SMED30002680

Overview
NameSMED30002680
Smed IDSMED30002680
Length (bp)985
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 SMED30002680 (SMED30002680) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30002680 (SMED30002680) 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 SMED30002680 (SMED30002680) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30002680 (SMED30002680) 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



SMED30002680

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
X1 cellSMED30002680 SmedASXL_072817SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30002680 SmedASXL_072817SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
pharynxSMED30002680 dd_Smed_v4_11691_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30002680 dd_Smed_v4_11691_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002680 dd_Smed_v4_11691_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30002680 dd_Smed_v4_11691_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30002680 dd_Smed_v4_11691_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
Homology
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BLAST of SMED30002680 vs. Planmine SMEST
Match: SMESG000058785.1 (SMESG000058785.1)

HSP 1 Score: 105.145 bits (261), Expect = 3.575e-33
Identity = 50/84 (59.52%), Postives = 61/84 (72.62%), Query Frame = 2 
Query:  206 ICTDKENEIKICMDVSSAVTTPPVVEEAQNSSTSVGY*TDDFGDELS*PILFFMDTKTNFHRKRKFPVDIDGENRDFVVDLCTL 457
            IC+D E+++KI MD+SSA+ TPPVV+E +N + SVGY TDDFGDEL   I   +  K   HRKRK  VDIDGENRD  +DLC L
Sbjct:  262 ICSDNEDDMKISMDISSAIVTPPVVDEDRNLAASVGYWTDDFGDELHHQIPSVVAAKCTSHRKRKLSVDIDGENRDLFIDLCEL 345

HSP 2 Score: 55.4546 bits (132), Expect = 3.575e-33
Identity = 31/50 (62.00%), Postives = 39/50 (78.00%), Query Frame = 1 
Query:    1 VGPAKTPKASKKHNPSKIXXXXXXXXAKGAIILENAAKVLEEATIRVAKQ 150
            +GPAK P+ SKKHNP+K + RRE  RA+GA++L NAAKVLEE TI +A  
Sbjct:  208 IGPAKIPRISKKHNPNKNQRRREGSRAEGAVLLANAAKVLEEDTIWIANN 257
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BLAST of SMED30002680 vs. Planmine SMEST
Match: SMESG000051967.1 (SMESG000051967.1)

HSP 1 Score: 120.168 bits (300), Expect = 9.699e-33
Identity = 60/101 (59.41%), Postives = 73/101 (72.28%), Query Frame = 2 
Query:  155 RNEQLPESAKPAESVPRICTDKENEIKICMDVSSAVTTPPVVEEAQNSSTSVGY*TDDFGDELS*PILFFMDTKTNFHRKRKFPVDIDGENRDFVVDLCTL 457
            +++Q PE  K  ESVPRIC DKE+++KI MD+ SA+  PPVVEE + SS SVGY TDDF DEL  P+   +  K N HRKRKF VDIDG+NRD  V+LC L
Sbjct:   73 QDKQHPEFVKSDESVPRICADKEDDMKIIMDILSAIIIPPVVEETRISSASVGYWTDDFSDELHHPVPSVVAAKCNSHRKRKFLVDIDGKNRDLFVNLCEL 173
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BLAST of SMED30002680 vs. Planmine SMEST
Match: SMESG000081381.1 (SMESG000081381.1)

HSP 1 Score: 99.7525 bits (247), Expect = 4.787e-32
Identity = 49/67 (73.13%), Postives = 56/67 (83.58%), Query Frame = 2 
Query:  158 NEQLPESAKPAESVPRICTDKENEIKICMDVSSAVTTPPVVEEAQNSSTSVGY*TDDFGDELS*PIL 358
            +EQLPESA+P E VP+IC  KE  +KICMDVSSAV TPPVVEEAQN STSVGY T++FGDEL  P+L
Sbjct:   69 DEQLPESAQPVEPVPQICAYKEERMKICMDVSSAVETPPVVEEAQNLSTSVGYLTNNFGDELPQPVL 135

HSP 2 Score: 56.9954 bits (136), Expect = 4.787e-32
Identity = 40/53 (75.47%), Postives = 44/53 (83.02%), Query Frame = 1 
Query:    1 VGPAKTPKASKKHNPSKIXXXXXXXXAKGAIILENAAKVLEEATIRVAKQFSE 159
            V PAKT ++ K HN SK R RRERRRA+GAI L NAAKVLEEATIRVA+QFSE
Sbjct:   12 VVPAKTHRSRKNHNSSKNRRRRERRRAEGAIELANAAKVLEEATIRVAEQFSE 64
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BLAST of SMED30002680 vs. Planmine SMEST
Match: SMESG000068480.1 (SMESG000068480.1)

HSP 1 Score: 73.559 bits (179), Expect = 2.533e-27
Identity = 43/53 (81.13%), Postives = 47/53 (88.68%), Query Frame = 1 
Query:    1 VGPAKTPKASKKHNPSKIXXXXXXXXAKGAIILENAAKVLEEATIRVAKQFSE 159
            VGPAKTPK SK+HNPSK R RRERR+A+GA IL NAAKVLEEATIRVA+QF E
Sbjct:  519 VGPAKTPKTSKRHNPSKTRRRRERRQAEGATILANAAKVLEEATIRVAEQFQE 571

HSP 2 Score: 67.3958 bits (163), Expect = 2.533e-27
Identity = 44/100 (44.00%), Postives = 48/100 (48.00%), Query Frame = 2 
Query:  158 NEQLPESAKPAESVPRICTDKENEIKICMDVSSAVTTPPVVEEAQNSSTSVGY*TDDFGDELS*PILFFMDTKTNFHRKRKFPVDIDGENRDFVVDLCTL 457
            +EQLPE  K  ESV RI   KE+E+ I  DVS   T P V                               TK NF RKRKFPVDIDGE+RDF VD  TL
Sbjct:  576 DEQLPELVKSVESVHRISASKEDEMNIYTDVSLEETVPQV-----------------------------GTTKFNFFRKRKFPVDIDGESRDFAVDFFTL 646
[Close]
BLAST of SMED30002680 vs. Planmine SMEST
Match: SMESG000001072.1 (SMESG000001072.1)

HSP 1 Score: 95.9005 bits (237), Expect = 7.487e-26
Identity = 57/102 (55.88%), Postives = 67/102 (65.69%), Query Frame = 2 
Query:  161 EQLPESAKPAE----SVPRICTDKENEIKICMDVSSAVTTPPVVEEAQNSSTSVGY*TDDFGDELS*PILFFMDTKTNFHRKRKFPVDIDGENRDFVVDLCT 454
            EQ PE  KP E    S+ +I  D+E+E+KI +DVSSA TTP VVEE +NSSTS+ Y TD FG ELS  +     T+  F RKRKF VDID E RDF VD  T
Sbjct:   71 EQFPEFVKPVEKSVESLHQISADEEDEMKIHIDVSSAETTPLVVEETRNSSTSIRYWTDGFGGELSHSVPQVGATEFKFPRKRKFSVDIDEERRDFAVDYFT 172

HSP 2 Score: 40.0466 bits (92), Expect = 7.487e-26
Identity = 19/27 (70.37%), Postives = 23/27 (85.19%), Query Frame = 1 
Query:   79 AKGAIILENAAKVLEEATIRVAKQFSE 159
            A+GA +L NAAKVLEEA +RVA+QF E
Sbjct:   49 AEGATVLANAAKVLEEAAVRVAEQFPE 75
The following BLAST results are available for this feature:
BLAST of SMED30002680 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 SMED30002680 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 SMED30002680 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 SMED30002680 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 SMED30002680 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 SMED30002680 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 SMED30002680 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 SMED30002680 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 SMED30002680 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 SMED30002680 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 SMED30002680 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 SMED30002680 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 SMED30002680 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 SMED30002680 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000058785.13.575e-3359.52SMESG000058785.1[more]
SMESG000051967.19.699e-3359.41SMESG000051967.1[more]
SMESG000081381.14.787e-3273.13SMESG000081381.1[more]
SMESG000068480.12.533e-2781.13SMESG000068480.1[more]
SMESG000001072.17.487e-2655.88SMESG000001072.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002680 ID=SMED30002680|Name=SMED30002680|organism=Schmidtea mediterranea sexual|type=transcript|length=985bp
GTTGGTCCGGCAAAAACCCCCAAAGCCAGTAAAAAGCACAACCCCAGCAA
AATCCGGTGACGCCGTGAACGTCGTCGAGCTAAAGGAGCCATCATATTGG
AAAATGCGGCCAAAGTGCTCGAAGAGGCCACCATTCGGGTCGCCAAGCAA
TTCTCGGAATGAACAATTGCCCGAATCGGCGAAACCAGCGGAATCAGTGC
CTCGAATTTGTACTGACAAGGAGAACGAGATTAAAATCTGCATGGACGTG
TCCTCGGCAGTAACAACCCCACCAGTAGTCGAGGAAGCTCAAAATTCATC
GACTTCAGTCGGATATTAAACCGACGACTTCGGCGACGAACTGTCTTAAC
CAATTCTTTTCTTCATGGATACCAAAACCAACTTTCATCGGAAGAGGAAA
TTCCCCGTCGATATCGATGGAGAAAATCGAGATTTCGTCGTCGATTTATG
TACCTTGTCTAACTAATATATTTTTTTCTTAATGTTTTAAATTTTAACAA
AAATTAAATTTTTGTAGTTATTCTTATTTTGCGTGAAATTTTGGTTTTTC
TTTATGAATAAATACTTAGCTAAGGTTAATAATCATTTCCGATTACGACA
GGAGGATAGTGGGAGCCTAAATACTACAAATAGTATTTTTAGAAAGGTTT
ATTCAACTAAGGGAGTTAAATTAGGAAGAATTAGAGTTCTTGTTAAATTA
ATTTTAAGTACTCGTGTGAGGGTTTTGAAAGTAAAAGGGTAATTTTCAGT
GAAAAACAAGATATAACCCTTAAGTCAACCTTATTTTTCTTTAAATTAAA
AAGAAAAATTTTATAAATTTAAAAACAGCTGATCTAACAGCGAATTAAAT
AATTTCGATGAATTTCAGAGAGCGGATCAAGAGGTAATAAGCTTAAAGAT
AAATCAATCAACCAAACAAATTAAATTCTTGCGCAACCAGTAGAGTATTG
TGAGTGTAGAATATTGTGAATTGAATCGATTTTTG
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protein sequence of SMED30002680-orf-1

>SMED30002680-orf-1 ID=SMED30002680-orf-1|Name=SMED30002680-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=106bp
LVRQKPPKPVKSTTPAKSGDAVNVVELKEPSYWKMRPKCSKRPPFGSPSN
SRNEQLPESAKPAESVPRICTDKENEIKICMDVSSAVTTPPVVEEAQNSS
TSVGY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0002109X1 cell
PLANA:0002111X2 cell
PLANA:0003116parenchymal cell