SMED30032665

Overview
NameSMED30032665
Smed IDSMED30032665
Length (bp)1163
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 SMED30032665 (SMED30032665) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30032665 (SMED30032665) 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 SMED30032665 (SMED30032665) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30032665 (SMED30032665) 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




SMED30032665

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
protonephridiaSMED30032665SMESG000024489.1 dd_Smed_v4_5366_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30032665SMESG000024489.1 dd_Smed_v4_5366_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30032665SMESG000024489.1 dd_Smed_v4_5366_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30032665SMESG000024489.1 dd_Smed_v4_5366_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30032665SMESG000024489.1 dd_Smed_v4_5366_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30032665SMESG000024489.1 dd_Smed_v4_5366_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30032665SMESG000024489.1 dd_Smed_v4_5366_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30032665 vs. Planmine SMEST
Match: SMESG000039117.1 (SMESG000039117.1)

HSP 1 Score: 133.65 bits (335), Expect = 4.146e-37
Identity = 76/143 (53.15%), Postives = 105/143 (73.43%), Query Frame = -2
Query:  164 GAKISVIDKSLLQKFGIRNLEKFYVKLRCANESPIEILGKINVQVQIIGISKRKVVEFIVAKEISPKVIGGIDFLKTFNIMLKIGSTTSNNKSEINKLTDMAIVKNVXXXXXXXXXXXXXXKYDCIFMKHKLDIGKTTLLNHE 592
            GAKISVID+S+L   G  N+EK  VKLRCANESP+ I+GK+NV VQI+G S+ +++EFIV KEIS K+IGGIDFL+ F+IML + S+ S N   I ++  +    +  +Q +D+N+++L  KYD IF+KHK D+ KT L+ HE
Sbjct:   26 GAKISVIDESVLDNIGKFNIEKCLVKLRCANESPVSIVGKVNVAVQIVGTSETRMIEFIVDKEISLKLIGGIDFLRKFDIMLNMKSSLSTNDENIARIMHLK-ESSESNQCQDSNVRELCRKYDSIFIKHKWDVCKTNLITHE 167          

HSP 2 Score: 40.4318 bits (93), Expect = 4.146e-37
Identity = 18/36 (50.00%), Postives = 24/36 (66.67%), Query Frame = -3
Query:   64 TMKIFISGKPKVIIPRRQPAHLIGKIDEQINEMERF 171
            T +I  +G+P  I PR QP+HLI KI+E + EME  
Sbjct:  165 THEILTAGRPMAINPRLQPSHLIEKIEENLKEMENM 200          
BLAST of SMED30032665 vs. Planmine SMEST
Match: SMESG000012744.1 (SMESG000012744.1)

HSP 1 Score: 129.028 bits (323), Expect = 3.956e-36
Identity = 61/79 (77.22%), Postives = 67/79 (84.81%), Query Frame = -3
Query:  922 NFYQRSRPRFNDFIFQENNRRILKCWACQEEGHKRFEFPNVKCNHCYKKGHFRHQCFELRSNKERKYREKVVAIKQADD 1158
             FY+R RPR NDF FQENNRR LKCWACQE+GHKR E  NVKCNHCY+ GHFR+QCF+ RSNKER+YREKV AI QADD
Sbjct:   64 TFYERFRPRVNDFRFQENNRRTLKCWACQEKGHKRSECSNVKCNHCYESGHFRYQCFQPRSNKERQYREKVAAIPQADD 142          
BLAST of SMED30032665 vs. Planmine SMEST
Match: SMESG000053907.1 (SMESG000053907.1)

HSP 1 Score: 119.013 bits (297), Expect = 4.227e-31
Identity = 70/149 (46.98%), Postives = 92/149 (61.74%), Query Frame = -2
Query:  182 GAKISVIDKSLLQKFGIRNLEKFYVKLRCANESPIEILGKINVQVQIIGISKRKVVEFIVAKEISPKVIGGIDFLKTFNIMLKIGSTTS------------NNKSEINKLTDMAIVKNVXXXXXXXXXXXXXXKYDCIFMKHKLDIGKT 592
            GA I +ID+S+L   G  N+EK  VKLRCA ESP+ I+GK+NV VQI+G  + +++EFIVAKEISPK+IGGIDFL+ FNIML   S+ S             + SE N+  DM + +             L  KY+  F+KHK D+GKT
Sbjct:   99 GANICMIDESILDNIGKFNIEKCLVKLRCAIESPVLIVGKVNVAVQIVGTRQTRMIEFIVAKEISPKLIGGIDFLRKFNIMLHTKSSLSKKDENIAGIMHLKSPSESNQCKDMNVRE-------------LCSKYESNFLKHKWDVGKT 234          
BLAST of SMED30032665 vs. Planmine SMEST
Match: SMESG000033246.1 (SMESG000033246.1)

HSP 1 Score: 115.931 bits (289), Expect = 3.899e-28
Identity = 58/95 (61.05%), Postives = 73/95 (76.84%), Query Frame = -2
Query:  308 GAKISVIDKSLLQKFGIRNLEKFYVKLRCANESPIEILGKINVQVQIIGISKRKVVEFIVAKEISPKVIGGIDFLKTFNIMLKIGSTTSNNKSEI 592
            GAKISVID+S+L   G  N+EK  VKLRCANESP+ I+ K+N+ VQI+G  + +++EFIVAKEISPK+IGGIDFLK F+IML + S  S N   I
Sbjct:  312 GAKISVIDESVLNNIGKFNIEKLLVKLRCANESPVSIVPKVNIAVQIVGTRETRMIEFIVAKEISPKLIGGIDFLKKFDIMLNMESKLSKNDENI 406          

HSP 2 Score: 92.4337 bits (228), Expect = 3.278e-20
Identity = 51/123 (41.46%), Postives = 71/123 (57.72%), Query Frame = -3
Query:  832 FNDFIFQENNRRILKCWACQEEGHKRFEFPNVKCNHCYKKGHFRHQCFEL-----------------------RSNKERKYREKVVAIKQADDENESQYQNGYAPLQEKVIRALQ*M*VMYEW 1131
            FN+ I Q NN+   KCW C EEGH+RFE PNVKC+HC+K  HF+H+CF+                        R+N++R+Y+  V A+   ++E+ +QY NGY  L+EKVI AL      +EW
Sbjct:  140 FNNKIVQRNNQPKFKCWVCFEEGHRRFECPNVKCHHCHKAEHFKHRCFQRTEKWIEVRENDQEYKRAKFQGNDRNNRDRQYQRPVAAMDDDEEEHGNQYPNGYDQLREKVIGAL------HEW 256          
BLAST of SMED30032665 vs. Planmine SMEST
Match: SMESG000029259.1 (SMESG000029259.1)

HSP 1 Score: 59.6918 bits (143), Expect = 7.472e-20
Identity = 29/51 (56.86%), Postives = 36/51 (70.59%), Query Frame = -3
Query:   13 KIFISGKPKVIIPRRQPAHLIGKIDEQINEMERFGIIKECNSPWNRP*VCV 165
            KI   G+P +I PRRQP +L  KI+E I  +E  GII++CNSPWN P VCV
Sbjct: 2720 KIITKGEPIMIKPRRQPINLEDKIEEAIKNLENNGIIRKCNSPWNTPLVCV 2770          

