SMED30035346

Overview
NameSMED30035346
Smed IDSMED30035346
Length (bp)455
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 SMED30035346 (SMED30035346) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30035346 (SMED30035346) 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




SMED30035346

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymal cellSMED30035346SMESG000063591.1 SMESG000063590.1 SMESG000063568.1 dd_Smed_v4_8628_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Category 2 cellSMED30035346SMESG000063591.1 SMESG000063590.1 SMESG000063568.1 dd_Smed_v4_8628_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30035346 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002102:38604..39164 -1321
v31.002102:40375..40935 +1313
v31.002102:49535..50095 -1266
v31.002102:32777..33342 +1249
Homology
BLAST of SMED30035346 vs. Planmine SMEST
Match: SMESG000063590.1 (SMESG000063590.1)

HSP 1 Score: 99.3673 bits (246), Expect = 2.597e-27
Identity = 60/97 (61.86%), Postives = 66/97 (68.04%), Query Frame = 2
Query:   77 QDPIDSRSNDNIIDANDGSMSSPRHGSRMTSGEGTARGNDDMEIHXXXXXXXXXXXXT-IRNFMKKIKGHNSNFILGEEMKHVRSLIDGALNGVAKP 364
            QDPIDSRSNDN+ID NDGSMSSPRHGS MTSGEGTARGNDDMEIHKRR R  R    +    FM K+K   S F    +M  V+ LI  A   + KP
Sbjct:   23 QDPIDSRSNDNVIDTNDGSMSSPRHGSGMTSGEGTARGNDDMEIHKRRSRMSRKGKPSKWSKFMNKLKKQKSKFRSNRKMNKVKGLISDAFYAI-KP 118          
BLAST of SMED30035346 vs. Planmine SMEST
Match: SMESG000063590.1 (SMESG000063590.1)

HSP 1 Score: 98.9821 bits (245), Expect = 2.998e-27
Identity = 60/97 (61.86%), Postives = 66/97 (68.04%), Query Frame = 2
Query:   77 QDPIDSRSNDNIIDANDGSMSSPRHGSRMTSGEGTARGNDDMEIHXXXXXXXXXXXXT-IRNFMKKIKGHNSNFILGEEMKHVRSLIDGALNGVAKP 364
            QDPIDSRSNDN+ID NDGSMSSPRHGS MTSGEGTARGNDDMEIHKRR R  R    +    FM K+K   S F    +M  V+ LI  A   + KP
Sbjct:   14 QDPIDSRSNDNVIDTNDGSMSSPRHGSGMTSGEGTARGNDDMEIHKRRSRMSRKGKPSKWSKFMNKLKKQKSKFRSNRKMNKVKGLISDAFYAI-KP 109          
BLAST of SMED30035346 vs. Planmine SMEST
Match: SMESG000063591.1 (SMESG000063591.1)

HSP 1 Score: 98.2117 bits (243), Expect = 7.702e-27
Identity = 61/96 (63.54%), Postives = 66/96 (68.75%), Query Frame = 2
Query:   80 DPIDSRSNDNIIDANDGSMSSPRHGSRMTSGEGTARGNDDMEIHXXXXXXXXXXXXT-IRNFMKKIKGHNSNFILGEEMKHVRSLIDGALNGVAKP 364
            DPIDSRSNDNIIDA DGSMSSPRHGSRMTSGEGTARGNDDMEIHKRR R  R    +    FM K+K   S F    +M  V  LI  A+  + KP
Sbjct:   15 DPIDSRSNDNIIDAIDGSMSSPRHGSRMTSGEGTARGNDDMEIHKRRSRMSRKGKPSKWSKFMNKLKTQKSKFRSNRKMNKVEGLISDAIYAI-KP 109          
BLAST of SMED30035346 vs. Planmine SMEST
Match: SMESG000063591.1 (SMESG000063591.1)

HSP 1 Score: 98.2117 bits (243), Expect = 7.926e-27
Identity = 61/96 (63.54%), Postives = 66/96 (68.75%), Query Frame = 2
Query:   80 DPIDSRSNDNIIDANDGSMSSPRHGSRMTSGEGTARGNDDMEIHXXXXXXXXXXXXT-IRNFMKKIKGHNSNFILGEEMKHVRSLIDGALNGVAKP 364
            DPIDSRSNDNIIDA DGSMSSPRHGSRMTSGEGTARGNDDMEIHKRR R  R    +    FM K+K   S F    +M  V  LI  A+  + KP
Sbjct:   24 DPIDSRSNDNIIDAIDGSMSSPRHGSRMTSGEGTARGNDDMEIHKRRSRMSRKGKPSKWSKFMNKLKTQKSKFRSNRKMNKVEGLISDAIYAI-KP 118          
The following BLAST results are available for this feature:
BLAST of SMED30035346 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 SMED30035346 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 SMED30035346 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 SMED30035346 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 SMED30035346 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 SMED30035346 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 SMED30035346 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 SMED30035346 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 SMED30035346 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 SMED30035346 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 SMED30035346 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 SMED30035346 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 SMED30035346 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 SMED30035346 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000063590.12.597e-2761.86SMESG000063590.1[more]
SMESG000063590.12.998e-2761.86SMESG000063590.1[more]
SMESG000063591.17.702e-2763.54SMESG000063591.1[more]
SMESG000063591.17.926e-2763.54SMESG000063591.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035346 ID=SMED30035346|Name=SMED30035346|organism=Schmidtea mediterranea sexual|type=transcript|length=455bp
CAACTCGACAATGAAAATTGCTATTTTGATTCTGTCAATGATTTCATTGA
TTTCCATTATTAATGGATCAATAATTCAAGATCCGATCGATTCCCGATCA
AATGATAATATAATTGATGCTAATGATGGGTCAATGAGTTCTCCTCGTCA
CGGGTCAAGGATGACATCAGGGGAGGGAACGGCACGTGGAAATGATGATA
TGGAAATCCATAAACGAAGATGGAGATCTGGTAGAGGAAAGTCCAGCACA
ATCAGAAATTTTATGAAAAAAATTAAGGGACATAATTCAAATTTTATATT
AGGTGAGGAAATGAAACACGTTAGAAGCCTTATTGATGGAGCGTTGAATG
GAGTTGCCAAGCCGTAAATTAGCCAATGAGGCATCTAAGTTCCTCAACAA
AATGATATTCAGGGTTCATTAAAACATGATTATATTCAATAAAATAAATT
CGTCG
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protein sequence of SMED30035346-orf-1

>SMED30035346-orf-1 ID=SMED30035346-orf-1|Name=SMED30035346-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=122bp
NSTMKIAILILSMISLISIINGSIIQDPIDSRSNDNIIDANDGSMSSPRH
GSRMTSGEGTARGNDDMEIHKRRWRSGRGKSSTIRNFMKKIKGHNSNFIL
GEEMKHVRSLIDGALNGVAKP*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000028Category 2 cell
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR011528NERD
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 41..59
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 41..82
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..22
score: 0.885
NoneNo IPR availableTMHMMTMhelixcoord: 6..25