SMED30035466

Overview
NameSMED30035466
Smed IDSMED30035466
Length (bp)666
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 SMED30035466 (SMED30035466) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30035466 (SMED30035466) 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 SMED30035466 (SMED30035466) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30035466 (SMED30035466) 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



SMED30035466

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
nervous systemSMED30035466SMESG000076498.1 dd_Smed_v4_30209_0_2dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30035466SMESG000076498.1 dd_Smed_v4_30209_0_2dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30035466SMESG000076498.1 dd_Smed_v4_30209_0_2dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30035466 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.019318:6862..7527 +3276
v31.003404:93713..94377 -3124
v31.004096:1319..1925 -1975
v31.002470:50169..50798 +1967
v31.011548:4761..5367 -1966
v31.011784:7349..7928 +1953
v31.002198:91237..91788 -1923
Homology
[Close]
BLAST of SMED30035466 vs. TrEMBL
Match: A0A433SLU9 (Uncharacterized protein OS=Elysia chlorotica OX=188477 GN=EGW08_022121 PE=4 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 9.845e-7
Identity = 41/149 (27.52%), Postives = 75/149 (50.34%), Query Frame = 2 
Query:   47 LDEWDNIKPIYMNVTIKDSNDLVVGWLFFKVTQTDSLLSWFTNTNLLKSSPWDVNKLLSNNYLFFSVIGDIQSNVQRNFFIAISYIGCANDNAVICIFGMADNCVYSQSNVGYPLIKYMINNGNAGLSDTSNIAKSLEIIAIYDQFIEV 493
            LD+W NI  +   +     N  +V  +FFK  Q+ + ++W+    L+KS  WD   L    +LFF + GD  +++QR FFI  +Y GC+ND   + +          + +  YP+IK+ +  G    + ++      E IA++ ++ ++
Sbjct:  187 LDQWKNIDEVLFAII---QNGEMVKTIFFKGEQS-TYMNWYEKARLIKSC-WD--DLRMGPHLFFGIEGD--ASLQRRFFIQRNYGGCSNDKGWMVVSDNPPRPCDWEKSTAYPIIKFAV--GPKAENWSTGEVLEAEAIAVFLKYKKL 324
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BLAST of SMED30035466 vs. Planmine SMEST
Match: SMESG000076498.1 (SMESG000076498.1)

HSP 1 Score: 312.383 bits (799), Expect = 2.956e-108
Identity = 153/166 (92.17%), Postives = 156/166 (93.98%), Query Frame = 2 
Query:    2 EDKRRINPANFRSPILDEWDNIKPIYMNVTIKDSNDLVVGWLFFKVTQTDSLLSWFTNTNLLKSSPWDVNKLLSNNYLFFSVIGDIQSNVQRNFFIAISYIGCANDNAVICIFGMADNCVYSQSNVGYPLIKYMINNGNAGLSDTSNIAKSLEIIAIYDQFIEVFS 499
            EDK+RIN +NFRSPILDEWDNIKPIYMNVTIKDSNDLVVGWLFFKV Q +SLLSWFT  NLLKSSPWDVNKLLSNNYLFFSVIGDIQSNVQRNFFIAISYIGC NDNAVICIF M DNC YSQSNVGYPLIKYMINNGNAGLSDTSNIAKSLEIIAIYDQFI VFS
Sbjct:  100 EDKKRINSSNFRSPILDEWDNIKPIYMNVTIKDSNDLVVGWLFFKVAQANSLLSWFTKINLLKSSPWDVNKLLSNNYLFFSVIGDIQSNVQRNFFIAISYIGCENDNAVICIFEMQDNCAYSQSNVGYPLIKYMINNGNAGLSDTSNIAKSLEIIAIYDQFIAVFS 265
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BLAST of SMED30035466 vs. Planmine SMEST
Match: SMESG000034452.1 (SMESG000034452.1)

