SMED30013474

Overview
NameSMED30013474
Smed IDSMED30013474
Length (bp)356
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 SMED30013474 (SMED30013474) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30013474 (SMED30013474) 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




SMED30013474

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
neuronSMED30013474SMESG000069967.1 dd_Smed_v4_6939_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
neuronSMED30013474SMESG000069967.1 dd_Smed_v4_6939_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
muscle cellSMED30013474SMESG000069967.1 dd_Smed_v4_6939_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parapharyngeal cellSMED30013474SMESG000069967.1 dd_Smed_v4_6939_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
headSMED30013474SMESG000069967.1 dd_Smed_v6_6939_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30013474 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001794:5612..5951 +1684
Homology
BLAST of SMED30013474 vs. Planmine SMEST
Match: SMESG000044971.1 (SMESG000044971.1)

HSP 1 Score: 73.1738 bits (178), Expect = 2.282e-17
Identity = 32/50 (64.00%), Postives = 40/50 (80.00%), Query Frame = -3
Query:  106 VSFELDDPRLMNMNTPTKLILPDRLVQSMLLSQPEQRQLGDHTYARQHPQ 255
            VSFELDDPRLM M  PTK+++P++LVQS L ++   RQ GDHTYA +HPQ
Sbjct: 1256 VSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRLGSRQTGDHTYASRHPQ 1305          

HSP 2 Score: 31.187 bits (69), Expect = 2.282e-17
Identity = 14/22 (63.64%), Postives = 15/22 (68.18%), Query Frame = -1
Query:  267 QWNADIASGLIPITDDFTSKYG 332
            Q N DIASG IP TD F  +YG
Sbjct: 1234 QVNRDIASGAIPSTDGFPPEYG 1255          
BLAST of SMED30013474 vs. Planmine SMEST
Match: SMESG000031842.1 (SMESG000031842.1)

HSP 1 Score: 72.7886 bits (177), Expect = 3.193e-17
Identity = 32/51 (62.75%), Postives = 40/51 (78.43%), Query Frame = -3
Query:  103 VSFELDDPRLMNMNTPTKLILPDRLVQSMLLSQPEQRQLGDHTYARQHPQL 255
            VSFELDDPRLM M  PTK+++P++LVQS L ++   RQ GDHTYA +HPQ 
Sbjct:  820 VSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRLGSRQTGDHTYASRHPQW 870          

HSP 2 Score: 31.187 bits (69), Expect = 3.193e-17
Identity = 14/22 (63.64%), Postives = 15/22 (68.18%), Query Frame = -1
Query:  267 QWNADIASGLIPITDDFTSKYG 332
            Q N DIASG IP TD F  +YG
Sbjct:  798 QVNRDIASGAIPSTDGFPPEYG 819          
BLAST of SMED30013474 vs. Planmine SMEST
Match: SMESG000031842.1 (SMESG000031842.1)

HSP 1 Score: 73.1738 bits (178), Expect = 3.604e-17
Identity = 32/51 (62.75%), Postives = 40/51 (78.43%), Query Frame = -3
Query:  103 VSFELDDPRLMNMNTPTKLILPDRLVQSMLLSQPEQRQLGDHTYARQHPQL 255
            VSFELDDPRLM M  PTK+++P++LVQS L ++   RQ GDHTYA +HPQ 
Sbjct:  894 VSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRLGSRQTGDHTYASRHPQW 944          

HSP 2 Score: 30.8018 bits (68), Expect = 3.604e-17
Identity = 14/22 (63.64%), Postives = 15/22 (68.18%), Query Frame = -1
Query:  267 QWNADIASGLIPITDDFTSKYG 332
            Q N DIASG IP TD F  +YG
Sbjct:  872 QVNRDIASGAIPSTDGFPPEYG 893          
BLAST of SMED30013474 vs. Planmine SMEST
Match: SMESG000027782.1 (SMESG000027782.1)

