SMED30014112

Overview
NameSMED30014112
Smed IDSMED30014112
Length (bp)748
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 SMED30014112 (SMED30014112) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30014112 (SMED30014112) 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 SMED30014112 (SMED30014112) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30014112 (SMED30014112) 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




SMED30014112

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30014112SMESG000043425.1 SMESG000036246.1 dd_Smed_v4_2014_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30014112SMESG000043425.1 SMESG000036246.1 dd_Smed_v4_2014_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30014112SMESG000043425.1 SMESG000036246.1 dd_Smed_v4_2014_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30014112SMESG000043425.1 SMESG000036246.1 dd_Smed_v4_2014_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30014112SMESG000054821.1 SMESG000054819.1 SMESG000028508.1 Contig31297newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30014112SMESG000054821.1 SMESG000054819.1 SMESG000028508.1 Contig31297uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30014112 vs. Planmine SMEST
Match: SMESG000036246.1 (SMESG000036246.1)

HSP 1 Score: 169.859 bits (429), Expect = 4.055e-54
Identity = 98/98 (100.00%), Postives = 98/98 (100.00%), Query Frame = 3
Query:  435 MPMKQXXXXXXXXXXXXXXXVLINLIFAETTDPLKRFKQEDWEKFNIISRRNPYFNELYGHQQIHDGKRSWMNKETKKTVKDSPEFFLLDHVLDDFSK 728
            MPMKQITSSFTSLFIFSMILVLINLIFAETTDPLKRFKQEDWEKFNIISRRNPYFNELYGHQQIHDGKRSWMNKETKKTVKDSPEFFLLDHVLDDFSK
Sbjct:    1 MPMKQITSSFTSLFIFSMILVLINLIFAETTDPLKRFKQEDWEKFNIISRRNPYFNELYGHQQIHDGKRSWMNKETKKTVKDSPEFFLLDHVLDDFSK 98          
BLAST of SMED30014112 vs. Planmine SMEST
Match: SMESG000011558.1 (SMESG000011558.1)

HSP 1 Score: 58.5362 bits (140), Expect = 3.009e-11
Identity = 28/77 (36.36%), Postives = 47/77 (61.04%), Query Frame = 3
Query:  495 VLINLIFAETTDPL---KRFKQEDWEKFNIISRRNPYFNELYGHQQIHDGKRSWMNKETKKTVKDSPEFFLLDHVLD 716
            ++I++     T+ L   KR ++ +W   + ++ R+P FNEL+GHQ+IHDGKRS      +   + +P FFL+D  +D
Sbjct:   10 LIISIALYRVTNALGAMKRVERREWNLLDALNNRSPLFNELFGHQEIHDGKRS------QGLQRYTPAFFLMDRAID 80          
The following BLAST results are available for this feature:
BLAST of SMED30014112 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 SMED30014112 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 SMED30014112 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 SMED30014112 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 SMED30014112 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 SMED30014112 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 SMED30014112 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 SMED30014112 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 SMED30014112 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 SMED30014112 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 SMED30014112 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 SMED30014112 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 SMED30014112 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 SMED30014112 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000036246.14.055e-54100.00SMESG000036246.1[more]
SMESG000011558.13.009e-1136.36SMESG000011558.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014112 ID=SMED30014112|Name=SMED30014112|organism=Schmidtea mediterranea sexual|type=transcript|length=748bp
ATCTTGTTATTTAAATTATTCTAGCTTTCACAAGTCGGCACGAGTCACCA
GCTGTTACCGCCTATCACATTTTCCGTTCAATCATTTCATATCATTTGAT
TTTCTTATCTCTACACTATTCGAAGTCAATTAATTTATGTTCATTTTCTG
TGAGAGATTTTTCAGTTGGATTTATTTTAGTTTTGTTGATCAAGTTATCA
AAATCAAGAAAAACTTAAAATAAGGAAAAATAAAAACGAATTTATTAATC
AGATAAGGAAGCTTCAGTACTCGTTTTATCGCAGAAAAAACAATTTATCA
TTTTTATTATTATTGGGAAATTTTTGATTGATATTGTCAGAAATTTATCC
TTATCGGCCAAAGAATTCATATAAAAAGAATAGATTTAATTATATTTTGC
TTTTTACTTCAATTGTCGGATATTACTAGATATAATGCCAATGAAACAAA
TCACCTCATCTTTTACTAGTTTATTTATTTTTTCAATGATTCTTGTGCTC
ATCAACCTAATTTTCGCAGAAACGACAGATCCCTTGAAAAGGTTTAAACA
AGAAGATTGGGAAAAATTTAATATTATTAGCAGAAGAAATCCTTATTTCA
ATGAATTATATGGACATCAACAAATTCACGATGGAAAACGATCTTGGATG
AATAAAGAAACAAAGAAAACAGTTAAAGATTCTCCAGAGTTCTTTTTGTT
GGACCATGTTTTGGATGATTTCAGTAAAAATAAATTTATTATATAGAG
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protein sequence of SMED30014112-orf-1

>SMED30014112-orf-1 ID=SMED30014112-orf-1|Name=SMED30014112-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=104bp
MPMKQITSSFTSLFIFSMILVLINLIFAETTDPLKRFKQEDWEKFNIISR
RNPYFNELYGHQQIHDGKRSWMNKETKKTVKDSPEFFLLDHVLDDFSKNK
FII*
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