SMED30002881

Overview
NameSMED30002881
Smed IDSMED30002881
Length (bp)722
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30002881 (SMED30002881) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30002881 (SMED30002881) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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



SMED30002881

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
parapharyngeal regionSMED30002881h1SMcG0019122 SmedASXL_003080SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30002881h1SMcG0019122 dd_Smed_v6_1577_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30002881h1SMcG0019122 OX_Smed_1.0.08913ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30002881 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000208:217487..218207 -3578
Homology
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BLAST of SMED30002881 vs. Planmine SMEST
Match: SMESG000026697.1 (SMESG000026697.1)

HSP 1 Score: 411.379 bits (1056), Expect = 4.326e-148
Identity = 197/197 (100.00%), Postives = 197/197 (100.00%), Query Frame = 1 
Query:   46 MQFFLTFLICVIVLVSGKEFDAEKQCCFGDRWGIKLHEHFVTKTWTNEDSFRIYYDYKQRKKLTHYLLFDTYSLVNETTMLTYSAKMPTFNMCLDNRGLIDTNLNDESLVGSVQCVGTASGYSEISRNRDIVYLYKESKDWKVTYQFKTDTCQFVSQRRETISGIITYKVELANLDTGILDVFPKIMEKSCEGNQKP 636
            MQFFLTFLICVIVLVSGKEFDAEKQCCFGDRWGIKLHEHFVTKTWTNEDSFRIYYDYKQRKKLTHYLLFDTYSLVNETTMLTYSAKMPTFNMCLDNRGLIDTNLNDESLVGSVQCVGTASGYSEISRNRDIVYLYKESKDWKVTYQFKTDTCQFVSQRRETISGIITYKVELANLDTGILDVFPKIMEKSCEGNQKP
Sbjct:    1 MQFFLTFLICVIVLVSGKEFDAEKQCCFGDRWGIKLHEHFVTKTWTNEDSFRIYYDYKQRKKLTHYLLFDTYSLVNETTMLTYSAKMPTFNMCLDNRGLIDTNLNDESLVGSVQCVGTASGYSEISRNRDIVYLYKESKDWKVTYQFKTDTCQFVSQRRETISGIITYKVELANLDTGILDVFPKIMEKSCEGNQKP 197
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BLAST of SMED30002881 vs. Planmine SMEST
Match: SMESG000026696.1 (SMESG000026696.1)

HSP 1 Score: 188.348 bits (477), Expect = 4.324e-60
Identity = 89/192 (46.35%), Postives = 123/192 (64.06%), Query Frame = 1 
Query:   46 MQFFLTFLICVIVLVSGKEFDAEKQCCFGDRWGIKLHEHFVTKTWTNEDSFRIYYDYKQRKKLTHYLLFDTYSLVNETTMLTYSAKMPTFNMCLDNRGLIDTNLNDESLVGSVQCVGTASGYSEISRNRDIVYLYKESKDWKVTYQFKTDTCQFVSQRRETISGIITYKVELANLDTGILDVFPKIMEKSCE 621
            M+  L  L+  + +V G  +D+ KQCCF +RWG+K+HEH+    WTN+DS RI+YDY +R KL HY+ F++Y L NET ++        F+ C DN+  I  NLND SL+G++QC+G ++G++E S++ +IV L K   + KV Y+FK D C  VS  RE  S   +Y VE   LDT ILD  PK MEK CE
Sbjct:    1 MRLVLLGLLISVAVVFGSSYDSTKQCCFPERWGLKVHEHYAENKWTNDDSQRIFYDYSKRVKLVHYISFNSYMLTNETKLIVLGKTTSIFDRCDDNKDYIHLNLNDYSLLGALQCIGASTGFTEASKSEEIVELQKTFPNAKVNYKFKVDNCNLVSLYREFDSESFSYTVEGDYLDTSILDTLPKEMEKVCE 192
[Close]
BLAST of SMED30002881 vs. Planmine SMEST
Match: SMESG000026698.1 (SMESG000026698.1)

HSP 1 Score: 174.866 bits (442), Expect = 9.447e-55
Identity = 86/197 (43.65%), Postives = 120/197 (60.91%), Query Frame = 1 
Query:   46 MQFFLTFLICVIVLVSGKEFDAEKQCCFGDRWGIKLHEHFVTKT--WTNEDSFRIYYDYKQRKKLTHYLLFDTYSLVNETTMLTYSAKMPTFNMCLDNRGLIDTNLNDESLVGSVQCVGTASGYSEISRNRDIVYLYKESKDWKVTYQFKTDTCQFVSQRRETISGIITYKVELANLDTGILDVFPKIMEKSCEGNQ 630
            MQ     +I  I  V  + F++ KQCCF D++G+ L EH+  K   W N DS RI+YDY Q++KLTH++ F+TY   N T +L YSA    +N C DN+ +ID NLN+ SL G+VQC+GT SGY+ ++ +   V L    +D  VTY+F T  C+ + Q R+  + I TY VE  N D  I+D F   M+  CEGN+
Sbjct:    1 MQLIYLLIIVAIETVLSENFESSKQCCFPDKYGVSLQEHYFEKQSKWNNYDSQRIFYDYSQKRKLTHFVNFNTYLFHNTTKLLVYSATHRNYNQCYDNKHIIDANLNERSLFGAVQCIGTGSGYNVVASSDTTVDLQITLQDVTVTYRFSTSDCKPILQIRDVPTAIYTYTVEENNEDASIIDEFEAKMQSVCEGNR 197
The following BLAST results are available for this feature:
BLAST of SMED30002881 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 SMED30002881 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 SMED30002881 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 SMED30002881 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 SMED30002881 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 SMED30002881 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 SMED30002881 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 SMED30002881 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 SMED30002881 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 SMED30002881 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 SMED30002881 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 SMED30002881 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 SMED30002881 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 SMED30002881 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000026697.14.326e-148100.00SMESG000026697.1[more]
SMESG000026696.14.324e-6046.35SMESG000026696.1[more]
SMESG000026698.19.447e-5543.65SMESG000026698.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002881 ID=SMED30002881|Name=SMED30002881|organism=Schmidtea mediterranea sexual|type=transcript|length=722bp
TTTTTTTGCTTTAAGATTTAATTAGTTATCCTAAAAATATTCGAAATGCA
ATTTTTTCTGACGTTTTTGATTTGCGTGATTGTGCTCGTTTCGGGAAAAG
AATTTGACGCAGAGAAGCAGTGCTGTTTCGGAGATCGGTGGGGCATTAAA
TTGCATGAGCACTTTGTGACGAAGACATGGACCAATGAAGACTCATTTAG
AATCTATTACGATTATAAACAACGAAAAAAGTTAACTCATTACTTGTTGT
TTGATACGTACTCATTGGTAAATGAGACAACCATGTTGACGTATAGTGCG
AAAATGCCGACTTTTAACATGTGTTTGGACAACAGAGGTTTGATAGATAC
TAATCTCAATGACGAGAGTCTTGTTGGTTCAGTGCAGTGCGTAGGAACTG
CAAGTGGATATAGTGAGATATCCCGAAATAGAGATATTGTCTATTTGTAT
AAAGAGTCAAAAGATTGGAAAGTGACGTATCAATTCAAAACCGACACTTG
CCAGTTCGTATCTCAAAGAAGAGAAACCATCTCGGGAATAATTACATATA
AAGTTGAACTGGCCAACCTAGATACTGGAATTCTTGATGTGTTCCCGAAA
ATTATGGAAAAATCCTGTGAAGGAAATCAAAAACCATGATAAATTGATTT
CAACTAAATAAAATTAAAATTAATTAAAAATGACTTTGTTTTAATAGAGT
AAATATAAAATTTCATTTAAAA
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protein sequence of SMED30002881-orf-1

>SMED30002881-orf-1 ID=SMED30002881-orf-1|Name=SMED30002881-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=198bp
MQFFLTFLICVIVLVSGKEFDAEKQCCFGDRWGIKLHEHFVTKTWTNEDS
FRIYYDYKQRKKLTHYLLFDTYSLVNETTMLTYSAKMPTFNMCLDNRGLI
DTNLNDESLVGSVQCVGTASGYSEISRNRDIVYLYKESKDWKVTYQFKTD
TCQFVSQRRETISGIITYKVELANLDTGILDVFPKIMEKSCEGNQKP*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000420parapharyngeal region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..17
score: 0.898