SMED30033138

Overview
NameSMED30033138
Smed IDSMED30033138
Length (bp)775
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 SMED30033138 (SMED30033138) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30033138 (SMED30033138) 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 SMED30033138 (SMED30033138) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30033138 (SMED30033138) 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



SMED30033138

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30033138 SmedASXL_058849SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30033138 Contig51470uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30033138 Contig51470newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
parenchymaSMED30033138 dd_Smed_v4_1379_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
prepharyngeal regionSMED30033138 dd_Smed_v6_1379_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30033138 OX_Smed_1.0.16574ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
prepharyngeal regionSMED30033138 SMU15014980SMUPMID:27074666
Lander et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30033138 vs. TrEMBL
Match: A0A5P8I4M6 (Uncharacterized protein OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 172.94 bits (437), Expect = 1.145e-51
Identity = 84/85 (98.82%), Postives = 85/85 (100.00%), Query Frame = -3 
Query:  120 MHFISIFTGCFCILLMLTHSTVGSSSVKLYHIVVVPKNICDRFIAVKLLKKYNFQIYRKNRQIHGFIGKKAMRNKVESLFMELSI 374
            MHFISIFTGCFCILLMLTHSTVGSSSVKLYH+VVVPKNICDRFIAVKLLKKYNFQIYRKNRQIHGFIGKKAMRNKVESLFMELSI
Sbjct:    1 MHFISIFTGCFCILLMLTHSTVGSSSVKLYHVVVVPKNICDRFIAVKLLKKYNFQIYRKNRQIHGFIGKKAMRNKVESLFMELSI 85
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BLAST of SMED30033138 vs. Planmine SMEST
Match: SMESG000075450.1 (SMESG000075450.1)

HSP 1 Score: 162.925 bits (411), Expect = 2.909e-51
Identity = 80/85 (94.12%), Postives = 82/85 (96.47%), Query Frame = -3 
Query:  120 MHFISIFTGCFCILLMLTHSTVGSSSVKLYHIVVVPKNICDRFIAVKLLKKYNFQIYRKNRQIHGFIGKKAMRNKVESLFMELSI 374
            MHFISIFTGCFCILLML HSTVGSSSVKLYHIVVVPK+ICDRFIAVKLLKKYNFQIYRKN QIHGFI +KAMRNKVESLFMELSI
Sbjct:    1 MHFISIFTGCFCILLMLMHSTVGSSSVKLYHIVVVPKDICDRFIAVKLLKKYNFQIYRKNSQIHGFIREKAMRNKVESLFMELSI 85
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BLAST of SMED30033138 vs. Planmine SMEST
Match: SMESG000075450.1 (SMESG000075450.1)

HSP 1 Score: 129.028 bits (323), Expect = 2.426e-38
Identity = 63/67 (94.03%), Postives = 65/67 (97.01%), Query Frame = -3 
Query:  120 HSTVGSSSVKLYHIVVVPKNICDRFIAVKLLKKYNFQIYRKNRQIHGFIGKKAMRNKVESLFMELSI 320
            HSTVGSSSVKLYHIVVVPK+ICDRFIAVKLLKKYNFQIYRKN QIHGFI +KAMRNKVESLFMELSI
Sbjct:    2 HSTVGSSSVKLYHIVVVPKDICDRFIAVKLLKKYNFQIYRKNSQIHGFIREKAMRNKVESLFMELSI 68
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BLAST of SMED30033138 vs. Planmine SMEST
Match: SMESG000034009.1 (SMESG000034009.1)

HSP 1 Score: 42.743 bits (99), Expect = 4.586e-9
Identity = 21/25 (84.00%), Postives = 22/25 (88.00%), Query Frame = 2 
Query:  440 EKLKRENQQLKLKETIGNEIGNHSS 514
            EKLKR+NQQLK KETI NEI NHSS
Sbjct:  124 EKLKRKNQQLKFKETIRNEIRNHSS 148

