SMED30007578

Overview
NameSMED30007578
Smed IDSMED30007578
Length (bp)749
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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Alignments
SMED30007578 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001392:39615..40396 +3601
Homology
BLAST of SMED30007578 vs. Planmine SMEST
Match: SMESG000010389.1 (SMESG000010389.1)

HSP 1 Score: 349.747 bits (896), Expect = 7.772e-123
Identity = 228/246 (92.68%), Postives = 228/246 (92.68%), Query Frame = 3
Query:   24 MNYLKYFVLILAVYESSGLDSYGTVGEGPIAYDAPNHGVHTTEVEYGKGNGGFDLSNDRYGKPLGGGELHEGYSEHHSDESSDNINVDKGYGSKDLGDSYSGVNGGEYQGNVVGT------------------NYGDNNPADEYRNGNEGTDGYKERDDDEARYRKGSKYIKNIYGEXXXXXXXXXXXXXXXXXXXXXXXXNCYGYGKKYQLRXXXXXXXXXXXXXXXTITKYATTKPAVHSKRYY 707
            MNYLKYFVLILAVYESSGLDSYGTVGEGPIAYDAPNHGVHTTEVEYGKGNGGFDLSNDRYGKPLGGGELHEGYSEHHSDESSDNINVDKGYGSKDLGDSYSGVNGGEYQGNVVGT                  NYGDNNPADEYRNGNEGTDGYKERDDDEARYRKGSKYIKNIYGEKKLAKLRNILNLKKLIKKRKYAKKNCYGYGKKYQLRKYIHKKPYGHHGHGKTITKYATTKPAVHSKRYY
Sbjct:    1 MNYLKYFVLILAVYESSGLDSYGTVGEGPIAYDAPNHGVHTTEVEYGKGNGGFDLSNDRYGKPLGGGELHEGYSEHHSDESSDNINVDKGYGSKDLGDSYSGVNGGEYQGNVVGTNYGNNDRDGGHKGSTLGLNYGDNNPADEYRNGNEGTDGYKERDDDEARYRKGSKYIKNIYGEKKLAKLRNILNLKKLIKKRKYAKKNCYGYGKKYQLRKYIHKKPYGHHGHGKTITKYATTKPAVHSKRYY 246          
BLAST of SMED30007578 vs. Planmine SMEST
Match: SMESG000010378.1 (SMESG000010378.1)

HSP 1 Score: 265.003 bits (676), Expect = 3.170e-90
Identity = 175/229 (76.42%), Postives = 178/229 (77.73%), Query Frame = 3
Query:   24 MNYLKYFVLILAVYESSGLDSYGTVGEGPIAYDAPNHGVHTTEVEYGKGNGGFDLSNDRYGKPLGGGELHEGYSEHHSDESSDNINVDKGYGSKDLGDSYSGVNGGEYQGNVVGTNYGDNNPADEYRNGNEGTDGYKERDDDEARYRKGSKYIKNIYGEXXXXXXXXXXXXXXXXXXXXXXXXNCYGYG-KKYQLRXXXXXXXXXXXXXXXTITKYATTKPAVHSKRYY 707
            MNYLKYFVLILAVYESSGLDSYGTVGE PIAYDAPNHGVHTTEVEYGKGNGGFDLSN+ Y                          VDKGYGSKDLGDSYSGVNGGEYQGNVVGTNYGDNNPADEYRNGNEGTDGYKERDDDEARYRKGSKYIKNIYGEKKL KLR+                   GYG  KYQLRKYIH+KPYGHHGHGKTITKYA TKPAVHSKRYY
Sbjct:    1 MNYLKYFVLILAVYESSGLDSYGTVGEEPIAYDAPNHGVHTTEVEYGKGNGGFDLSNNPY--------------------------VDKGYGSKDLGDSYSGVNGGEYQGNVVGTNYGDNNPADEYRNGNEGTDGYKERDDDEARYRKGSKYIKNIYGEKKLTKLRHGKRRT--------------GYGINKYQLRKYIHQKPYGHHGHGKTITKYAPTKPAVHSKRYY 189          
The following BLAST results are available for this feature:
BLAST of SMED30007578 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 SMED30007578 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 SMED30007578 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 SMED30007578 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 SMED30007578 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 SMED30007578 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 SMED30007578 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 SMED30007578 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 SMED30007578 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 SMED30007578 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 SMED30007578 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 SMED30007578 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 SMED30007578 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 SMED30007578 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000010389.17.772e-12392.68SMESG000010389.1[more]
SMESG000010378.13.170e-9076.42SMESG000010378.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007578 ID=SMED30007578|Name=SMED30007578|organism=Schmidtea mediterranea sexual|type=transcript|length=749bp
GATCTTGGAATATTCATTCAGAAATGAATTATTTGAAATATTTTGTTTTA
ATCTTAGCTGTTTATGAAAGTTCCGGATTGGATTCCTATGGCACCGTTGG
TGAGGGGCCGATTGCGTATGACGCCCCTAATCATGGAGTCCATACAACTG
AGGTTGAGTATGGTAAAGGCAATGGAGGATTTGATCTTTCTAATGACCGT
TATGGAAAGCCACTGGGAGGTGGGGAGTTACACGAGGGATATAGTGAACA
TCATTCTGATGAAAGTTCTGATAATATTAATGTTGACAAGGGGTATGGAA
GTAAAGATTTAGGAGATAGTTATAGTGGAGTAAATGGAGGTGAATATCAA
GGAAATGTTGTCGGAACTAATTACGGTGATAATAATCCTGCAGACGAATA
TCGCAATGGTAATGAAGGAACAGATGGATATAAAGAGAGAGATGATGATG
AGGCAAGATATAGAAAAGGTTCCAAATATATTAAAAATATTTATGGTGAG
AAAAAGTTGGCAAAGCTTCGAAATATTTTAAATCTTAAAAAGCTCATCAA
AAAACGAAAATATGCGAAGAAGAATTGTTACGGATATGGCAAAAAGTATC
AATTGAGGAAATATATTCACAAGAAACCTTACGGCCACCATGGCCATGGG
AAGACCATAACCAAGTACGCCACTACCAAGCCGGCGGTCCACAGCAAGCG
CTATTATTAGCTTAATAAATTTGTCATTTGAAAAAAAAAGATCGGAAGA
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protein sequence of SMED30007578-orf-1

>SMED30007578-orf-1 ID=SMED30007578-orf-1|Name=SMED30007578-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=236bp
SWNIHSEMNYLKYFVLILAVYESSGLDSYGTVGEGPIAYDAPNHGVHTTE
VEYGKGNGGFDLSNDRYGKPLGGGELHEGYSEHHSDESSDNINVDKGYGS
KDLGDSYSGVNGGEYQGNVVGTNYGDNNPADEYRNGNEGTDGYKERDDDE
ARYRKGSKYIKNIYGEKKLAKLRNILNLKKLIKKRKYAKKNCYGYGKKYQ
LRKYIHKKPYGHHGHGKTITKYATTKPAVHSKRYY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 36..58