SMED30021117

Overview
NameSMED30021117
Smed IDSMED30021117
Length (bp)1752
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 SMED30021117 (SMED30021117) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021117 (SMED30021117) 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 SMED30021117 (SMED30021117) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021117 (SMED30021117) 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



SMED30021117

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 systemSMED30021117SMESG000079744.1 SMESG000074656.1 SMESG000054243.1 SMESG000040345.1 SMESG000035927.1 SMESG000022375.1 SMESG000019267.1 dd_Smed_v4_12375_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30021117SMESG000076821.1 SMESG000055285.1 SMESG000054243.1 SMESG000021425.1 SMESG000013482.1 Contig53275newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
neuronSMED30021117SMESG000076821.1 SMESG000055285.1 SMESG000054243.1 SMESG000021425.1 SMESG000013482.1 Contig53275uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30021117 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000004:42660..44451 +7845
v31.009681:17507..19298 +7744
v31.000682:100126..101914 -7256
v31.004330:9560..11348 -7231
v31.020194:8609..10057 +6740
v31.000391:66665..68097 +6680
v31.003061:8863..10385 +6649
v31.000523:38287..39857 +6636
v31.001279:46428..47951 -6521
v31.009866:16704..18187 +6507
v31.005570:9351..10876 +6501
v31.003328:21765..23241 -6466
v31.000806:18880..20364 -6452
v31.001031:22250..23736 +6428
v31.000025:14418..15905 +6413
v31.002118:52219..53702 +6381
v31.006576:20873..22357 -6371
v31.001669:70200..71685 -6369
v31.000124:196134..197625 -6364
v31.024382:419..1902 +6360
v31.001694:27433..28917 -6317
v31.000463:152561..153998 +6308
v31.000616:52720..54241 +6307
v31.014418:4278..5803 +6305
v31.000001:408868..410394 +6294
v31.002543:32619..34103 +6290
v31.000026:239761..241289 -6272
v31.004657:13741..15264 +6253
v31.016686:3368..4888 -6219
v31.000450:135091..136611 -6213
v31.000341:143095..144611 -6200
v31.008426:9417..10944 -6193
v31.041422:327..1853 -6183
v31.002754:17461..18993 +6183
v31.005499:33469..34992 -6180
v31.000695:76293..77810 +6176
v31.006018:10820..12349 -6152
v31.002311:53857..55380 -6151
v31.003665:23908..25425 -6140
v31.007390:14047..15565 +6128
v31.007281:3457..4975 +6111
v31.006842:1380..2895 -6061
v31.000724:98770..100287 -6056
v31.000240:181461..182989 -6015
v31.000168:139875..141385 +5986
v31.001916:22186..23640 -5977
v31.011029:12630..14109 +5939
v31.027780:2593..4047 +5885
v31.000391:86105..87600 -5869
v31.000072:118114..119578 +5651
v31.003108:21894..23355 +5649
v31.010517:1821..3278 +5639
v31.020403:7893..9350 +5576
v31.003868:21088..22531 +5330
v31.002141:3374..4804 +5150
v31.000567:116808..118279 +4541
Homology
[Close]
BLAST of SMED30021117 vs. Planmine SMEST
Match: SMESG000074656.1 (SMESG000074656.1)

HSP 1 Score: 335.495 bits (859), Expect = 1.418e-113
Identity = 158/164 (96.34%), Postives = 162/164 (98.78%), Query Frame = 3 
Query:  447 MNYSGKADPDLIPIQLADRWREAWKLYWHSKFPSNFQRSSSRPEYLDQTHEVPEPFWEEWHPTAEIYAHARCLLDDLLEHQQQVDLRVARARQCLANIEEDLEAGRIADIYYHPRARGHLYEDAEKGKNAQMTRTHRGRNLRRPVMIIPNCSPEDWVARGFSDS 938
            MNYSG ADPDLIP+QLADRWREAWKLYWHSKFPSNFQRSSSRPEYLD+THEVPEPFWEEWHPTAEIYAHARCLLDDLLEHQQQVDLRVARARQCLANIEEDLEAGRIADIYYHPR+RGHLY DAEKGKNAQMTRTHRGRNLRRPVMIIPNCSPEDWVARGF+DS
Sbjct:    1 MNYSGNADPDLIPMQLADRWREAWKLYWHSKFPSNFQRSSSRPEYLDRTHEVPEPFWEEWHPTAEIYAHARCLLDDLLEHQQQVDLRVARARQCLANIEEDLEAGRIADIYYHPRSRGHLYGDAEKGKNAQMTRTHRGRNLRRPVMIIPNCSPEDWVARGFTDS 164
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BLAST of SMED30021117 vs. Planmine SMEST
Match: SMESG000040345.1 (SMESG000040345.1)

HSP 1 Score: 335.495 bits (859), Expect = 1.418e-113
Identity = 158/164 (96.34%), Postives = 162/164 (98.78%), Query Frame = 3 
Query:  447 MNYSGKADPDLIPIQLADRWREAWKLYWHSKFPSNFQRSSSRPEYLDQTHEVPEPFWEEWHPTAEIYAHARCLLDDLLEHQQQVDLRVARARQCLANIEEDLEAGRIADIYYHPRARGHLYEDAEKGKNAQMTRTHRGRNLRRPVMIIPNCSPEDWVARGFSDS 938
            MNYSG ADPDLIP+QLADRWREAWKLYWHSKFPSNFQRSSSRPEYLD+THEVPEPFWEEWHPTAEIYAHARCLLDDLLEHQQQVDLRVARARQCLANIEEDLEAGRIADIYYHPR+RGHLY DAEKGKNAQMTRTHRGRNLRRPVMIIPNCSPEDWVARGF+DS
Sbjct:    1 MNYSGNADPDLIPMQLADRWREAWKLYWHSKFPSNFQRSSSRPEYLDRTHEVPEPFWEEWHPTAEIYAHARCLLDDLLEHQQQVDLRVARARQCLANIEEDLEAGRIADIYYHPRSRGHLYGDAEKGKNAQMTRTHRGRNLRRPVMIIPNCSPEDWVARGFTDS 164
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BLAST of SMED30021117 vs. Planmine SMEST
Match: SMESG000066543.1 (SMESG000066543.1)

HSP 1 Score: 332.413 bits (851), Expect = 2.529e-112
Identity = 157/164 (95.73%), Postives = 162/164 (98.78%), Query Frame = 3 
Query:  447 MNYSGKADPDLIPIQLADRWREAWKLYWHSKFPSNFQRSSSRPEYLDQTHEVPEPFWEEWHPTAEIYAHARCLLDDLLEHQQQVDLRVARARQCLANIEEDLEAGRIADIYYHPRARGHLYEDAEKGKNAQMTRTHRGRNLRRPVMIIPNCSPEDWVARGFSDS 938
            MN+ G ADPDLIP+QLADRWREAWKLYWHSKFPSNFQRSSSRPEYLD+THEVPEPFWEEWHPTAEIYAHARCLLDDLLEHQQQVDLRVARARQCLANIEEDLEAGRIADIYYHPR+RGHL+EDAEKGKNAQMTRTHRGRNLRRPVMIIPNCSPEDWVARGFSDS
Sbjct:    1 MNHLGNADPDLIPMQLADRWREAWKLYWHSKFPSNFQRSSSRPEYLDRTHEVPEPFWEEWHPTAEIYAHARCLLDDLLEHQQQVDLRVARARQCLANIEEDLEAGRIADIYYHPRSRGHLHEDAEKGKNAQMTRTHRGRNLRRPVMIIPNCSPEDWVARGFSDS 164
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BLAST of SMED30021117 vs. Planmine SMEST
Match: SMESG000062616.1 (SMESG000062616.1)

HSP 1 Score: 324.324 bits (830), Expect = 3.208e-109
Identity = 154/164 (93.90%), Postives = 160/164 (97.56%), Query Frame = 3 
Query:  447 MNYSGKADPDLIPIQLADRWREAWKLYWHSKFPSNFQRSSSRPEYLDQTHEVPEPFWEEWHPTAEIYAHARCLLDDLLEHQQQVDLRVARARQCLANIEEDLEAGRIADIYYHPRARGHLYEDAEKGKNAQMTRTHRGRNLRRPVMIIPNCSPEDWVARGFSDS 938
            MN+SG ADPDLIP+QLADRWREAWKLY HSKFPSNF+RSS RPEYLD+THEVPEPFWEEWHPTAEIYAHARCLLDDLLEHQQQVDLRVARARQCLANIEEDLEAGRIADIYYHPR+RGHL+EDAEK KNAQMTRTHRGRNLRRPVMIIPNCSPEDWVARGFSDS
Sbjct:    1 MNHSGNADPDLIPMQLADRWREAWKLYEHSKFPSNFRRSSGRPEYLDRTHEVPEPFWEEWHPTAEIYAHARCLLDDLLEHQQQVDLRVARARQCLANIEEDLEAGRIADIYYHPRSRGHLHEDAEKVKNAQMTRTHRGRNLRRPVMIIPNCSPEDWVARGFSDS 164
[Close]
BLAST of SMED30021117 vs. Planmine SMEST
Match: SMESG000019267.1 (SMESG000019267.1)

HSP 1 Score: 322.398 bits (825), Expect = 4.818e-108
Identity = 151/169 (89.35%), Postives = 160/169 (94.67%), Query Frame = 3 
Query:  432 RSILIMNYSGKADPDLIPIQLADRWREAWKLYWHSKFPSNFQRSSSRPEYLDQTHEVPEPFWEEWHPTAEIYAHARCLLDDLLEHQQQVDLRVARARQCLANIEEDLEAGRIADIYYHPRARGHLYEDAEKGKNAQMTRTHRGRNLRRPVMIIPNCSPEDWVARGFSDS 938
            RS +   ++G ADPDLIP+QLADRWREAWKLYWHSKFPSNFQRSS+RPEYLD+ HE PEPFWEEWHPTAEIYAHARCLLDDLLEHQ+QVDLRVARARQCLANIEEDLEAGRIADIYYHPR+RGHLY DAEK KNAQMTRTHRGRNLRRPVMIIPNCSPEDWVARGF+DS
Sbjct:   20 RSTVESEHAGNADPDLIPMQLADRWREAWKLYWHSKFPSNFQRSSNRPEYLDRVHETPEPFWEEWHPTAEIYAHARCLLDDLLEHQRQVDLRVARARQCLANIEEDLEAGRIADIYYHPRSRGHLYGDAEKEKNAQMTRTHRGRNLRRPVMIIPNCSPEDWVARGFTDS 188

HSP 2 Score: 52.7582 bits (125), Expect = 9.150e-8
Identity = 23/30 (76.67%), Postives = 28/30 (93.33%), Query Frame = 3 
Query:   66 MYSQQNPKRRIISNSPTGRRSTIESEHAGS 155
            MY Q+NPK+R IS+SPTGRRST+ESEHAG+
Sbjct:    1 MYPQRNPKKRTISDSPTGRRSTVESEHAGN 30
The following BLAST results are available for this feature:
BLAST of SMED30021117 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 SMED30021117 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 SMED30021117 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 SMED30021117 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 SMED30021117 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 SMED30021117 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 SMED30021117 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 SMED30021117 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 SMED30021117 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 SMED30021117 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 SMED30021117 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 SMED30021117 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 SMED30021117 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 SMED30021117 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000074656.11.418e-11396.34SMESG000074656.1[more]
SMESG000040345.11.418e-11396.34SMESG000040345.1[more]
SMESG000066543.12.529e-11295.73SMESG000066543.1[more]
SMESG000062616.13.208e-10993.90SMESG000062616.1[more]
SMESG000019267.14.818e-10889.35SMESG000019267.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021117 ID=SMED30021117|Name=SMED30021117|organism=Schmidtea mediterranea sexual|type=transcript|length=1752bp
AACAAAAATGAACTCCATAATAGTGATATAAATCTTCACCGAAGATCAGC
CAATCAAACGCACCAATGTACTCACAACAAAACCCAAAGAGGAGAATCAT
TTCGAATAGCCCAACTGGCCGAAGGTCCACAATTGAATCCGAACACGCAG
GTAGTGATTTGTGCACATATGATGTTTAAACATAAGGGTTTAATGAGCAC
CCGCCGCATAATGATATTCGCACCTTCATTTAAAAATGAAAACGAAACAG
TATATTCAAGTCATTGGAAATTCTTTTTCCCACCGAGAACGGATGACGCA
AATAGCAACTGTTAGCAATGGATAAGGAAGCATTAAGCAGAAAGGATTCG
TCATCCGTAACATCGTCAAGCCAGTTAACACCCCTCTTAGAATAACTGAA
ACGATTATATCACCTCTTATCATATTATACAAGAAGCATACTAATTATGA
ATTATTCAGGAAAAGCAGACCCCGATCTCATCCCAATACAACTCGCCGAC
CGATGGAGGGAAGCCTGGAAACTCTACTGGCACTCAAAATTCCCGTCCAA
CTTCCAACGTAGCAGCAGCAGACCCGAGTATCTCGACCAAACTCACGAGG
TACCAGAACCGTTCTGGGAGGAGTGGCACCCCACGGCAGAGATCTACGCC
CATGCGCGGTGTCTACTTGACGACCTTCTCGAACACCAGCAACAAGTGGA
TCTGAGGGTAGCTCGAGCCCGTCAATGTTTGGCAAACATTGAGGAGGATC
TCGAAGCCGGCAGGATTGCCGATATTTATTATCATCCACGAGCACGCGGA
CACCTGTATGAAGACGCCGAGAAAGGAAAAAATGCACAGATGACGAGAAC
TCACCGAGGTCGAAACCTCAGAAGGCCGGTGATGATTATACCGAATTGCT
CCCCCGAGGATTGGGTAGCCAGAGGTTTCTCAGACTCATGAGAATCATAT
TGTGAACTCTTTTTAGTTTGATATTTGTTAAAGTAGAAATTGCGTTCGAA
TAAACATTAATTTTGTTTTATTTTTGGTTGCTGTTATAACAATTCATCAG
GAAAGTTTTGTTTAATTAGTTACTTCGGTGGTGATACCTATTGTTTTAAC
GTTATAAATTCCAGACATGGATTCCACACACACTCTGAGGATGGAACTAG
CCACAGCCCGAAAAGATAACAAGAACCTCTACAATCAAATAATTCAATTA
ACACGAGAGGTACATCAAATACGAGCCACCTGGATAGATCCAGTAAAGGT
TAAATCCTTATATCAGAGGCTCACAGCTGCTCAGAAAGGATGGGCCGAAG
AAAAACAAATCAATCAAAGTTTACGCACACAAATCCGAGGACTGGAGGTC
GCCCTATCGGCCAGTCAGGAAGGAGCGGCTGTCACCTATCCGCTCGTGTT
CGCACCGGCTCAGTTAGCGTACCGGGAGCCGGCAGCTGCTTCAACTTCGA
CCCCAAATTCTACAACGAACATAAAGACGTACTCGCGTCCCGGACGCAAA
GAGAGAGCTAGACGTCGTGCCGCCAAACTACCAACTTGATCCGAGCCAGA
TTTCACCGACCATTGTAGTTCCTGTAAAAAATACATTTTTGTAGTTTGAT
TTCATTAACCTAGGTGAGAAGATCCAGAAAAGCATGATAGAATTCCTGAA
ACTCACTAGACTTTAAATGATATAGGACATAAAGGGGACCAAATACAAAG
AAAATCGAGCACATGTCTTCTAACGACGGCTCGTTGAACCCGAGGGTTGT
CC
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protein sequence of SMED30021117-orf-1

>SMED30021117-orf-1 ID=SMED30021117-orf-1|Name=SMED30021117-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=165bp
MNYSGKADPDLIPIQLADRWREAWKLYWHSKFPSNFQRSSSRPEYLDQTH
EVPEPFWEEWHPTAEIYAHARCLLDDLLEHQQQVDLRVARARQCLANIEE
DLEAGRIADIYYHPRARGHLYEDAEKGKNAQMTRTHRGRNLRRPVMIIPN
CSPEDWVARGFSDS*
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protein sequence of SMED30021117-orf-2

>SMED30021117-orf-2 ID=SMED30021117-orf-2|Name=SMED30021117-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=141bp
MDSTHTLRMELATARKDNKNLYNQIIQLTREVHQIRATWIDPVKVKSLYQ
RLTAAQKGWAEEKQINQSLRTQIRGLEVALSASQEGAAVTYPLVFAPAQL
AYREPAAASTSTPNSTTNIKTYSRPGRKERARRRAAKLPT*
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protein sequence of SMED30021117-orf-3

>SMED30021117-orf-3 ID=SMED30021117-orf-3|Name=SMED30021117-orf-3|organism=Schmidtea mediterranea sexual|type=polypeptide|length=105bp
NKNELHNSDINLHRRSANQTHQCTHNKTQRGESFRIAQLAEGPQLNPNTQ
VVICAHMMFKHKGLMSTRRIMIFAPSFKNENETVYSSHWKFFFPPRTDDA
NSNC*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron