SMED30033485

Overview
NameSMED30033485
Smed IDSMED30033485
Length (bp)839
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 SMED30033485 (SMED30033485) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30033485 (SMED30033485) 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.
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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



SMED30033485

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
oocyteSMED30033485 Contig21774newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30033485 Contig21774uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30033485 Contig21774newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30033485 Contig21774uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30033485 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000940:29255..29993 +3610
Homology
[Close]
BLAST of SMED30033485 vs. Planmine SMEST
Match: SMESG000014051.1 (SMESG000014051.1)

HSP 1 Score: 81.6481 bits (200), Expect = 1.771e-28
Identity = 45/76 (59.21%), Postives = 54/76 (71.05%), Query Frame = 2 
Query:  275 WKNEKALTQAQRTQIGGLEVALLGCQEGSAVTYQLIFARHNSRIVIR---VDRMG*KK*QSHSRPGRAERNRRRLQ 493
            WK+E+AL QAQRTQI GLEVAL  CQEGSAVTY L+FA   +++  R     +   KK +SH+RPGR ER RRR Q
Sbjct:  431 WKDERALNQAQRTQIKGLEVALSACQEGSAVTYPLVFA--PAQLAYRDQEKPQSTNKKPRSHARPGRTERLRRRAQ 504

HSP 2 Score: 62.7734 bits (151), Expect = 1.771e-28
Identity = 30/64 (46.88%), Postives = 48/64 (75.00%), Query Frame = 3 
Query:   99 DMDATRILSQKLKKL*QANTDMHQQLLQLCREIQEVKANWFKSTRVKLLYQRLTATQQSGKTKK 290
            +M+ATRI+ ++LK+L + N  +H+QLLQ  R+IQ++KA W +  ++K LYQRLTA Q+  K ++
Sbjct:  372 EMEATRIIHRELKELRRENQHLHRQLLQQSRDIQQLKATWAEPAKMKALYQRLTAAQRGWKDER 435
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BLAST of SMED30033485 vs. Planmine SMEST
Match: SMESG000073618.1 (SMESG000073618.1)

HSP 1 Score: 70.8626 bits (172), Expect = 6.103e-26
Identity = 41/76 (53.95%), Postives = 50/76 (65.79%), Query Frame = 2 
Query:  275 WKNEKALTQAQRTQIGGLEVALLGCQEGSAVTYQLIFARHNSRIVIRVDRMG---*KK*QSHSRPGRAERNRRRLQ 493
            WK E+ L Q+Q+TQI  LEVAL  CQEGSAVTY L+FA   +++  R         KK +SH+RPGR ER RRR Q
Sbjct:  201 WKEERVLNQSQQTQIKRLEVALSACQEGSAVTYPLVFA--PAQLAYRDQEKAQSTNKKPRSHARPGRTERLRRRSQ 274

HSP 2 Score: 65.0846 bits (157), Expect = 6.103e-26
Identity = 32/64 (50.00%), Postives = 48/64 (75.00%), Query Frame = 3 
Query:   99 DMDATRILSQKLKKL*QANTDMHQQLLQLCREIQEVKANWFKSTRVKLLYQRLTATQQSGKTKK 290
            +M+ATRI+ ++LK+L + N  +H+QLLQ  RE+Q+VKA W +  ++K LYQRLTA QQ  K ++
Sbjct:  142 EMEATRIIHRELKELRRENQHLHRQLLQQGRELQQVKATWAEPAKMKALYQRLTAAQQGWKEER 205
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BLAST of SMED30033485 vs. Planmine SMEST
Match: SMESG000001279.1 (SMESG000001279.1)

HSP 1 Score: 75.0998 bits (183), Expect = 1.043e-25
Identity = 40/74 (54.05%), Postives = 50/74 (67.57%), Query Frame = 2 
Query:  275 WKNEKALTQAQRTQIGGLEVALLGCQEGSAVTYQLIFARHNSRIVIR---VDRMG*KK*QSHSRPGRAERNRRR 487
            W++EK+L QAQRTQI GLEVAL  CQEGSAVTY  +FA   +++  R     +   K+   H+RPGR ER RRR
Sbjct:  100 WRDEKSLNQAQRTQIKGLEVALSACQEGSAVTYPFVFA--PAQLAYRDQDKQKSSNKRSHPHARPGRTERLRRR 171

HSP 2 Score: 60.077 bits (144), Expect = 1.043e-25
Identity = 30/64 (46.88%), Postives = 44/64 (68.75%), Query Frame = 3 
Query:   99 DMDATRILSQKLKKL*QANTDMHQQLLQLCREIQEVKANWFKSTRVKLLYQRLTATQQSGKTKK 290
            +M A RIL+ +LK+L + N  +HQQLLQ   E+Q +KA W +  ++K +YQRLTA QQ  + +K
Sbjct:   41 EMKAMRILNHELKELRRENAHLHQQLLQQSPELQRIKATWAEPEKMKSVYQRLTAAQQGWRDEK 104
[Close]
BLAST of SMED30033485 vs. Planmine SMEST
Match: SMESG000064545.1 (SMESG000064545.1)

