SMED30028195

Overview
NameSMED30028195
Smed IDSMED30028195
Length (bp)896
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 SMED30028195 (SMED30028195) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30028195 (SMED30028195) 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 SMED30028195 (SMED30028195) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30028195 (SMED30028195) 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



SMED30028195

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
nervous systemSMED30028195h1SMcG0010282 dd_Smed_v4_8456_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30028195h1SMcG0010282 dd_Smed_v4_8456_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30028195h1SMcG0010282 dd_Smed_v4_8456_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30028195h1SMcG0010282 dd_Smed_v4_8456_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30028195h1SMcG0010282 dd_Smed_v4_8456_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30028195h1SMcG0010282 Contig48450uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30028195h1SMcG0010282 Contig48450newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
tail regionSMED30028195h1SMcG0010282 dd_Smed_v6_8456_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
reproductive organSMED30028195h1SMcG0004540 Contig3033GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30028195h1SMcG0010282 Contig3033GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30028195 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000655:25171..26066 +4435
Homology
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BLAST of SMED30028195 vs. TrEMBL
Match: A0A183KDP4 (Uncharacterized protein OS=Schistosoma curassoni OX=6186 GN=SCUD_LOCUS13136 PE=4 SV=1)

HSP 1 Score: 74.7146 bits (182), Expect = 7.685e-13
Identity = 42/101 (41.58%), Postives = 61/101 (60.40%), Query Frame = 1 
Query:  382 TELSLRYEPSICRKLE--QHLEDDIWAEVMAQYDRSNDRELLCQLEEGCCNHPELYQITRLEKQKNRHIIIEMQPKPVFKVINISRRNS-VNSCDTSITEV 675
            +E SL Y   I R L+   +LEDD+WA  + Q D S++  LL QLE GC   PE Y++ R++  KNR  +I+   KP  + I +SR NS  +S +T++T V
Sbjct:   41 SETSLSY---ITRGLQIIDYLEDDLWAATILQCDNSSNAGLLRQLEAGCRLEPEAYKMERVQTVKNRETVIDFPSKPTVRTIGLSRSNSDTDSINTTLTGV 138
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BLAST of SMED30028195 vs. TrEMBL
Match: A0A183NGJ7 (Uncharacterized protein OS=Schistosoma mattheei OX=31246 GN=SMTD_LOCUS1233 PE=4 SV=1)

HSP 1 Score: 73.9442 bits (180), Expect = 7.865e-13
Identity = 42/101 (41.58%), Postives = 61/101 (60.40%), Query Frame = 1 
Query:  382 TELSLRYEPSICRKLE--QHLEDDIWAEVMAQYDRSNDRELLCQLEEGCCNHPELYQITRLEKQKNRHIIIEMQPKPVFKVINISRRNS-VNSCDTSITEV 675
            +E SL Y   I R L+   +LEDD+WA  + Q D S++  LL QLE GC   PE Y++ R++  KNR  +I+   KP  + I +SR NS  +S +T++T V
Sbjct:   11 SETSLSY---ITRGLQIIDYLEDDLWAATILQCDNSSNAGLLRQLEAGCRLEPEAYKMERVQTVKNRETVIDFPSKPTVRTIGLSRSNSDTDSINTTLTGV 108
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BLAST of SMED30028195 vs. TrEMBL
Match: A0A183LR17 (Uncharacterized protein OS=Schistosoma margrebowiei OX=48269 GN=SMRZ_LOCUS6242 PE=4 SV=1)

