SMED30023740

Overview
NameSMED30023740
Smed IDSMED30023740
Length (bp)805
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell 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 SMED30023740 (SMED30023740) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023740 (SMED30023740) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30023740 (SMED30023740) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023740 (SMED30023740) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30023740

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30023740h1SMcG0009896 SmedASXL_001359SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30023740h1SMcG0009896 dd_Smed_v4_11762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023740h1SMcG0009896 dd_Smed_v4_11762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30023740h1SMcG0009896 dd_Smed_v4_11762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30023740h1SMcG0009896 dd_Smed_v4_11762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30023740h1SMcG0009896 dd_Smed_v4_11762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
anterior sideSMED30023740h1SMcG0009896 dd_Smed_v4_11762_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30023740h1SMcG0009896 dd_Smed_v6_11762_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30023740h1SMcG0009896 OX_Smed_1.0.16451ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
enteric muscle cellSMED30023740h1SMcG0009896 dd_Smed_v4_11762_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30023740 vs. TrEMBL
Match: A0A1I8HSG9 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig023001g1 PE=4 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 4.888e-6
Identity = 26/64 (40.62%), Postives = 38/64 (59.38%), Query Frame = 3 
Query:  312 SYTPSDTIEVWNCIVDGHNISIALDKETEEIWCNDSLLKTKNESHKKMICKQFGLYNHVARLEI 503
            SY P++   VWN  VDG + S+AL K+T E+WCND L++T ++         F L +  AR+ I
Sbjct:   36 SYLPTEETAVWNVRVDGVHFSVALSKDTLEVWCNDQLMETTDDFSDMGSTVDFDLGSKKARIWI 99
[Close]
BLAST of SMED30023740 vs. Planmine SMEST
Match: SMESG000064469.1 (SMESG000064469.1)

HSP 1 Score: 250.366 bits (638), Expect = 5.577e-85
Identity = 133/133 (100.00%), Postives = 133/133 (100.00%), Query Frame = 3 
Query:  234 GQNKSXXXXXXXXXXSDPVIQCESFSSYTPSDTIEVWNCIVDGHNISIALDKETEEIWCNDSLLKTKNESHKKMICKQFGLYNHVARLEIARKSESSLSLCVKPKPSGNKIVIATLRIDNKIVPTVVNSDLMN 632
            GQNKSKKPKPAPAQASDPVIQCESFSSYTPSDTIEVWNCIVDGHNISIALDKETEEIWCNDSLLKTKNESHKKMICKQFGLYNHVARLEIARKSESSLSLCVKPKPSGNKIVIATLRIDNKIVPTVVNSDLMN
Sbjct:    8 GQNKSKKPKPAPAQASDPVIQCESFSSYTPSDTIEVWNCIVDGHNISIALDKETEEIWCNDSLLKTKNESHKKMICKQFGLYNHVARLEIARKSESSLSLCVKPKPSGNKIVIATLRIDNKIVPTVVNSDLMN 140
[Close]
BLAST of SMED30023740 vs. Planmine SMEST
Match: SMESG000004029.1 (SMESG000004029.1)

HSP 1 Score: 60.077 bits (144), Expect = 3.548e-11
Identity = 34/104 (32.69%), Postives = 53/104 (50.96%), Query Frame = 3 
Query:  303 SFSSYTPSDTIEVWNCIVDGHNISIALDKETEEIWCNDSLLKTKNESHKKMICKQFGLYNHVARLEIARKSESSLSLCVKPKPSGNKIVIATLRIDNKIVPTVV 614
            + +SY PSD+++VWNC++ G  +SIAL K+  EIWC+D L+ T            F + +H  R+ ++    S             K  I+ L ID +I+P  V
Sbjct:   31 TVNSYLPSDSVDVWNCVLGGSPVSIALCKDNFEIWCDDVLINTIETLDATETKMDFVMMSHKMRITVSFDKHS-------------KHPISVLTIDGEIIPRAV 121
[Close]
BLAST of SMED30023740 vs. Planmine SMEST
Match: SMESG000004029.1 (SMESG000004029.1)