HSP 1 Score: 71.633 bits (174), Expect = 6.797e-17
Identity = 32/49 (65.31%), Postives = 39/49 (79.59%), Query Frame = -3
Query:  109 VSFELDDPRLMNMNTPTKLILPDRLVQSMLLSQPEQRQLGDHTYARQHP 255
            VSFELDDPRLM M  PTKL+LP++L+QS L ++   RQ GDHTYA +HP
Sbjct:  156 VSFELDDPRLMQMTAPTKLVLPEKLIQSTLRNRLGSRQTGDHTYASRHP 204          

HSP 2 Score: 31.187 bits (69), Expect = 6.797e-17
Identity = 14/22 (63.64%), Postives = 15/22 (68.18%), Query Frame = -1
Query:  267 QWNADIASGLIPITDDFTSKYG 332
            Q N DIASG IP TD F  +YG
Sbjct:  134 QVNRDIASGAIPSTDGFPPEYG 155          
BLAST of SMED30013474 vs. Planmine SMEST
Match: SMESG000042475.1 (SMESG000042475.1)

HSP 1 Score: 72.0182 bits (175), Expect = 7.458e-17
Identity = 32/49 (65.31%), Postives = 39/49 (79.59%), Query Frame = -3
Query:  109 VSFELDDPRLMNMNTPTKLILPDRLVQSMLLSQPEQRQLGDHTYARQHP 255
            VSFELDDPRLM M  PTKL+LP++L+QS L ++   RQ GDHTYA +HP
Sbjct: 1451 VSFELDDPRLMQMTAPTKLVLPEKLIQSTLRNRLGSRQTGDHTYASRHP 1499          

HSP 2 Score: 30.4166 bits (67), Expect = 7.458e-17
Identity = 14/22 (63.64%), Postives = 15/22 (68.18%), Query Frame = -1
Query:  267 QWNADIASGLIPITDDFTSKYG 332
            Q N DIASG IP TD F  +YG
Sbjct: 1429 QVNRDIASGAIPSTDGFPQEYG 1450          
The following BLAST results are available for this feature:
BLAST of SMED30013474 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 SMED30013474 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 SMED30013474 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 SMED30013474 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 SMED30013474 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 SMED30013474 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 SMED30013474 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 SMED30013474 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 SMED30013474 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 SMED30013474 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 SMED30013474 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 SMED30013474 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 SMED30013474 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 SMED30013474 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000044971.12.282e-1764.00SMESG000044971.1[more]
SMESG000031842.13.193e-1762.75SMESG000031842.1[more]
SMESG000031842.13.604e-1762.75SMESG000031842.1[more]
SMESG000027782.16.797e-1765.31SMESG000027782.1[more]
SMESG000042475.17.458e-1765.31SMESG000042475.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013474 ID=SMED30013474|Name=SMED30013474|organism=Schmidtea mediterranea sexual|type=transcript|length=356bp
AACTTCATGTAGCTATTCATTGGTACCATAATTCAAGTCTTGCTTTTCGG
TTCATCGTTGACTCTCGGACGGATTATTTCGGTGAAGATGGTCCGTACGT
TTCAATTGTGGGTGTTGTCGAGCATATGTGTGATCTCCGAGCTGCCGTTG
TTCTGGCTGACTCAGTAGCATTGACTGTACCAGTCGATCTGGTAAAATTA
GCTTTGTTGGTGTGTTCATATTCATCAGTCTGGGGTCATCTAGTTCGAAT
GAAACTTACTTCGAAATCCGTACTTCGAAGTGAAGTCATCGGTGATTGGA
ATTAGTCCGCTGGCAATATCAGCATTCCATTGGATTCAAGATTAATAATG
TCATTT
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protein sequence of SMED30013474-orf-1

>SMED30013474-orf-1 ID=SMED30013474-orf-1|Name=SMED30013474-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=101bp
LHVAIHWYHNSSLAFRFIVDSRTDYFGEDGPYVSIVGVVEHMCDLRAAVV
LADSVALTVPVDLVKLALLVCSYSSVWGHLVRMKLTSKSVLRSEVIGDWN
*
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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:0000418head
PLANA:0003117parapharyngeal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 22..57
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 36..57