SMED30021328

Overview
NameSMED30021328
Smed IDSMED30021328
Length (bp)1019
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell 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 SMED30021328 (SMED30021328) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021328 (SMED30021328) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30021328 (SMED30021328) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021328 (SMED30021328) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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



SMED30021328

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
X2 cellSMED30021328SMESG000028190.1 SmedASXL_008523SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
cephalic gangliaSMED30021328SMESG000028190.1 dd_Smed_v4_17722_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30021328SMESG000028190.1 dd_Smed_v4_17722_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30021328SMESG000028190.1 dd_Smed_v4_17722_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30021328SMESG000028190.1 dd_Smed_v4_17722_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
SMED30021328 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011476:7214..8235 -5075
v31.016301:6585..7603 +4951
v31.000249:44830..45836 -3463
v31.019454:4035..5001 +3305
Homology
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BLAST of SMED30021328 vs. Planmine SMEST
Match: SMESG000028190.1 (SMESG000028190.1)

HSP 1 Score: 185.652 bits (470), Expect = 5.759e-59
Identity = 107/124 (86.29%), Postives = 107/124 (86.29%), Query Frame = 2 
Query:  539 MPHVHKSDRYILLITKESVSFPQSQFRKMNIQWDTIEMTPKPXXXXXXXXXXXRRCETRRNELMERKEDEGIDIVLFIKKFLTIYLRETHRPPRFDYRPSNNSGTSPKSEYRRDQHEKTNNTLI 910
            MPHVHKSDRYILLITKESVSFPQSQFRKMNIQWDTIEMTPKPNNGNQNGINFNRRCETRRNELMERKEDE                 ETHRPPRFDYRPSNNSGTSPKSEYRRDQHEKTNNTLI
Sbjct:    1 MPHVHKSDRYILLITKESVSFPQSQFRKMNIQWDTIEMTPKPNNGNQNGINFNRRCETRRNELMERKEDE-----------------ETHRPPRFDYRPSNNSGTSPKSEYRRDQHEKTNNTLI 107
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BLAST of SMED30021328 vs. Planmine SMEST
Match: SMESG000028190.1 (SMESG000028190.1)

HSP 1 Score: 124.405 bits (311), Expect = 1.828e-44
Identity = 71/71 (100.00%), Postives = 71/71 (100.00%), Query Frame = 2 
Query:  539 MPHVHKSDRYILLITKESVSFPQSQFRKMNIQWDTIEMTPKPXXXXXXXXXXXRRCETRRNELMERKEDEG 751
            MPHVHKSDRYILLITKESVSFPQSQFRKMNIQWDTIEMTPKPNNGNQNGINFNRRCETRRNELMERKEDEG
Sbjct:    1 MPHVHKSDRYILLITKESVSFPQSQFRKMNIQWDTIEMTPKPNNGNQNGINFNRRCETRRNELMERKEDEG 71

HSP 2 Score: 73.9442 bits (180), Expect = 1.828e-44
Identity = 36/36 (100.00%), Postives = 36/36 (100.00%), Query Frame = 3 
Query:  810 GRHDSTIARAITLERPQRASTEETSMRKQIIPSYER 917
            GRHDSTIARAITLERPQRASTEETSMRKQIIPSYER
Sbjct:   71 GRHDSTIARAITLERPQRASTEETSMRKQIIPSYER 106
[Close]
BLAST of SMED30021328 vs. Planmine SMEST
Match: SMESG000028190.1 (SMESG000028190.1)

HSP 1 Score: 74.3294 bits (181), Expect = 3.960e-27
Identity = 36/36 (100.00%), Postives = 36/36 (100.00%), Query Frame = 3 
Query:  810 GRHDSTIARAITLERPQRASTEETSMRKQIIPSYER 917
            GRHDSTIARAITLERPQRASTEETSMRKQIIPSYER
Sbjct:   43 GRHDSTIARAITLERPQRASTEETSMRKQIIPSYER 78

HSP 2 Score: 66.2402 bits (160), Expect = 3.960e-27
Identity = 43/43 (100.00%), Postives = 43/43 (100.00%), Query Frame = 2 
Query:  623 MNIQWDTIEMTPKPXXXXXXXXXXXRRCETRRNELMERKEDEG 751
            MNIQWDTIEMTPKPNNGNQNGINFNRRCETRRNELMERKEDEG
Sbjct:    1 MNIQWDTIEMTPKPNNGNQNGINFNRRCETRRNELMERKEDEG 43
[Close]
BLAST of SMED30021328 vs. Planmine SMEST
Match: SMESG000077820.1 (SMESG000077820.1)

