SMED30031269

Overview
NameSMED30031269
Smed IDSMED30031269
Length (bp)1275
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 SMED30031269 (SMED30031269) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031269 (SMED30031269) in cells (dots) of each of the 12 neoblast clusters.

 

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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 SMED30031269 (SMED30031269) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031269 (SMED30031269) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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.
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

 

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Anatomical Expression

PAGE et. al., 2020




SMED30031269

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30031269SMESG000018562.1 SmedASXL_018121SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30031269 SmedASXL_018123SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30031269SMESG000023258.1 dd_Smed_v4_3718_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30031269SMESG000023258.1 dd_Smed_v4_3718_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30031269SMESG000023258.1 dd_Smed_v4_3718_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30031269SMESG000023258.1 dd_Smed_v4_3718_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30031269SMESG000023258.1 dd_Smed_v4_3718_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30031269SMESG000023258.1 dd_Smed_v4_3718_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30031269SMESG000023258.1 dd_Smed_v6_3718_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
reproductive organSMED30031269SMESG000041325.1 Contig3765GPL15192PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30031269SMESG000018562.1 Contig3765GPL15192PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30031269 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006161:46469..53756 +3284
v31.004671:858..7704 +3011
Homology
BLAST of SMED30031269 vs. Planmine SMEST
Match: SMESG000033246.1 (SMESG000033246.1)

HSP 1 Score: 176.792 bits (447), Expect = 6.187e-90
Identity = 108/213 (50.70%), Postives = 113/213 (53.05%), Query Frame = -2
Query:  633 MATTMANFIKAPENFEMGADIEDLFKEAERFFELMSIAEDFKGRFIKGFLSNEAIKKYDCTDEKQSYVDRLRSAFR*QMNLMKYLIEAMEYRQDEDSVDDFCEKLERRILKHELNEEELQKLLIFNEVGDQNLKKDLMLNEYKSVLEMKKRIKMHEKVNKELNRNNSSMAVMGTXXXXXXXXXRTSNIPAQPMP*RYNYISNRHTVGESRKNK 1271
            MATTMANFIKAPENFE+GADIED  KEAERFFELMSIAEDFKG                          RL  AF               Y+                 LKHE NEE LQK LIFN VGDQNLK DLMLNEYKSV EMK RIKMH K  K                          NIPAQPMP RYNY+SNR TVGESR+N+
Sbjct:    1 MATTMANFIKAPENFEIGADIEDFIKEAERFFELMSIAEDFKG--------------------------RLIKAF---------------YQ-----------------LKHEFNEEVLQKFLIFNAVGDQNLKNDLMLNEYKSVFEMKNRIKMHAKSEK------------------------PQNIPAQPMPQRYNYVSNRFTVGESRQNR 131          

HSP 2 Score: 174.096 bits (440), Expect = 6.187e-90
Identity = 86/119 (72.27%), Postives = 93/119 (78.15%), Query Frame = -3
Query:  281 KNQHNFNKQVVQRNSQPKFKFWACFEEGRRRSECPNVKCHHL---SHFKHQCSQRTESWRDVRENDQ*YARAKSLGNNRNKRD*QYQRPVAAMDDDKEEHGNQYQNGYAPPRE-VIGAL 625
            K Q NFN ++VQRN+QPKFK W CFEEG RR ECPNVKCHH     HFKH+C QRTE W +VRENDQ Y RAK  GN+RN RD QYQRPVAAMDDD+EEHGNQY NGY   RE VIGAL
Sbjct:  135 KKQQNFNNKIVQRNNQPKFKCWVCFEEGHRRFECPNVKCHHCHKAEHFKHRCFQRTEKWIEVRENDQEYKRAKFQGNDRNNRDRQYQRPVAAMDDDEEEHGNQYPNGYDQLREKVIGAL 253          
BLAST of SMED30031269 vs. Planmine SMEST
Match: SMESG000018562.1 (SMESG000018562.1)

HSP 1 Score: 182.185 bits (461), Expect = 8.012e-55
Identity = 90/93 (96.77%), Postives = 91/93 (97.85%), Query Frame = -1
Query:    1 NQIPPSINHQIIEQRRGNFSQVNQYDEIILSNMSLDSLAPGCSNSVVIDRFFDQVISMKIFNKTNLDIIRSSVNIDSRYSNKRHVLIRIDKGA 279
            +QIPPSINHQIIEQRRGNFS VNQYDEIILSNMSLDSLAPGCSNSVVIDRFFDQVISMKIFNKTNLDIIRSSVNIDSRYSNKRHVLIRIDKG 
Sbjct:  141 DQIPPSINHQIIEQRRGNFSLVNQYDEIILSNMSLDSLAPGCSNSVVIDRFFDQVISMKIFNKTNLDIIRSSVNIDSRYSNKRHVLIRIDKGT 233          
BLAST of SMED30031269 vs. Planmine SMEST
Match: SMESG000018562.1 (SMESG000018562.1)

