SMED30005835

Overview
NameSMED30005835
Smed IDSMED30005835
Length (bp)579
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 SMED30005835 (SMED30005835) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30005835 (SMED30005835) 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 SMED30005835 (SMED30005835) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30005835 (SMED30005835) 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




SMED30005835

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30005835SMESG000012702.1 SMESG000012701.1 SMESG000012690.1 SMESG000012688.1 SMESG000012672.1 dd_Smed_v4_55_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30005835SMESG000012702.1 SMESG000012701.1 SMESG000012690.1 SMESG000012688.1 SMESG000012672.1 dd_Smed_v4_55_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30005835SMESG000012702.1 SMESG000012701.1 SMESG000012690.1 SMESG000012688.1 SMESG000012672.1 dd_Smed_v4_55_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30005835SMESG000012702.1 SMESG000012701.1 SMESG000012690.1 SMESG000012688.1 SMESG000012672.1 dd_Smed_v4_55_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30005835SMESG000012702.1 SMESG000012701.1 SMESG000012690.1 SMESG000012688.1 SMESG000012672.1 dd_Smed_v4_55_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005835SMESG000012702.1 SMESG000012701.1 SMESG000012690.1 SMESG000012688.1 SMESG000012672.1 Contig50417newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005835SMESG000012702.1 SMESG000012701.1 SMESG000012690.1 SMESG000012688.1 SMESG000012672.1 Contig50417uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
tail regionSMED30005835SMESG000012702.1 SMESG000012701.1 SMESG000012690.1 SMESG000012688.1 SMESG000012672.1 dd_Smed_v6_55_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Category 3 cellSMED30005835SMESG000012702.1 SMESG000012701.1 SMESG000012690.1 SMESG000012688.1 SMESG000012672.1 dd_Smed_v6_55_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30005835SMESG000012702.1 SMESG000012701.1 SMESG000012690.1 SMESG000012688.1 SMESG000012672.1 dd_Smed_v4_55_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30005835 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.024405:7539..8069 +2451
v31.014026:5027..5533 +2446
v31.001937:104268..104776 +2440
v31.008383:12257..12763 +2437
v31.014150:448..954 +2401
v31.014208:21142..21644 -2398
v31.027002:6041..6547 +2347
v31.014150:10855..11361 +2320
v31.029225:5654..6153 +2294
Homology
BLAST of SMED30005835 vs. TrEMBL
Match: I1ZIF6 (Uncharacterized protein (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 149.828 bits (377), Expect = 1.258e-43
Identity = 74/75 (98.67%), Postives = 74/75 (98.67%), Query Frame = 3
Query:  276 STNATLKEKKFVGEIIGNVQCTINSVVCTAFYLGTDAVCLLAITDDTRDRCADVDQGIREKCTSLNDVCDWRNRG 500
            STNATLKEKKFVGEIIGNVQCTINSVVCTAFYLGTDAVCLLAITD TRDRCADVDQGIREKCTSLNDVCDWRNRG
Sbjct:   16 STNATLKEKKFVGEIIGNVQCTINSVVCTAFYLGTDAVCLLAITDATRDRCADVDQGIREKCTSLNDVCDWRNRG 90          
BLAST of SMED30005835 vs. Planmine SMEST
Match: SMESG000012672.1 (SMESG000012672.1)

HSP 1 Score: 152.525 bits (384), Expect = 3.579e-48
Identity = 75/75 (100.00%), Postives = 75/75 (100.00%), Query Frame = 3
Query:  276 STNATLKEKKFVGEIIGNVQCTINSVVCTAFYLGTDAVCLLAITDDTRDRCADVDQGIREKCTSLNDVCDWRNRG 500
            STNATLKEKKFVGEIIGNVQCTINSVVCTAFYLGTDAVCLLAITDDTRDRCADVDQGIREKCTSLNDVCDWRNRG
Sbjct:   15 STNATLKEKKFVGEIIGNVQCTINSVVCTAFYLGTDAVCLLAITDDTRDRCADVDQGIREKCTSLNDVCDWRNRG 89          
BLAST of SMED30005835 vs. Planmine SMEST
Match: SMESG000012702.1 (SMESG000012702.1)

HSP 1 Score: 150.214 bits (378), Expect = 3.010e-47
Identity = 74/75 (98.67%), Postives = 74/75 (98.67%), Query Frame = 3
Query:  276 STNATLKEKKFVGEIIGNVQCTINSVVCTAFYLGTDAVCLLAITDDTRDRCADVDQGIREKCTSLNDVCDWRNRG 500
            STNATLKEKKFVGEIIGNVQCTINSVVCTAFYLGTDAVCLLAITD TRDRCADVDQGIREKCTSLNDVCDWRNRG
Sbjct:   15 STNATLKEKKFVGEIIGNVQCTINSVVCTAFYLGTDAVCLLAITDATRDRCADVDQGIREKCTSLNDVCDWRNRG 89          
BLAST of SMED30005835 vs. Planmine SMEST
Match: SMESG000012701.1 (SMESG000012701.1)