HSP 1 Score: 100.523 bits (249), Expect = 3.409e-26
Identity = 68/116 (58.62%), Postives = 78/116 (67.24%), Query Frame = 2 
Query:  539 MPHVHKSDRYILLITKESVSFPQSQFRKMNIQWDTIEMTPKPXXXXXXXXXXXRRCETRRNELMERKEDEGIDIVLFIKKFLTIYLRETHRPPRFDYRPSNNSG----TSPKSEYR 874
            M H+H+ DRYIL IT+ESVS PQ QFRKMN+Q D IEMT KPNNGN+N IN+NRR ETR NELME+  DEG                  HRPP+F+YRP NNSG    TS K EY+
Sbjct:    1 MSHMHEPDRYILTITEESVSIPQHQFRKMNVQRDVIEMTHKPNNGNKNCINYNRRGETRLNELMEK--DEG-----------------AHRPPQFEYRPINNSGPSQITSIKEEYQ 97
The following BLAST results are available for this feature:
BLAST of SMED30021328 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 SMED30021328 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 SMED30021328 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 SMED30021328 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 SMED30021328 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 SMED30021328 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 SMED30021328 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 SMED30021328 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 SMED30021328 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 SMED30021328 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 SMED30021328 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 SMED30021328 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 SMED30021328 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 SMED30021328 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000028190.15.759e-5986.29SMESG000028190.1[more]
SMESG000028190.11.828e-44100.00SMESG000028190.1[more]
SMESG000028190.13.960e-27100.00SMESG000028190.1[more]
SMESG000077820.13.409e-2658.62SMESG000077820.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021328 ID=SMED30021328|Name=SMED30021328|organism=Schmidtea mediterranea sexual|type=transcript|length=1019bp
TTAACCAAACACAGAACATTTATTTTAATAGTTCACACTTCTTAACATGT
AAGCTCGGTTTTCCCTTTTAAATCTGCAGGAGGACGTAAAATTTCTGTTT
ATCACTTATGATTTAAAACAGCTATATTTTGGTAAAATTAGGAATATTAA
CTCAAAGGCAATTCGATTATGAATCTGATTGAGAAGAACCACGAAATCCA
ATGATTTCAAAACCAAGCAGATATAAATGAATAAGAAGTTTACGAAAATG
CACTTACCGTTAGCCGAAAAATCAACAAATGGAGTTATGACTGGAATCAG
ATAATACGTTCATCCAATAATTAAAACTCTCCGGGATTAATGATAAAATT
GTGATGAAGATATCGATTAAATGATCACGTGGTCAATGACGTCATGACAC
ACCAACAATGATAGAGCGGCAGTGCAGAAAGTGTGGTGTACAGTATGCTA
GAATCTCTAACAAAAATTCTTCAACGATGAAGAATCAAAATATCAGGTCG
AACAAATGGAAGGGAATTTATAGATCATCCCCGACTAAATGCCACACGTG
CACAAATCAGACAGGTATATATTACTGATCACAAAAGAATCAGTCAGTTT
TCCGCAATCTCAATTTAGAAAAATGAACATACAATGGGATACGATAGAAA
TGACTCCGAAACCGAATAATGGGAACCAGAACGGTATCAACTTCAACCGA
CGATGCGAAACCAGAAGGAATGAACTGATGGAGAGAAAGGAGGACGAAGG
TATAGATATAGTTCTATTTATTAAAAAGTTTTTAACCATTTATCTACGAG
AAACACATAGGCCGCCACGATTCGACTATCGCCCGAGCAATAACTCTGGA
ACGTCCCCAAAGAGCGAGTACCGAAGAGACCAGCATGAGAAAACAAATAA
TACCCTCATATGAGCGTTGATCATGTCCAATAAATTATTTACTAAAAACA
AGAAGCGTACTGTTGTGTTTTGTTTTCCAAATTCTATGTGGATACAATTT
ATTCCTTCATATGAGCATC
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protein sequence of SMED30021328-orf-1

>SMED30021328-orf-1 ID=SMED30021328-orf-1|Name=SMED30021328-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=125bp
MPHVHKSDRYILLITKESVSFPQSQFRKMNIQWDTIEMTPKPNNGNQNGI
NFNRRCETRRNELMERKEDEGIDIVLFIKKFLTIYLRETHRPPRFDYRPS
NNSGTSPKSEYRRDQHEKTNNTLI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell
PLANA:0000101muscle cell
PLANA:0002111X2 cell