SMED30011431

Overview
NameSMED30011431
Smed IDSMED30011431
Length (bp)545
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 SMED30011431 (SMED30011431) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30011431 (SMED30011431) 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 SMED30011431 (SMED30011431) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30011431 (SMED30011431) 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



SMED30011431

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30011431h1SMcG0011542 SmedASXL_009933SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30011431h1SMcG0011542 Contig54493newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011431h1SMcG0011542 Contig54493uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011431h1SMcG0009490 Contig54493newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011431h1SMcG0009490 Contig54493uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30011431h1SMcG0011542 dd_Smed_v4_2217_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30011431h1SMcG0011542 dd_Smed_v4_2217_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30011431h1SMcG0011542 dd_Smed_v4_2217_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynxSMED30011431h1SMcG0011542 dd_Smed_v6_2217_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30011431h1SMcG0011542 dd_Smed_v4_2217_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
Homology
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BLAST of SMED30011431 vs. TrEMBL
Match: A0A4Z2DTV2 (Uncharacterized protein OS=Schistosoma japonicum OX=6182 GN=EWB00_005950 PE=4 SV=1)

HSP 1 Score: 69.3218 bits (168), Expect = 1.948e-11
Identity = 46/151 (30.46%), Postives = 67/151 (44.37%), Query Frame = 2 
Query:  149 YWMTHWKKGDQVVKSRQLLGAAHWLQLRD-LTE------------------TCQPIEHDESGRILIHSRTDKELHRRLRDLDN--------------------HFIR-----DARLGLRYWLIDPPKPTKFGHYATGAKYTYYGLGNAPRT 469
            YW  HWK  D V+ ++++ G  +W+ LRD L E                      +E   SG  +I ++ + E     + ++                      F R      AR G R+W+ + PKPTKFGHY+ GAKYT+ GL NAPR+
Sbjct:   16 YWRYHWKNSDPVMIAKRI-GTVNWVLLRDKLNEMNDMHEKEANPHSIRAQIITSQLESMTSGTTMIPTKNEDESESCAKKINKETCNYKCGPYTKGMTPKERKQFFRTTLNQKAREGFRFWVTERPKPTKFGHYSMGAKYTFLGLCNAPRS 165
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BLAST of SMED30011431 vs. TrEMBL
Match: C1LFB3 (Uncharacterized protein OS=Schistosoma japonicum OX=6182 PE=2 SV=1)

HSP 1 Score: 68.9366 bits (167), Expect = 2.186e-11
Identity = 46/151 (30.46%), Postives = 67/151 (44.37%), Query Frame = 2 
Query:  149 YWMTHWKKGDQVVKSRQLLGAAHWLQLRD-LTE------------------TCQPIEHDESGRILIHSRTDKELHRRLRDLDN--------------------HFIR-----DARLGLRYWLIDPPKPTKFGHYATGAKYTYYGLGNAPRT 469
            YW  HWK  D V+ ++++ G  +W+ LRD L E                      +E   SG  +I ++ + E     + ++                      F R      AR G R+W+ + PKPTKFGHY+ GAKYT+ GL NAPR+
Sbjct:   16 YWRYHWKNSDPVMIAKRI-GTVNWVLLRDKLNEMNDMHEKEANPHSIRAQIITSQLESMTSGTTMIPTKNEDESESCAKKINKETCNYKGGPYTKGMTPKERKQFFRTTLNQKAREGFRFWVTERPKPTKFGHYSMGAKYTFLGLCNAPRS 165
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BLAST of SMED30011431 vs. TrEMBL
Match: A0A095CCN0 (Uncharacterized protein OS=Schistosoma haematobium OX=6185 GN=MS3_08778 PE=4 SV=1)