HSP 1 Score: 265.003 bits (676), Expect = 7.105e-90
Identity = 126/166 (75.90%), Postives = 142/166 (85.54%), Query Frame = 2 
Query:    2 EDKRRINPANFRSPILDEWDNIKPIYMNVTIKDSNDLVVGWLFFKVTQTDSLLSWFTNTNLLKSSPWDVNKLLSNNYLFFSVIGDIQSNVQRNFFIAISYIGCANDNAVICIFGMADNCVYSQSNVGYPLIKYMINNGNAGLSDTSNIAKSLEIIAIYDQFIEVFS 499
            EDKRRINP+NFRSPILDEW+NIKPI+MNVTIKDSNDLVVGWLFFKV Q DSLLSWFT  NLL S PWD++KLLSNNY FFSVIGDI  N QRNFFI+I Y GC ND  ++CIFG++D C YSQS  GYPLIKY+INNGN GL +TS++AKSLEIIA YDQ I ++S
Sbjct:   80 EDKRRINPSNFRSPILDEWNNIKPIFMNVTIKDSNDLVVGWLFFKVGQADSLLSWFTKANLLNSFPWDIDKLLSNNYRFFSVIGDINLNKQRNFFISILYYGCPNDTGILCIFGLSDPCSYSQSTAGYPLIKYVINNGNGGLWNTSSLAKSLEIIATYDQLIAIYS 245
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BLAST of SMED30035466 vs. Planmine SMEST
Match: SMESG000034404.1 (SMESG000034404.1)

HSP 1 Score: 255.373 bits (651), Expect = 7.913e-86
Identity = 121/166 (72.89%), Postives = 138/166 (83.13%), Query Frame = 2 
Query:    2 EDKRRINPANFRSPILDEWDNIKPIYMNVTIKDSNDLVVGWLFFKVTQTDSLLSWFTNTNLLKSSPWDVNKLLSNNYLFFSVIGDIQSNVQRNFFIAISYIGCANDNAVICIFGMADNCVYSQSNVGYPLIKYMINNGNAGLSDTSNIAKSLEIIAIYDQFIEVFS 499
            EDKRRINP+NFRSPILDEW+NIKPI+MNVTIKDSNDLVVGWLFFKV Q DSLLSWFT  NLLKS PWD++KLLS+ Y  FSVIGD Q NVQRNFFI+I Y GC+ D+ ++CIFG++D C Y QS  GYPLI+Y IN GN G   TSN+AKSLEIIA YDQ I ++S
Sbjct:   99 EDKRRINPSNFRSPILDEWNNIKPIFMNVTIKDSNDLVVGWLFFKVGQADSLLSWFTKANLLKSFPWDIDKLLSSYYPVFSVIGDTQPNVQRNFFISILYNGCSYDSGILCIFGLSDPCSYGQSTAGYPLIRYAINYGNGGPWTTSNLAKSLEIIATYDQLIAIYS 264
[Close]
BLAST of SMED30035466 vs. Planmine SMEST
Match: SMESG000032522.1 (SMESG000032522.1)

HSP 1 Score: 177.948 bits (450), Expect = 2.704e-55
Identity = 92/168 (54.76%), Postives = 114/168 (67.86%), Query Frame = 2 
Query:    5 DKRRINPANFRSPILDEWDNIKPIYMNVTIKDSNDLVVGWLFFKVTQTDSLLSWFTNTNLLKSSPWDVNKLLSNNYLFFSVIGDIQSN--VQRNFFIAISYIGCANDNAVICIFGMADNCVYSQSNVGYPLIKYMINNGN-AGLSDTSNIAKSLEIIAIYDQFIEVFS 499
            DK+R    NFRS ILDEW++IKPI MNVTIKDSND  V WLFFKV +TD+L+SWF   NLL S PW++  LL N Y +F++ G    +  V R FFI +SY GC ND  V C+F  AD C + +S  GYPLIKY I+NGN A  +  S  AKS+EI+A YD+ I  +S
Sbjct:  107 DKKRNYSQNFRSLILDEWNSIKPINMNVTIKDSNDFTVAWLFFKVDKTDTLISWFKKENLLSSHPWNIKMLLGNLYNYFNISGHAPPDQPVIRLFFINLSYGGCPNDVGVFCVFDRADPCPFGKSTCGYPLIKYAIHNGNGANWNHYSTAAKSMEIVATYDEMIYFYS 274
[Close]
BLAST of SMED30035466 vs. Planmine SMEST
Match: SMESG000076260.1 (SMESG000076260.1)