HSP 1 Score: 182.956 bits (463), Expect = 8.458e-55
Identity = 90/93 (96.77%), Postives = 91/93 (97.85%), Query Frame = -1
Query:    1 NQIPPSINHQIIEQRRGNFSQVNQYDEIILSNMSLDSLAPGCSNSVVIDRFFDQVISMKIFNKTNLDIIRSSVNIDSRYSNKRHVLIRIDKGA 279
            +QIPPSINHQIIEQRRGNFS VNQYDEIILSNMSLDSLAPGCSNSVVIDRFFDQVISMKIFNKTNLDIIRSSVNIDSRYSNKRHVLIRIDKG 
Sbjct:  165 DQIPPSINHQIIEQRRGNFSLVNQYDEIILSNMSLDSLAPGCSNSVVIDRFFDQVISMKIFNKTNLDIIRSSVNIDSRYSNKRHVLIRIDKGT 257          
BLAST of SMED30031269 vs. Planmine SMEST
Match: SMESG000018562.1 (SMESG000018562.1)

HSP 1 Score: 182.956 bits (463), Expect = 1.011e-54
Identity = 90/93 (96.77%), Postives = 91/93 (97.85%), Query Frame = -1
Query:    1 NQIPPSINHQIIEQRRGNFSQVNQYDEIILSNMSLDSLAPGCSNSVVIDRFFDQVISMKIFNKTNLDIIRSSVNIDSRYSNKRHVLIRIDKGA 279
            +QIPPSINHQIIEQRRGNFS VNQYDEIILSNMSLDSLAPGCSNSVVIDRFFDQVISMKIFNKTNLDIIRSSVNIDSRYSNKRHVLIRIDKG 
Sbjct:  170 DQIPPSINHQIIEQRRGNFSLVNQYDEIILSNMSLDSLAPGCSNSVVIDRFFDQVISMKIFNKTNLDIIRSSVNIDSRYSNKRHVLIRIDKGT 262          
BLAST of SMED30031269 vs. Planmine SMEST
Match: SMESG000023258.1 (SMESG000023258.1)

HSP 1 Score: 165.236 bits (417), Expect = 4.762e-44
Identity = 83/176 (47.16%), Postives = 127/176 (72.16%), Query Frame = -2
Query:  756 NMATTMANFIKAPENFEMGADIEDLFKEAERFFELMSIAEDFKGRFIKGFLSNEAIKKYDCTDEKQSYVDRLRSAFR*QMNLMKYLIEAMEYRQDEDSVDDFC---EKLERRILKHELNEEELQKLLIFNEVGDQNLKKDLMLNEYKSVLEMKKRIKMHEKVNKELNRNNSSMAVM 1274
            NMATT+ANFIK PE ++M +D+ED   E ERFFE+ +I ++++ +F+K FLS  + KKY+ T+E   Y +RLR+AF    +L+  L EA+ YRQ  ++ ++FC   EKL + ILKH+L+EEEL+K L+FN + D+ +KKDL + + KS  EMK+R+K H++V+KE+N  ++ +A M
Sbjct: 1048 NMATTIANFIKPPETYDMDSDVEDFILETERFFEMTNIVDEYRSKFVKAFLSINSTKKYELTNETLHYTERLRNAFSKNRSLIDDLNEALNYRQGNEAAEEFCSKIEKLAKNILKHKLDEEELKKFLLFNSLEDKEVKKDLKMQDLKSFDEMKERLKRHDQVSKEINVFHADVASM 1223          

