SMED30031307

Overview
NameSMED30031307
Smed IDSMED30031307
Length (bp)2169
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 SMED30031307 (SMED30031307) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031307 (SMED30031307) 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 SMED30031307 (SMED30031307) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031307 (SMED30031307) 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



SMED30031307

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pigment cellSMED30031307 SmedASXL_012683SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017		whole organism asexual adult RNA-sequencing evidence
X1 cellSMED30031307 SmedASXL_012683SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30031307 SmedASXL_012683SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30031307 Contig37084newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
gutSMED30031307 SMED30031307smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
parenchymaSMED30031307 SMED30031307smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30031307 vs. Planmine SMEST
Match: SMESG000057533.1 (SMESG000057533.1)

HSP 1 Score: 86.6557 bits (213), Expect = 3.560e-24
Identity = 42/99 (42.42%), Postives = 61/99 (61.62%), Query Frame = 3 
Query: 1149 ARNRQALLDHGYVILAMGDLDWPMRQAYRNGDV*MLSIAIKKEPVRNPE*KARHRIEFELFQLEAAGKRMKWKVSAAR*RLARVNVDVTLGLIPSTDEY 1445
            AR RQ L D+GY++   GD  WP R  Y+  ++ + SIAIK+EP  NP  +AR R ++   ++E   ++   K  +AR RLA+VN D+  G IPSTD +
Sbjct: 1662 ARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHNPAREARQRAKYAAMKMEELERKYHRKAVSARQRLAQVNRDIASGSIPSTDGF 1760

HSP 2 Score: 45.0542 bits (105), Expect = 3.560e-24
Identity = 22/61 (36.07%), Postives = 38/61 (62.30%), Query Frame = 2 
Query: 1448 YGVS*RMGDPVLRKMTAPTSIVVPQRILPLSVKKHFGERSYRVDHSYSNGN--WNRQSLNR 1624
            YGVS  + DP L +MTAPT +V+P++++  +++   G      DH+Y++ +  WN +  NR
Sbjct: 1764 YGVSFELDDPRLTQMTAPTKMVIPEKLVQSTLRNQLGSHQTG-DHTYASRHPQWNSKLNNR 1823
[Close]
BLAST of SMED30031307 vs. Planmine SMEST
Match: SMESG000035366.1 (SMESG000035366.1)

HSP 1 Score: 83.5741 bits (205), Expect = 1.835e-23
Identity = 45/99 (45.45%), Postives = 60/99 (60.61%), Query Frame = 3 
Query: 1149 ARNRQALLDHGYVILAMGDLDWPMRQAYRNGDV*MLSIAIKKEPVRNPE*KARHRIEFELFQLEAAGKRMKWKVSAAR*RLARVNVDVTLGLIPSTDEY 1445
            AR RQ L D+GY++   GD  WP R  Y+  +V + SIAIK EP +NP  +AR R EF   ++E   ++   K   AR RLA+VN D+  G IPSTD +
Sbjct:  683 ARYRQVLWDNGYLLSIYGDSSWPRRSEYQAEEVELPSIAIKCEPGKNPAREARQRAEFSAMKMEQMEQKYHRKAVLARQRLAQVNWDIASGAIPSTDGF 781

HSP 2 Score: 45.8246 bits (107), Expect = 1.835e-23
Identity = 25/61 (40.98%), Postives = 38/61 (62.30%), Query Frame = 2 
Query: 1448 YGVS*RMGDPVLRKMTAPTSIVVPQRILPLSVKKHFGERSYRVDHSYSNGN--WNRQSLNR 1624
            YGVS  + DP L +M+APT +V+P+RI+  +++   G R    DH Y++ +  WN  S NR
Sbjct:  785 YGVSFELDDPRLLQMSAPTKLVLPERIIQSTLRNRLGSRQ-TGDHMYTSRHPRWNFNSNNR 844
[Close]
BLAST of SMED30031307 vs. Planmine SMEST
Match: SMESG000035366.1 (SMESG000035366.1)

HSP 1 Score: 83.5741 bits (205), Expect = 1.881e-23
Identity = 45/99 (45.45%), Postives = 60/99 (60.61%), Query Frame = 3 
Query: 1149 ARNRQALLDHGYVILAMGDLDWPMRQAYRNGDV*MLSIAIKKEPVRNPE*KARHRIEFELFQLEAAGKRMKWKVSAAR*RLARVNVDVTLGLIPSTDEY 1445
            AR RQ L D+GY++   GD  WP R  Y+  +V + SIAIK EP +NP  +AR R EF   ++E   ++   K   AR RLA+VN D+  G IPSTD +
Sbjct:  684 ARYRQVLWDNGYLLSIYGDSSWPRRSEYQAEEVELPSIAIKCEPGKNPAREARQRAEFSAMKMEQMEQKYHRKAVLARQRLAQVNWDIASGAIPSTDGF 782