HSP 1 Score: 137.887 bits (346), Expect = 1.744e-42
Identity = 68/75 (90.67%), Postives = 68/75 (90.67%), Query Frame = 3
Query:  276 STNATLKEKKFVGEIIGNVQCTINSVVCTAFYLGTDAVCLLAITDDTRDRCADVDQGIREKCTSLNDVCDWRNRG 500
            STNATLKEKK   EII NVQCTINSVVCTAFYLGTDAVCLLAITD TRDRCADVDQGIREKC SLND CDWRNRG
Sbjct:   15 STNATLKEKKLFKEIIENVQCTINSVVCTAFYLGTDAVCLLAITDATRDRCADVDQGIREKCASLNDACDWRNRG 89          
BLAST of SMED30005835 vs. Planmine SMEST
Match: SMESG000012688.1 (SMESG000012688.1)

HSP 1 Score: 137.887 bits (346), Expect = 1.882e-42
Identity = 68/75 (90.67%), Postives = 68/75 (90.67%), Query Frame = 3
Query:  276 STNATLKEKKFVGEIIGNVQCTINSVVCTAFYLGTDAVCLLAITDDTRDRCADVDQGIREKCTSLNDVCDWRNRG 500
            STNATLKEKK   EII NVQCTINSVVCTAFYLGTDAVCLLAITD TRDRCADVDQGIREKC SLND CDWRNRG
Sbjct:   15 STNATLKEKKLFKEIIENVQCTINSVVCTAFYLGTDAVCLLAITDATRDRCADVDQGIREKCASLNDACDWRNRG 89          
BLAST of SMED30005835 vs. Planmine SMEST
Match: SMESG000012690.1 (SMESG000012690.1)

HSP 1 Score: 112.849 bits (281), Expect = 1.978e-32
Identity = 55/60 (91.67%), Postives = 56/60 (93.33%), Query Frame = 3
Query:  321 IGNVQCTINSVVCTAFYLGTDAVCLLAITDDTRDRCADVDQGIREKCTSLNDVCDWRNRG 500
            + NVQCTINSVVCTAFYLGTDAVCLLAITD TRDRCADVDQGIREKC SLND CDWRNRG
Sbjct:    1 MENVQCTINSVVCTAFYLGTDAVCLLAITDATRDRCADVDQGIREKCASLNDACDWRNRG 60          
The following BLAST results are available for this feature:
BLAST of SMED30005835 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 SMED30005835 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 SMED30005835 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 SMED30005835 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 SMED30005835 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 SMED30005835 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 SMED30005835 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 SMED30005835 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZIF61.258e-4398.67Uncharacterized protein (Fragment) OS=Schmidtea me... [more]
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BLAST of SMED30005835 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 SMED30005835 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 SMED30005835 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 SMED30005835 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 SMED30005835 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 SMED30005835 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000012672.13.579e-48100.00SMESG000012672.1[more]
SMESG000012702.13.010e-4798.67SMESG000012702.1[more]
SMESG000012701.11.744e-4290.67SMESG000012701.1[more]
SMESG000012688.11.882e-4290.67SMESG000012688.1[more]
SMESG000012690.11.978e-3291.67SMESG000012690.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005835 ID=SMED30005835|Name=SMED30005835|organism=Schmidtea mediterranea sexual|type=transcript|length=579bp
TTAATGATCCGGCGCCCACCGAGTTCTACACTCTTCCCCTAGACGACGCT
CTTCCGATCTTGAAAACCAAAGCACTGTAGTAAAATATTTCTGTAAACAA
ATAAAAATATTGAAAACGTCAAGATAAACAAACCTACACAGAAAGCAGTC
CAGAACCAATTTCTAGAGGGCCCACTCAGTATTACCTAGAGCTATAAATT
GAGGTGAAAACTCAACTGTATTGTTGTTGAGAAATGAAATTTATTTGCAT
ATTTTTGTTGGCGCTCTGCATTCTATCAACCAATGCAACCTTAAAGGAAA
AGAAATTTGTCGGAGAAATTATAGGAAATGTTCAATGTACAATAAATAGT
GTGGTTTGTACTGCGTTCTATTTAGGAACCGATGCGGTCTGCCTGCTTGC
CATAACTGATGATACTCGAGATCGCTGTGCAGATGTCGACCAAGGAATAA
GGGAGAAATGTACCAGTCTCAATGATGTCTGCGACTGGAGAAACCGAGGT
TAAGCAAATGTATTCTTTCCTCGCTTTGTGATGCGTGAAATAAATTTTAA
TTTTTTAAAAAAAAAAAAAAAAAATGCGA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell
PLANA:0000421tail
PLANA:0002032epidermal cell
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..18
score: 0.866