SMED30021645

Overview
NameSMED30021645
Smed IDSMED30021645
Length (bp)644
Neoblast Clusters

Zeng et. al., 2018



 

 

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



Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
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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



SMED30021645

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
protonephridiaSMED30021645SMESG000014085.1 SMESG000014086.1 SMESG000014087.1 dd_Smed_v4_10249_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30021645SMESG000014085.1 SMESG000014086.1 SMESG000014087.1 dd_Smed_v4_10249_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30021645SMESG000014085.1 SMESG000014086.1 SMESG000014087.1 dd_Smed_v4_10249_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30021645SMESG000014085.1 SMESG000014086.1 SMESG000014087.1 dd_Smed_v4_10249_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30021645SMESG000014085.1 SMESG000014086.1 SMESG000014087.1 dd_Smed_v4_10249_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30021645SMESG000014085.1 SMESG000014086.1 SMESG000014087.1 dd_Smed_v4_10249_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30021645SMESG000014085.1 SMESG000014086.1 SMESG000014087.1 dd_Smed_v4_10249_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30021645SMESG000014085.1 SMESG000014086.1 SMESG000014087.1 dd_Smed_v4_10249_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30021645SMESG000014085.1 SMESG000014086.1 SMESG000014087.1 dd_Smed_v4_10249_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30021645SMESG000014085.1 SMESG000014086.1 SMESG000014087.1 dd_Smed_v4_10249_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30021645SMESG000014085.1 SMESG000014087.1 SMESG000014086.1 Contig53671newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30021645SMESG000014085.1 SMESG000014087.1 SMESG000014086.1 Contig53671uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30021645 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001868:4255..4855 -2146
v31.019695:3691..4271 -1700
v31.012290:13080..13660 -1695
v31.025273:2063..2651 +1689
v31.002147:57307..57844 +1672
v31.000096:202887..203442 -1626
v31.005822:34583..35069 +1475
Homology
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BLAST of SMED30021645 vs. TrEMBL
Match: A0A034V1L6 (Uncharacterized protein (Fragment) OS=Bactrocera dorsalis OX=27457 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 5.388e-8
Identity = 43/156 (27.56%), Postives = 73/156 (46.79%), Query Frame = 2 
Query:   98 EMESLNEEARRRVILIFFENNVHREKRYTVQQFKEMNIRPSTTYRILQRLDNNSTAQRKLESRGANKIMNGNQLRALKVIALNRVGVYSRRLASRFKVSKSTISRALKRMGATCRARTKSPLYTPEQLARAEECSTKLAVDLSNKTLIMDDEFYFS 565
            +M S  +  R RV+  F++ +    K++T   F    +   T Y IL  L      +R+  S     IM    +R LK +  N   +    +A +F+ S+  I + L R+    R + + P YT EQ+++ +     +  + S K+ I+DDE YFS
Sbjct:    7 KMASKQQHLRDRVVQ-FYKKHETAGKKFTCAHFMAEGVSRRTIYSILSTLK----IERQPGSGRKPTIMTPQNVRKLKTLFNNNYCISQTEVARKFECSQPYICKTLNRLHIKARKKQRCPGYTEEQISQVKSQCRWMCKNFSGKSFILDDESYFS 157
The following BLAST results are available for this feature:
BLAST of SMED30021645 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 SMED30021645 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 SMED30021645 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 SMED30021645 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 SMED30021645 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 SMED30021645 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 SMED30021645 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 SMED30021645 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A034V1L65.388e-827.56Uncharacterized protein (Fragment) OS=Bactrocera d... [more]
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BLAST of SMED30021645 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 SMED30021645 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 SMED30021645 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 SMED30021645 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 SMED30021645 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 SMED30021645 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021645 ID=SMED30021645|Name=SMED30021645|organism=Schmidtea mediterranea sexual|type=transcript|length=644bp
GCTTTCATAATTTGCTGTTCGATATTGTCATTGATATTCGTGATTTCATT
GATTCGATTGGTTTTGTCTATCAGATCTTGTTTCAAATCATTCAACTGAG
ATGGAGTCGCTCAATGAAGAAGCACGCAGAAGAGTGATTTTGATCTTTTT
TGAGAACAATGTACATCGTGAAAAACGGTACACAGTCCAGCAATTCAAGG
AAATGAATATTCGTCCCAGTACAACGTATCGAATCCTGCAACGTCTAGAT
AATAATTCTACTGCACAGCGGAAGTTAGAAAGTAGAGGAGCCAACAAAAT
CATGAATGGCAATCAACTGCGAGCACTCAAAGTCATTGCGCTTAACCGAG
TTGGTGTCTATTCACGCAGACTAGCATCCAGATTCAAAGTGAGCAAATCA
ACAATCAGCAGAGCACTCAAGCGTATGGGAGCAACATGTCGAGCTCGAAC
GAAATCACCTCTGTACACACCTGAGCAATTGGCACGAGCTGAAGAGTGCT
CTACAAAACTCGCAGTCGATTTGAGTAATAAAACTCTTATCATGGACGAT
GAATTTTATTTTTCTTTTTGTCTCTTTTCTGGTGAGCCACCCGTTATTTT
GTAAGTCACACAATAACTCGCTCTTTTTCAACCTTTCTATCCAC
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protein sequence of SMED30021645-orf-1

>SMED30021645-orf-1 ID=SMED30021645-orf-1|Name=SMED30021645-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=168bp
MESLNEEARRRVILIFFENNVHREKRYTVQQFKEMNIRPSTTYRILQRLD
NNSTAQRKLESRGANKIMNGNQLRALKVIALNRVGVYSRRLASRFKVSKS
TISRALKRMGATCRARTKSPLYTPEQLARAEECSTKLAVDLSNKTLIMDD
EFYFSFCLFSGEPPVIL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0003117parapharyngeal cell
Vocabulary: INTERPRO
TermDefinition
IPR011991WHTH_DNA-bd_dom
IPR009057Homeobox-like_sf
Vocabulary: molecular function
TermDefinition
GO:0003677DNA binding