HSP 2 Score: 45.8246 bits (107), Expect = 1.881e-23
Identity = 25/61 (40.98%), Postives = 38/61 (62.30%), Query Frame = 2 
Query: 1448 YGVS*RMGDPVLRKMTAPTSIVVPQRILPLSVKKHFGERSYRVDHSYSNGN--WNRQSLNR 1624
            YGVS  + DP L +M+APT +V+P+RI+  +++   G R    DH Y++ +  WN  S NR
Sbjct:  786 YGVSFELDDPRLLQMSAPTKLVLPERIIQSTLRNRLGSRQ-TGDHMYTSRHPRWNFNSNNR 845
[Close]
BLAST of SMED30031307 vs. Planmine SMEST
Match: SMESG000044971.1 (SMESG000044971.1)

HSP 1 Score: 81.6481 bits (200), Expect = 1.883e-23
Identity = 43/99 (43.43%), Postives = 60/99 (60.61%), Query Frame = 3 
Query: 1149 ARNRQALLDHGYVILAMGDLDWPMRQAYRNGDV*MLSIAIKKEPVRNPE*KARHRIEFELFQLEAAGKRMKWKVSAAR*RLARVNVDVTLGLIPSTDEY 1445
            AR RQ L D+GY++   GD  WP R  Y+  ++ + SIAIK+EP  NP  +AR R E+   ++E   ++   K   AR RLA+VN D+  G IPSTD +
Sbjct: 1152 ARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHNPAREARQRAEYVAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGF 1250

HSP 2 Score: 47.7506 bits (112), Expect = 1.883e-23
Identity = 23/61 (37.70%), Postives = 39/61 (63.93%), Query Frame = 2 
Query: 1448 YGVS*RMGDPVLRKMTAPTSIVVPQRILPLSVKKHFGERSYRVDHSYSNGN--WNRQSLNR 1624
            YGVS  + DP L +MTAPT +V+P++++  +++   G R    DH+Y++ +  WN +  NR
Sbjct: 1254 YGVSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRLGSRQTG-DHTYASRHPQWNPKRNNR 1313
[Close]
BLAST of SMED30031307 vs. Planmine SMEST
Match: SMESG000077847.1 (SMESG000077847.1)

HSP 1 Score: 82.4185 bits (202), Expect = 6.245e-23
Identity = 43/99 (43.43%), Postives = 60/99 (60.61%), Query Frame = 3 
Query: 1149 ARNRQALLDHGYVILAMGDLDWPMRQAYRNGDV*MLSIAIKKEPVRNPE*KARHRIEFELFQLEAAGKRMKWKVSAAR*RLARVNVDVTLGLIPSTDEY 1445
            AR RQ L D+GY++   GD  WP R  Y+  ++ + SIAIK+EP  NP  +AR R E+   ++E   ++   K   AR RLA+VN D+  G IPSTD +
Sbjct:  695 ARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHNPAREARQRAEYAAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGF 793

