SMED30018270

Overview
NameSMED30018270
Smed IDSMED30018270
Length (bp)422
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 SMED30018270 (SMED30018270) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30018270 (SMED30018270) 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 SMED30018270 (SMED30018270) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30018270 (SMED30018270) 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



SMED30018270

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
X1 cellSMED30018270 SmedASXL_060978SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
muscle cellSMED30018270 dd_Smed_v4_7704_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30018270 dd_Smed_v4_7704_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30018270 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003986:28117..28535 +2000
v31.006207:10188..10613 -1954
Homology
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BLAST of SMED30018270 vs. UniProt/SwissProt
Match: sp|O60068|ISD11_SCHPO (Protein isd11 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=isd11 PE=3 SV=1)

HSP 1 Score: 51.6026 bits (122), Expect = 3.220e-8
Identity = 22/56 (39.29%), Postives = 41/56 (73.21%), Query Frame = -3 
Query:   82 YREYFFDRTKYQFQKIKSENNPVVVEEFLRKCNEELKVLQRQAVISGLYGESNLVV 249
            YREY   RT+ +F+++K E++P   E+ ++   + L+++QRQ++I+G+Y + NLVV
Sbjct:   26 YREYTIRRTRDKFKELKVESDPAKFEQGIKDSEKLLEIIQRQSIINGMYNKRNLVV 81
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BLAST of SMED30018270 vs. TrEMBL
Match: A0A197KA33 (Uncharacterized protein OS=Mortierella elongata AG-77 OX=1314771 GN=K457DRAFT_134397 PE=3 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 5.047e-7
Identity = 24/56 (42.86%), Postives = 37/56 (66.07%), Query Frame = -3 
Query:   82 YREYFFDRTKYQFQKIKSENNPVVVEEFLRKCNEELKVLQRQAVISGLYGESNLVV 249
            +R+Y   RT+  F   K+E +P  +E  +RK  ++L+V++RQ+VIS LYG   LVV
Sbjct:   29 FRDYAVRRTRDAFHAAKNETDPAKIEALIRKAEQQLEVVKRQSVISQLYGGQKLVV 84
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BLAST of SMED30018270 vs. TrEMBL
Match: A0A4Y7PX22 (Uncharacterized protein OS=Rickenella mellea OX=50990 GN=BD410DRAFT_792048 PE=3 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 6.105e-7
Identity = 26/58 (44.83%), Postives = 37/58 (63.79%), Query Frame = -3 
Query:   76 YREYFFDRTKYQFQKIKSENNPVVVEEFLRKCNEELKVLQRQAVISGLYGESNLVVNK 249
            +REYF  RTK  F++I++E +P+      RK  EE  VL+R A+++ LYG   LVV K
Sbjct:   28 FREYFVRRTKSTFREIQAEKDPLRAASLFRKAAEEHTVLKRSALVNQLYGGWRLVVEK 85
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BLAST of SMED30018270 vs. TrEMBL
Match: A0A4R0R7T7 (Uncharacterized protein OS=Steccherinum ochraceum OX=92696 GN=EIP91_008991 PE=3 SV=1)

HSP 1 Score: 53.1434 bits (126), Expect = 1.933e-6
Identity = 27/58 (46.55%), Postives = 38/58 (65.52%), Query Frame = -3 
Query:   76 YREYFFDRTKYQFQKIKSENNPVVVEEFLRKCNEELKVLQRQAVISGLYGESNLVVNK 249
            +R+YF  RTK  FQ+IK E +PV +  F  +  +EL VL+R A+++ LYG   LVV K
Sbjct:   30 FRQYFVRRTKSVFQEIKDEQDPVKLRTFYAEKKKELDVLKRSAIVNQLYGGWKLVVEK 87
[Close]
BLAST of SMED30018270 vs. TrEMBL
Match: A0A5B1QR38 (Uncharacterized protein OS=Dentipellis sp. KUC8613 OX=1883078 GN=DENSPDRAFT_929943 PE=3 SV=1)

HSP 1 Score: 52.7582 bits (125), Expect = 2.713e-6
Identity = 25/58 (43.10%), Postives = 37/58 (63.79%), Query Frame = -3 
Query:   76 YREYFFDRTKYQFQKIKSENNPVVVEEFLRKCNEELKVLQRQAVISGLYGESNLVVNK 249
            +REYF  RTK  F+ I++E +P  + +F     +EL VL+R A+++ LYG   LVV K
Sbjct:   29 FREYFLRRTKSTFRAIQNEQDPAKLSQFYNDTAKELAVLKRSAIVNQLYGGWRLVVEK 86
[Close]
BLAST of SMED30018270 vs. TrEMBL
Match: A0A4S4MMY7 (Uncharacterized protein OS=Antrodiella citrinella OX=2447956 GN=EUX98_g6971 PE=3 SV=1)

