SMED30017150

Overview
NameSMED30017150
Smed IDSMED30017150
Length (bp)515
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 SMED30017150 (SMED30017150) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30017150 (SMED30017150) 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 SMED30017150 (SMED30017150) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30017150 (SMED30017150) 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



SMED30017150

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
posterior sideSMED30017150 dd_Smed_v4_5666_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30017150 dd_Smed_v4_5666_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
[Close]
BLAST of SMED30017150 vs. Ensembl Fly
Match: QIL1 (gene:FBgn0036726 transcript:FBtr0075220)

HSP 1 Score: 48.521 bits (114), Expect = 1.511e-7
Identity = 30/97 (30.93%), Postives = 49/97 (50.52%), Query Frame = 1 
Query:  145 VGGFMYMTYKCGVWSDNDSSRSSFNTLRHSI------IAKSC--DIPS--RAGEIKEAAKACWNGGVNYTFDHISRSPEYAKKGIEYVKHKAKDF*Q 405
            V   +Y T K G+W D+D +   +N ++  +      + K    ++P   + GE++  AK  +N GV  TF  I   P YA +G++ VK   +DF Q
Sbjct:   12 VAATVYYTQKVGIWGDSDQTDKLYNDIKSELRPHVQKLEKQLPFEVPQLPKTGEMRFLAKHYYNEGVKNTFRFIHMLPCYAGRGLKKVKDTFQDFAQ 108
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BLAST of SMED30017150 vs. UniProt/SwissProt
Match: sp|Q9VVH3|MIC13_DROME (MICOS complex subunit MIC13 homolog QIL1 OS=Drosophila melanogaster OX=7227 GN=QIL1 PE=2 SV=1)

HSP 1 Score: 48.521 bits (114), Expect = 1.515e-6
Identity = 30/97 (30.93%), Postives = 49/97 (50.52%), Query Frame = 1 
Query:  145 VGGFMYMTYKCGVWSDNDSSRSSFNTLRHSI------IAKSC--DIPS--RAGEIKEAAKACWNGGVNYTFDHISRSPEYAKKGIEYVKHKAKDF*Q 405
            V   +Y T K G+W D+D +   +N ++  +      + K    ++P   + GE++  AK  +N GV  TF  I   P YA +G++ VK   +DF Q
Sbjct:   12 VAATVYYTQKVGIWGDSDQTDKLYNDIKSELRPHVQKLEKQLPFEVPQLPKTGEMRFLAKHYYNEGVKNTFRFIHMLPCYAGRGLKKVKDTFQDFAQ 108
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BLAST of SMED30017150 vs. TrEMBL
Match: A0A2T7PKV7 (MICOS complex subunit MIC13 OS=Pomacea canaliculata OX=400727 GN=C0Q70_05296 PE=3 SV=1)

HSP 1 Score: 54.299 bits (129), Expect = 2.330e-6
Identity = 34/107 (31.78%), Postives = 54/107 (50.47%), Query Frame = 1 
Query:   76 NLNKFLKMPAILKFLNNSAKLFAVGGFMYMTYKCGVWS-DNDSSRSSFNTLRHSIIAKSCD----IPSRAGEIKEAAKACWNGGVNYTFDHISRSPEYAKKGIEYVK 381
             L K L   A++    N AK+    G +Y+T + G+WS D        N++R S++  + +    IPS A ++  +A   WN GV   F+ ++  PEY KK + Y K
Sbjct:   10 TLKKILSGQAVI----NLAKVGVGAGAIYVTIQQGIWSTDTKQGYQVLNSVRSSVLPTASEYVSKIPS-AEQMCISATQTWNKGVTKVFEGVAEVPEYGKKVVTYTK 111
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BLAST of SMED30017150 vs. Planmine SMEST
Match: SMESG000072322.1 (SMESG000072322.1)