HSP 1 Score: 65.0846 bits (157), Expect = 7.420e-10
Identity = 43/151 (28.48%), Postives = 63/151 (41.72%), Query Frame = 2 
Query:  149 YWMTHWKKGDQVVKSRQLLGAAHWLQLRDLTETCQPIEHDESG-------------------RILIHSRTDKELHRRLRDLD--------------------NHFIR-----DARLGLRYWLIDPPKPTKFGHYATGAKYTYYGLGNAPRT 469
            YW  HWK  D V+ +R++ G  +W+ LRD           E+                      L H++ +    +  +++                       F R      AR G R+W+ + PKPTKFGHY+ GAKYT+ GL NAPR+
Sbjct:   21 YWRYHWKNSDPVMIARRI-GTINWVLLRDKINEMNDRHEKEANPHTIRAQIIASQLQNISRETTLTHTKHEDGFEKCTKEMSIESTDHKGGPYTKGMTPEERKQFFRTKLNQKAREGFRFWVTERPKPTKFGHYSMGAKYTFLGLCNAPRS 170
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BLAST of SMED30011431 vs. TrEMBL
Match: A0A3Q0KP63 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 PE=4 SV=1)

HSP 1 Score: 64.6994 bits (156), Expect = 1.113e-9
Identity = 46/151 (30.46%), Postives = 64/151 (42.38%), Query Frame = 2 
Query:  149 YWMTHWKKGDQVVKSRQLLGAAHWLQLRD----------------------LTETCQPIEHDESGRILIH----SRTDKELHRRLRDLD-------------NHFIR-----DARLGLRYWLIDPPKPTKFGHYATGAKYTYYGLGNAPRT 469
            YW  HWK  D V+ +R++ G  +W+ LRD                      +    Q +  + +     H     +  KE+ R   D                 F R      AR G R+W+ + PKPTKFGHY+ GAKYT+ GL NAPR+
Sbjct:   21 YWRYHWKNSDPVMIARRI-GTINWVLLRDKLNEMNDRHQKETNPHTMRAQIIASQLQNMSRETTIADTKHKDDFEKCTKEISRESTDHKGGPYTKGMTPEERKQFFRTKLNQKAREGFRFWVTERPKPTKFGHYSMGAKYTFLGLCNAPRS 170
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BLAST of SMED30011431 vs. TrEMBL
Match: A0A2T7NU63 (Uncharacterized protein OS=Pomacea canaliculata OX=400727 GN=C0Q70_15180 PE=4 SV=1)

HSP 1 Score: 64.6994 bits (156), Expect = 3.793e-9
Identity = 29/46 (63.04%), Postives = 33/46 (71.74%), Query Frame = 2 
Query:  332 LDNHFIRDARLGLRYWLIDPPKPTKFGHYATGAKYTYYGLGNAPRT 469
            +DN F R AR G RYWLI+ PKPTKFG Y  G+  T  G+GNAPRT
Sbjct:  206 MDNEFNRRAREGFRYWLIEKPKPTKFGRYGIGSYKTALGVGNAPRT 251
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BLAST of SMED30011431 vs. Planmine SMEST
Match: SMESG000063184.1 (SMESG000063184.1)

HSP 1 Score: 252.292 bits (643), Expect = 2.223e-87
Identity = 120/120 (100.00%), Postives = 120/120 (100.00%), Query Frame = 2 
Query:  110 MSSRNNLNSNYPNYWMTHWKKGDQVVKSRQLLGAAHWLQLRDLTETCQPIEHDESGRILIHSRTDKELHRRLRDLDNHFIRDARLGLRYWLIDPPKPTKFGHYATGAKYTYYGLGNAPRT 469
            MSSRNNLNSNYPNYWMTHWKKGDQVVKSRQLLGAAHWLQLRDLTETCQPIEHDESGRILIHSRTDKELHRRLRDLDNHFIRDARLGLRYWLIDPPKPTKFGHYATGAKYTYYGLGNAPRT
Sbjct:    1 MSSRNNLNSNYPNYWMTHWKKGDQVVKSRQLLGAAHWLQLRDLTETCQPIEHDESGRILIHSRTDKELHRRLRDLDNHFIRDARLGLRYWLIDPPKPTKFGHYATGAKYTYYGLGNAPRT 120
[Close]
BLAST of SMED30011431 vs. Planmine SMEST
Match: SMESG000063184.1 (SMESG000063184.1)

