SMED30017561

Overview
NameSMED30017561
Smed IDSMED30017561
Length (bp)1066
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 SMED30017561 (SMED30017561) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30017561 (SMED30017561) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

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 SMED30017561 (SMED30017561) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30017561 (SMED30017561) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30017561

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 cellSMED30017561SMESG000004026.1 SmedASXL_009281SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
epidermisSMED30017561SMESG000004026.1 dd_Smed_v4_14537_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
tail regionSMED30017561SMESG000004026.1 dd_Smed_v6_14537_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30017561 vs. Planmine SMEST
Match: SMESG000026733.1 (SMESG000026733.1)

HSP 1 Score: 139.043 bits (349), Expect = 5.479e-40
Identity = 72/143 (50.35%), Postives = 95/143 (66.43%), Query Frame = 3 
Query:  486 NLKGSSNNDGKDRQSL*DAGYSLSTFSDSSWPVWNNSRDDEVEVPSLVIKREPGRNTAHEAR*HAEYSLCRFEALEWKFHWRMMMVH*HLRRNNMAIASGEIPSTDEHALDYGISFELDDPALDQLSAPTRVILPAKLFNGPV 914
             +K + +   + RQSL D  YSL+T  D+SWP+ + SRD+E+E+ SL IKREP RN A E    AE+SL R E L  KF W++ M   HL++ N  IA+GEIPSTD +A DYG+ FEL+DP L Q+   T  ILPA+LFN  +
Sbjct:   12 TIKVTPDMAAQYRQSLWDVSYSLATLGDNSWPIRDKSRDNEIELLSLAIKREPDRNLAREPCQRAEFSLYRLEELVRKFQWKVRMTQRHLKQINATIATGEIPSTDGYAQDYGLLFELNDPVLTQMH--TNAILPAQLFNERI 152
[Close]
BLAST of SMED30017561 vs. Planmine SMEST
Match: SMESG000027782.1 (SMESG000027782.1)

HSP 1 Score: 138.658 bits (348), Expect = 3.420e-39
Identity = 74/163 (45.40%), Postives = 104/163 (63.80%), Query Frame = 3 
Query:  486 NLKGSSNNDGKDRQSL*DAGYSLSTFSDSSWPVWNNSRDDEVEVPSLVIKREPGRNTAHEAR*HAEYSLCRFEALEWKFHWRMMMVH*HLRRNNMAIASGEIPSTDEHALDYGISFELDDPALDQLSAPTRVILPAKLFNGPVWSKPGLQRGREDNSYGSPYP 974
             L+  S +  + RQ L D GY LST+ DSSWP  +  + +E+E+PS+ IKREPG N A EAR  AEY+  + E LE K+H + ++    L + N  IASG IPSTD    +YG+SFELDDP L Q++APT+++LP KL    + ++ G  R   D++Y S +P
Sbjct:   43 TLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSKYQAEEIELPSIAIKREPGHNPAREARQRAEYAAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKLVLPEKLIQSTLRNRLG-SRQTGDHTYASRHP 204
[Close]
BLAST of SMED30017561 vs. Planmine SMEST
Match: SMESG000004883.1 (SMESG000004883.1)

HSP 1 Score: 132.494 bits (332), Expect = 3.515e-36
Identity = 76/172 (44.19%), Postives = 107/172 (62.21%), Query Frame = 3 
Query:  489 LKGSSNNDGKDRQSL*DAGYSLSTFSDSSWPVWNNSRDDEVEVPSLVIKREPGRNTAHEAR*HAEYSLCRFEALEWKFHWRMMMVH*HLRRNNMAIASGEIPSTDEHALDYGISFELDDPALDQLSAPTRVILPAKLFNGPVWSKPG-LQRGREDNSYGSPYPSTSGKMQEL 1001
            L+  S +  + RQ L D GY LST+ DSSWP  +  + +EVE+PS+ IKREPG N A EAR  AEY+  + E LE K+  + ++    L + N  IASG IPSTD    +YG+SFELDDP L Q++APT++++P KL    + ++ G  Q G  D++Y S +P  + K   L
Sbjct:   97 LQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEVELPSVAIKREPGHNPAREARQRAEYAAMKKEELERKYQRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVRSTLRNRLGSSQTG--DHTYASRHPQWNSKHNNL 266

HSP 2 Score: 75.0998 bits (183), Expect = 3.364e-15
Identity = 40/86 (46.51%), Postives = 54/86 (62.79%), Query Frame = 3 
Query:  738 MVH*HLRRNNMAIASGEIPSTDEHALDYGISFELDDPALDQLSAPTRVILPAKLFNGPVWSKPGLQRGREDNSYGSPYPSTSGKMQ 995
            M    L R N  IASGEIPSTD +A DYG+SFEL DPA  ++ APT ++LP  LFNGP+  +      R+++SY   +P+   + Q
Sbjct:    1 MARRRLERINAVIASGEIPSTDGYAPDYGVSFELRDPA--RMKAPTNIVLPVNLFNGPIRHRD----RRDEHSYQCQHPTKKERNQ 80
[Close]
BLAST of SMED30017561 vs. Planmine SMEST
Match: SMESG000046313.1 (SMESG000046313.1)