HSP 1 Score: 60.4622 bits (145), Expect = 3.582e-11
Identity = 34/104 (32.69%), Postives = 53/104 (50.96%), Query Frame = 3 
Query:  303 SFSSYTPSDTIEVWNCIVDGHNISIALDKETEEIWCNDSLLKTKNESHKKMICKQFGLYNHVARLEIARKSESSLSLCVKPKPSGNKIVIATLRIDNKIVPTVV 614
            + +SY PSD+++VWNC++ G  +SIAL K+  EIWC+D L+ T            F + +H  R+ ++    S             K  I+ L ID +I+P  V
Sbjct:   36 TVNSYLPSDSVDVWNCVLGGSPVSIALCKDNFEIWCDDVLINTIETLDATETKMDFVMMSHKMRITVSFDKHS-------------KHPISVLTIDGEIIPRAV 126
The following BLAST results are available for this feature:
BLAST of SMED30023740 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023740 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023740 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023740 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023740 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023740 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023740 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023740 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A1I8HSG94.888e-640.63Uncharacterized protein OS=Macrostomum lignano OX=... [more]
back to top
BLAST of SMED30023740 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023740 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023740 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023740 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023740 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30023740 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000064469.15.577e-85100.00SMESG000064469.1[more]
SMESG000004029.13.548e-1132.69SMESG000004029.1[more]
SMESG000004029.13.582e-1132.69SMESG000004029.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023740 ID=SMED30023740|Name=SMED30023740|organism=Schmidtea mediterranea sexual|type=transcript|length=805bp
CACAGAACTGTATGGATTTTATTTCCTTTAAATATATAGAGAATTCAATT
TAGAATTTAATTTTTAAAAATTCATTTCCCCATTTGAAAATTCTTTGTTT
TTCAATTTGGATTTCCTCATAATCTAATTGGATCGTAGAAATTTCTCTGT
TAATTCTATTTGGAATTTGAATATTTTTATCAACTGTTGATAGTTTTTCT
TTATTTGTTTCGATGTCTGTACTATTGAATTCCGGACAGAACAAATCCAA
AAAACCCAAACCAGCACCGGCACAGGCATCGGATCCAGTCATTCAATGCG
AATCATTTTCTTCATATACTCCTTCAGATACCATAGAGGTTTGGAATTGC
ATTGTTGATGGACACAATATCAGTATAGCTTTGGATAAAGAAACTGAAGA
GATTTGGTGCAATGATTCTTTACTCAAAACTAAAAATGAATCGCATAAAA
AAATGATCTGCAAACAATTCGGATTATATAACCATGTGGCGAGATTGGAA
ATCGCGAGAAAGTCAGAATCGTCTCTGTCATTGTGCGTTAAGCCCAAACC
AAGCGGAAATAAAATCGTAATTGCTACGTTACGAATTGATAATAAAATCG
TACCAACAGTTGTCAATTCCGACCTGATGAATTAGTGACTGTGGAGAGAG
GGGGGCTGCTGTAAATAATATTACTCCTATAATCATTTTGTGTTGAATGC
TTCATTTAATCCGTGTTTAGCTACCGGAAACTAAATCCAGATTCATATAA
AAATGCGACTATAAATTCTTTTAGATTTTCTGAGTATAATGACATCATGG
GCTTA
back to top

protein sequence of SMED30023740-orf-1

>SMED30023740-orf-1 ID=SMED30023740-orf-1|Name=SMED30023740-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=141bp
MSVLLNSGQNKSKKPKPAPAQASDPVIQCESFSSYTPSDTIEVWNCIVDG
HNISIALDKETEEIWCNDSLLKTKNESHKKMICKQFGLYNHVARLEIARK
SESSLSLCVKPKPSGNKIVIATLRIDNKIVPTVVNSDLMN*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000140anterior region of the whole animal
PLANA:0000418head
PLANA:0000420parapharyngeal region
PLANA:0003104enteric muscle cell
Vocabulary: INTERPRO
TermDefinition
IPR038513FAIM1_dom_sf
IPR010695FAIM1
Vocabulary: biological process
TermDefinition
GO:0043066negative regulation of apoptotic process
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR038513FAIM1 domain superfamilyGENE3DG3DSA:2.40.128.180coord: 40..134
e-value: 1.4E-8
score: 36.5
IPR010695Fas apoptotic inhibitory molecule 1PFAMPF06905FAIM1coord: 30..96
e-value: 4.0E-7
score: 29.9
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..16
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..24