HSP 1 Score: 51.9878 bits (123), Expect = 3.557e-6
Identity = 27/58 (46.55%), Postives = 36/58 (62.07%), Query Frame = -3 
Query:   76 YREYFFDRTKYQFQKIKSENNPVVVEEFLRKCNEELKVLQRQAVISGLYGESNLVVNK 249
            +R+YF  RTK  FQ IK E +P  +  F  +  +EL VL+R AV++ LYG   LVV K
Sbjct:   13 FRQYFVHRTKSVFQDIKDEQDPAKLRAFYDEKRKELDVLKRSAVVNQLYGGWRLVVEK 70
[Close]
BLAST of SMED30018270 vs. Ensembl Yeast
Match: ISD11 (Cysteine desulfurase (Nfs1p) activator; essential for the formation of the persulfide intermediate at the desulfurase active site during pyridoxal phosphate-dependent desulfuration of cysteine; required for mitochondrial iron-sulfur cluster biosynthesis; exclusive to eukaryotes, implicated as eukaryotic supplement to the bacterium-derived Fe-S cluster (ISC) assembly apparatus; involved in regulation of iron metabolism; member of the LYR protein family [Source:SGD;Acc:S000007237])

HSP 1 Score: 43.5134 bits (101), Expect = 4.953e-7
Identity = 21/56 (37.50%), Postives = 35/56 (62.50%), Query Frame = -3 
Query:   82 YREYFFDRTKYQFQKIKSENNPVVVEEFLRKCNEELKVLQRQAVISGLYGESNLVV 249
            +REYF  +T+  F+K  ++ +P V+    ++   +L VL+RQ+VIS +Y    LVV
Sbjct:   31 FREYFLSKTRTTFRKNMNQQDPKVLMNLFKEAKNDLGVLKRQSVISQMYTFDRLVV 86
The following BLAST results are available for this feature:
BLAST of SMED30018270 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 SMED30018270 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 SMED30018270 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 SMED30018270 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 SMED30018270 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 SMED30018270 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 SMED30018270 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|O60068|ISD11_SCHPO3.220e-839.29Protein isd11 OS=Schizosaccharomyces pombe (strain... [more]
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BLAST of SMED30018270 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A197KA335.047e-742.86Uncharacterized protein OS=Mortierella elongata AG... [more]
A0A4Y7PX226.105e-744.83Uncharacterized protein OS=Rickenella mellea OX=50... [more]
A0A4R0R7T71.933e-646.55Uncharacterized protein OS=Steccherinum ochraceum ... [more]
A0A5B1QR382.713e-643.10Uncharacterized protein OS=Dentipellis sp. KUC8613... [more]
A0A4S4MMY73.557e-646.55Uncharacterized protein OS=Antrodiella citrinella ... [more]
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BLAST of SMED30018270 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 SMED30018270 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 SMED30018270 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 1
Match NameE-valueIdentityDescription
ISD114.953e-737.50Cysteine desulfurase (Nfs1p) activator; essential ... [more]
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BLAST of SMED30018270 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 SMED30018270 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 SMED30018270 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018270 ID=SMED30018270|Name=SMED30018270|organism=Schmidtea mediterranea sexual|type=transcript|length=422bp
AAAAAAATATTTATATTAAATTAATTTAAATTTAATATACAATTGTAAAT
AAATAAAAAAAATACTAAAACTTCATTTATTAACAACTAAATTGGATTCA
CCATAAAGCCCTGATATAACGGCCTGTCTTTGGAGAACTTTTAATTCTTC
ATTACATTTTCTTAAAAATTCTTCTACAACAACTGGATTATTTTCTGATT
TTATTTTTTGAAATTGATATTTCGTTCTGTCAAAAAAATATTCTCTATAA
AAAGATTGCTTAAATTTTAAACTTTCTTTTAACAAAGACTTATATAATGA
TAGAATGTACATTTTATTCATGTATAAAATAGTTATAACTTAAACTGAAA
TGCTTGATTAACAAACTAGTGACAAATTAAATTTAAAACGCAAAATTTGA
GATAATATAAAAACAAAATTAC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR008011Complex1_LYR
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR008011Complex 1 LYR proteinPFAMPF05347Complex1_LYRcoord: 6..61
e-value: 5.2E-12
score: 45.6
NoneNo IPR availablePANTHERPTHR13166PROTEIN C6ORF149coord: 3..82