SMED30006315

Overview
NameSMED30006315
Smed IDSMED30006315
Length (bp)1752
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 SMED30006315 (SMED30006315) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30006315 (SMED30006315) 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 SMED30006315 (SMED30006315) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30006315 (SMED30006315) 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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Homology
[Close]
BLAST of SMED30006315 vs. Planmine SMEST
Match: SMESG000004983.1 (SMESG000004983.1)

HSP 1 Score: 357.451 bits (916), Expect = 7.286e-122
Identity = 179/179 (100.00%), Postives = 179/179 (100.00%), Query Frame = -3 
Query:   32 MFMNIKERITNLKNRIQIKNIFRMPDRDSQTNCHVETDSDQYLYDVTLKMALEDLQEEVVQANQIKETLIYQQQNLEKKYNEIWKENAELHKQINQLKIETEQLQLKNSEDNMKHRIAEMEFESTIVELKQQLNNENFHREMNSTSSKINLENRLLIQNVQFTDSVADLFLDNSCFDIQ 568
            MFMNIKERITNLKNRIQIKNIFRMPDRDSQTNCHVETDSDQYLYDVTLKMALEDLQEEVVQANQIKETLIYQQQNLEKKYNEIWKENAELHKQINQLKIETEQLQLKNSEDNMKHRIAEMEFESTIVELKQQLNNENFHREMNSTSSKINLENRLLIQNVQFTDSVADLFLDNSCFDIQ
Sbjct:    1 MFMNIKERITNLKNRIQIKNIFRMPDRDSQTNCHVETDSDQYLYDVTLKMALEDLQEEVVQANQIKETLIYQQQNLEKKYNEIWKENAELHKQINQLKIETEQLQLKNSEDNMKHRIAEMEFESTIVELKQQLNNENFHREMNSTSSKINLENRLLIQNVQFTDSVADLFLDNSCFDIQ 179
[Close]
BLAST of SMED30006315 vs. Planmine SMEST
Match: SMESG000004983.1 (SMESG000004983.1)

HSP 1 Score: 352.829 bits (904), Expect = 3.485e-120
Identity = 177/177 (100.00%), Postives = 177/177 (100.00%), Query Frame = -3 
Query:   32 MNIKERITNLKNRIQIKNIFRMPDRDSQTNCHVETDSDQYLYDVTLKMALEDLQEEVVQANQIKETLIYQQQNLEKKYNEIWKENAELHKQINQLKIETEQLQLKNSEDNMKHRIAEMEFESTIVELKQQLNNENFHREMNSTSSKINLENRLLIQNVQFTDSVADLFLDNSCFDIQ 562
            MNIKERITNLKNRIQIKNIFRMPDRDSQTNCHVETDSDQYLYDVTLKMALEDLQEEVVQANQIKETLIYQQQNLEKKYNEIWKENAELHKQINQLKIETEQLQLKNSEDNMKHRIAEMEFESTIVELKQQLNNENFHREMNSTSSKINLENRLLIQNVQFTDSVADLFLDNSCFDIQ
Sbjct:    1 MNIKERITNLKNRIQIKNIFRMPDRDSQTNCHVETDSDQYLYDVTLKMALEDLQEEVVQANQIKETLIYQQQNLEKKYNEIWKENAELHKQINQLKIETEQLQLKNSEDNMKHRIAEMEFESTIVELKQQLNNENFHREMNSTSSKINLENRLLIQNVQFTDSVADLFLDNSCFDIQ 177
[Close]
BLAST of SMED30006315 vs. Planmine SMEST
Match: SMESG000075431.1 (SMESG000075431.1)

HSP 1 Score: 55.0694 bits (131), Expect = 1.288e-7
Identity = 29/51 (56.86%), Postives = 34/51 (66.67%), Query Frame = -1 
Query: 1045 F*ILLRLCSDLDYNFKCYGCNITHIQMTIRHPRSQVLDLFRLKELIDISRQ 1197
            F +LLR CSDL + F  +GCN T+I MT  H RSQV    RL ELIDIS+ 
Sbjct:  439 FQVLLRFCSDLGFQFIRHGCNTTYIGMTPHHFRSQVFIHSRLMELIDISKH 489
[Close]
BLAST of SMED30006315 vs. Planmine SMEST
Match: SMESG000075431.1 (SMESG000075431.1)

HSP 1 Score: 55.0694 bits (131), Expect = 1.386e-7
Identity = 29/51 (56.86%), Postives = 34/51 (66.67%), Query Frame = -1 
Query: 1045 F*ILLRLCSDLDYNFKCYGCNITHIQMTIRHPRSQVLDLFRLKELIDISRQ 1197
            F +LLR CSDL + F  +GCN T+I MT  H RSQV    RL ELIDIS+ 
Sbjct:  428 FQVLLRFCSDLGFQFIRHGCNTTYIGMTPHHFRSQVFIHSRLMELIDISKH 478
[Close]
BLAST of SMED30006315 vs. Planmine SMEST
Match: SMESG000075431.1 (SMESG000075431.1)

HSP 1 Score: 52.7582 bits (125), Expect = 7.581e-7
Identity = 28/49 (57.14%), Postives = 33/49 (67.35%), Query Frame = -1 
Query: 1051 F*ILLRLCSDLDYNFKCYGCNITHIQMTIRHPRSQVLDLFRLKELIDIS 1197
            F +LLR CSDL + F  +GCN T+I MT  H RSQV    RL ELIDI+
Sbjct:  439 FQVLLRFCSDLGFQFIRHGCNTTYIGMTPHHFRSQVFIHSRLMELIDIN 487
The following BLAST results are available for this feature:
BLAST of SMED30006315 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 SMED30006315 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 SMED30006315 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 SMED30006315 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 SMED30006315 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 SMED30006315 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 SMED30006315 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 SMED30006315 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 SMED30006315 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 SMED30006315 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 SMED30006315 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 SMED30006315 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 SMED30006315 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 SMED30006315 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000004983.17.286e-122100.00SMESG000004983.1[more]
SMESG000004983.13.485e-120100.00SMESG000004983.1[more]
SMESG000075431.11.288e-756.86SMESG000075431.1[more]
SMESG000075431.11.386e-756.86SMESG000075431.1[more]
SMESG000075431.17.581e-757.14SMESG000075431.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006315 ID=SMED30006315|Name=SMED30006315|organism=Schmidtea mediterranea sexual|type=transcript|length=1752bp
CGGAACTAACGGAAACGAATATAAATAATTATTGGATGTCAAAACATGAA
TTGTCAAGAAATAGATCAGCCACTGAATCTGTGAACTGTACATTTTGAAT
CAAAAGTCGATTTTCTAAGTTTATTTTTGAACTTGTTGAATTCATTTCTC
TATGAAAGTTTTCATTGTTCAATTGCTGCTTAAGCTCTACAATTGTCGAT
TCGAACTCCATTTCTGCTATACGATGTTTCATGTTATCTTCAGAATTTTT
GAGTTGAAGCTGTTCCGTTTCTATTTTTAATTGGTTGATTTGTTTATGAA
GTTCCGCATTTTCTTTCCAAATTTCGTTGTATTTCTTTTCCAAGTTTTGT
TGTTGGTAAATCAATGTTTCTTTTATTTGGTTGGCTTGAACAACCTCTTC
TTGTAAGTCTTCTAAAGCCATTTTCAAAGTAACATCATACAAATACTGAT
CTGAATCTGTTTCAACATGACAGTTTGTTTGACTATCTCTATCAGGCATT
CTGAATATATTTTTTATTTGAATTCTATTCTTTAAGTTAGTTATTCTTTC
TTTGATATTCATAAACATAAAAATCCAAATTTCATTCAATAAATCCAAAG
TGACAAAAAATAGTGTTAAACAATATGAATTTGAAAAAAAATTTAAATAA
AAGAGAATTTTCATGGTAAGCGAAAAGAACATTTCGGTATGAAATAAAAT
GGGAAAATTCCACTCAGCAAGACGCAGAAGTGATTTCTACATACACTCGC
GGACATCGACACCAAGAAAAAACTAACAGCTCCTATTAGAAAGTTGCATT
TCTATCAAATTAATGGAATCGATATCCAGCTGAAAATATCGAGTTCTCCT
AAGCGCATAAAAAACTGAAAAAATATTCCCAACAAAAAAACTCCGAATTA
AATTTTAATTTTAAAAATTTTAAAAAATTATATAAAAATTAATTAATTTT
TAATAAATTTTTAATGTTTTTTTACATACATATTATCATTTTTCATTTAT
TTTCTTCCATTTATCACTTCAAAACAACAAAACAAACTCAAAAATTGTCT
ACTAATATCAATCAATTCCTTCAGTCGAAAAAGATCAAGAACTTGAGAAC
GGGGGTGGCGGATAGTCATTTGAATGTGTGTAATATTACACCCATAACAT
TTAAAATTATAATCAAGATCTGAACACAGTCTAAGCAGAATTTAAAATCT
ACCTGATGATGACAATGAATCCATCGAAAAATATTATTGGTTTAGATTTA
TAAGTCCATAATTGATGTTAGAAATAATATATATATATGGGGTAAAAAGA
AAAATTTGAAGGAAATGAAGGCAAAAAAATACAAATATTTATACTATTTG
AAATCAATTTACGAAATTTACACCCAAGGATTAATATCAGTGCGAACAAT
AAAAGTTCGGACTAGTAGCTGAAAAAAATTACCCGACTCCTGATCTACAC
AAACAAAGTAAAATATATCAAATTTTCATTATTGACAAATTTCTAAATAA
TTTTAACTATAAGATATTTCAATGTTAATTTATTTCTCCTTAATCCATTC
AAGTTTTATTGAAGAATTCTAAAAAAAAATTTCTAAAAATGAATCATTTA
GATTAATCGATTTTTAGCAGATTAGCTAGAACTGCATTCTGTGAGAAATA
AAAATTAATTAATGCATGAATTTAATATTGCCTCAAAAATTTTATCATAT
TATTTTTTAATTAAATCAATATTAGAAAATAAATTATAAAACTAATCAAC
AT
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protein sequence of SMED30006315-orf-1

>SMED30006315-orf-1 ID=SMED30006315-orf-1|Name=SMED30006315-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=218bp
MFFSLTMKILFYLNFFSNSYCLTLFFVTLDLLNEIWIFMFMNIKERITNL
KNRIQIKNIFRMPDRDSQTNCHVETDSDQYLYDVTLKMALEDLQEEVVQA
NQIKETLIYQQQNLEKKYNEIWKENAELHKQINQLKIETEQLQLKNSEDN
MKHRIAEMEFESTIVELKQQLNNENFHREMNSTSSKINLENRLLIQNVQF
TDSVADLFLDNSCFDIQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000420parapharyngeal region
PLANA:0002089reproductive organ