HSP 1 Score: 137.502 bits (345), Expect = 1.837e-35
Identity = 72/163 (44.17%), Postives = 106/163 (65.03%), Query Frame = 3 
Query:  486 NLKGSSNNDGKDRQSL*DAGYSLSTFSDSSWPVWNNSRDDEVEVPSLVIKREPGRNTAHEAR*HAEYSLCRFEALEWKFHWRMMMVH*HLRRNNMAIASGEIPSTDEHALDYGISFELDDPALDQLSAPTRVILPAKLFNGPVWSKPGLQRGREDNSYGSPYP 974
             L+ S+ +  + RQ+L D GY+LST+ +SSWP     R+DEVE+PS+ IKREPGRN A E    AEY+  + E +E K+H + ++    L + N  IASG IPSTD     YG+SFELDDP L Q++APT++++P +L    + ++ G +R   D++Y S +P
Sbjct:  677 TLQISNASAARYRQALWDNGYTLSTYGESSWPRRPKDREDEVELPSIAIKREPGRNPAREVHQRAEYTSMKMEEMERKYHRKAVLARQRLAQINRDIASGVIPSTDSFPPTYGVSFELDDPRLLQMTAPTKLVIPEELIQPGLRNRLGSRRT-GDHTYASRHP 838
[Close]
BLAST of SMED30017561 vs. Planmine SMEST
Match: SMESG000046313.1 (SMESG000046313.1)

HSP 1 Score: 137.502 bits (345), Expect = 1.856e-35
Identity = 72/162 (44.44%), Postives = 106/162 (65.43%), Query Frame = 3 
Query:  489 LKGSSNNDGKDRQSL*DAGYSLSTFSDSSWPVWNNSRDDEVEVPSLVIKREPGRNTAHEAR*HAEYSLCRFEALEWKFHWRMMMVH*HLRRNNMAIASGEIPSTDEHALDYGISFELDDPALDQLSAPTRVILPAKLFNGPVWSKPGLQRGREDNSYGSPYP 974
            L+ S+ +  + RQ+L D GY+LST+ +SSWP     R+DEVE+PS+ IKREPGRN A E    AEY+  + E +E K+H + ++    L + N  IASG IPSTD     YG+SFELDDP L Q++APT++++P +L    + ++ G +R   D++Y S +P
Sbjct:  626 LQISNASAARYRQALWDNGYTLSTYGESSWPRRPKDREDEVELPSIAIKREPGRNPAREVHQRAEYTSMKMEEMERKYHRKAVLARQRLAQINRDIASGVIPSTDSFPPTYGVSFELDDPRLLQMTAPTKLVIPEELIQPGLRNRLGSRRT-GDHTYASRHP 786
The following BLAST results are available for this feature:
BLAST of SMED30017561 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017561 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017561 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017561 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017561 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017561 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017561 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017561 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017561 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017561 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017561 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017561 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017561 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30017561 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000026733.15.479e-4050.35SMESG000026733.1[more]
SMESG000027782.13.420e-3945.40SMESG000027782.1[more]
SMESG000004883.13.515e-3644.19SMESG000004883.1[more]
SMESG000046313.11.837e-3544.17SMESG000046313.1[more]
SMESG000046313.11.856e-3544.44SMESG000046313.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017561 ID=SMED30017561|Name=SMED30017561|organism=Schmidtea mediterranea sexual|type=transcript|length=1066bp
TTAAATTAATACTGAGGGCTAATAACAAAACTTTATCGACACCGCCGGTC
CAAGTAGTAGAACTTGCATAAGGGAATTCGGAGCGATCGAGGTGGGTGCA
AGAAGAAAGGACCAAGCAACCGGACCAAACTCGTACAGTTCGATCGAGTT
CATAGAAGGTAAACCACTATGATCTAATAGGAATTAGGAATGAGTGTCGC
GAGAGCGGAACAGTTACTTAGAATAATTTAGTTCTACGAGAATATAGTTA
GAGTAATTTGGACCTGTGATGTACCTTATAAATGATAGACCTCAATGAAT
ACCCACTGGATTTGACGGACATGTGAGATTATTGAACAAGGAATTGAGAC
CTACTGATACTAATTTCTTCTAATAATGTTTTGCGAATAAAGAGCCACGG
GTTTAAGAGCGACATTGTTTCAAATTAACTTCTTTAAGTACCAAACCTAG
AGAATCGAAATCATGTGGAAAGATGCAGGACGAGTAACCTTAAAGGTTCC
TCAAACAATGACGGCAAAGATCGACAGTCGTTGTAAGACGCAGGGTACAG
TTTGTCCACATTCAGTGACAGTAGCTGGCCAGTCTGGAACAACTCAAGAG
ACGATGAAGTGGAAGTACCAAGCCTCGTTATAAAACGCGAGCCAGGTCGG
AATACGGCCCACGAAGCACGCTAGCACGCTGAATACTCTTTATGTCGATT
CGAAGCGCTCGAGTGGAAGTTCCACTGGAGGATGATGATGGTTCATTGAC
ACCTGAGGCGGAATAACATGGCAATCGCCTCCGGAGAAATTCCAAGTACC
GATGAACACGCACTCGATTATGGAATCTCTTTTGAACTGGATGATCCAGC
TTTGGATCAGCTGAGTGCTCCAACGAGAGTCATATTGCCAGCCAAGCTGT
TCAATGGACCGGTGTGGAGTAAACCGGGATTACAACGAGGACGGGAAGAC
AATTCTTATGGTAGCCCTTACCCATCAACTAGCGGAAAGATGCAAGAGCT
TAACCCTGGTACACCAGGATGGAAACCAACGAAGAAACCAATACAAGCAT
TTTGTTTCCTTATCTT
back to top

protein sequence of SMED30017561-orf-1

>SMED30017561-orf-1 ID=SMED30017561-orf-1|Name=SMED30017561-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=99bp
MAIASGEIPSTDEHALDYGISFELDDPALDQLSAPTRVILPAKLFNGPVW
SKPGLQRGREDNSYGSPYPSTSGKMQELNPGTPGWKPTKKPIQAFCFLI
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000421tail
PLANA:0002032epidermal cell
PLANA:0002111X2 cell