SMED30001567

Overview
NameSMED30001567
Smed IDSMED30001567
Length (bp)542
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 SMED30001567 (SMED30001567) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30001567 (SMED30001567) 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 SMED30001567 (SMED30001567) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30001567 (SMED30001567) 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



SMED30001567

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30001567SMESG000022139.1 SmedASXL_002794SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30001567SMESG000022139.1 dd_Smed_v4_715_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30001567SMESG000022139.1 dd_Smed_v4_715_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30001567SMESG000022139.1 Contig35009newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30001567SMESG000022139.1 Contig35009uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30001567SMESG000022139.1 dd_Smed_v6_715_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30001567SMESG000022139.1 OX_Smed_1.0.09137ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
gutSMED30001567SMESG000022139.1 SMED30001567smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
parenchymaSMED30001567SMESG000022139.1 SMED30001567smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
Category 3 cellSMED30001567SMESG000022139.1 dd_Smed_v6_715_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30001567SMESG000022139.1 dd_Smed_v4_715_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
Alignments
SMED30001567 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011567:16064..16633 -2557
Homology
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BLAST of SMED30001567 vs. Planmine SMEST
Match: SMESG000022139.1 (SMESG000022139.1)

HSP 1 Score: 218.394 bits (555), Expect = 5.390e-74
Identity = 122/123 (99.19%), Postives = 122/123 (99.19%), Query Frame = 3 
Query:   54 MKKFSIIAFSIFVTLAVADVWIPPSARCKNVLVPASKQCDKNYKETDEFCNGGFAKLNKVCYGKDTVECGDAYKAFTALCKEKQDNFWDECDPVYTAYRKECATPXXXXXXXXXXXXXXXDNK 422
            MKKFSIIAFSIFVTLAVADVWIPPSARCKNVLVPASKQCDKNYKETDEFCNGGFAKLNKVCYGKDTVECGDAYKAFT LCKEKQDNFWDECDPVYTAYRKECATPEEIKEENQEIAEEAKDNK
Sbjct:    1 MKKFSIIAFSIFVTLAVADVWIPPSARCKNVLVPASKQCDKNYKETDEFCNGGFAKLNKVCYGKDTVECGDAYKAFTTLCKEKQDNFWDECDPVYTAYRKECATPEEIKEENQEIAEEAKDNK 123
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BLAST of SMED30001567 vs. Planmine SMEST
Match: SMESG000061767.1 (SMESG000061767.1)

HSP 1 Score: 120.939 bits (302), Expect = 2.484e-35
Identity = 53/105 (50.48%), Postives = 70/105 (66.67%), Query Frame = 3 
Query:   54 MKKFSIIAFSIFVTLAVADVWIPPSARCKNVLVPASKQCDKNYKETDEFCNGGFAKLNKVCYGKDTVECGDAYKAFTALCKEKQDNFWDECDPVYTAYRKECATP 368
            MK  SI    + V +  +  W+PPS RC  +L PA+++CD+ YKE D FC+ G+  +NK C GK+T++CG  +    A CKEKQD FWD CD VYTAYR ECA+P
Sbjct:    1 MKNLSIFLCFLSVAVVFSTKWVPPSNRCSKILTPAARRCDRKYKEADNFCSAGYVAINKDCKGKETIDCGKRFDQHDADCKEKQDIFWDLCDSVYTAYRNECASP 105
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BLAST of SMED30001567 vs. Planmine SMEST
Match: SMESG000020501.1 (SMESG000020501.1)

HSP 1 Score: 106.686 bits (265), Expect = 4.312e-30
Identity = 54/104 (51.92%), Postives = 67/104 (64.42%), Query Frame = 3 
Query:   54 MKKFSIIAFSIFVTLAVADVWIPPSARCKNVLVPASKQCDKNYKETDEFCNGGFAKLNKVCYGKDTVECGDAYKAFTALCKEKQDNFWDECDPVYTAYRKECAT 365
            M K SI A  +FV       +   S RC   L PA+K+CDK Y ETD FCNGG+A +NKVC G DT+ECG  YK F   CKE+Q+NFW++CD VY  Y+  CA+
Sbjct:    1 MSKLSIFAL-LFVI-----AYCHCSPRCDLELAPAAKRCDKKYAETDAFCNGGYAAINKVCKGVDTIECGLEYKRFAVKCKERQNNFWNDCDQVYKTYQTVCAS 98
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BLAST of SMED30001567 vs. Planmine SMEST
Match: SMESG000029095.1 (SMESG000029095.1)

