SMED30010450

Overview
NameSMED30010450
Smed IDSMED30010450
Length (bp)666
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 SMED30010450 (SMED30010450) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30010450 (SMED30010450) 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




SMED30010450

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
prepharyngeal regionSMED30010450 SmedASXL_060927SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
muscle progenitor cellSMED30010450 SMED30010450smed_20140614PMID:29906446
Zeng et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
X1 cellSMED30010450 SmedASXL_060927SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30010450 SmedASXL_060927SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
neoblastSMED30010450 dd_Smed_v4_13055_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
SMED30010450 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.012344:11385..12039 -3187
v31.008079:21984..22637 -3134
Homology
BLAST of SMED30010450 vs. Planmine SMEST
Match: SMESG000056869.1 (SMESG000056869.1)

HSP 1 Score: 88.9669 bits (219), Expect = 1.169e-21
Identity = 48/102 (47.06%), Postives = 62/102 (60.78%), Query Frame = 3
Query:  195 DDAAYTSIAIKREPHRNPAHEDRNSAEYTLARLEQEFRKAQGRVKMTHQHLAQMNSDIRSGRIISTDAHVPAYNVVYKPDSPILRSILAPTIMVVSTPLIHP 500
            D+    SIAIKREP RNPA E R  AEYT+ ++E+  RK   +  +  Q LAQ+N DI SG I STD+  P Y V ++ D P L  + APT +V+   LI P
Sbjct:   63 DEVELPSIAIKREPGRNPAREVRQQAEYTVMKMEEMERKYHRKAVLARQRLAQINRDIASGVIPSTDSFPPTYEVSFELDDPRLLQMTAPTKLVIPEELIQP 164          
BLAST of SMED30010450 vs. Planmine SMEST
Match: SMESG000056869.1 (SMESG000056869.1)

HSP 1 Score: 88.5817 bits (218), Expect = 1.297e-21
Identity = 48/102 (47.06%), Postives = 62/102 (60.78%), Query Frame = 3
Query:  195 DDAAYTSIAIKREPHRNPAHEDRNSAEYTLARLEQEFRKAQGRVKMTHQHLAQMNSDIRSGRIISTDAHVPAYNVVYKPDSPILRSILAPTIMVVSTPLIHP 500
            D+    SIAIKREP RNPA E R  AEYT+ ++E+  RK   +  +  Q LAQ+N DI SG I STD+  P Y V ++ D P L  + APT +V+   LI P
Sbjct:   61 DEVELPSIAIKREPGRNPAREVRQQAEYTVMKMEEMERKYHRKAVLARQRLAQINRDIASGVIPSTDSFPPTYEVSFELDDPRLLQMTAPTKLVIPEELIQP 162          
BLAST of SMED30010450 vs. Planmine SMEST
Match: SMESG000044971.1 (SMESG000044971.1)

HSP 1 Score: 88.5817 bits (218), Expect = 4.718e-20
Identity = 52/128 (40.62%), Postives = 70/128 (54.69%), Query Frame = 3
Query:  213 SIAIKREPHRNPAHEDRNSAEYTLARLEQEFRKAQGRVKMTHQHLAQMNSDIRSGRIISTDAHVPAYNVVYKPDSPILRSILAPTIMVVSTPLIHP*ILQCMQPMLELTDNTHVRRPP--GPKRSRQQ 590
            SIAIKREP  NPA E R  AEY   ++E+  RK   +  +  Q LAQ+N DI SG I STD   P Y V ++ D P L  + APT MV+   L+    L+      +  D+T+  R P   PKR+ ++
Sbjct: 1188 SIAIKREPGHNPAREARQRAEYVAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKMVIPEKLVQS-TLRNRLGSRQTGDHTYASRHPQWNPKRNNRR 1314          
BLAST of SMED30010450 vs. Planmine SMEST
Match: SMESG000048378.1 (SMESG000048378.1)

