SMED30018170

Overview
NameSMED30018170
Smed IDSMED30018170
Length (bp)952
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 SMED30018170 (SMED30018170) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30018170 (SMED30018170) 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 SMED30018170 (SMED30018170) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30018170 (SMED30018170) 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



SMED30018170

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30018170h1SMcG0009335 SmedASXL_016243SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30018170h1SMcG0009333 SmedASXL_016243SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30018170h1SMcG0009397 Contig51710newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018170h1SMcG0009397 Contig51710uc_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
Homology
[Close]
BLAST of SMED30018170 vs. Planmine SMEST
Match: SMESG000079382.1 (SMESG000079382.1)

HSP 1 Score: 172.555 bits (436), Expect = 4.829e-52
Identity = 110/226 (48.67%), Postives = 131/226 (57.96%), Query Frame = 3 
Query:  144 YSCLKDVVTMDYHFRNKHSAKGYAYHVTKIDCCDKTLDDMDKINWKQNPI-----------KGESQPNQQ--------------------NEDIELKAFQIRECKFYPYVEGVGGVFMNTTLFGGLLPPHTIYGPYPYVHP---ISHYYQRISIKFDKISATYPQCKFWSITDDGNQRHYICYNKDTEIEKFN-IKEAQAGIKLCNKSSDSEF----VRKGGKTKD 704
            Y C+KD    D  FRNK  A GYAYHVT IDCC +T  +M KINW +N +            GESQPNQ                     NED+EL+ F+IR+  ++P VEGV GVFMNTTL+ G LP  T+   YP+  P   + HYYQRISIKFDKIS  YPQCKFW I D   QRHYICY  +++I+ FN  K A AGIK      DSE     ++K G TKD
Sbjct:    5 YHCIKDKNMED--FRNKDPANGYAYHVTNIDCCGRTKLNMKKINWIRNRVDERVESIKSILSGESQPNQPNQPNQQDMTGLADQLAAINLNEDLELRPFEIRKSNYHPAVEGVEGVFMNTTLYDGHLPDWTV---YPFGKPQCQVDHYYQRISIKFDKISEKYPQCKFWCIKD--KQRHYICYKSESKIKNFNKTKSATAGIKFSEDFQDSELEVMGIKKEGATKD 223
[Close]
BLAST of SMED30018170 vs. Planmine SMEST
Match: SMESG000079382.1 (SMESG000079382.1)

HSP 1 Score: 169.088 bits (427), Expect = 7.234e-51
Identity = 105/213 (49.30%), Postives = 125/213 (58.69%), Query Frame = 3 
Query:  183 FRNKHSAKGYAYHVTKIDCCDKTLDDMDKINWKQNPI-----------KGESQPNQQ--------------------NEDIELKAFQIRECKFYPYVEGVGGVFMNTTLFGGLLPPHTIYGPYPYVHP---ISHYYQRISIKFDKISATYPQCKFWSITDDGNQRHYICYNKDTEIEKFN-IKEAQAGIKLCNKSSDSEF----VRKGGKTKD 704
            FRNK  A GYAYHVT IDCC +T  +M KINW +N +            GESQPNQ                     NED+EL+ F+IR+  ++P VEGV GVFMNTTL+ G LP  T+   YP+  P   + HYYQRISIKFDKIS  YPQCKFW I D   QRHYICY  +++I+ FN  K A AGIK      DSE     ++K G TKD
Sbjct:    4 FRNKDPANGYAYHVTNIDCCGRTKLNMKKINWIRNRVDERVESIKSILSGESQPNQPNQPNQQDMTGLADQLAAINLNEDLELRPFEIRKSNYHPAVEGVEGVFMNTTLYDGHLPDWTV---YPFGKPQCQVDHYYQRISIKFDKISEKYPQCKFWCIKD--KQRHYICYKSESKIKNFNKTKSATAGIKFSEDFQDSELEVMGIKKEGATKD 211
[Close]
BLAST of SMED30018170 vs. Planmine SMEST
Match: SMESG000079668.1 (SMESG000079668.1)