HSP 1 Score: 73.1738 bits (178), Expect = 2.603e-12
Identity = 41/101 (40.59%), Postives = 61/101 (60.40%), Query Frame = 1 
Query:  382 TELSLRYEPSICRKLE--QHLEDDIWAEVMAQYDRSNDRELLCQLEEGCCNHPELYQITRLEKQKNRHIIIEMQPKPVFKVINISRRNS-VNSCDTSITEV 675
            +E SL Y   + R L+   +LEDD+WA  + Q D S++  LL QLE GC   PE Y++ R++  KNR  +I+   KP  + I +SR NS  +S +T++T V
Sbjct:   27 SETSLSY---LTRGLQIIDYLEDDLWAATILQCDNSSNAGLLRQLEAGCRLEPEAYKMERVQTVKNRETVIDFPSKPTVRTIGLSRSNSDTDSINTTLTGV 124
[Close]
BLAST of SMED30028195 vs. TrEMBL
Match: A0A095AQG8 (Uncharacterized protein OS=Schistosoma haematobium OX=6185 GN=MS3_04871 PE=4 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 3.682e-12
Identity = 42/101 (41.58%), Postives = 61/101 (60.40%), Query Frame = 1 
Query:  382 TELSLRYEPSICRKLE--QHLEDDIWAEVMAQYDRSNDRELLCQLEEGCCNHPELYQITRLEKQKNRHIIIEMQPKPVFKVINISRRNS-VNSCDTSITEV 675
            +E SL Y   I R L+   +LEDD+WA  + Q D S++  LL QLE GC   PE Y++ R++  KNR  +I+   KP  + I +SR NS  +S +T++T V
Sbjct:   53 SETSLSY---ITRGLQIIDYLEDDLWAATILQCDNSSNAGLLRQLEAGCRLEPEAYKMERVQTVKNRETVIDFPSKPTVRTIGLSRSNSDTDSINTTLTGV 150
[Close]
BLAST of SMED30028195 vs. TrEMBL
Match: A0A068YCI0 (Uncharacterized protein OS=Echinococcus multilocularis OX=6211 GN=EmuJ_001018700 PE=4 SV=1)

HSP 1 Score: 72.7886 bits (177), Expect = 2.633e-11
Identity = 50/187 (26.74%), Postives = 88/187 (47.06%), Query Frame = 1 
Query:  232 SIAQMGKNILREYRSDFLLPCQTHVAITRQEISQPVKQLKIVSVDLVV------------------------GYT-------ELSLRYEPSIC-RKLEQ--------HLEDDIWAEVMAQYDRSNDRELLCQLEEGCCNHPELYQITRLEKQKNRHIIIEMQPKPVFKVINISRRNS-VNSCDTSIT 669
            S+  + + + R+Y S+F+LP  T +A+ R E S P    ++V+V L V                        G T       E +   E  +   KL +        +L+DD WA  + ++D   + ELL QLE GC   P+ +++ RL++++N   ++++Q +P  + +  SR+ S   S +TS T
Sbjct:   36 SVILLSQRVKRQYMSEFVLPDDTRIAVRRVESSMPADHKQVVTVSLAVRHPFDSILPQFVTTQTSEVWKSECGSTTTLETLGEATTDSEDEVTLEKLSEKGNLRILDYLDDDAWAATLLEWDSGANGELLKQLEAGCRLDPDSFRMERLQRRRNWKTVVDIQQEPQTRSLGFSRKGSESGSLNTSTT 222
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BLAST of SMED30028195 vs. Planmine SMEST
Match: SMESG000078660.1 (SMESG000078660.1)

