SMED30013744

Overview
NameSMED30013744
Smed IDSMED30013744
Length (bp)1394
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 SMED30013744 (SMED30013744) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30013744 (SMED30013744) 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 SMED30013744 (SMED30013744) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30013744 (SMED30013744) 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




SMED30013744

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



PAGE Curations: 18

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30013744SMESG000074160.1 SMESG000029555.1 Contig7552uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30013744SMESG000074160.1 SMESG000029555.1 Contig7552newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
protonephridiaSMED30013744SMESG000001468.1 dd_Smed_v4_5675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
neuronSMED30013744SMESG000001468.1 dd_Smed_v4_5675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
neuronSMED30013744SMESG000001468.1 dd_Smed_v4_5675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
parenchymal cellSMED30013744SMESG000001468.1 dd_Smed_v4_5675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
epidermal cellSMED30013744SMESG000001468.1 dd_Smed_v4_5675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
neuronSMED30013744 Contig47745uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
neuronSMED30013744 Contig47745newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
neuronSMED30013744SMESG000066529.1 SMESG000053822.1 SMESG000029555.1 SMESG000010523.1 SMESG000023758.1 SMESG000074160.1 SMESG000019863.1 SMESG000001468.1 dd_Smed_v6_5675_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cholinergic neuronSMED30013744SMESG000066529.1 SMESG000053822.1 SMESG000029555.1 SMESG000010523.1 SMESG000023758.1 SMESG000074160.1 SMESG000019863.1 SMESG000001468.1 dd_Smed_v6_5675_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
GABAergic neuronSMED30013744SMESG000066529.1 SMESG000053822.1 SMESG000029555.1 SMESG000010523.1 SMESG000023758.1 SMESG000074160.1 SMESG000019863.1 SMESG000001468.1 dd_Smed_v6_5675_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30013744SMESG000066529.1 SMESG000053822.1 SMESG000029555.1 SMESG000010523.1 SMESG000023758.1 SMESG000074160.1 SMESG000019863.1 SMESG000001468.1 dd_Smed_v6_5675_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
glial cellSMED30013744SMESG000066529.1 SMESG000053822.1 SMESG000029555.1 SMESG000010523.1 SMESG000023758.1 SMESG000074160.1 SMESG000019863.1 SMESG000001468.1 dd_Smed_v6_5675_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
oocyteSMED30013744SMESG000074160.1 SMESG000073782.1 SMESG000048852.1 SMESG000029555.1 SMESG000017813.1 SMESG000001468.1 Contig36008uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30013744SMESG000074160.1 SMESG000073782.1 SMESG000048852.1 SMESG000029555.1 SMESG000017813.1 SMESG000001468.1 Contig36008uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30013744SMESG000074160.1 SMESG000073782.1 SMESG000048852.1 SMESG000029555.1 SMESG000017813.1 SMESG000001468.1 Contig36008newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30013744SMESG000074160.1 SMESG000073782.1 SMESG000048852.1 SMESG000029555.1 SMESG000017813.1 SMESG000001468.1 Contig36008newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30013744 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000702:12078..13478 -6773
Homology
BLAST of SMED30013744 vs. Planmine SMEST
Match: SMESG000052099.1 (SMESG000052099.1)

HSP 1 Score: 657.907 bits (1696), Expect = 0.000e+0
Identity = 332/332 (100.00%), Postives = 332/332 (100.00%), Query Frame = 3
Query:   54 MSLLKVKCLKNQIAQLERQIFISLQNVCCLQDHYQNIYNGLLGFLDSFKMIFQVNFFGNQCTIAHSDIIQMLELANKLKEILHTNIPNCINDKFPNNLLVLHFHNVMPSDQKFQIIPSTSFLNLSPIINLESKLLELYKNMIHISIQLKVCLTKDFVTKQNCNFQNSFFQYKSRHKEIVEIVAQFSYLIFDRHKKLINEFDEIIKSYNGKIQSKDYELIIKQAQLSQHKLSILAAQNDILENQLKFYSNNSIDKPENASQIEIERKRGNVNDFIGNNLLLPLKVLIDSYKNLESNPDSDNALKEFLSCCQSSDVLRKDFSKNFIEKLSFINC 1049
            MSLLKVKCLKNQIAQLERQIFISLQNVCCLQDHYQNIYNGLLGFLDSFKMIFQVNFFGNQCTIAHSDIIQMLELANKLKEILHTNIPNCINDKFPNNLLVLHFHNVMPSDQKFQIIPSTSFLNLSPIINLESKLLELYKNMIHISIQLKVCLTKDFVTKQNCNFQNSFFQYKSRHKEIVEIVAQFSYLIFDRHKKLINEFDEIIKSYNGKIQSKDYELIIKQAQLSQHKLSILAAQNDILENQLKFYSNNSIDKPENASQIEIERKRGNVNDFIGNNLLLPLKVLIDSYKNLESNPDSDNALKEFLSCCQSSDVLRKDFSKNFIEKLSFINC
Sbjct:    1 MSLLKVKCLKNQIAQLERQIFISLQNVCCLQDHYQNIYNGLLGFLDSFKMIFQVNFFGNQCTIAHSDIIQMLELANKLKEILHTNIPNCINDKFPNNLLVLHFHNVMPSDQKFQIIPSTSFLNLSPIINLESKLLELYKNMIHISIQLKVCLTKDFVTKQNCNFQNSFFQYKSRHKEIVEIVAQFSYLIFDRHKKLINEFDEIIKSYNGKIQSKDYELIIKQAQLSQHKLSILAAQNDILENQLKFYSNNSIDKPENASQIEIERKRGNVNDFIGNNLLLPLKVLIDSYKNLESNPDSDNALKEFLSCCQSSDVLRKDFSKNFIEKLSFINC 332          
BLAST of SMED30013744 vs. Planmine SMEST
Match: SMESG000019863.1 (SMESG000019863.1)

