTAACAGATCCTTTTAGG
GTATATCCATAGGCATAATTGCCATTATGCTGTGCATATACCTAATGATT
TGAAATTGCAGATGGAGGGGACAAAGGATGTTGAATAGGATTATTCTCTC
CCGTCCAACTACACAAATTTCATAACTTTTATTATAGACTTTAGATTGGT
ATTGTTTTAGGCTCAAATGGCACGACCAATGGCATCACTCAATTATTGCG
ATTGGTCAAAATTAAAATTAAACATTGGCTGAAACCAGAAATTGAATGTT
TATTTTGTCATTTAATGACAACTGGAAATTAATAATAATAGAATAATATA
TTCCAATAGCAAAGTCATTGTCTAAGAATTATTTTTGAAATTCTACAGTT
TGAAAGAATTTAAAATTTCCCCCTTTTACTTACCTATTAAATCTATTATT
ATGGAATAAACTCAGAAAACGTTGGACATCTAATATCTGGTCATTTATTC
TTTGTATGTCTTGTTATGTACACTGAGATTTCGCAGGGGATCTTGTGACA
ATCTCCCTTTATATGAAATTGAATCTCAAACTGTAATTACATTTAAACAG
ATTATACTAATTATTTAATTATTTAATTATTCAATCCAAAACGAGATAGC
TCCATAAAAAAGGTCTCACATCATACTTGTAATCAAGAATTAGATATTAT
AACAAAGAAGAATTTCTCACTTCAATGCTTGCACGCTGTTCTTGTCAACT
AAATTTCTTCAACCACTTTGGCAAATTGACTAAAATATATAATTTTTCAT
AGAGCTCAAGCCTCATCTATCAATTAATCTCGACTAAACAGTCTGCCAAT
TTACCTGTCAAACTTAGAGATTTTGTTTACTAATTGAATTGATTAATTCT
TATCAACAAATTAATTATTCTGCATTTCTTAAATAATATTGCTTAGGGAC
TCCCATTTTTTTATAAATAAATATTTATACTCGTTTAAGTTACAAATTCG
TAATAAAATTGTCCGTAACTTATTATGGAAATGTAAAATTTCTTTATTGA
GTAATATTTATTACACTTTGCCTACATTTTTATTGGCGCTAGGAAATGCT
TGTTATTTCCGGTTCCCTTTCTACAGGCTTAGCCCGCATTAATTGCCCGT
CTATGACAATCTGTATAACGTTTCTCATAACGGCTTAGGCCGTTTCTTTT
AATGAATATATTTATAAATTATTAAAATAAAAAATTTATTCCTGAGATTA
ATATAATGTTTAAATGCTGACTTGAAGACCCCCTTTTCCATTTTACTCGG
TTTTTATTTGTATTTTTTAAAGAAAAATCGGCATTAAATTTGCTTGAAAC
TCAAGCTGTTTTAAAGAAAAAGAATTTGAAGTCTTTTTAAGAACTTCTAA
TTTCAGGAGATATATTATATTTTATTTGAAATAATTTTATTAAATTAATA
TTAAATTTTATTTTTATTAATATGAAATAG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000106ciliated epithelial cell
PLANA:0002032epidermal cell
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availablePROSITEPS51257PROKAR_LIPOPROTEINcoord: 1..15
score: 5.0
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..21
score: 0.665