SMED30016347

Overview
NameSMED30016347
Smed IDSMED30016347
Length (bp)641
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 SMED30016347 (SMED30016347) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016347 (SMED30016347) 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 SMED30016347 (SMED30016347) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30016347 (SMED30016347) 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



SMED30016347

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
pigment cellSMED30016347h1SMcG0006621 SmedASXL_070308SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017		whole organism asexual adult RNA-sequencing evidence
pigment cellSMED30016347h1SMcG0019532 SmedASXL_070308SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017		whole organism asexual adult RNA-sequencing evidence
protonephridiaSMED30016347h1SMcG0006621 dd_Smed_v4_10981_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30016347h1SMcG0006621 dd_Smed_v4_10981_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30016347h1SMcG0006621 dd_Smed_v4_10981_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30016347h1SMcG0006621 dd_Smed_v4_10981_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30016347h1SMcG0006621 dd_Smed_v4_10981_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30016347h1SMcG0006621 dd_Smed_v4_10981_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30016347h1SMcG0006621 Contig31763newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30016347h1SMcG0006621 Contig31763uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30016347 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.014465:10104..10746 +2974
v31.033258:834..1474 +2963
v31.014465:1691..2325 +2950
v31.014465:12248..12890 +2920
Homology
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BLAST of SMED30016347 vs. Ensembl Nematostella
Match: EDO37470 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SFI6])

HSP 1 Score: 46.595 bits (109), Expect = 3.390e-6
Identity = 34/119 (28.57%), Postives = 56/119 (47.06%), Query Frame = 3 
Query:   27 QSDRICHSDPQCPLYGDCCYGHQDNGKPGLLKDVLSCKPYNKLFPSAMW-VTNKC-KNPNHPLSDFCTKK----IFNPKNHLKSWIPVISNRKIIYDNLFCAKCNEEIDFTYLPVKVNC 365
            Q + +C+ D  C   GDCC+ ++      + K  LS KP  K   S  + VTN C K  +  L   C++     +  P + L++      ++ I Y N+FCA+CN   + +Y     +C
Sbjct:   53 QIETLCYCDSICLQIGDCCHDYRK-----VCKAKLSEKPQVKQVCSNHYIVTNSCPKGTDQYLDGLCSETHGEILRRPYDLLRNLHVFDHDKNISYRNVFCARCNGARNTSYWTTTADC 166
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BLAST of SMED30016347 vs. Planmine SMEST
Match: SMESG000033614.1 (SMESG000033614.1)

HSP 1 Score: 421.779 bits (1083), Expect = 2.749e-147
Identity = 202/212 (95.28%), Postives = 204/212 (96.23%), Query Frame = 3 
Query:    6 RSGYNGSQSDRICHSDPQCPLYGDCCYGHQDNGKPGLLKDVLSCKPYNKLFPSAMWVTNKCKNPNHPLSDFCTKKIFNPKNHLKSWIPVISNRKIIYDNLFCAKCNEEIDFTYLPVKVNCGPLEIYDYASANQAVIDNPNHCEIFPYFNRTLQRSCEGEIITNCTNTKLIQNKFVIDKCENGGKDYFVFRLQKYKNVFCCKCWNKNCFVRGK 641
            RSGYNGSQSDRICHSDPQCPLYGDCCYGHQD+GKPGLLKDVLSCKPYNKLFPSAMW+ NKCKN NHPLSDFCTKKIF PK  LKSWIPVISNRKIIYDNLFCAKCNEEIDFTYLPVKVNCGPLEIYDYASANQAVIDNPNHCEIFPYFNRTLQRSCEGEIITNCTNTKLIQNKFVIDKCENG KDYFVFRLQKYKNVFCCKCWNKNCF R K
Sbjct:   14 RSGYNGSQSDRICHSDPQCPLYGDCCYGHQDHGKPGLLKDVLSCKPYNKLFPSAMWLINKCKNLNHPLSDFCTKKIFYPKAPLKSWIPVISNRKIIYDNLFCAKCNEEIDFTYLPVKVNCGPLEIYDYASANQAVIDNPNHCEIFPYFNRTLQRSCEGEIITNCTNTKLIQNKFVIDKCENGEKDYFVFRLQKYKNVFCCKCWNKNCFGRRK 225
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BLAST of SMED30016347 vs. Planmine SMEST
Match: SMESG000033611.1 (SMESG000033611.1)

