SMED30004502

Overview
NameSMED30004502
Smed IDSMED30004502
Length (bp)582
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ 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




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 SMED30004502 (SMED30004502) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004502 (SMED30004502) 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




SMED30004502

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymal cellSMED30004502h1SMcG0019305 dd_Smed_v4_11793_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004502h1SMcG0019305 Contig50494newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004502h1SMcG0019305 Contig50494uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30004502h1SMcG0019305 dd_Smed_v6_11793_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30004502h1SMcG0019305 OX_Smed_1.0.05288ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30004502 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007259:14675..15255 -2851
v31.009078:5548..6125 +2684
Homology
BLAST of SMED30004502 vs. Planmine SMEST
Match: SMESG000067312.1 (SMESG000067312.1)

HSP 1 Score: 299.671 bits (766), Expect = 2.168e-105
Identity = 147/151 (97.35%), Postives = 149/151 (98.68%), Query Frame = 1
Query:   70 MPFNYLSDKMDENRIGIDLKNLIFGVMFLTCGLIQTYFSFAILIGLHEEWITLILGLFLTTSGAMSILSFKQRTRRILLITFIFECLSSLFHMMFTIVYYNLNFHNPYSLHLFQDIQHLLYYIIMASILFGHSLLLYWQMKIPMGYVRESL 522
            MPFNYLSDKMDENRIGIDLKNLIFGVMFLTCGLIQTYFSFAILIGLHEEWITLILGLFLTTSGAMSILSFKQRT+RILLITFIFEC+SSLFHMMFTIVYYNLNFHNPYSLHLFQDIQHLLYYIIMASILFGHS LLYWQMK PMGYVRESL
Sbjct:    1 MPFNYLSDKMDENRIGIDLKNLIFGVMFLTCGLIQTYFSFAILIGLHEEWITLILGLFLTTSGAMSILSFKQRTKRILLITFIFECISSLFHMMFTIVYYNLNFHNPYSLHLFQDIQHLLYYIIMASILFGHSFLLYWQMKRPMGYVRESL 151          
BLAST of SMED30004502 vs. Planmine SMEST
Match: SMESG000067307.1 (SMESG000067307.1)

HSP 1 Score: 286.96 bits (733), Expect = 2.078e-100
Identity = 142/151 (94.04%), Postives = 145/151 (96.03%), Query Frame = 1
Query:   70 MPFNYLSDKMDENRIGIDLKNLIFGVMFLTCGLIQTYFSFAILIGLHEEWITLILGLFLTTSGAMSILSFKQRTRRILLITFIFECLSSLFHMMFTIVYYNLNFHNPYSLHLFQDIQHLLYYIIMASILFGHSLLLYWQMKIPMGYVRESL 522
            MPFNYLSDKMDENRIGIDLKNLIFGVMFLTCGLIQTYFSFAILIGLHEEWITLILGLFLTTSGAMSILSFKQRT+RILLITFIFEC+SSLFHMMFTIVYYNLNF N YSLH + DIQHLLYYIIMASILFGHS LLYWQMK PMGYVRESL
Sbjct:    1 MPFNYLSDKMDENRIGIDLKNLIFGVMFLTCGLIQTYFSFAILIGLHEEWITLILGLFLTTSGAMSILSFKQRTKRILLITFIFECISSLFHMMFTIVYYNLNFQNLYSLHFYPDIQHLLYYIIMASILFGHSFLLYWQMKRPMGYVRESL 151          
BLAST of SMED30004502 vs. Planmine SMEST
Match: SMESG000067313.1 (SMESG000067313.1)

