SMED30029472

Overview
NameSMED30029472
Smed IDSMED30029472
Length (bp)646
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 SMED30029472 (SMED30029472) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30029472 (SMED30029472) 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 SMED30029472 (SMED30029472) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30029472 (SMED30029472) 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




SMED30029472

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30029472h1SMcG0022539 SmedASXL_016187SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30029472h1SMcG0022539 SmedASXL_016187SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30029472h1SMcG0022520 Contig44698newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30029472h1SMcG0022520 Contig44698uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30029472h1SMcG0022517 Contig51564newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
protonephridiaSMED30029472h1SMcG0022517 dd_Smed_v4_2090_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30029472h1SMcG0022517 dd_Smed_v4_2090_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30029472h1SMcG0022517 dd_Smed_v4_2090_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30029472h1SMcG0022517 dd_Smed_v4_2090_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30029472h1SMcG0022517 dd_Smed_v4_2090_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30029472h1SMcG0022517 dd_Smed_v4_2090_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30029472h1SMcG0022517 dd_Smed_v6_2090_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30029472 vs. Planmine SMEST
Match: SMESG000016257.1 (SMESG000016257.1)

HSP 1 Score: 149.828 bits (377), Expect = 4.909e-47
Identity = 75/75 (100.00%), Postives = 75/75 (100.00%), Query Frame = 3
Query:  210 MKQITFLVLILSISGIQSSEIICSSGLKMLTCATSGSCDYACDQPVNCGQCRDCVQYCCKVNLVEKISSRCVEGL 434
            MKQITFLVLILSISGIQSSEIICSSGLKMLTCATSGSCDYACDQPVNCGQCRDCVQYCCKVNLVEKISSRCVEGL
Sbjct:    1 MKQITFLVLILSISGIQSSEIICSSGLKMLTCATSGSCDYACDQPVNCGQCRDCVQYCCKVNLVEKISSRCVEGL 75          
BLAST of SMED30029472 vs. Planmine SMEST
Match: SMESG000016256.1 (SMESG000016256.1)

HSP 1 Score: 72.4034 bits (176), Expect = 1.128e-14
Identity = 35/42 (83.33%), Postives = 39/42 (92.86%), Query Frame = 2
Query:   50 YRFRNHLNDLLGSTRVPPSPTAENQRVPLNESAQDSKNPKIV 175
            YRFRN+LNDLL S + PPSPTA+NQRVPLNESAQ+SKNPKIV
Sbjct:  763 YRFRNNLNDLLRSKQKPPSPTAKNQRVPLNESAQESKNPKIV 804          
BLAST of SMED30029472 vs. Planmine SMEST
Match: SMESG000016256.1 (SMESG000016256.1)

HSP 1 Score: 66.6254 bits (161), Expect = 1.284e-12
Identity = 34/43 (79.07%), Postives = 39/43 (90.70%), Query Frame = 2
Query:   50 YRFRNHLNDLLGSTRVPPSPTAEN-QRVPLNESAQDSKNPKIV 175
            YRFRN+LNDLL S + PPSPTA+N +RVPLNESAQ+SKNPKIV
Sbjct:  763 YRFRNNLNDLLRSKQKPPSPTAKNPERVPLNESAQESKNPKIV 805          
The following BLAST results are available for this feature:
BLAST of SMED30029472 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 SMED30029472 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 SMED30029472 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 SMED30029472 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 SMED30029472 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 SMED30029472 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 SMED30029472 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 SMED30029472 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 SMED30029472 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 SMED30029472 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 SMED30029472 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 SMED30029472 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 SMED30029472 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 SMED30029472 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000016257.14.909e-47100.00SMESG000016257.1[more]
SMESG000016256.11.128e-1483.33SMESG000016256.1[more]
SMESG000016256.11.284e-1279.07SMESG000016256.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029472 ID=SMED30029472|Name=SMED30029472|organism=Schmidtea mediterranea sexual|type=transcript|length=646bp
CATTTGCCTTATTCTATTAATTCTCCTAGCTGCCATTGGAGCATTAATAT
ATCGGTTTCGGAATCACCTAAATGATCTGCTAGGAAGTACGCGGGTACCT
CCAAGTCCTACAGCTGAAAACCAGAGGGTGCCACTCAATGAAAGTGCCCA
AGATTCCAAAAATCCCAAAATTGTTTAGAATGCGATTAATTGTTCAAATT
GAATTAAAAATGAAACAGATCACATTCCTAGTTCTCATCCTTTCCATAAG
TGGTATTCAGTCGTCAGAGATTATCTGCAGCTCCGGCCTGAAAATGCTGA
CTTGCGCCACCAGTGGCTCTTGTGATTACGCCTGTGATCAGCCAGTTAAT
TGCGGCCAATGCCGAGATTGCGTCCAATATTGTTGCAAAGTCAATCTAGT
TGAAAAAATTTCCAGCCGATGCGTTGAAGGACTCTAATAAATAATTATAT
GGAGCTGATTTCTCAGTTTTTCCCTCTAAATAAATTACGCTTGCTAAATC
ATTCTCACATGCAAAACCCGAATCGACGGGAAATTTAATTTCAAAGTTTT
GTTTCATTAACTCATTTCTTGCTACTAAACATTTCATTTTGGGGCTTTAT
TTATCATTGACTTTCATTGCTGAATTTTCCCAAAACAATACACACT
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protein sequence of SMED30029472-orf-1

>SMED30029472-orf-1 ID=SMED30029472-orf-1|Name=SMED30029472-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=100bp
MKVPKIPKIPKLFRMRLIVQIELKMKQITFLVLILSISGIQSSEIICSSG
LKMLTCATSGSCDYACDQPVNCGQCRDCVQYCCKVNLVEKISSRCVEGL*
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