HSP 1 Score: 98.9821 bits (245), Expect = 4.426e-27
Identity = 48/103 (46.60%), Postives = 61/103 (59.22%), Query Frame = 3 
Query:   54 MKKFSIIAFSIFVTLAVADVWIPPSARCKNVLVPASKQCDKNYKETDEFCNGGFAKLNKVCYGKDTVECGDAYKAFTALCKEKQDNFWDECDPVYTAYRKECA 362
            M + S+ A    V       +   S +C   LVPA+K CD+ Y ETD FCNGG+AK+NKVC G DT+EC   YK F   C+E+QD FW  C PVY  Y+  C+
Sbjct:    1 MSRISLFAIVYLVA------YCHCSEQCDRELVPAAKDCDRKYAETDNFCNGGYAKINKVCKGVDTIECALKYKKFGEACRERQDYFWKNCGPVYKIYQTLCS 97
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BLAST of SMED30001567 vs. Planmine SMEST
Match: SMESG000061765.1 (SMESG000061765.1)

HSP 1 Score: 98.9821 bits (245), Expect = 8.232e-27
Identity = 43/102 (42.16%), Postives = 62/102 (60.78%), Query Frame = 3 
Query:   60 KFSIIAFSIFVTLAVADVWIPPSARCKNVLVPASKQCDKNYKETDEFCNGGFAKLNKVCYGKDTVECGDAYKAFTALCKEKQDNFWDECDPVYTAYRKECAT 365
            K SI+ F + ++    D     S  C  VL P SK CD+ Y   D FC+ G+AK+NK+C GK++V CG  Y+     CK+ Q+NFW+ CD +Y  YR++CA+
Sbjct:    2 KTSILIFCVLISAVFTDEEFQLSKHCIEVLTPLSKDCDRRYHVADTFCSQGYAKINKICTGKESVYCGLQYENHDKACKQVQNNFWNHCDDIYRNYRQQCAS 103
The following BLAST results are available for this feature:
BLAST of SMED30001567 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 SMED30001567 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 SMED30001567 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 SMED30001567 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 SMED30001567 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 SMED30001567 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 SMED30001567 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 SMED30001567 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 SMED30001567 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 SMED30001567 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 SMED30001567 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 SMED30001567 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 SMED30001567 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 SMED30001567 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000022139.15.390e-7499.19SMESG000022139.1[more]
SMESG000061767.12.484e-3550.48SMESG000061767.1[more]
SMESG000020501.14.312e-3051.92SMESG000020501.1[more]
SMESG000029095.14.426e-2746.60SMESG000029095.1[more]
SMESG000061765.18.232e-2742.16SMESG000061765.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001567 ID=SMED30001567|Name=SMED30001567|organism=Schmidtea mediterranea sexual|type=transcript|length=542bp
ACATATTTAAATTAATTTTTTTGTACTATTTGATATTGTTTTAATTATAA
CAAATGAAGAAATTTTCAATTATCGCATTTTCTATATTCGTTACTTTGGC
AGTTGCTGATGTTTGGATTCCTCCGTCAGCGAGATGTAAAAATGTACTCG
TGCCAGCATCAAAACAGTGCGACAAAAATTATAAAGAAACAGATGAGTTT
TGTAATGGTGGATTTGCAAAATTGAATAAAGTCTGTTATGGAAAAGACAC
CGTTGAATGCGGCGATGCGTATAAAGCATTCACCGCTTTATGTAAAGAAA
AACAAGACAACTTTTGGGATGAATGTGACCCAGTCTATACAGCTTACAGA
AAAGAGTGTGCTACACCTGAAGAAATAAAAGAAGAGAATCAAGAAATTGC
TGAAGAAGCAAAAGATAACAAATAGAAAAGCGCAGTAAATCATAGACCAA
AGATTCCTCGTTTCAAATTAATTGTAAAAAACAATTATTTGTTCGCTAAA
TATATTTTTTTCTTTTGTCAAAAAAAAAAAAAAAAAATGCGA
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protein sequence of SMED30001567-orf-1

>SMED30001567-orf-1 ID=SMED30001567-orf-1|Name=SMED30001567-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=124bp
MKKFSIIAFSIFVTLAVADVWIPPSARCKNVLVPASKQCDKNYKETDEFC
NGGFAKLNKVCYGKDTVECGDAYKAFTALCKEKQDNFWDECDPVYTAYRK
ECATPEEIKEENQEIAEEAKDNK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000035Category 3 cell
PLANA:0000418head
PLANA:0002032epidermal cell
PLANA:0002142parenchyma
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..18
score: 0.831