HSP 1 Score: 88.1965 bits (217), Expect = 5.763e-20
Identity = 47/111 (42.34%), Postives = 65/111 (58.56%), Query Frame = 3
Query:  189 DQD-DAAYTSIAIKREPHRNPAHEDRNSAEYTLARLEQEFRKAQGRVKMTHQHLAQMNSDIRSGRIISTDAHVPAYNVVYKPDSPILRSILAPTIMVVSTPLIHP*ILQCM 518
            DQD D    S+AIK +P RNPA E  +  E+ L + E   RK + +  +  + LA++NSDI SGRI+S+D H+P Y V +  D P L SI AP  + V   +I P IL  +
Sbjct: 1206 DQDEDVEMPSLAIKSKPGRNPAREIGHDDEFMLQQFENLERKCRWKASLQRRRLARINSDISSGRILSSDGHLPKYGVAFNLDDPALLSIDAPVHLAVPKQIIQPDILDSL 1316          
BLAST of SMED30010450 vs. Planmine SMEST
Match: SMESG000048378.1 (SMESG000048378.1)

HSP 1 Score: 88.1965 bits (217), Expect = 5.941e-20
Identity = 47/111 (42.34%), Postives = 65/111 (58.56%), Query Frame = 3
Query:  189 DQD-DAAYTSIAIKREPHRNPAHEDRNSAEYTLARLEQEFRKAQGRVKMTHQHLAQMNSDIRSGRIISTDAHVPAYNVVYKPDSPILRSILAPTIMVVSTPLIHP*ILQCM 518
            DQD D    S+AIK +P RNPA E  +  E+ L + E   RK + +  +  + LA++NSDI SGRI+S+D H+P Y V +  D P L SI AP  + V   +I P IL  +
Sbjct: 1225 DQDEDVEMPSLAIKSKPGRNPAREIGHDDEFMLQQFENLERKCRWKASLQRRRLARINSDISSGRILSSDGHLPKYGVAFNLDDPALLSIDAPVHLAVPKQIIQPDILDSL 1335          
The following BLAST results are available for this feature:
BLAST of SMED30010450 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 SMED30010450 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 SMED30010450 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 SMED30010450 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 SMED30010450 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 SMED30010450 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 SMED30010450 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 SMED30010450 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 SMED30010450 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 SMED30010450 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 SMED30010450 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 SMED30010450 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 SMED30010450 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 SMED30010450 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000056869.11.169e-2147.06SMESG000056869.1[more]
SMESG000056869.11.297e-2147.06SMESG000056869.1[more]
SMESG000044971.14.718e-2040.63SMESG000044971.1[more]
SMESG000048378.15.763e-2042.34SMESG000048378.1[more]
SMESG000048378.15.941e-2042.34SMESG000048378.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010450 ID=SMED30010450|Name=SMED30010450|organism=Schmidtea mediterranea sexual|type=transcript|length=666bp
AAATTATATAAACGACCGAGTCATTCTAGATAATTTGGTTATCATGGGAA
AATATTCACCCCTGACTGAATACAAAAAATAATAACAAAGACTCCATGGT
CAAACCATTCTTCAATATTTATTCACCAGCCATCAAAGAACCAATCATAT
AAATTCATATCCTGGAAATAGGTAAGTTTCGGGACGGCGATCAAGATGAT
GCGGCATATACGAGTATCGCAATTAAGCGGGAGCCTCACCGCAACCCCGC
CCACGAGGACAGAAACAGTGCCGAATATACACTAGCTAGACTCGAACAGG
AATTTAGAAAGGCCCAAGGGAGAGTNAAGATGACTCACCAGCACTTAGCC
CAAATGAACAGTGACATCCGGAGTGGCCGAATTATAAGCACAGACGCACA
TGTGCCAGCCTACAATGTGGTTTACAAACCAGACAGCCCGATATTGCGGT
CGATATTGGCCCCTACAATAATGGTAGTCTCAACACCATTAATCCATCCA
TGAATATTGCAATGTATGCAACCAATGTTGGAGCTGACGGACAACACCCA
TGTCAGAAGGCCACCCGGACCAAAGAGAAGCAGACAGCAATGGCAATGAA
ATAATAGAACCCAGTCAATGATCCTGTTGCTTGTAATAGTTTAATAAAGT
GTTTTAGATCGGAAGA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000019muscle progenitor cell
PLANA:0000419prepharyngeal region
PLANA:0002109X1 cell
PLANA:0002111X2 cell