SMED30013125

Overview
NameSMED30013125
Smed IDSMED30013125
Length (bp)445
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



Anatomical Expression

PAGE et. al., 2020



SMED30013125

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



PAGE Curations: 33

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30013125h1SMcG0019647 Contig49384uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0019647 Contig49384newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0019646 Contig44595newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0019646 Contig44595uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0019646 Contig5172GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0019646 Contig49384uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0019646 Contig49384newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0019647 Contig39421uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0019647 Contig39421newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0019646 Contig39421uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0019646 Contig39421newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0019646 Contig42646uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0019646 Contig42646newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0019646 Contig37177newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0019646 Contig37176newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0019646 Contig37176uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0019646 Contig5216GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30013125h1SMcG0019646 dd_Smed_v4_1721_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30013125h1SMcG0019646 dd_Smed_v4_1721_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30013125h1SMcG0019646 dd_Smed_v4_1721_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
muscle cellSMED30013125h1SMcG0019646 dd_Smed_v4_1721_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30013125h1SMcG0019646 dd_Smed_v4_1721_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30013125h1SMcG0019646 dd_Smed_v4_1721_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30013125h1SMcG0019646 dd_Smed_v4_1721_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30013125h1SMcG0019646 dd_Smed_v4_1721_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30013125h1SMcG0019646 dd_Smed_v4_1721_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30013125h1SMcG0019646 dd_Smed_v4_1721_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013125h1SMcG0021452 Contig5216GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30013125h1SMcG0019646 dd_Smed_v6_1721_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
neuronSMED30013125h1SMcG0019646 dd_Smed_v6_1721_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cholinergic neuronSMED30013125h1SMcG0019646 dd_Smed_v6_1721_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pigment cellSMED30013125h1SMcG0019646 dd_Smed_v6_1721_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
secretory systemSMED30013125h1SMcG0019646 dd_Smed_v6_1721_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30013125 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003018:4645..5032 +1471
Homology
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BLAST of SMED30013125 vs. Planmine SMEST
Match: SMESG000014734.1 (SMESG000014734.1)

HSP 1 Score: 73.9442 bits (180), Expect = 6.873e-16
Identity = 34/41 (82.93%), Postives = 36/41 (87.80%), Query Frame = -1 
Query:  323 RGSSSLQTQMNTLRVVDAFRMPNGQRRDMHRGSIGAIRAAR 445
            RG S LQTQMNT+RVVDAFRM N QR+DMHR SIGAIRAAR
Sbjct: 1130 RGLSRLQTQMNTIRVVDAFRMTNDQRQDMHRSSIGAIRAAR 1170
[Close]
BLAST of SMED30013125 vs. Planmine SMEST
Match: SMESG000014734.1 (SMESG000014734.1)

HSP 1 Score: 63.929 bits (154), Expect = 1.810e-12
Identity = 29/37 (78.38%), Postives = 33/37 (89.19%), Query Frame = -1 
Query:  323 SLQTQMNTLRVVDAFRMPNGQRRDMHRGSIGAIRAAR 433
            SL ++MNT+RVVDAFRM N QR+DMHR SIGAIRAAR
Sbjct: 1169 SLLSEMNTIRVVDAFRMTNDQRQDMHRSSIGAIRAAR 1205
The following BLAST results are available for this feature:
BLAST of SMED30013125 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 SMED30013125 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 SMED30013125 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 SMED30013125 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 SMED30013125 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 SMED30013125 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 SMED30013125 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 SMED30013125 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 SMED30013125 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 SMED30013125 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 SMED30013125 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 SMED30013125 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 SMED30013125 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 SMED30013125 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000014734.16.873e-1682.93SMESG000014734.1[more]
SMESG000014734.11.810e-1278.38SMESG000014734.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013125 ID=SMED30013125|Name=SMED30013125|organism=Schmidtea mediterranea sexual|type=transcript|length=445bp
TTTTTTTTTTTTTTTTTTTGATTTGTGAAGCAAATCTGAAGCTCAAGAGA
CATATCTAAAACCAATCATTACCATCGGAACAAAACGCACATATATGCAG
AAATACACTACCATACATGACAACTACGTATCACCATAGGAAAAGAGAGA
ATCGCAGACATACTGATCCAAGGGAAAAGGAAATACACTCGATCTTCACC
AAAGCTAAACGGAACTTGAAAATGAGTCAAATAGGAAAATCTCAGGCGTC
AACGGTGCCCATCGCACTGGATGCCGCGAGCGCGGACGCTGCACACAAGC
TTGGCGAGCGATTTGCACATGTCCGGGCTGCCCTAATTGCACCAATACTA
CCCCTATGCATATCCCGCCTCTGACCATTGGGCATCCTGAATGCGTCCAC
NACCCGGAGCGTATTCATCTGAGTCTGAAGACTAGATGAACCTCG
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