HSP 1 Score: 211.846 bits (538), Expect = 8.021e-72
Identity = 100/101 (99.01%), Postives = 101/101 (100.00%), Query Frame = 1 
Query:   97 MPAILKFLNNSAKLFAVGGFMYMTYKCGVWSDNDSSRSSFNTLRHSIIAKSCDIPSRAGEIKEAAKACWNGGVNYTFDHISRSPEYAKKGIEYVKHKAKDF 399
            MPAILKF+NNSAKLFAVGGFMYMTYKCGVWSDNDSSRSSFNTLRHSIIAKSCDIPSRAGEIKEAAKACWNGGVNYTFDHISRSPEYAKKGIEYVKHKAKDF
Sbjct:    1 MPAILKFMNNSAKLFAVGGFMYMTYKCGVWSDNDSSRSSFNTLRHSIIAKSCDIPSRAGEIKEAAKACWNGGVNYTFDHISRSPEYAKKGIEYVKHKAKDF 101
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BLAST of SMED30017150 vs. Planmine SMEST
Match: SMESG000072322.1 (SMESG000072322.1)

HSP 1 Score: 207.223 bits (526), Expect = 5.513e-70
Identity = 100/102 (98.04%), Postives = 101/102 (99.02%), Query Frame = 1 
Query:   97 MPAILKFLNNSAKLFAVGGFMYMTYKCGVWSDNDSSRSSFNTLRHSIIAKSCD-IPSRAGEIKEAAKACWNGGVNYTFDHISRSPEYAKKGIEYVKHKAKDF 399
            MPAILKF+NNSAKLFAVGGFMYMTYKCGVWSDNDSSRSSFNTLRHSIIAKSCD IPSRAGEIKEAAKACWNGGVNYTFDHISRSPEYAKKGIEYVKHKAKDF
Sbjct:    1 MPAILKFMNNSAKLFAVGGFMYMTYKCGVWSDNDSSRSSFNTLRHSIIAKSCDVIPSRAGEIKEAAKACWNGGVNYTFDHISRSPEYAKKGIEYVKHKAKDF 102
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BLAST of SMED30017150 vs. Planmine SMEST
Match: SMESG000072322.1 (SMESG000072322.1)

HSP 1 Score: 197.208 bits (500), Expect = 3.952e-66
Identity = 93/94 (98.94%), Postives = 94/94 (100.00%), Query Frame = 1 
Query:  118 LNNSAKLFAVGGFMYMTYKCGVWSDNDSSRSSFNTLRHSIIAKSCDIPSRAGEIKEAAKACWNGGVNYTFDHISRSPEYAKKGIEYVKHKAKDF 399
            +NNSAKLFAVGGFMYMTYKCGVWSDNDSSRSSFNTLRHSIIAKSCDIPSRAGEIKEAAKACWNGGVNYTFDHISRSPEYAKKGIEYVKHKAKDF
Sbjct:    1 MNNSAKLFAVGGFMYMTYKCGVWSDNDSSRSSFNTLRHSIIAKSCDIPSRAGEIKEAAKACWNGGVNYTFDHISRSPEYAKKGIEYVKHKAKDF 94
[Close]
BLAST of SMED30017150 vs. Planmine SMEST
Match: SMESG000062986.1 (SMESG000062986.1)

HSP 1 Score: 140.969 bits (354), Expect = 4.912e-43
Identity = 73/93 (78.49%), Postives = 79/93 (84.95%), Query Frame = 1 
Query:   97 MPAILKFLNNSAKLFAVGGFMYMTYKCGVWSDNDSSRSSFNTLRHSIIAKSCD-IPSRAGEIKEAAKACWNGGVNYTFDHISRSPEYAKKGIE 372
            MPAIL++L+NSAKLFAVGGFM+MTYKCGVWSDNDSSRSSFNTLRHSIIAKSCD IPSRAGEIKEAAKA WNG        I RSP  + +GIE
Sbjct:    1 MPAILEYLDNSAKLFAVGGFMFMTYKCGVWSDNDSSRSSFNTLRHSIIAKSCDVIPSRAGEIKEAAKARWNGA-------IQRSPTLS-EGIE 85
[Close]
BLAST of SMED30017150 vs. Planmine SMEST
Match: SMESG000009672.1 (SMESG000009672.1)

