SMED30001308

Overview
NameSMED30001308
Smed IDSMED30001308
Length (bp)856
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 SMED30001308 (SMED30001308) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30001308 (SMED30001308) 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 SMED30001308 (SMED30001308) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30001308 (SMED30001308) 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



SMED30001308

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X2 cellSMED30001308 SmedASXL_062303SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30001308SMESG000077179.1 SMESG000076896.1 SMESG000068998.1 SMESG000036236.1 SMESG000036145.1 Contig16112newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30001308SMESG000077179.1 SMESG000076896.1 SMESG000068998.1 SMESG000036236.1 SMESG000036145.1 Contig16112uc_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
Alignments
SMED30001308 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002682:13582..14413 -4031
v31.017268:14612..15479 -3092
v31.004472:50461..51328 -3074
Homology
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BLAST of SMED30001308 vs. Planmine SMEST
Match: SMESG000004514.1 (SMESG000004514.1)

HSP 1 Score: 78.5666 bits (192), Expect = 3.024e-31
Identity = 37/67 (55.22%), Postives = 45/67 (67.16%), Query Frame = 3 
Query:  420 IERHVSKQGRRIIQFSSNEAAQYHRILWEYGYTVSIPGNVTWSARLGSLEDLNLPSIEIKMETGRNP 620
            + RHV    R IIQFSS  +AQ   ILW+Y Y+VS PG+ T  AR G +EDL++P I IK E GRNP
Sbjct:   18 VRRHVPGPEREIIQFSSTASAQCRHILWDYEYSVSTPGDSTLPARPGLIEDLDIPGIAIKREPGRNP 84

HSP 2 Score: 71.2478 bits (173), Expect = 3.024e-31
Identity = 33/57 (57.89%), Postives = 47/57 (82.46%), Query Frame = 2 
Query:  620 AREARQGVEFYLLRLDEKDKQLRHRRQIAQRKLNQINLEIAAGKILCSDVYVLEYNA 790
            ARE RQ VEFYLL L E++++L+HRR++ Q +L++IN +IAAG+ILC+ VY  +YNA
Sbjct:   85 ARETRQKVEFYLLLLVEEERRLQHRRRMPQVELDKINRDIAAGRILCTGVYAPDYNA 141

HSP 3 Score: 24.2534 bits (51), Expect = 3.024e-31
Identity = 10/18 (55.56%), Postives = 14/18 (77.78%), Query Frame = 1 
Query:  277 MMPELLPQISTNEKRNCV 330
            MM EL PQ+STN +++ V
Sbjct:    1 MMSELTPQLSTNGRQSTV 18
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BLAST of SMED30001308 vs. Planmine SMEST
Match: SMESG000074058.1 (SMESG000074058.1)

HSP 1 Score: 90.5077 bits (223), Expect = 2.507e-28
Identity = 45/64 (70.31%), Postives = 53/64 (82.81%), Query Frame = 2 
Query:  620 AREARQGVEFYLLRLDEKDKQLRHRRQIAQRKLNQINLEIAAGKILCSDVYVLEYNASYEINDP 811
            AREARQ VE+YL RL EK++QL+HRR++AQR+L +IN EIAAG ILC D Y  EYN SYEINDP
Sbjct:   51 AREARQRVEYYLFRL-EKNRQLQHRRRMAQRELCRINFEIAAGIILCLDTYAPEYNVSYEINDP 113

HSP 2 Score: 53.9138 bits (128), Expect = 2.507e-28
Identity = 28/55 (50.91%), Postives = 37/55 (67.27%), Query Frame = 3 
Query:  456 IQFSSNEAAQYHRILWEYGYTVSIPGNVTWSARLGSLEDLNLPSIEIKMETGRNP 620
            +QF SN AAQ  +ILW+Y Y V+     T S  LGSL+++N+ SI IK + GRNP
Sbjct:    1 MQFDSNTAAQCRQILWDYRYMVT-----TRSDPLGSLKEMNIHSITIKRKPGRNP 50
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BLAST of SMED30001308 vs. Planmine SMEST
Match: SMESG000014849.1 (SMESG000014849.1)

HSP 1 Score: 67.781 bits (164), Expect = 2.078e-21
Identity = 29/79 (36.71%), Postives = 52/79 (65.82%), Query Frame = 2 
Query:  620 AREARQGVEFYLLRLDEKDKQLRHRRQIAQRKLNQINLEIAAGKILCSDVYVLEYNASYEINDPTLKTQMAPTRAAIPD 856
            AREARQ  E+  ++++E +++   +  +A+++L Q+N +IA+G I  +D +  EY  S+E++DP L    APT+  IP+
Sbjct:  947 AREARQRAEYAAMKMEELERKYHRKAVLARQRLAQVNRDIASGVIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPE 1025

HSP 2 Score: 52.7582 bits (125), Expect = 2.078e-21
Identity = 26/63 (41.27%), Postives = 36/63 (57.14%), Query Frame = 3 
Query:  435 SKQGRRIIQFSSNEAAQYHRILWEYGYTVSIPGNVTWSARLG-SLEDLNLPSIEIKMETGRNP 620
            S   R  +Q  S  AA+Y ++LW+ GY +S  G+ +W  R     E++ LPSI IK E G NP
Sbjct:  884 SDNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYRAEEIELPSIAIKREPGHNP 946
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BLAST of SMED30001308 vs. Planmine SMEST
Match: SMESG000044971.1 (SMESG000044971.1)