HSP 1 Score: 169.859 bits (429), Expect = 7.392e-51
Identity = 108/235 (45.96%), Postives = 128/235 (54.47%), Query Frame = 3 
Query:  171 MDYHFRNKHS-----AKGYAYHVTKIDCCDKTLDDMDKINWKQNPI-----------------------------KGESQPNQQNED---------------IELKAFQIRECKFYPYVEGVGGVFMNTTLFGGLLPPHTIYGPYPYVHP---ISHYYQRISIKFDKISATYPQCKFWSITDDGNQRHYICYNKDTEIEKFN-IKEAQAGIKLCNKSSDSEF----VRKGGKTKD 704
            M   FRNK+S     A GYAYHVT  DCC +T +DM +INW +N +                              GESQPNQQ ED                ELKAF+IRE  ++P VEGV GVFM+TTL+ G LP  T+Y   P+  P   + HYYQRISIKFDKIS  YPQCKFW I D   QRHYICY  +++I+ FN  K A AGIK      DSE     ++K G TKD
Sbjct:    1 MSKGFRNKNSMNEDPANGYAYHVTSTDCCGRTDNDMLQINWIRNRVDGKKIFVFIKFFYILFGVKECLDHNSSILSGESQPNQQEEDEKDLTYPFKMKTEINCELKAFRIRESYYHPTVEGVEGVFMSTTLYDGHLPDWTVY---PFGKPQCQVDHYYQRISIKFDKISEKYPQCKFWCIKD--KQRHYICYKSESKIKNFNKTKSATAGIKFSEDFQDSELEVMGIKKEGATKD 230
[Close]
BLAST of SMED30018170 vs. Planmine SMEST
Match: SMESG000079644.1 (SMESG000079644.1)

HSP 1 Score: 120.553 bits (301), Expect = 6.500e-32
Identity = 67/174 (38.51%), Postives = 89/174 (51.15%), Query Frame = 3 
Query:  171 MDYHFRNKHSAKGYAYHVTKIDCCDKTLDDMDKINWKQNPIKG--------ESQPNQQNEDIE------------------LKAFQIRECKFYPYVEGVGGVFMNTTLFGGLLPPHTIYGPYP--------------YVHPISHYYQRISIKFDKISATYPQCKFWSITDDGNQ 572
            M+  FR  HS +GYAYHVT IDCC KT + M  I+W  NP +         ESQ + +   +E                  LKAF+I++CK++P  EGV  VF+N TLF   LP  T   P+                 +P  H+YQRISIKF +IS  YP+CKFW +  D ++
Sbjct:    1 MNSLFRTTHSMRGYAYHVTSIDCCGKTDNTMRIIDWDHNPPRDGFHYLDAEESQTSNEENSVEDLIDQMGKKVHIKDNKNILKAFEIKKCKYHPSAEGVKAVFLNLTLFNNSLPNSTKVYPHARQIFSEDYCIPSRRLEYPYGHFYQRISIKFKRISKRYPKCKFWCLMKDEDK 174
[Close]
BLAST of SMED30018170 vs. Planmine SMEST
Match: SMESG000079644.1 (SMESG000079644.1)

HSP 1 Score: 110.538 bits (275), Expect = 2.779e-28
Identity = 62/163 (38.04%), Postives = 83/163 (50.92%), Query Frame = 3 
Query:  204 KGYAYHVTKIDCCDKTLDDMDKINWKQNPIKG--------ESQPNQQNEDIE------------------LKAFQIRECKFYPYVEGVGGVFMNTTLFGGLLPPHTIYGPYP--------------YVHPISHYYQRISIKFDKISATYPQCKFWSITDDGNQ 572
            +GYAYHVT IDCC KT + M  I+W  NP +         ESQ + +   +E                  LKAF+I++CK++P  EGV  VF+N TLF   LP  T   P+                 +P  H+YQRISIKF +IS  YP+CKFW +  D ++
Sbjct:    2 RGYAYHVTSIDCCGKTDNTMRIIDWDHNPPRDGFHYLDAEESQTSNEENSVEDLIDQMGKKVHIKDNKNILKAFEIKKCKYHPSAEGVKAVFLNLTLFNNSLPNSTKVYPHARQIFSEDYCIPSRRLEYPYGHFYQRISIKFKRISKRYPKCKFWCLMKDEDK 164
The following BLAST results are available for this feature:
BLAST of SMED30018170 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 SMED30018170 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 SMED30018170 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 SMED30018170 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 SMED30018170 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 SMED30018170 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 SMED30018170 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 SMED30018170 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30018170 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 SMED30018170 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 SMED30018170 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 SMED30018170 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 SMED30018170 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 SMED30018170 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000079382.14.829e-5248.67SMESG000079382.1[more]
SMESG000079382.17.234e-5149.30SMESG000079382.1[more]
SMESG000079668.17.392e-5145.96SMESG000079668.1[more]
SMESG000079644.16.500e-3238.51SMESG000079644.1[more]
SMESG000079644.12.779e-2838.04SMESG000079644.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018170 ID=SMED30018170|Name=SMED30018170|organism=Schmidtea mediterranea sexual|type=transcript|length=952bp
AAATAAACTAAAAATCAAGTTTTGATGAGATTTTGTAATAATTTCATTGA
TTATTTTAGATTTTAGGAAGAAAAATAAAAACTTGTGGAAAACGAAAAAG
TCGTAACAAGAAAATGGCAGAGGCAATAGATGATACATATAAATATTCCT
GCTTGAAAGATGTTGTAACGATGGATTATCATTTCCGGAATAAACATTCA
GCAAAAGGTTATGCCTATCACGTGACCAAAATTGATTGCTGTGACAAAAC
TTTAGATGACATGGATAAGATAAATTGGAAACAAAATCCCATAAAAGGAG
AATCGCAACCAAATCAGCAAAATGAAGACATAGAACTAAAGGCTTTTCAA
ATCAGAGAATGTAAATTTTATCCATATGTGGAGGGTGTTGGAGGTGTCTT
TATGAACACAACCTTATTCGGTGGCCTCCTACCGCCACACACCATATATG
GTCCATATCCTTATGTACATCCAATTAGTCATTATTATCAAAGAATTTCA
ATTAAATTTGATAAAATATCTGCAACATATCCCCAATGCAAGTTCTGGTC
AATTACAGACGATGGCAACCAGCGTCATTATATTTGCTATAATAAGGATA
CCGAAATAGAAAAATTCAATATAAAGGAAGCACAAGCTGGCATTAAGTTA
TGTAATAAGTCTAGTGATTCAGAATTCGTTAGGAAAGGAGGAAAAACTAA
AGATATTCTGCCTTTACTTCAAAATAACTATAATAACAATGAGGAAAAAT
TTATTAACAATCTCTTTTTGTTAGGTGGCATCACGGTGGCACCGGAAGAC
AGGAAATGAGATATTGTTAAACGTAAAATAGATACCAAATAACCTGATAA
ATTCAACCGCATATCCTGATCTGAATCTGATTGGCTGTTATATCTCAATA
TTAATTATAACAATTATTAGTGCATATCCACAATAAAGTTATACAAAACG
CG
back to top

protein sequence of SMED30018170-orf-1

>SMED30018170-orf-1 ID=SMED30018170-orf-1|Name=SMED30018170-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=232bp
MAEAIDDTYKYSCLKDVVTMDYHFRNKHSAKGYAYHVTKIDCCDKTLDDM
DKINWKQNPIKGESQPNQQNEDIELKAFQIRECKFYPYVEGVGGVFMNTT
LFGGLLPPHTIYGPYPYVHPISHYYQRISIKFDKISATYPQCKFWSITDD
GNQRHYICYNKDTEIEKFNIKEAQAGIKLCNKSSDSEFVRKGGKTKDILP
LLQNNYNNNEEKFINNLFLLGGITVAPEDRK*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000420parapharyngeal region