HSP 2 Score: 56.225 bits (134), Expect = 7.472e-20
Identity = 51/156 (32.69%), Postives = 85/156 (54.49%), Query Frame = -2
Query:  167 GAKISVIDKSLLQKFGIRNLEKFYVK--LRCANESPIEILGKINVQVQIIGISKRKVVEFIVAKEISPKVIGGIDFLKTFNIMLKIGSTTSNNKSEI---------NKLTDMAIVKNVXXXXXXXXXXXXXXKYDC---IFMKHKLDIGKTTLLNH 592
            GA+I+V+ KS++ +  + N+E    +  LRCAN S +E +GK+N+ V+ +G  +R V  FI+ K + P++IGG++  + F I LK        +S+            +TD   +++  D LK    K+LL+ +     +FM  K DIG T L+ H
Sbjct: 2568 GARINVMAKSVIDR--LENIEILETRESLRCANNSRLETMGKLNINVK-MGSMERNVT-FIIVKNLIPEIIGGVELQRLFGIELKCILEEHEKRSDFICEIEARFGRIITDEERLRHAIDVLKVTGNKRLLEIFQANKNVFMADKWDIGCTNLIKH 2719          
The following BLAST results are available for this feature:
BLAST of SMED30032665 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 SMED30032665 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 SMED30032665 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 SMED30032665 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 SMED30032665 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 SMED30032665 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 SMED30032665 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 SMED30032665 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 SMED30032665 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 SMED30032665 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 SMED30032665 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 SMED30032665 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 SMED30032665 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 SMED30032665 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000039117.14.146e-3753.15SMESG000039117.1[more]
SMESG000012744.13.956e-3677.22SMESG000012744.1[more]
SMESG000053907.14.227e-3146.98SMESG000053907.1[more]
SMESG000033246.13.899e-2861.05SMESG000033246.1[more]
SMESG000029259.17.472e-2056.86SMESG000029259.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30032665 ID=SMED30032665|Name=SMED30032665|organism=Schmidtea mediterranea sexual|type=transcript|length=1163bp
ATTTTTATTTTTGACACATACTTACGGTCTGTTCCACGGGGAATTACATT
CTTTTATTATGCCAAACCTTTCCATTTCATTAATCTGTTCATCAATTTTT
CCTATCAAATGAGCGGGCTGTCGCCTAGGGATAATGACTTTAGGTTTACC
TGAAATAAAAATTTTCATGGTTTAACAAAGTTGTTTTTCCTATATCCAAT
TTGTGTTTCATAAAAATGCAATCATATTTATCCAACAATTTTTTAATATT
ATTATCTTTCAGTTGATCATCTACATTTTTCACTATTGCCATATCTGTCA
ATTTATTTATTTCACTTTTATTATTACTAGTAGTGCTTCCAATTTTTAAC
ATAATATTAAACGTTTTCAAAAAATCTATTCCTCCAATAACTTTAGGAGA
TATCTCTTTAGCTACAATAAATTCGACAACTTTCCTTTTCGATATTCCAA
TAATTTGCACTTGCACATTAATTTTCCCCAATATTTCAATAGGTGATTCA
TTTGCACATCTTAATTTCACATAAAATTTCTCTAAATTTCTAATTCCAAA
CTTTTGTAGCAAACTTTTATCAATCACACTTATTTTTGCGCCCTAACCTA
CCCTAACCCATTTAATTTATAGTATTAATTATTTAAATTATTATTATCAT
TAATTATACAAAAATATTCATCGAAATTTAAATTTTCCTCATTATTACAT
CCTAAATCATCCATTCTCCATTTATCAACACACCAATCACTATACGCGTT
CGAGTCTAACCAACAATCACAACTATTATCTAAAGGTTTAATTTTTTATC
ATTCACAGCATACAAACAATCATAAATCATCCCATTCATACATTACTTAC
ATTTACTGTAGAGCTCTGATCACCTTCTCTTGTAATGGAGCATATCCGTT
TTGGTATTGACTTTCATTTTCATCATCAGCTTGCTTGATTGCTACCACTT
TTTCTCGATATTTTCGTTCTTTGTTTGAGCGAAGCTCGAAGCACTGGTGA
CGAAAGTGTCCTTTTTTATAGCAATGATTGCATTTTACATTTGGGAATTC
AAATCTCTTATGCCCTTCTTCTTGACAAGCCCAACATTTTAAAATTCGTC
TATTATTTTCCTGAAATATAAAATCGTTAAATCTGGGTCGAGATCTTTGA
TAAAAATTATTGG
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protein sequence of SMED30032665-orf-1

>SMED30032665-orf-1 ID=SMED30032665-orf-1|Name=SMED30032665-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=103bp
NNFYQRSRPRFNDFIFQENNRRILKCWACQEEGHKRFEFPNVKCNHCYKK
GHFRHQCFELRSNKERKYREKVVAIKQADDENESQYQNGYAPLQEKVIRA
LQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000101muscle cell
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR001878Znf_CCHC
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0008270zinc ion binding