HSP 1 Score: 66.2402 bits (160), Expect = 7.448e-21
Identity = 29/79 (36.71%), Postives = 52/79 (65.82%), Query Frame = 2 
Query:  620 AREARQGVEFYLLRLDEKDKQLRHRRQIAQRKLNQINLEIAAGKILCSDVYVLEYNASYEINDPTLKTQMAPTRAAIPD 856
            AREARQ  E+  ++++E +++   +  +A+++L Q+N +IA+G I  +D +  EY  S+E++DP L    APT+  IP+
Sbjct: 1200 AREARQRAEYVAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKMVIPE 1278

HSP 2 Score: 52.373 bits (124), Expect = 7.448e-21
Identity = 26/63 (41.27%), Postives = 36/63 (57.14%), Query Frame = 3 
Query:  435 SKQGRRIIQFSSNEAAQYHRILWEYGYTVSIPGNVTWSARLG-SLEDLNLPSIEIKMETGRNP 620
            S   R  +Q  S  AA+Y ++LW+ GY +S  G+ +W  R     E++ LPSI IK E G NP
Sbjct: 1137 SDNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHNP 1199
[Close]
BLAST of SMED30001308 vs. Planmine SMEST
Match: SMESG000035366.1 (SMESG000035366.1)

HSP 1 Score: 64.3142 bits (155), Expect = 4.876e-20
Identity = 28/79 (35.44%), Postives = 52/79 (65.82%), Query Frame = 2 
Query:  620 AREARQGVEFYLLRLDEKDKQLRHRRQIAQRKLNQINLEIAAGKILCSDVYVLEYNASYEINDPTLKTQMAPTRAAIPD 856
            AREARQ  EF  +++++ +++   +  +A+++L Q+N +IA+G I  +D +  EY  S+E++DP L    APT+  +P+
Sbjct:  732 AREARQRAEFSAMKMEQMEQKYHRKAVLARQRLAQVNWDIASGAIPSTDGFPPEYGVSFELDDPRLLQMSAPTKLVLPE 810

HSP 2 Score: 51.6026 bits (122), Expect = 4.876e-20
Identity = 25/59 (42.37%), Postives = 37/59 (62.71%), Query Frame = 3 
Query:  447 RRIIQFSSNEAAQYHRILWEYGYTVSIPGNVTWSARLG-SLEDLNLPSIEIKMETGRNP 620
            R  ++  S  AA+Y ++LW+ GY +SI G+ +W  R     E++ LPSI IK E G+NP
Sbjct:  673 RVTLRIPSASAARYRQVLWDNGYLLSIYGDSSWPRRSEYQAEEVELPSIAIKCEPGKNP 731
The following BLAST results are available for this feature:
BLAST of SMED30001308 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 SMED30001308 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 SMED30001308 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 SMED30001308 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 SMED30001308 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 SMED30001308 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 SMED30001308 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 SMED30001308 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 SMED30001308 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 SMED30001308 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 SMED30001308 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 SMED30001308 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 SMED30001308 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 SMED30001308 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000004514.13.024e-3155.22SMESG000004514.1[more]
SMESG000074058.12.507e-2870.31SMESG000074058.1[more]
SMESG000014849.12.078e-2136.71SMESG000014849.1[more]
SMESG000044971.17.448e-2136.71SMESG000044971.1[more]
SMESG000035366.14.876e-2035.44SMESG000035366.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001308 ID=SMED30001308|Name=SMED30001308|organism=Schmidtea mediterranea sexual|type=transcript|length=856bp
TAATAATACAATAACCATTCCAGAAAATACGCACACCCAAATAATATCAA
TGACAAGGATTGAAAAATTTAACAATAACAATACGCCTGACTGAACTAGA
AAATGACGTGGCAGGTGACGCAGCTAGAGAATGGAGCACACTATGTAAGT
TCTCTCGATGATCATTGGAATAGAATTAGAATGAATATTAAAAAAAACTC
AATATGCGAATCGAACACCAGGGAAAAGGTTCAGAGAGCAGCAGAGACAA
GGATGACCTCGCAAAATGCGTATCCAATGATGCCAGAGTTACTGCCACAA
ATTTCCACAAACGAAAAAAGGAATTGTGTTTACTTCATATTATCTTCTAT
GAAACCTTTTATCATAAAGTGCAACGTAATGATCGTTGTTAACCCAAACG
AATATCATGTGGAATCGAAATCGAACGGCATGTATCAAAGCAAGGAAGAA
GGATTATTCAATTTAGTTCGAATGAGGCAGCCCAATATCATCGAATCCTG
TGGGAATATGGGTACACGGTCTCTATACCAGGAAATGTCACGTGGTCGGC
TCGACTAGGATCGCTGGAAGATCTAAACCTTCCAAGTATTGAAATCAAAA
TGGAGACTGGTCGGAATCCGCCAGAGAGGCCCGTCAAGGAGTAGAATTTT
ACTTACTTCGTCTGGATGAGAAGGACAAACAGTTACGACACCGACGACAG
ATAGCCCAGAGAAAGTTGAACCAAATAAATCTCGAAATAGCCGCAGGCAA
AATCCTTTGTTCAGATGTATATGTTCTGGAATATAATGCTTCTTATGAAA
TCAATGATCCTACCCTGAAAACTCAAATGGCCCCGACTCGGGCGGCTATT
CCAGAC
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protein sequence of SMED30001308-orf-1

>SMED30001308-orf-1 ID=SMED30001308-orf-1|Name=SMED30001308-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=152bp
MTWQVTQLENGAHYVSSLDDHWNRIRMNIKKNSICESNTREKVQRAAETR
MTSQNAYPMMPELLPQISTNEKRNCVYFILSSMKPFIIKCNVMIVVNPNE
YHVESKSNGMYQSKEEGLFNLVRMRQPNIIESCGNMGTRSLYQEMSRGRL
D*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell