SMED30035542

Overview
NameSMED30035542
Smed IDSMED30035542
Length (bp)306
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30035542 (SMED30035542) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30035542 (SMED30035542) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30035542

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
central nervous systemSMED30035542 dd_Smed_v4_18000_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
posterior region of the whole animalSMED30035542 dd_Smed_v4_18000_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
pigment cellSMED30035542 SmedASXL_075274SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30035542 dd_Smed_v4_18000_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30035542 dd_Smed_v4_18000_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30035542 dd_Smed_v4_18000_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30035542 dd_Smed_v4_18000_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30035542 dd_Smed_v4_18000_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
Alignments
SMED30035542 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.014194:6207..6511 -1471
Homology
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BLAST of SMED30035542 vs. Planmine SMEST
Match: SMESG000062936.1 (SMESG000062936.1)

HSP 1 Score: 203.756 bits (517), Expect = 4.680e-62
Identity = 100/102 (98.04%), Postives = 101/102 (99.02%), Query Frame = 1 
Query:    1 VGLLIRDNKNKTIKLVDVKCPLDTEFNFINTHELNMSKYNDLKLNIEKALPNYKVTLSTCIFGSLGSIPDKTFDVLDDIGVRFTDRNSLSVECALSNIEYSA 306
            V LLIRDNKNKTIKLVDVKCPLDTEFNFINTHELNMSKYNDLKLNIEKALPNYKVTLSTCIFGSLGSIPDKTFDVLDDIGV+FTDRNSLSVECALSNIEYSA
Sbjct: 1396 VDLLIRDNKNKTIKLVDVKCPLDTEFNFINTHELNMSKYNDLKLNIEKALPNYKVTLSTCIFGSLGSIPDKTFDVLDDIGVKFTDRNSLSVECALSNIEYSA 1497
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BLAST of SMED30035542 vs. Planmine SMEST
Match: SMESG000046455.1 (SMESG000046455.1)

HSP 1 Score: 95.1301 bits (235), Expect = 4.804e-24
Identity = 53/102 (51.96%), Postives = 66/102 (64.71%), Query Frame = 1 
Query:    1 VGLLIRDNKNKTIKLVDVKCPLDTEFNFINTHELNMSKYNDLKLNIEKALPNYKVTLSTCIFGSLGSIPDKTFDVLDDIGVRFTDRNSLSVECALSNIEYSA 306
            V L+I D   K I LVD+KCP DT  NF     LN+ KY+ LK+ I+ A P++KV L TCI GSLGS P KT ++L  IGV  T    L ++CALSNI +SA
Sbjct: 2173 VDLMITDMVRKKIFLVDMKCPCDTINNFALVDLLNLQKYDSLKMQIQDAKPDFKVELDTCIIGSLGSFPPKTPELLLKIGVDRTHLKGLLIDCALSNISHSA 2274
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BLAST of SMED30035542 vs. Planmine SMEST
Match: SMESG000021486.1 (SMESG000021486.1)

HSP 1 Score: 95.1301 bits (235), Expect = 5.146e-24
Identity = 52/102 (50.98%), Postives = 66/102 (64.71%), Query Frame = 1 
Query:    1 VGLLIRDNKNKTIKLVDVKCPLDTEFNFINTHELNMSKYNDLKLNIEKALPNYKVTLSTCIFGSLGSIPDKTFDVLDDIGVRFTDRNSLSVECALSNIEYSA 306
            V L+I D   K I LVD+KCP D+  NF     LN+ KY+ LK  I+   P++KV L TC+FGSLGS P KT ++L  IGV+ T+   L  ECALSNI +SA
Sbjct: 3713 VDLMITDLSRKKIFLVDMKCPCDSVNNFEQVDLLNLRKYDSLKNQIQAVKPDFKVELDTCVFGSLGSFPLKTSEILVKIGVKRTELKPLLKECALSNIAHSA 3814