HSP 1 Score: 144.821 bits (364), Expect = 2.659e-40
Identity = 75/196 (38.27%), Postives = 116/196 (59.18%), Query Frame = 3 
Query:   42 CHSDPQCPLYGDCCYGHQDNGKPGLLKDVLSCKPYNKLFPSAMWVTNKCKN-PNHPLSDFCTKKIFNPKNHLKSWIPVISNRKIIYDNLFCAKCNEEIDFTYLPVKVNCGPLEIYDYASANQAVIDNPNHCEIFPYFNRTLQRSCEGEIITNCTNTKLIQNKFVIDKCENGGKDYFVFRLQKYKNVFCCKCWNKNC 626
            C+ D +C LYGDCC GH+   K G L+++L CK +      +++V +KCKN   H LS  C K++   K  +KS+IPVI+   +I++N FCAKCN E  ++YL + ++C  + I D   ANQA+  + + CEI P     ++R C+ ++I  C+N+     + +  KC NG + + V     Y+N FCCKCW  +C
Sbjct:   29 CNCDDKCTLYGDCCSGHESFNKTGSLRNILKCKLFKPSVAESIYVVDKCKNNTKHILSKLCRKEVIFSKIPVKSFIPVINENGVIFENSFCAKCNNEDLYSYLNISISCPDVNITDIYDANQAIAKSRDSCEIQPEIESNIKRICKTKLIDFCSNSFEDIGENITGKCTNGPESFEVHGEILYRNTFCCKCWKIHC 224
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BLAST of SMED30016347 vs. Planmine SMEST
Match: SMESG000033610.1 (SMESG000033610.1)

HSP 1 Score: 124.79 bits (312), Expect = 5.083e-33
Identity = 72/204 (35.29%), Postives = 105/204 (51.47%), Query Frame = 3 
Query:   18 NGSQSDRICHSDPQCPLYGDCCYGHQDNGKPGLLKDVLSCKPYNKLFPSAMWVTNKCKNPNHPLSDFCTKKIFNPKNHLKSWIPVISNRKIIYDNLFCAKCNEEIDFTYLPVKVNCGPLEIYDYASANQAVIDNPNHCEIFPYFNRTLQRSCEGEIITNCTNTKLIQNKFVIDKCENGGKDYFVFRLQKYKNVFCCKCWNKNCF 629
            N  +SD+ C  D  C  +GDCC GH+   + G L+ + SCK + K     M V NKC N NH  S +CTK++ +PK  +KS+  V+   K+IY+N +CA+CN    + Y  + V+C    I ++   N+ +I +P  C I P  +  LQR+C   +   C      +   V D C NG  D        Y+N  CC C N +CF
Sbjct:   19 NCRKSDQYCQCDKICVQFGDCCPGHEKFQQTGSLESISSCKVFAKNSYENMRVINKCVNDNHYYSKYCTKELMDPKLPIKSFAAVMGENKLIYENYYCARCNNIKRYQYFSLSVSCFGHNITNFKQVNEIMIKSPYSCSILPLIDSELQRTCFINLTRLCQEPLSKRFDNVSDMCLNGKLDIVSDGRNFYRNDHCCSCRNISCF 222
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BLAST of SMED30016347 vs. Planmine SMEST
Match: SMESG000067292.1 (SMESG000067292.1)