HSP 1 Score: 98.9821 bits (245), Expect = 1.797e-26
Identity = 54/137 (39.42%), Postives = 86/137 (62.77%), Query Frame = 1
Query:   97 MDENRIGIDLKNLIFGVMFLTCGLIQTYFSFAILIGLHEEWITLILGLFLTTSGAMSILSFKQRTRRILLITFIFECLSSLFHMMFTIVY-----YNLNFHNPYSLHLFQDIQHLLYYIIMASILFGHSLLLYWQMK 492
            M+ ++IG DLK+L FG+ FL+CG IQTYF+  +++  H     L  G+FL   GA+ I ++  +T+RI  +  +FECLS   +++  IV+     Y +  H  YS+ +F  +QH L+Y ++ ++L  HS+LLY QMK
Sbjct:    1 MEVHKIGKDLKDLCFGISFLSCGSIQTYFAVGVILLSHRGLGDLFSGVFLAIVGALIIFAYNSKTKRIFKVILVFECLSCALNVIHPIVFNAYFIYKIKDHLHYSI-IFFIVQHTLFYFLLVALLCYHSVLLYRQMK 136          
BLAST of SMED30004502 vs. Planmine SMEST
Match: SMESG000018458.1 (SMESG000018458.1)

HSP 1 Score: 47.3654 bits (111), Expect = 6.638e-7
Identity = 21/65 (32.31%), Postives = 35/65 (53.85%), Query Frame = 1
Query:  202 GLHEEWITLILGLFLTTSGAMSILSFKQRTRRILLITFIFECLSSLFHMMFTIVYYNLNFHNPYS 396
            G+ + W  +I G  L  +G++ + S     +R L+I  +FEC+SS  H +F I    + +HN  S
Sbjct:   49 GVEKSWAAIISGSILIAAGSLCVHSSDHARKRFLVIALVFECVSSAMHYLFCIACIAVLYHNNTS 113          
The following BLAST results are available for this feature:
BLAST of SMED30004502 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 SMED30004502 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 SMED30004502 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 SMED30004502 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 SMED30004502 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 SMED30004502 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 SMED30004502 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 SMED30004502 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 SMED30004502 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 SMED30004502 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 SMED30004502 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 SMED30004502 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 SMED30004502 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 SMED30004502 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000067312.12.168e-10597.35SMESG000067312.1[more]
SMESG000067307.12.078e-10094.04SMESG000067307.1[more]
SMESG000067313.11.797e-2639.42SMESG000067313.1[more]
SMESG000018458.16.638e-732.31SMESG000018458.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004502 ID=SMED30004502|Name=SMED30004502|organism=Schmidtea mediterranea sexual|type=transcript|length=582bp
GTAAATATTATTGTTATTGTTTCCGTAGAATGTGCAAGTTTAATTTAATA
ACTGAAGTCTACTACGTTTATGCCATTCAATTATCTGTCAGATAAAATGG
ACGAAAACAGAATTGGCATTGACTTAAAAAATCTAATCTTTGGTGTTATG
TTTTTGACCTGTGGACTGATCCAGACATATTTCTCCTTTGCAATTTTGAT
CGGGCTTCACGAAGAATGGATAACCTTGATCTTGGGATTATTTCTAACGA
CTTCCGGTGCAATGTCTATTCTTAGTTTCAAGCAAAGAACAAGAAGGATT
CTTCTCATAACCTTTATTTTTGAATGTTTATCCAGCTTATTTCATATGAT
GTTCACGATCGTATACTACAATCTAAATTTTCATAATCCTTACTCTCTTC
ATTTATTCCAGGATATCCAACATTTGTTGTACTACATCATAATGGCCAGT
ATTTTATTTGGTCATTCTTTGTTGCTATACTGGCAAATGAAGATACCCAT
GGGATATGTTAGAGAATCTCTCTGATTGAGAATCGAATGAATTTTCATTA
ATAATCATTTTATTAATTAAAACAAACAGATC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 77..99
NoneNo IPR availableTMHMMTMhelixcoord: 48..70
NoneNo IPR availableTMHMMTMhelixcoord: 21..43
NoneNo IPR availableTMHMMTMhelixcoord: 119..138