HSP 2 Score: 60.4622 bits (145), Expect = 1.665e-9
Identity = 37/98 (37.76%), Postives = 46/98 (46.94%), Query Frame = -3
Query:  281 WACFEEGRRRSECPNVKCHHL---SHFKHQCSQRTESWRDVRENDQ*YARAKSLGNNRNKRD*QYQRPVAAMDDDKEEHGNQYQNGYAPP-REVIGAL 562
            WAC EEG RRSEC N++C H     HFKHQC +                           R  ++ + VAA  D+  E   +Y NG APP  EVIGA+
Sbjct: 1315 WACHEEGHRRSECSNIQCAHCKRSGHFKHQCHELFPG-----------------------RSRKFHKSVAAFGDEDPEADCEYPNGNAPPHEEVIGAI 1389          
The following BLAST results are available for this feature:
BLAST of SMED30031269 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 SMED30031269 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 SMED30031269 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 SMED30031269 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 SMED30031269 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 SMED30031269 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 SMED30031269 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 SMED30031269 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 SMED30031269 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 SMED30031269 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 SMED30031269 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 SMED30031269 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 SMED30031269 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 SMED30031269 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000033246.16.187e-9050.70SMESG000033246.1[more]
SMESG000018562.18.012e-5596.77SMESG000018562.1[more]
SMESG000018562.18.458e-5596.77SMESG000018562.1[more]
SMESG000018562.11.011e-5496.77SMESG000018562.1[more]
SMESG000023258.14.762e-4447.16SMESG000023258.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031269 ID=SMED30031269|Name=SMED30031269|organism=Schmidtea mediterranea sexual|type=transcript|length=1275bp
TGCCCCTTTATCAATTCTTATCAGTACATGTCTCTTATTGGAATATCGGC
TATCAATATTGACAGAAGAGCGGATGATATCTAAATTAGTTTTGTTAAAT
ATTTTCATACTGATTACTTGATCGAAGAATCTATCTATTACTACTGAATT
ACTACATCCCGGTGCCAGAGAATCCAATGACATGTTTGATAAAATTATTT
CGTCGTATTGATTAACTTGGGAGAAATTCCCACGGCGTTGTTCAATGATT
TGATGATTTATCGAAGGAGGAATTTGATTGCAATGCTCCTATCACCTCTC
GCGGTGGAGCATATCCATTTTGGTATTGGTTTCCATGTTCCTCTTTGTCG
TCGTCCATTGCTGCAACTGGTCTCTGATATTGTCAGTCTCGTTTATTTCG
ATTATTACCTAGGGACTTTGCTCGTGCGTATTATTGGTCATTTTCTCTCA
CATCTCTCCAACTTTCAGTTCTCTGCGAGCATTGGTGCTTAAAATGACTT
AAATGGTGACATTTCACATTAGGACATTCTGATCTCCTACGTCCCTCTTC
AAAACATGCCCAGAATTTGAATTTTGGCTGGCTATTTCTCTGTACAACTT
GCTTGTTGAAATTGTGTTGGTTTTTCGGATATTTTGTTTTTTCTAGATTC
GCCGACTGTATGTCTGTTCGAAATGTAGTTGTATCTTTATGGCATTGGTT
GTGCTGGAATATTTGAGGTCCTTCTGACTACATCTACGTATCTTCTATCT
GTTCCCATAACTGCCATAGAGCTATTGTTTCGATTTAATTCTTTATTTAC
CTTTTCGTGCATTTTAATTCTCTTTTTCATTTCCAAGACCGATTTATATT
CGTTTAACATTAAATCTTTTTTTAAATTTTGATCTCCCACCTCATTGAAA
ATAAGAAGTTTTTGTAGCTCCTCTTCATTTAATTCATGTTTCAGAATTCT
TCTCTCCAATTTCTCACAAAAATCATCGACAGAATCTTCATCTTGTCTGT
ATTCCATTGCTTCAATTAAGTATTTCATCAAATTCATTTGTTATCTGAAA
GCTGATCTCAATCTGTCCACATAACTCTGCTTCTCGTCAGTGCAGTCATA
TTTCTTGATTGCCTCATTTGATAAAAAACCTTTTATAAATCTTCCTTTGA
AATCCTCAGCAATTGACATTAATTCGAAGAATCTCTCTGCTTCTTTGAAC
AAATCTTCGATATCAGCTCCCATTTCGAAGTTTTCAGGTGCCTTGATAAA
GTTGGCCATCGTGGTCGCCATATTA
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protein sequence of SMED30031269-orf-1

>SMED30031269-orf-1 ID=SMED30031269-orf-1|Name=SMED30031269-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=117bp
MNLMKYLIEAMEYRQDEDSVDDFCEKLERRILKHELNEEELQKLLIFNEV
GDQNLKKDLMLNEYKSVLEMKKRIKMHEKVNKELNRNNSSMAVMGTDRRY
VDVVRRTSNIPAQPMP*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000429neoblast
PLANA:0002089reproductive organ
PLANA:0002109X1 cell