HSP 2 Score: 95.1301 bits (235), Expect = 5.146e-24
Identity = 52/102 (50.98%), Postives = 66/102 (64.71%), Query Frame = 1 
Query:    1 VGLLIRDNKNKTIKLVDVKCPLDTEFNFINTHELNMSKYNDLKLNIEKALPNYKVTLSTCIFGSLGSIPDKTFDVLDDIGVRFTDRNSLSVECALSNIEYSA 306
            V L+I D   K I LVD+KCP D+  NF     LN+ KY+ LK  I+   P++KV L TC+FGSLGS P KT ++L  IGV+ T+   L  ECALSNI +SA
Sbjct: 6040 VDLMITDLSRKKIFLVDMKCPCDSVNNFEQVDLLNLRKYDSLKNQIQAVKPDFKVELDTCVFGSLGSFPLKTSEILVKIGVKRTELKPLLKECALSNIAHSA 6141

HSP 3 Score: 93.5893 bits (231), Expect = 1.768e-23
Identity = 52/102 (50.98%), Postives = 67/102 (65.69%), Query Frame = 1 
Query:    1 VGLLIRDNKNKTIKLVDVKCPLDTEFNFINTHELNMSKYNDLKLNIEKALPNYKVTLSTCIFGSLGSIPDKTFDVLDDIGVRFTDRNSLSVECALSNIEYSA 306
            V L+I + + KTI LVD+KCP+D+  NF     LN+ KY  LKL+I+   P+YKV L TCI GSLGSI  KT D+L  +GV+      L  ECA+SNI +SA
Sbjct: 1422 VDLIITNTEKKTILLVDMKCPIDSVSNFQLVDNLNLEKYAKLKLDIQAVKPDYKVELHTCIMGSLGSIESKTEDLLLKMGVQPNRIIGLMKECAISNIAHSA 1523
[Close]
BLAST of SMED30035542 vs. Planmine SMEST
Match: SMESG000021486.1 (SMESG000021486.1)

HSP 1 Score: 94.7449 bits (234), Expect = 5.456e-24
Identity = 52/102 (50.98%), Postives = 66/102 (64.71%), Query Frame = 1 
Query:    1 VGLLIRDNKNKTIKLVDVKCPLDTEFNFINTHELNMSKYNDLKLNIEKALPNYKVTLSTCIFGSLGSIPDKTFDVLDDIGVRFTDRNSLSVECALSNIEYSA 306
            V L+I D   K I LVD+KCP D+  NF     LN+ KY+ LK  I+   P++KV L TC+FGSLGS P KT ++L  IGV+ T+   L  ECALSNI +SA
Sbjct: 3742 VDLMITDLSRKKIFLVDMKCPCDSVNNFEQVDLLNLRKYDSLKNQIQAVKPDFKVELDTCVFGSLGSFPLKTSEILVKIGVKRTELKPLLKECALSNIAHSA 3843

HSP 2 Score: 94.7449 bits (234), Expect = 5.456e-24
Identity = 52/102 (50.98%), Postives = 66/102 (64.71%), Query Frame = 1 
Query:    1 VGLLIRDNKNKTIKLVDVKCPLDTEFNFINTHELNMSKYNDLKLNIEKALPNYKVTLSTCIFGSLGSIPDKTFDVLDDIGVRFTDRNSLSVECALSNIEYSA 306
            V L+I D   K I LVD+KCP D+  NF     LN+ KY+ LK  I+   P++KV L TC+FGSLGS P KT ++L  IGV+ T+   L  ECALSNI +SA
Sbjct: 6098 VDLMITDLSRKKIFLVDMKCPCDSVNNFEQVDLLNLRKYDSLKNQIQAVKPDFKVELDTCVFGSLGSFPLKTSEILVKIGVKRTELKPLLKECALSNIAHSA 6199

HSP 3 Score: 93.5893 bits (231), Expect = 1.786e-23
Identity = 52/102 (50.98%), Postives = 67/102 (65.69%), Query Frame = 1 
Query:    1 VGLLIRDNKNKTIKLVDVKCPLDTEFNFINTHELNMSKYNDLKLNIEKALPNYKVTLSTCIFGSLGSIPDKTFDVLDDIGVRFTDRNSLSVECALSNIEYSA 306
            V L+I + + KTI LVD+KCP+D+  NF     LN+ KY  LKL+I+   P+YKV L TCI GSLGSI  KT D+L  +GV+      L  ECA+SNI +SA
Sbjct: 1422 VDLIITNTEKKTILLVDMKCPIDSVSNFQLVDNLNLEKYAKLKLDIQAVKPDYKVELHTCIMGSLGSIESKTEDLLLKMGVQPNRIIGLMKECAISNIAHSA 1523
[Close]
BLAST of SMED30035542 vs. Planmine SMEST
Match: SMESG000044750.1 (SMESG000044750.1)