HSP 1 Score: 430.254 bits (1105), Expect = 3.185e-154
Identity = 221/222 (99.55%), Postives = 222/222 (100.00%), Query Frame = 1 
Query:  115 MSLEDSSNASESPKVLRRQSIQSRLPXXXXXXXXXXCTHSIAQMGKNILREYRSDFLLPCQTHVAITRQEISQPVKQLKIVSVDLVVGYTELSLRYEPSICRKLEQHLEDDIWAEVMAQYDRSNDRELLCQLEEGCCNHPELYQITRLEKQKNRHIIIEMQPKPVFKVINISRRNSVNSCDTSITEVTDLSDICLQETNNDSTDINSDFNLSLSDSTANSDI 780
            MSLEDSSNASESPKVLRRQSIQSRLPFFEFNE+TTNCTHSIAQMGKNILREYRSDFLLPCQTHVAITRQEISQPVKQLKIVSVDLVVGYTELSLRYEPSICRKLEQHLEDDIWAEVMAQYDRSNDRELLCQLEEGCCNHPELYQITRLEKQKNRHIIIEMQPKPVFKVINISRRNSVNSCDTSITEVTDLSDICLQETNNDSTDINSDFNLSLSDSTANSDI
Sbjct:    1 MSLEDSSNASESPKVLRRQSIQSRLPFFEFNESTTNCTHSIAQMGKNILREYRSDFLLPCQTHVAITRQEISQPVKQLKIVSVDLVVGYTELSLRYEPSICRKLEQHLEDDIWAEVMAQYDRSNDRELLCQLEEGCCNHPELYQITRLEKQKNRHIIIEMQPKPVFKVINISRRNSVNSCDTSITEVTDLSDICLQETNNDSTDINSDFNLSLSDSTANSDI 222
The following BLAST results are available for this feature:
BLAST of SMED30028195 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 SMED30028195 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 SMED30028195 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 SMED30028195 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 SMED30028195 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 SMED30028195 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 SMED30028195 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 SMED30028195 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A183KDP47.685e-1341.58Uncharacterized protein OS=Schistosoma curassoni O... [more]
A0A183NGJ77.865e-1341.58Uncharacterized protein OS=Schistosoma mattheei OX... [more]
A0A183LR172.603e-1240.59Uncharacterized protein OS=Schistosoma margrebowie... [more]
A0A095AQG83.682e-1241.58Uncharacterized protein OS=Schistosoma haematobium... [more]
A0A068YCI02.633e-1126.74Uncharacterized protein OS=Echinococcus multilocul... [more]
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BLAST of SMED30028195 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 SMED30028195 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 SMED30028195 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 SMED30028195 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 SMED30028195 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 SMED30028195 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000078660.13.185e-15499.55SMESG000078660.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028195 ID=SMED30028195|Name=SMED30028195|organism=Schmidtea mediterranea sexual|type=transcript|length=896bp
ATACACTCAATAATTAATTAATCTGTTTGCCTGACATTCTAATTGGTTTA
TTTTCTGACTAATAGAAAGCGGTGTACTATTAATATCTAACAGCTATGAC
ACAATTCACCAGAAATGAGTTTAGAAGATTCTTCAAATGCATCTGAAAGT
CCAAAAGTATTGAGACGGCAATCAATTCAGTCAAGGCTTCCATTTTTTGA
ATTCAATGAAACCACAACTAACTGTACTCATTCGATAGCACAAATGGGAA
AAAATATTCTTCGGGAATATCGATCGGATTTTCTACTGCCATGTCAAACT
CATGTTGCCATAACTCGACAAGAGATCTCTCAACCGGTCAAACAATTGAA
AATCGTGTCAGTTGATTTGGTTGTTGGATACACCGAACTCAGCTTGCGAT
ATGAACCTTCGATTTGCCGAAAGCTCGAGCAACATCTAGAAGATGATATC
TGGGCAGAAGTTATGGCACAATACGATAGGTCGAATGATCGAGAATTACT
ATGTCAACTCGAAGAAGGATGTTGTAATCATCCGGAACTTTATCAAATTA
CTCGATTAGAAAAACAGAAAAATCGACATATAATTATAGAAATGCAACCG
AAGCCAGTGTTCAAAGTAATCAACATAAGCAGAAGAAATAGTGTGAATTC
ATGCGATACGAGCATTACGGAAGTGACAGATCTATCAGATATTTGTCTTC
AGGAAACCAATAATGACTCCACTGATATCAATTCAGATTTCAACTTGAGT
TTATCCGATTCGACCGCCAACAGTGACATATGAAATGGAATGCCTTTGAA
ATTCTATAACATATTACCCTTCATATCTCTGTATACTTGCCTTGTAAAAC
AATTATTAATTTCTTGTTTAAATTTCTATAAGAAATTATTCGTCAG
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protein sequence of SMED30028195-orf-1

>SMED30028195-orf-1 ID=SMED30028195-orf-1|Name=SMED30028195-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=223bp
MSLEDSSNASESPKVLRRQSIQSRLPFFEFNETTTNCTHSIAQMGKNILR
EYRSDFLLPCQTHVAITRQEISQPVKQLKIVSVDLVVGYTELSLRYEPSI
CRKLEQHLEDDIWAEVMAQYDRSNDRELLCQLEEGCCNHPELYQITRLEK
QKNRHIIIEMQPKPVFKVINISRRNSVNSCDTSITEVTDLSDICLQETNN
DSTDINSDFNLSLSDSTANSDI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000421tail
PLANA:0002089reproductive organ