HSP 1 Score: 64.3142 bits (155), Expect = 4.153e-22
Identity = 33/63 (52.38%), Postives = 47/63 (74.60%), Query Frame = 3 
Query:  102 MDATRILSQKLKKL*QANTDMHQQLLQLCREIQEVKANWFKSTRVKLLYQRLTATQQSGKTKK 290
            M AT+IL Q+LK+L + N  +H+QLLQ  REIQ++KA W +  ++K LYQRLTA+QQ  K ++
Sbjct:    1 MKATKILHQELKELRRENQHLHRQLLQQSREIQQLKATWAEPEKMKALYQRLTASQQGWKEER 63

HSP 2 Score: 58.9214 bits (141), Expect = 4.153e-22
Identity = 26/37 (70.27%), Postives = 30/37 (81.08%), Query Frame = 2 
Query:  275 WKNEKALTQAQRTQIGGLEVALLGCQEGSAVTYQLIF 385
            WK E+ L QA+RTQI GLEVAL  CQEGSAVTY L++
Sbjct:   59 WKEERVLNQARRTQIKGLEVALSACQEGSAVTYPLMY 95
[Close]
BLAST of SMED30033485 vs. Planmine SMEST
Match: SMESG000033890.1 (SMESG000033890.1)

HSP 1 Score: 64.6994 bits (156), Expect = 4.914e-22
Identity = 33/71 (46.48%), Postives = 45/71 (63.38%), Query Frame = 2 
Query:  275 WKNEKALTQAQRTQIGGLEVALLGCQEGSAVTYQLIFARHNSRIVIRVDRMG*KK*QSHSRPGRAERNRRR 487
            W++EK L Q+Q+ QI  LEVAL  CQEG+A+TYQL+FA      +   +     K  +  RPG+AER +RR
Sbjct:   66 WEDEKQLGQSQKIQILSLEVALSACQEGNAITYQLVFAPAQLAYMETTEATKPAKKPAERRPGKAERAKRR 136

HSP 2 Score: 58.151 bits (139), Expect = 4.914e-22
Identity = 29/66 (43.94%), Postives = 44/66 (66.67%), Query Frame = 3 
Query:   93 FLDMDATRILSQKLKKL*QANTDMHQQLLQLCREIQEVKANWFKSTRVKLLYQRLTATQQSGKTKK 290
             LDM+    L+++L K  Q N  +H QLLQL +EIQ+++A+W +  R K +YQRLTA Q+  + +K
Sbjct:    5 ILDMNRIGTLTKELTKSRQQNEKLHSQLLQLNKEIQQIRASWIEPARPKRIYQRLTAAQRGWEDEK 70
The following BLAST results are available for this feature:
BLAST of SMED30033485 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 SMED30033485 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 SMED30033485 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 SMED30033485 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 SMED30033485 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 SMED30033485 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 SMED30033485 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 SMED30033485 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 SMED30033485 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 SMED30033485 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 SMED30033485 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 SMED30033485 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 SMED30033485 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 SMED30033485 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000014051.11.771e-2859.21SMESG000014051.1[more]
SMESG000073618.16.103e-2653.95SMESG000073618.1[more]
SMESG000001279.11.043e-2554.05SMESG000001279.1[more]
SMESG000064545.14.153e-2252.38SMESG000064545.1[more]
SMESG000033890.14.914e-2246.48SMESG000033890.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033485 ID=SMED30033485|Name=SMED30033485|organism=Schmidtea mediterranea sexual|type=transcript|length=839bp
TAATAAAAAATATGGATATAAACGAAATACGCTAGGACAATCTGAATAAT
AACCCTTTATGGTCTAAATAGTTTATTTGAATTTTATTTGGATTTTTAGA
TATGGATGCGACTCGAATACTCAGCCAAAAGCTAAAGAAACTATGACAGG
CAAATACGGATATGCACCAACAATTGCTACAACTATGCCGGGAGATACAG
GAGGTCAAAGCCAATTGGTTCAAATCAACGCGAGTCAAGCTGCTGTATCA
ACGCCTCACCGCGACTCAGCAGAGTGGAAAAACGAAAAAGCGTTGACTCA
GGCTCAGCGAACCCAAATTGGAGGGTTAGAAGTCGCGCTCTTGGGGTGCC
AAGAAGGGAGTGCAGTAACCTACCAACTGATTTTTGCCCGACACAACTCA
CGTATCGTAATCAGAGTCGACCGGATGGGTTGAAAAAAATGACAATCCCA
TTCAAGGCCGGGTAGGGCAGAGCGAAATCGGAGACGACTCCAGCAATTCA
ATAATGAAAACTCATTAGCAAAAGTTTTCCTTCAGAAATTTCTTAAATTA
CANNNTCNAAGTTTTATTAATGAATTAGTTGAAATAAGGTTGCTTTAAAT
TGAATTAGTAAATAACGAAAAGGGAACCAATGCCATTTAGGCATGTTTTT
CAACAGTAATAAACGCTAACATTTACAGATAAACTTAGTGAGACCTTAAG
GGAACTCTACTCCGGACGTATGCATGGGATCGATAGTAACGGACGGGAAA
GGGGGTGTTAATATCGAGAAAGTCAGAGACATTAAGTAGACGTAAGTCCT
TCTATCGGCAGTCAGGAACCCGAAAGCGAAAATATCATG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland