SMED30028359

Overview
NameSMED30028359
Smed IDSMED30028359
Length (bp)311
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



SMED30028359

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30028359SMESG000010591.1 dd_Smed_v4_10661_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30028359SMESG000038869.1 OX_Smed_1.0.03638ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Category 4 cellSMED30028359SMESG000010591.1 dd_Smed_v4_10661_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30028359 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001170:25327..31505 -1481
Homology
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BLAST of SMED30028359 vs. Planmine SMEST
Match: SMESG000005062.1 (SMESG000005062.1)

HSP 1 Score: 52.7582 bits (125), Expect = 1.050e-9
Identity = 31/73 (42.47%), Postives = 46/73 (63.01%), Query Frame = 3 
Query:    9 LNSYISNESNNKQVGISIT--NSTYERI*HFQKTIKRTQNIEFLYIALKTASPTSTNSERIFSVSGNFYTKLH 221
            +N+ ++N S  K+VG+  T  NS  E    ++KT+KRT+ ++ L+ A+ T  PT T SER+FS S NF  KL 
Sbjct:    1 MNACLNNAS--KEVGVQETPYNSLKEEFVIYKKTVKRTETLQQLFDAVLTVGPTYTESERVFSFSANFTRKLR 71
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BLAST of SMED30028359 vs. Planmine SMEST
Match: SMESG000061313.1 (SMESG000061313.1)

HSP 1 Score: 46.2098 bits (108), Expect = 5.912e-7
Identity = 20/43 (46.51%), Postives = 32/43 (74.42%), Query Frame = 3 
Query:   93 FQKTIKRTQNIEFLYIALKTASPTSTNSERIFSVSGNFYTKLH 221
            F  T ++++ ++ L+  L +  PTST+SER+FS++GNF TKLH
Sbjct:  525 FGVTKQKSKTVQNLFNVLASIQPTSTDSERVFSIAGNFCTKLH 567
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BLAST of SMED30028359 vs. Planmine SMEST
Match: SMESG000060816.1 (SMESG000060816.1)

HSP 1 Score: 45.4394 bits (106), Expect = 1.070e-6
Identity = 28/66 (42.42%), Postives = 38/66 (57.58%), Query Frame = 3 
Query:    9 LNSYISNESNNKQVGISITNSTYERI*HFQKTIKRTQNIEFLYIALKTASPTSTNSERIFSVSGNF 206
            +N+ I+N S    V  +   S  E    ++KT KRTQ ++ LY A+ T  P  T SER+FSVS NF
Sbjct:  234 MNACINNASKEGGVKETPYKSLKEEFAIYKKTGKRTQTLQQLYDAVLTVRPKFTESERVFSVSTNF 299
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BLAST of SMED30028359 vs. Planmine SMEST
Match: SMESG000022344.1 (SMESG000022344.1)

HSP 1 Score: 44.669 bits (104), Expect = 1.978e-6
Identity = 22/49 (44.90%), Postives = 34/49 (69.39%), Query Frame = 3 
Query:   93 FQKTIK-------RTQNIEFLYIALKTASPTSTNSERIFSVSGNFYTKL 218
            FQK +K       +++ ++ L+ AL +  PTST+SER+FS++GNF TKL
Sbjct:  522 FQKELKMFGVTKQKSKTVQNLFNALASIQPTSTDSERVFSIAGNFCTKL 570
The following BLAST results are available for this feature:
BLAST of SMED30028359 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 SMED30028359 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 SMED30028359 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 SMED30028359 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 SMED30028359 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 SMED30028359 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 SMED30028359 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 SMED30028359 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 SMED30028359 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 SMED30028359 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 SMED30028359 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 SMED30028359 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 SMED30028359 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 SMED30028359 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000005062.11.050e-942.47SMESG000005062.1[more]
SMESG000061313.15.912e-746.51SMESG000061313.1[more]
SMESG000060816.11.070e-642.42SMESG000060816.1[more]
SMESG000022344.11.978e-644.90SMESG000022344.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028359 ID=SMED30028359|Name=SMED30028359|organism=Schmidtea mediterranea sexual|type=transcript|length=311bp
TGGAAGCACTCAATTCATATATTTCAAATGAATCCAACAATAAACAAGTA
GGAATATCAATAACTAATAGTACTTATGAAAGAATTTAGCATTTTCAAAA
AACAATTAAAAGAACACAAAATATTGAATTTCTCTATATAGCACTAAAAA
CAGCGAGTCCGACTTCTACAAATTCAGAGAGAATTTTTTCAGTTTCTGGA
AATTTCTATACTAAATTACATTTCGTCTTTCTTGTGCGCCACTTAATGCA
TTAGCCTTCTTCCTGAAATCCAAATTAAAATAATAAATTAAATTTCAGCT
AAATTTTCAAG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000418head
PLANA:0002032epidermal cell