HSP 1 Score: 220.32 bits (560), Expect = 6.880e-75
Identity = 105/105 (100.00%), Postives = 105/105 (100.00%), Query Frame = 2 
Query:  155 MTHWKKGDQVVKSRQLLGAAHWLQLRDLTETCQPIEHDESGRILIHSRTDKELHRRLRDLDNHFIRDARLGLRYWLIDPPKPTKFGHYATGAKYTYYGLGNAPRT 469
            MTHWKKGDQVVKSRQLLGAAHWLQLRDLTETCQPIEHDESGRILIHSRTDKELHRRLRDLDNHFIRDARLGLRYWLIDPPKPTKFGHYATGAKYTYYGLGNAPRT
Sbjct:    1 MTHWKKGDQVVKSRQLLGAAHWLQLRDLTETCQPIEHDESGRILIHSRTDKELHRRLRDLDNHFIRDARLGLRYWLIDPPKPTKFGHYATGAKYTYYGLGNAPRT 105
The following BLAST results are available for this feature:
BLAST of SMED30011431 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 SMED30011431 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 SMED30011431 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 SMED30011431 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 SMED30011431 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 SMED30011431 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 SMED30011431 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 SMED30011431 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4Z2DTV21.948e-1130.46Uncharacterized protein OS=Schistosoma japonicum O... [more]
C1LFB32.186e-1130.46Uncharacterized protein OS=Schistosoma japonicum O... [more]
A0A095CCN07.420e-1028.48Uncharacterized protein OS=Schistosoma haematobium... [more]
A0A3Q0KP631.113e-930.46Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A2T7NU633.793e-963.04Uncharacterized protein OS=Pomacea canaliculata OX... [more]
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BLAST of SMED30011431 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 SMED30011431 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 SMED30011431 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 SMED30011431 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 SMED30011431 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 SMED30011431 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000063184.12.223e-87100.00SMESG000063184.1[more]
SMESG000063184.16.880e-75100.00SMESG000063184.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011431 ID=SMED30011431|Name=SMED30011431|organism=Schmidtea mediterranea sexual|type=transcript|length=545bp
CCCGTCTAACTAATGTCATTAGAAATGACATTTAAATTGTTCACTTTTGG
TAAGTCACAGACCCAGTGAAAGGTATCTCATTTGGACAAATTTGTGTTTA
ATTTTTAGAATGTCTAGCAGAAATAATTTGAATTCTAATTATCCCAATTA
TTGGATGACTCACTGGAAGAAAGGTGACCAAGTTGTAAAATCCAGACAAT
TACTGGGTGCTGCACATTGGCTTCAATTAAGAGATTTAACCGAAACCTGC
CAACCAATCGAACACGACGAGAGCGGTCGAATATTAATCCATTCAAGAAC
TGACAAAGAATTACACAGACGATTAAGGGATTTGGATAATCATTTCATAC
GGGACGCTCGTTTGGGGTTGCGCTATTGGCTGATCGATCCTCCTAAGCCA
ACCAAATTTGGTCATTATGCTACTGGAGCAAAATATACTTATTACGGCCT
TGGAAATGCCCCAAGAACATAGAAGGAATCTGGATGCAAAAATATTATTG
AAAAGAAATTTTAAAATTAATAATTTAGTAATCATTATGTGGTTG
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protein sequence of SMED30011431-orf-1

>SMED30011431-orf-1 ID=SMED30011431-orf-1|Name=SMED30011431-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=121bp
MSSRNNLNSNYPNYWMTHWKKGDQVVKSRQLLGAAHWLQLRDLTETCQPI
EHDESGRILIHSRTDKELHRRLRDLDNHFIRDARLGLRYWLIDPPKPTKF
GHYATGAKYTYYGLGNAPRT*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000420parapharyngeal region