HSP 1 Score: 79.7221 bits (195), Expect = 2.179e-15
Identity = 38/52 (73.08%), Postives = 41/52 (78.85%), Query Frame = -2
Query: 1235 PAMNQFIPRAQQMFKPPATRNPEDRGNNQVSYNNNFRKDDNGDKMKY*CVIC 1390
            PAMNQFIPRAQQMFKPP TRNPED+GNNQVSYNNNFR   N ++    C  C
Sbjct:  223 PAMNQFIPRAQQMFKPPTTRNPEDKGNNQVSYNNNFRNKPNANEQ---CSTC 271          
BLAST of SMED30013744 vs. Planmine SMEST
Match: SMESG000019863.1 (SMESG000019863.1)

HSP 1 Score: 79.7221 bits (195), Expect = 2.219e-15
Identity = 38/52 (73.08%), Postives = 41/52 (78.85%), Query Frame = -2
Query: 1235 PAMNQFIPRAQQMFKPPATRNPEDRGNNQVSYNNNFRKDDNGDKMKY*CVIC 1390
            PAMNQFIPRAQQMFKPP TRNPED+GNNQVSYNNNFR   N ++    C  C
Sbjct:  223 PAMNQFIPRAQQMFKPPTTRNPEDKGNNQVSYNNNFRNKPNANEQ---CSTC 271          
BLAST of SMED30013744 vs. Planmine SMEST
Match: SMESG000019863.1 (SMESG000019863.1)

HSP 1 Score: 79.7221 bits (195), Expect = 2.254e-15
Identity = 38/52 (73.08%), Postives = 41/52 (78.85%), Query Frame = -2
Query: 1235 PAMNQFIPRAQQMFKPPATRNPEDRGNNQVSYNNNFRKDDNGDKMKY*CVIC 1390
            PAMNQFIPRAQQMFKPP TRNPED+GNNQVSYNNNFR   N ++    C  C
Sbjct:  223 PAMNQFIPRAQQMFKPPTTRNPEDKGNNQVSYNNNFRNKPNANEQ---CSTC 271          
BLAST of SMED30013744 vs. Planmine SMEST
Match: SMESG000059476.1 (SMESG000059476.1)