HSP 1 Score: 92.8189 bits (229), Expect = 2.654e-23
Identity = 53/102 (51.96%), Postives = 65/102 (63.73%), Query Frame = 1 
Query:    1 VGLLIRDNKNKTIKLVDVKCPLDTEFNFINTHELNMSKYNDLKLNIEKALPNYKVTLSTCIFGSLGSIPDKTFDVLDDIGVRFTDRNSLSVECALSNIEYSA 306
            V L+I D   K I LVD+KCP DT  NF     LN+ KY+ LK+ I+ A P++KV L TCI GSLGS P KT ++L  IGV  T    L  +CALSNI +SA
Sbjct: 2270 VDLMITDMVRKKIFLVDMKCPCDTINNFALVDLLNLQKYDSLKMQIQDAKPDFKVELDTCIIGSLGSFPPKTPELLLKIGVDRTHLKGLLKDCALSNISHSA 2371

HSP 2 Score: 92.8189 bits (229), Expect = 3.384e-23
Identity = 53/102 (51.96%), Postives = 65/102 (63.73%), Query Frame = 1 
Query:    1 VGLLIRDNKNKTIKLVDVKCPLDTEFNFINTHELNMSKYNDLKLNIEKALPNYKVTLSTCIFGSLGSIPDKTFDVLDDIGVRFTDRNSLSVECALSNIEYSA 306
            V L+I D   K I LVD+KCP DT  NF     LN+ KY+ LK+ I+ A P++KV L TCI GSLGS P KT ++L  IGV  T    L  +CALSNI +SA
Sbjct: 1897 VDLMITDMVRKKIFLVDMKCPCDTINNFALVDLLNLQKYDSLKIQIQDAKPDFKVELDTCIIGSLGSFPPKTPELLLKIGVDRTHLKGLLKDCALSNISHSA 1998
The following BLAST results are available for this feature:
BLAST of SMED30035542 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 SMED30035542 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 SMED30035542 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 SMED30035542 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 SMED30035542 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 SMED30035542 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 SMED30035542 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 SMED30035542 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 SMED30035542 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 SMED30035542 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 SMED30035542 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 SMED30035542 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 SMED30035542 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 SMED30035542 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000062936.14.680e-6298.04SMESG000062936.1[more]
SMESG000046455.14.804e-2451.96SMESG000046455.1[more]
SMESG000021486.15.146e-2450.98SMESG000021486.1[more]
SMESG000021486.15.456e-2450.98SMESG000021486.1[more]
SMESG000044750.12.654e-2351.96SMESG000044750.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035542 ID=SMED30035542|Name=SMED30035542|organism=Schmidtea mediterranea sexual|type=transcript|length=306bp
GTTGGTCTACTAATTAGAGATAATAAAAATAAAACCATAAAACTTGTCGA
TGTAAAATGCCCATTGGACACAGAATTTAACTTTATCAACACCCACGAAT
TAAATATGTCTAAATATAATGATTTAAAATTAAACATTGAAAAAGCTCTT
CCTAATTATAAAGTTACTTTGTCAACTTGTATCTTTGGTTCTCTTGGCTC
TATACCTGATAAAACTTTTGACGTTTTGGATGACATTGGTGTCAGATTTA
CTGATAGAAATTCGTTGTCTGTTGAATGCGCTCTTTCGAATATAGAATAC
TCTGCC
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protein sequence of SMED30035542-orf-1

>SMED30035542-orf-1 ID=SMED30035542-orf-1|Name=SMED30035542-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
VGLLIRDNKNKTIKLVDVKCPLDTEFNFINTHELNMSKYNDLKLNIEKAL
PNYKVTLSTCIFGSLGSIPDKTFDVLDDIGVRFTDRNSLSVECALSNIEY
SA
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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:0000103central nervous system
PLANA:0000142posterior region of the whole animal
PLANA:0002075pigment cell