SMED30007442

Overview
NameSMED30007442
Smed IDSMED30007442
Length (bp)622
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 SMED30007442 (SMED30007442) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30007442 (SMED30007442) 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 SMED30007442 (SMED30007442) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30007442 (SMED30007442) 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



SMED30007442

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30007442h1SMcG0016185 Contig4568newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30007442h1SMcG0016185 Contig4568uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30007442h1SMcG0015487 Contig4568newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30007442h1SMcG0015487 Contig4568uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
pigment cellSMED30007442h1SMcG0016185 SmedASXL_005480SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017		whole organism asexual adult RNA-sequencing evidence
gutSMED30007442h1SMcG0016185 dd_Smed_v4_5530_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30007442h1SMcG0016185 dd_Smed_v4_5530_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30007442h1SMcG0016185 dd_Smed_v4_5530_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30007442h1SMcG0016185 dd_Smed_v4_5530_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
SMED30007442 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000168:221370..221990 -3033
Homology
[Close]
BLAST of SMED30007442 vs. Planmine SMEST
Match: SMESG000069832.1 (SMESG000069832.1)

HSP 1 Score: 275.018 bits (702), Expect = 1.383e-95
Identity = 140/143 (97.90%), Postives = 142/143 (99.30%), Query Frame = 3 
Query:  111 MAALYNETLNPSKSKEYGAGLYXXXXXXFYCVGGAFLTCSGIKRKQKSKLTEEEQVEVYIQQRRVIEKQEKVDQIWQTDRMLRRNFMDYPRKKSESGTQTETIVQKSIARSNSLKDLISKSKRNNFSIPPEVQPLKRYSIPLI 539
            MAALYNETL+ SKSKEYGAGLYIIIILIFYCVGGAFLTCSGIKRKQKSKLTEEEQVEVYIQQRRVIEKQEKVDQ+WQTDRMLRRNFMDYPRKKSESGTQTETIVQKSIARSNSLKDLISKSKRNNFSIPPEVQPLKRYSIPLI
Sbjct:    1 MAALYNETLHQSKSKEYGAGLYIIIILIFYCVGGAFLTCSGIKRKQKSKLTEEEQVEVYIQQRRVIEKQEKVDQMWQTDRMLRRNFMDYPRKKSESGTQTETIVQKSIARSNSLKDLISKSKRNNFSIPPEVQPLKRYSIPLI 143
[Close]
BLAST of SMED30007442 vs. Planmine SMEST
Match: SMESG000069780.1 (SMESG000069780.1)

HSP 1 Score: 110.923 bits (276), Expect = 6.285e-31
Identity = 64/135 (47.41%), Postives = 92/135 (68.15%), Query Frame = 3 
Query:  105 TVMAALYNETLNPSKSKEYGAGLYXXXXXXFYCVGGAFLTCSGIKRKQKSKLTEEEQVEVYIQQRRVIEKQEKVDQIWQTDRMLRRNFMDYPRKKSESGTQTETIVQKSIARSNSLKDLISKSKRNNFSIPPEVQ 509
            T+MAA        + SK+Y AGLYII+I++FYCVGGA L  SG+K K+  +  EEEQ+E YI Q++ +EKQ KVDQIWQTDR+LR  F +  +  +E+GT+   +     +  +S+++LISKS  N +SIP +V+
Sbjct:   13 TLMAA-------AATSKDYEAGLYIIMIILFYCVGGALLIMSGMKNKENLRSREEEQIEYYIDQKQFVEKQAKVDQIWQTDRLLREFFNERQQSNTENGTRNGELK----SDFHSIQNLISKSPINIYSIPQKVK 136
[Close]
BLAST of SMED30007442 vs. Planmine SMEST
Match: SMESG000069778.1 (SMESG000069778.1)

HSP 1 Score: 70.4774 bits (171), Expect = 2.429e-15
Identity = 52/140 (37.14%), Postives = 77/140 (55.00%), Query Frame = 3 
Query:  105 TVMAALYNETLNPSKSK--EYGAGLYXXXXXXFYCVGGAFLTCSGIKRKQKSKLTEEEQVEVYIQQRRVIEKQEKVDQIWQTDRMLRRNFMDYPRK----KSESGTQTETIVQKSIARSNSLKDLISKSKRNNFSIPPEV 506
            +V  A    T N SK    EY +G+YII +LIF+  G  F      K + K+KL EE+QV+ +I+QR  ++KQEKVD+IW T+  LR+    +       K++ G +          R + ++ L+SKS RN FSIP  +
Sbjct:   15 SVSQAQNGSTTNISKVNLSEYESGIYIIFVLIFFGSGAGFYLICEFKNRWKNKLREEDQVKSFIEQRGNVQKQEKVDKIWMTENHLRQIIFLHNNNRRCSKADGGKR----------RMSEVRVLLSKSPRNVFSIPNRI 144
The following BLAST results are available for this feature:
BLAST of SMED30007442 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 SMED30007442 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 SMED30007442 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 SMED30007442 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 SMED30007442 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 SMED30007442 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 SMED30007442 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 SMED30007442 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 SMED30007442 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 SMED30007442 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 SMED30007442 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 SMED30007442 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 SMED30007442 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 SMED30007442 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000069832.11.383e-9597.90SMESG000069832.1[more]
SMESG000069780.16.285e-3147.41SMESG000069780.1[more]
SMESG000069778.12.429e-1537.14SMESG000069778.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007442 ID=SMED30007442|Name=SMED30007442|organism=Schmidtea mediterranea sexual|type=transcript|length=622bp
TTTACTCTTCTCTTATCTCTAATGCATGATTGGTCAGGTACCTATAAACA
ATGATTTTTGTAAAATTCACGATTGTGAGCTTCAGTTTTTAGTGACCTTT
ATATACCGTCATGGCTGCACTTTATAATGAAACATTGAACCCATCGAAAT
CGAAGGAATACGGAGCAGGCTTGTACATCATAATAATATTGATATTTTAC
TGTGTAGGGGGAGCATTTTTAACATGCAGCGGAATAAAACGGAAACAGAA
AAGCAAATTAACAGAAGAAGAACAGGTTGAAGTTTACATTCAACAAAGAA
GAGTTATTGAAAAACAGGAAAAGGTAGACCAAATTTGGCAGACAGATAGA
ATGCTTCGTAGAAACTTTATGGATTATCCCAGGAAGAAAAGCGAATCTGG
AACTCAAACTGAAACGATCGTCCAGAAATCTATTGCAAGATCCAATAGTT
TAAAGGATTTAATTTCAAAATCTAAACGAAACAATTTCTCCATTCCTCCG
GAAGTTCAGCCGTTGAAAAGATATTCTATTCCCTTGATTTGAAAGGAACT
TTTATGAATATTTGTATAATTTGCTTTTATAAAAGATTTTAAATTAGAAT
AAATTTTTTATTTATTAAAAAA
back to top

protein sequence of SMED30007442-orf-1

>SMED30007442-orf-1 ID=SMED30007442-orf-1|Name=SMED30007442-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=144bp
MAALYNETLNPSKSKEYGAGLYIIIILIFYCVGGAFLTCSGIKRKQKSKL
TEEEQVEVYIQQRRVIEKQEKVDQIWQTDRMLRRNFMDYPRKKSESGTQT
ETIVQKSIARSNSLKDLISKSKRNNFSIPPEVQPLKRYSIPLI*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0002075pigment cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 20..42