HSP 2 Score: 45.0542 bits (105), Expect = 6.245e-23
Identity = 23/61 (37.70%), Postives = 38/61 (62.30%), Query Frame = 2 
Query: 1448 YGVS*RMGDPVLRKMTAPTSIVVPQRILPLSVKKHFGERSYRVDHSYSNGN--WNRQSLNR 1624
            YGVS  + DP L +MTAPT +V+P+ ++  +++   G R    DH+Y++ +  WN +  NR
Sbjct:  797 YGVSFELDDPRLTQMTAPTKMVIPENLVQSTLRNRLGSRQTG-DHTYASRHPQWNSKHNNR 856
The following BLAST results are available for this feature:
BLAST of SMED30031307 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 SMED30031307 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 SMED30031307 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 SMED30031307 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 SMED30031307 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 SMED30031307 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 SMED30031307 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 SMED30031307 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 SMED30031307 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 SMED30031307 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 SMED30031307 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 SMED30031307 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 SMED30031307 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 SMED30031307 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000057533.13.560e-2442.42SMESG000057533.1[more]
SMESG000035366.11.835e-2345.45SMESG000035366.1[more]
SMESG000035366.11.881e-2345.45SMESG000035366.1[more]
SMESG000044971.11.883e-2343.43SMESG000044971.1[more]
SMESG000077847.16.245e-2343.43SMESG000077847.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031307 ID=SMED30031307|Name=SMED30031307|organism=Schmidtea mediterranea sexual|type=transcript|length=2169bp
TACACAATCATTGAAATTAAACTAACAACAATAAGACAAAAGGAATTTTA
CTATCAAATCGAAAATCAACCAAGAAATAGGTGTAACCATAACCGATGAA
GTACTCAAAATAACATAGTATCACAAAACTCTAGAGTGGCNNNANNTATN
NCNNTCCNANNATNTNNANNACNNAANCATCCAGTACAGGCCTCTGCACC
TTGATCGGAGGATATAATCATCTAATAATCATCATCCAAGGCTACAACGA
GAGAATGGTAACGCCGGGGAATGATCCTCGCATAGCAAAATCACACTGTT
AGAGTATCTAAACCAAAATTCTAAATCCAGTTACTAGAATGAAATATGAC
TAATGTATGAATCAGCCAAGTTTAATCACATCAAAATGAGTCATGAACGA
GCAGTAACTTGGACTTCATAGAGATAGTAATGAATATAGANTTAAAATGC
TGATGTGTCTTTAATATATCAATTAGCAATAAATAATACGTTAAATGATG
AAAATACACGTGAATTAACTACCAGTTGGAGCGCGAAGCGAAGCACATGA
TGAACTATATAAATACAATACCAAATGTGAATGTTATTAGTTATTTATGA
TAAATCCAGTGAAACTGAAGATATTAGAAGAGGTACACTCGAAAACACCA
GTATTCCACTCACCCTCTCCGGGACACAGGATCAACTGCGATGTCGGAAG
TCGCCAACTCATGGTTGCAGAGCAAGGCGAATCGAAGTAGTTAATACAAA
ACCCATCGGAAGGTTAATTTTATTTTTCTCAAATTTTGTTTATTAGAATG
AACGAATGAAAGCAAAAAGTTAATGAAAGTGCCTTGAACAACAACTTTAT
TTATCTGTTTAATGTCACGATTGAGATAGACCATGGATGAAGGAGATGAA
AATGTTTCTAATTTGGATCACCGCCCTGTGTGAGTTACGTCAGTGGAGGG
CTCATTTCATTATTAGATACATCTCGTAGGAAGGCAGATTAATCGTGAAT
TCATTTTAGACGTCAAATTCATTATCAATCTGATTGAACATTACTATTTG
TTCACATTTCTTTTATTATCAGGAATGTCTGAACTACTGCCGGATTATTC
TTGGTTTTACGATGAAAGGGAAACTCTCTATATCACAGGCCCGTAGTGGC
CAGAAATCGCCAAGCATTATTGGACCATGGATACGTCATATTAGCAATGG
GTGATCTGGATTGGCCCATGCGCCAAGCGTACAGAAATGGGGACGTGTAG
ATGCTGAGCATTGCCATAAAGAAGGAGCCGGTTAGGAACCCGGAATGAAA
GGCGCGTCATCGCATTGAATTCGAGTTATTTCAATTGGAAGCCGCAGGAA
AAAGAATGAAATGGAAGGTATCTGCAGCTCGGTGACGCCTCGCGAGAGTG
AATGTCGACGTCACCTTAGGCCTGATCCCAAGTACAGATGAATATGCTAT
GGTGTGTCGTAACGAATGGGCGACCCAGTGCTCCGGAAGATGACTGCTCC
CACGAGTATTGTGGTGCCACAACGAATTTTACCACTATCAGTGAAGAAAC
ATTTTGGAGAACGATCTTATAGGGTAGACCATTCTTATTCTAATGGCAAT
TGGAACCGACAAAGTTTAAACCGAAATAAATGTGCAAAGTATGCGTATCA
AAGCCTTGTAATGCTTCAATAATGTAGTGGTCGTTAAAAATAAATTTTAG
TTGTATTGAAAAAAANATTCAAATAGCTGAATTTATTATTTTCTTTTTCT
ATCGCTTTCTTCTTGCTTCTTTAACCACTTTTACGTAATAGTGACTGTTA
ATTATGACGCCTGATGCAGCAAAATCCATATTTAAAAATCCTTTCATCTT
TGGTGATTTTTGTTTCAGAAAGGCATACCCAAGTTTTGCAAAGCTTTCTA
AATTTTACTAGCAACACTCATATCGCCTTTGTTACATGCCACCCGTAAGA
AATAGTCCCACAACTCATGAACACAGTTTGTTGATATTCATTTTATTTGG
CCAAGTTTAGCAACATACCTTTATAGATACTGATACGTTATGCCAGATCT
TTTATTACAATGTGAAAGTTTTCTCATTTTTAAATTCCACAGGCCTGCCA
GGCTTTTTCAGATCAAAAACACCAGTTCGTCGACTTATACAATCATGAAT
CCAGTTGTAAATAGTTGCG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0002075pigment cell
PLANA:0002109X1 cell
PLANA:0002111X2 cell
PLANA:0002142parenchyma