HSP 1 Score: 176.407 bits (446), Expect = 9.085e-55
Identity = 87/158 (55.06%), Postives = 109/158 (68.99%), Query Frame = 2 
Query:   29 NFRSPILDEWDNIKPIYMNVTIKDSNDLVVGWLFFKVTQTDSLLSWFTNTNLLKSSPWDVNKLLSNNYLFFSVIGDIQSNVQRNFFIAISYIGCANDNAVICIFGMADNCVYSQSNVGYPLIKYMINNGNAG-LSDTSNIAKSLEIIAIYDQFIEVFS 499
            NFRS +LDEW N+KP++MNVTIKDS+ +   WLFFKV   DSL SWF  TNLLKS PW+V  LL NNY +F + G     ++RNFFI I Y  C  D  V+C+FG+AD C Y Q+N GYPLIKY+I NGN G  +  S  A+++EI AIYD    ++S
Sbjct:  117 NFRSILLDEWSNVKPMFMNVTIKDSSAITKAWLFFKVDPNDSLSSWFRKTNLLKSFPWNVEILLRNNYNYFDITGHTTDQLKRNFFINIYYNYCPGDVGVLCVFGIADGCSYGQTNSGYPLIKYVIKNGNGGNWTSYSVTAQAMEITAIYDDSTLIYS 274
The following BLAST results are available for this feature:
BLAST of SMED30035466 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 SMED30035466 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 SMED30035466 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 SMED30035466 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 SMED30035466 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 SMED30035466 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 SMED30035466 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 SMED30035466 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A433SLU99.845e-727.52Uncharacterized protein OS=Elysia chlorotica OX=18... [more]
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BLAST of SMED30035466 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 SMED30035466 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 SMED30035466 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 SMED30035466 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 SMED30035466 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 SMED30035466 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000076498.12.956e-10892.17SMESG000076498.1[more]
SMESG000034452.17.105e-9075.90SMESG000034452.1[more]
SMESG000034404.17.913e-8672.89SMESG000034404.1[more]
SMESG000032522.12.704e-5554.76SMESG000032522.1[more]
SMESG000076260.19.085e-5555.06SMESG000076260.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035466 ID=SMED30035466|Name=SMED30035466|organism=Schmidtea mediterranea sexual|type=transcript|length=666bp
GGAAGACAAAAGAAGAATCAATCCCGCAAATTTCCGAAGTCCCATTCTAG
ATGAATGGGATAACATTAAACCGATCTATATGAATGTCACAATCAAGGAT
TCGAATGACTTGGTAGTTGGTTGGCTGTTTTTCAAAGTTACTCAAACTGA
CTCTTTATTATCATGGTTCACCAACACAAATCTATTGAAATCATCTCCAT
GGGATGTCAACAAATTATTAAGCAACAATTATCTCTTTTTCAGTGTTATT
GGCGATATACAGTCAAATGTACAGCGAAATTTCTTCATTGCTATATCTTA
TATCGGTTGCGCAAATGACAATGCGGTTATATGTATATTTGGAATGGCAG
ATAACTGCGTTTACAGTCAAAGCAATGTAGGATACCCCTTGATAAAATAT
ATGATAAATAATGGCAATGCAGGTCTTTCGGATACTTCAAATATAGCGAA
ATCTTTGGAGATCATAGCAATATATGATCAATTCATTGAAGTATTCTCAT
AGAACTTGAACTATCGTATAGCCTTTTTCTTCCTGTTCTATTATTCGTGA
GTCTCACTAAAGATAAAAATAGGATAAATTCCAGATGTTTTTTTTCTATA
TTAAATGTTCATCATTATCACGGCTCATTTACATTGAGCCTACCACAAAG
AATGTATGAAACCCAT
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protein sequence of SMED30035466-orf-1

>SMED30035466-orf-1 ID=SMED30035466-orf-1|Name=SMED30035466-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=167bp
EDKRRINPANFRSPILDEWDNIKPIYMNVTIKDSNDLVVGWLFFKVTQTD
SLLSWFTNTNLLKSSPWDVNKLLSNNYLFFSVIGDIQSNVQRNFFIAISY
IGCANDNAVICIFGMADNCVYSQSNVGYPLIKYMINNGNAGLSDTSNIAK
SLEIIAIYDQFIEVFS*
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