HSP 2 Score: 35.8094 bits (81), Expect = 4.586e-9
Identity = 29/40 (72.50%), Postives = 33/40 (82.50%), Query Frame = 3 
Query:  594 MQKPKHYXXXXXXXXXXXXXXXXAARLMGQLKKLISNILD 713
            +QKPKH KPR  K K ERR+RLK+ARLMGQ+KK I NILD
Sbjct:  176 IQKPKHNKPRLSKAKWERRRRLKSARLMGQIKKFIPNILD 215
[Close]
BLAST of SMED30033138 vs. Planmine SMEST
Match: SMESG000079784.1 (SMESG000079784.1)

HSP 1 Score: 49.6766 bits (117), Expect = 1.640e-7
Identity = 39/103 (37.86%), Postives = 52/103 (50.49%), Query Frame = 2 
Query:  401 NL*KISYY-IVTETEKLKRENQQLKLKETIGNEIGNHSSTMQASRQISPRLYQAPVKQIHPITQINAKTETL*ASSTQN*ERKTAKAQSSSIDGTIEEAHIEY 706
            +L K+ Y  +  E EK K+ENQQLKLKETI NEIG H ST   +      +     K I+    I+         S    ER+T K + S  +GT EE H+ +
Sbjct:   26 DLLKLQYSEMAIEKEKTKKENQQLKLKETIRNEIGYHPSTATTTCIDRTFIPSCSSKSINVDRNIDKTKSNKNRPSKAERERETPKIEDSQSNGTNEEVHVAH 128
The following BLAST results are available for this feature:
BLAST of SMED30033138 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 SMED30033138 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 SMED30033138 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 SMED30033138 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 SMED30033138 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 SMED30033138 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 SMED30033138 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 SMED30033138 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A5P8I4M61.145e-5198.82Uncharacterized protein OS=Schmidtea mediterranea ... [more]
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BLAST of SMED30033138 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 SMED30033138 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 SMED30033138 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 SMED30033138 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 SMED30033138 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 SMED30033138 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000075450.12.909e-5194.12SMESG000075450.1[more]
SMESG000075450.12.426e-3894.03SMESG000075450.1[more]
SMESG000034009.14.586e-984.00SMESG000034009.1[more]
SMESG000079784.11.640e-737.86SMESG000079784.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033138 ID=SMED30033138|Name=SMED30033138|organism=Schmidtea mediterranea sexual|type=transcript|length=775bp
TTCAAAAGTATTATTAATTATTCATGCATTAATTTAAACAAAGTTTTCAA
TTTTAATAAAATAACAAATGATTGAATGGAATTGTATTAATAATAATATT
AGTTTTTAAACTTATAATTGATGCTGAGTTCCATGAATAAGGATTCGACT
TTGTTTCTCATGGCTTTCTTGCCAATAAAGCCATGAATTTGGCGATTTTT
TCGATAGATTTGAAAATTGTACTTTTTCAATAGTTTTACAGCAATGAATC
TATCACAAATATTCTTTGGAACCACAACTATATGATACAGCTTCACAGAC
GAAGAACCAACTGTTGAATGCGTAAGCATAAGCAAAATGCAAAAGCATCC
AGTGAAAATTGAAATGAAATGCATATTAATTAAAGTAATTAAATTTCGTC
AATTTATAGAAAATTAGTTATTATATTGTAACCGAAACAGAGAAGTTGAA
AAGAGAAAACCAACAATTAAAGTTAAAGGAAACAATCGGAAACGAGATCG
GGAACCATTCAAGTACGATGCAAGCTTCAAGACAAATCTCACCTCGCTTA
TACCAAGCTCCAGTCAAACAAATACATCCAATAACACAGATTAATGCAAA
AACCGAAACATTATAAGCCTCGTCCACGCAAAACTAAGAGAGAAAGACGG
CAAAGGCTCAAAGCAGCTCGATTGATGGGACAATTGAAGAAGCTCATATC
GAATATCTTGGATTGAAATTTAATTGACGTGTTAGTTTGTTAAAATATTT
TAATAAATGATTTAGCGTTTCTCGA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000419prepharyngeal region