HSP 1 Score: 74.3294 bits (181), Expect = 1.039e-13
Identity = 38/58 (65.52%), Postives = 43/58 (74.14%), Query Frame = -2
Query: 1226 NPAMNQFIPRAQQMFKPPATRNPEDRGNNQVSYNNNFRKDDNGDKMKY*CVIC--INH 1393
            N AMNQFIPRAQQMFKPP TRNPE+ GNNQVSYNNNFR +   +++   C  C  I H
Sbjct:  297 NSAMNQFIPRAQQMFKPPPTRNPENGGNNQVSYNNNFRNNPKANEI---CTTCQRIGH 351          
The following BLAST results are available for this feature:
BLAST of SMED30013744 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 SMED30013744 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 SMED30013744 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 SMED30013744 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 SMED30013744 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 SMED30013744 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 SMED30013744 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 SMED30013744 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 SMED30013744 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 SMED30013744 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 SMED30013744 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 SMED30013744 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 SMED30013744 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 SMED30013744 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000052099.10.000e+0100.00SMESG000052099.1[more]
SMESG000019863.12.179e-1573.08SMESG000019863.1[more]
SMESG000019863.12.219e-1573.08SMESG000019863.1[more]
SMESG000019863.12.254e-1573.08SMESG000019863.1[more]
SMESG000059476.11.039e-1365.52SMESG000059476.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013744 ID=SMED30013744|Name=SMED30013744|organism=Schmidtea mediterranea sexual|type=transcript|length=1394bp
TTTAAATCGCAAATTTTAATTAATTATTTTAGTAGCAAGCTCTAATTTTC
AAAATGAGTTTATTAAAAGTTAAGTGTTTGAAAAATCAAATAGCACAATT
AGAAAGGCAGATTTTTATAAGTTTGCAAAATGTTTGTTGCTTACAGGATC
ATTATCAGAATATTTATAATGGTTTATTAGGATTTCTTGATTCTTTTAAA
ATGATATTTCAAGTTAATTTTTTCGGGAATCAGTGTACCATTGCCCATTC
AGACATCATACAAATGTTAGAATTGGCGAATAAACTAAAAGAAATTTTAC
ATACAAATATACCCAATTGTATAAATGATAAATTTCCTAATAATCTATTG
GTTCTCCATTTTCACAACGTAATGCCTTCAGATCAAAAATTTCAAATCAT
TCCGAGTACTTCATTCTTAAATTTGTCTCCGATAATTAATTTGGAGTCTA
AATTATTGGAGTTATATAAAAACATGATTCATATATCAATCCAGCTGAAA
GTGTGTTTAACGAAAGATTTTGTCACTAAACAAAACTGTAATTTCCAAAA
TTCATTTTTTCAATACAAATCACGACATAAAGAAATTGTTGAAATTGTCG
CTCAATTTTCTTATTTGATATTTGATCGACATAAGAAATTGATCAATGAA
TTCGATGAAATTATTAAAAGTTATAATGGTAAAATCCAATCGAAAGATTA
CGAATTAATAATAAAACAAGCCCAGTTAAGTCAGCATAAATTATCAATAT
TAGCAGCTCAAAATGATATTTTGGAAAATCAATTGAAATTTTATTCCAAT
AATTCGATTGACAAGCCGGAAAATGCGAGTCAAATAGAAATTGAAAGAAA
ACGGGGAAATGTTAATGATTTTATTGGGAATAATCTTTTGCTACCTTTAA
AGGTTTTAATAGATTCTTACAAGAATTTAGAATCAAATCCAGACAGTGAT
AATGCTCTTAAAGAATTCCTCAGTTGCTGCCAATCTTCAGATGTGTTACG
CAAGGATTTCTCGAAAAATTTCATTGAAAAATTATCTTTTATAAATTGTT
AAATTAGTTTTTATGCATTTTATGATTTTAGCAATGTGTCCCATTTAGTT
GGGGAGGGGTATTTGTTTCTCTAGAAGTCAGATTTGGAATTGCCGTAAAG
TGTGTGCGTGTCAAAACCGGGTGAATGTATATTACATATCAATGAACGCT
TTACAACTCGGATTGGTTTTCACGAATGATTTATACAAATAACGCATCAA
TATTTCATTTTGTCTCCATTGTCGTCCTTCCTGAAATTATTATTATAACT
TACTTGGTTATTACCTCTATCCTCCGGATTTCTCGTTGCTGGTGGCTTGA
ACATCTGCTGTGCTCTTGGAATGAATTGATTCATAGCTGGATTG
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protein sequence of SMED30013744-orf-1

>SMED30013744-orf-1 ID=SMED30013744-orf-1|Name=SMED30013744-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=333bp
MSLLKVKCLKNQIAQLERQIFISLQNVCCLQDHYQNIYNGLLGFLDSFKM
IFQVNFFGNQCTIAHSDIIQMLELANKLKEILHTNIPNCINDKFPNNLLV
LHFHNVMPSDQKFQIIPSTSFLNLSPIINLESKLLELYKNMIHISIQLKV
CLTKDFVTKQNCNFQNSFFQYKSRHKEIVEIVAQFSYLIFDRHKKLINEF
DEIIKSYNGKIQSKDYELIIKQAQLSQHKLSILAAQNDILENQLKFYSNN
SIDKPENASQIEIERKRGNVNDFIGNNLLLPLKVLIDSYKNLESNPDSDN
ALKEFLSCCQSSDVLRKDFSKNFIEKLSFINC*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000070intestinal phagocyte
PLANA:0000074oocyte
PLANA:0000099neuron
PLANA:0000231vitelline gland
PLANA:0000463cholinergic neuron
PLANA:0000464GABAergic neuron
PLANA:0002032epidermal cell
PLANA:0003116parenchymal cell
PLANA:0007528glial cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 6..26
NoneNo IPR availableCOILSCoilCoilcoord: 230..250