HSP 1 Score: 129.028 bits (323), Expect = 4.921e-39
Identity = 63/68 (92.65%), Postives = 65/68 (95.59%), Query Frame = 1 
Query:   97 MPAILKFLNNSAKLFAVGGFMYMTYKCGVWSDNDSSRSSFNTLRHSIIAKSCD-IPSRAGEIKEAAKA 297
            MPAILKFLNNS KLFAVGGFM+MTYKCGVWSDNDSSRSSFNTLRHSIIAKSCD IPSRAGEIKEA+ A
Sbjct:    1 MPAILKFLNNSDKLFAVGGFMFMTYKCGVWSDNDSSRSSFNTLRHSIIAKSCDVIPSRAGEIKEASTA 68
The following BLAST results are available for this feature:
BLAST of SMED30017150 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 SMED30017150 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 SMED30017150 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
QIL11.511e-730.93gene:FBgn0036726 transcript:FBtr0075220[more]
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BLAST of SMED30017150 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 SMED30017150 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 SMED30017150 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 SMED30017150 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|Q9VVH3|MIC13_DROME1.515e-630.93MICOS complex subunit MIC13 homolog QIL1 OS=Drosop... [more]
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BLAST of SMED30017150 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A2T7PKV72.330e-631.78MICOS complex subunit MIC13 OS=Pomacea canaliculat... [more]
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BLAST of SMED30017150 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 SMED30017150 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 SMED30017150 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 SMED30017150 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 SMED30017150 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 SMED30017150 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000072322.18.021e-7299.01SMESG000072322.1[more]
SMESG000072322.15.513e-7098.04SMESG000072322.1[more]
SMESG000072322.13.952e-6698.94SMESG000072322.1[more]
SMESG000062986.14.912e-4378.49SMESG000062986.1[more]
SMESG000009672.14.921e-3992.65SMESG000009672.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017150 ID=SMED30017150|Name=SMED30017150|organism=Schmidtea mediterranea sexual|type=transcript|length=515bp
GTTATACTTTGTTAACTTTTTTGGCGCTTAGTGAAATTCTTTAAGTTGTA
ATTATAATTTGTAAATTATTATCAGAATTTGAATAAATTCCTCAAAATGC
CTGCTATTCTTAAATTTTTGAATAATTCTGCTAAATTATTTGCCGTTGGT
GGATTTATGTATATGACATACAAATGTGGTGTCTGGTCAGATAATGATTC
TAGTCGGAGCTCATTTAATACATTACGGCATTCTATCATTGCAAAATCTT
GTGACATTCCTAGTAGAGCCGGCGAAATTAAAGAGGCTGCCAAAGCTTGT
TGGAATGGAGGAGTGAATTATACTTTTGATCACATTAGTCGTTCACCAGA
ATATGCAAAGAAAGGGATCGAATATGTGAAGCATAAAGCTAAGGATTTTT
AACAATAGCTATTTGTGTTTGTAATCAAAGATTTAATTTTAAGTTGGATT
TTTCAGTTAATTTTCGATCAGTCGTTAGGTTTAAAAAATAAATATTAATT
TGTATGTTATTAGAA
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protein sequence of SMED30017150-orf-1

>SMED30017150-orf-1 ID=SMED30017150-orf-1|Name=SMED30017150-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
MPAILKFLNNSAKLFAVGGFMYMTYKCGVWSDNDSSRSSFNTLRHSIIAK
SCDIPSRAGEIKEAAKACWNGGVNYTFDHISRSPEYAKKGIEYVKHKAKD
F*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal
Vocabulary: INTERPRO
TermDefinition
IPR026769Mic13