HSP 1 Score: 51.2174 bits (121), Expect = 1.491e-7
Identity = 54/206 (26.21%), Postives = 87/206 (42.23%), Query Frame = 3 
Query:   30 SDRICHSDPQCPLYGDCCYGHQDNGKPGLLKDVLSCKPYNKLFPSAMWVTNKC--KNPNHPLSDFCTKKIFNPKNHLKSWIPVISNRK---IIYDNLFCAKCNEEIDFTYLPVKVNCGPLEIYDYASANQAVIDNPNHCEIFPYFNRTLQRSCEGEIITNCTNTK------LIQNKFVIDKCENGGKDYFVFRLQK-YKNVFCCKC 611
            S+  C+ D QC ++GDCC+ HQ + +P     + SC           +V +KC  K+ +  L D C +K     N+L   +P   N +   + + N FCA CN +  F +  V+ +   L+            +  N+   FP   +  QR C   +I  C +        L +N+      EN G       +QK Y+N +C  C
Sbjct:   32 SETHCYCDDQCSMFGDCCHKHQQHHEP-----IASCHD-------GYYVIDKCLYKSTDGNLKDKCERKSEISVNNLLYHVPTYGNYENVSLTFKNAFCAVCNGKNQFEFARVEKHKTSLK-----RKKDNTTEKSNYKYTFP---KEFQRICHENVIITCDDDSEDALKLLCRNQPTFYVTENRG------MVQKIYRNAYCFLC 211
The following BLAST results are available for this feature:
BLAST of SMED30016347 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 SMED30016347 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 SMED30016347 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 SMED30016347 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 SMED30016347 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 SMED30016347 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 SMED30016347 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 SMED30016347 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 SMED30016347 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 SMED30016347 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 SMED30016347 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 SMED30016347 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO374703.390e-628.57Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30016347 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 SMED30016347 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000033614.12.749e-14795.28SMESG000033614.1[more]
SMESG000033611.12.659e-4038.27SMESG000033611.1[more]
SMESG000033610.15.083e-3335.29SMESG000033610.1[more]
SMESG000067292.11.491e-726.21SMESG000067292.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016347 ID=SMED30016347|Name=SMED30016347|organism=Schmidtea mediterranea sexual|type=transcript|length=641bp
TATAAAGATCAGGTTATAACGGTTCACAATCTGATCGAATATGTCATTCA
GATCCTCAATGTCCTCTATATGGTGACTGCTGTTATGGCCACCAGGATAA
CGGTAAGCCAGGATTGCTTAAGGATGTTTTATCATGCAAGCCATACAATA
AATTATTTCCATCGGCTATGTGGGTAACTAATAAATGCAAAAATCCCAAT
CATCCTCTCTCGGATTTTTGCACGAAGAAAATATTCAATCCCAAGAATCA
TCTGAAATCCTGGATTCCTGTGATTTCAAACAGAAAGATAATCTATGACA
ATCTATTCTGTGCCAAATGCAATGAGGAAATTGATTTTACATATCTGCCA
GTGAAAGTCAATTGTGGACCTTTAGAAATCTATGATTATGCCAGTGCAAA
TCAAGCTGTTATTGACAATCCAAACCACTGCGAAATCTTTCCGTATTTTA
ATAGAACTTTACAGAGAAGTTGTGAAGGCGAAATAATTACAAATTGTACA
AACACAAAACTCATACAAAATAAATTTGTTATAGACAAATGTGAAAATGG
GGGAAAAGATTATTTCGTTTTTAGGTTGCAGAAATATAAAAATGTTTTTT
GTTGTAAATGTTGGAATAAAAATTGCTTCGTTAGAGGGAAG
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protein sequence of SMED30016347-orf-1

>SMED30016347-orf-1 ID=SMED30016347-orf-1|Name=SMED30016347-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=158bp
MWVTNKCKNPNHPLSDFCTKKIFNPKNHLKSWIPVISNRKIIYDNLFCAK
CNEEIDFTYLPVKVNCGPLEIYDYASANQAVIDNPNHCEIFPYFNRTLQR
SCEGEIITNCTNTKLIQNKFVIDKCENGGKDYFVFRLQKYKNVFCCKCWN
KNCFVRGK
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000099neuron