SMED30026854

Overview
NameSMED30026854
Smed IDSMED30026854
Length (bp)745
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 SMED30026854 (SMED30026854) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30026854 (SMED30026854) 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 SMED30026854 (SMED30026854) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30026854 (SMED30026854) 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
Alignments
SMED30026854 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002260:59612..60354 +3475
v31.005292:18205..18945 -3394
v31.007782:1529..8044 -3114
v31.005790:14792..15521 -3098
v31.008263:24113..26738 +3078
v31.009673:2343..4135 -3076
v31.000981:1823..2551 -3074
v31.009673:4986..9713 -3058
v31.000969:38197..38924 -3050
v31.022391:7879..8607 -3040
v31.000237:35673..36401 +3038
v31.000728:32956..33685 -3035
v31.005271:7868..8598 -3031
v31.010123:10017..10745 -3030
v31.000450:121418..122147 -3028
v31.012055:293..1019 +3023
v31.000419:74290..75019 -3019
v31.008589:6592..7318 -3014
v31.001138:31778..32499 -3002
v31.000116:157245..157970 -2986
v31.001208:89378..90103 +2979
v31.000549:10413..11147 -2979
v31.013217:3737..4466 +2976
v31.007000:3162..3903 +2973
v31.010626:15883..16588 -2969
v31.000154:32907..33632 +2969
v31.026547:2543..3274 +2968
v31.009924:1511..2240 +2965
v31.000058:128884..129614 -2961
v31.000299:5228..5957 +2947
v31.005229:22398..23125 +2930
v31.002716:2550..3295 -2920
v31.001761:47101..47818 -2919
v31.008775:21338..22075 -2915
v31.021075:598..1318 +2912
v31.018446:10411..11139 +2912
v31.002447:63572..64298 -2899
v31.005894:42495..43218 +2888
v31.000766:117574..118302 +2887
v31.000327:5094..5841 -2886
v31.013376:7079..7804 -2879
v31.004914:17279..17989 -2869
v31.007268:28639..29343 -2859
v31.000467:159078..159853 +2855
v31.003046:42393..43111 -2850
v31.007616:5458..6172 -2846
v31.025905:4852..5566 +2829
v31.008485:12709..13419 +2814
v31.001650:53236..53965 -2813
v31.019570:7413..8135 +2808
v31.006642:11061..11787 -2806
v31.025379:4937..5651 +2803
v31.012150:1907..2621 -2803
v31.000710:91186..91886 -2801
v31.000726:54717..55415 -2783
v31.000013:391320..392033 -2756
v31.001967:45197..45916 +2753
v31.000120:149943..150651 -2717
v31.027007:3396..4117 +2705
v31.005690:6633..7360 +2664
v31.002638:40110..40783 -2653
v31.001466:46250..46976 +2634
v31.003436:7556..8222 +2589
v31.003010:11742..12445 +2548
v31.000141:235971..236677 +2521
v31.003396:20094..20849 -2499
v31.019608:8578..9235 +2404
v31.002349:53232..53821 +2376
v31.017834:3739..4477 -2374
v31.015330:13845..14501 -2369
v31.025831:2274..2959 -2366
v31.009922:3475..4171 +2358
v31.000696:90058..90773 -2321
v31.003788:45267..45972 +2303
v31.000206:141574..142274 +2271
v31.003044:41578..42297 -2265
v31.021735:9180..9882 +2244
v31.001402:124623..125331 -2198
v31.000581:128862..129486 +2150
v31.012388:2184..2912 -2141
v31.000774:71533..72194 -2066
v31.006736:16421..17167 +2046
v31.009103:1526..2251 +1992
v31.002837:54630..55325 +1955
v31.000308:35019..35737 -1932
v31.009872:16425..17042 +1929
v31.004818:18809..19556 -1929
v31.000707:75998..77299 -1918
v31.000618:42556..43183 +1890
v31.025365:4995..5751 -1838
v31.000871:48592..49188 -1781
v31.001040:100771..101368 -1777
v31.003612:1622..2356 -1775
v31.007936:23655..24411 +1456
v31.018414:116..866 +1441
Homology
BLAST of SMED30026854 vs. Planmine SMEST
Match: SMESG000029285.1 (SMESG000029285.1)

HSP 1 Score: 217.238 bits (552), Expect = 7.024e-68
Identity = 147/189 (77.78%), Postives = 159/189 (84.13%), Query Frame = 2
Query:   32 TRIIER*INCLLLQNAIEDKDIKREIKMRNISNVXXXXXXXXXXXXXXXXXXXXXXAAMKPFKRSYANVVQNQSQYLDXXXXXXXXXXXXXXXXXXXXXENTLTRREPFRNNNRFLDQRSLPSRPSVLPTQNRSDFSNSYERSNRRYE*LRSN**WGCKEV*LIRVQCPNIKCSHCKKASHLKFQCFDL 598
            TRIIE+ +   LLQ+AIEDKD+KREIKMRNI NVKEI+EIITKIEEINKEMKN+DIAAMKPFKR+Y+NVVQNQ+QYL       + RQ    QQHQRFRENTL +REPFRNNNRFLDQRSLPSRPS LPTQNRSDFSNSYERSNRRYE       WGCKEV  IR QCPNIKCSHCKKA HLKFQCF+L
Sbjct:  305 TRIIEKKLTAFLLQDAIEDKDVKREIKMRNIFNVKEIEEIITKIEEINKEMKNKDIAAMKPFKRTYSNVVQNQNQYL-----VQQYRQSQPTQQHQRFRENTLPQREPFRNNNRFLDQRSLPSRPSGLPTQNRSDFSNSYERSNRRYEQC-----WGCKEVGQIRAQCPNIKCSHCKKAGHLKFQCFNL 483          
BLAST of SMED30026854 vs. Planmine SMEST
Match: SMESG000029285.1 (SMESG000029285.1)

HSP 1 Score: 217.238 bits (552), Expect = 1.076e-67
Identity = 147/189 (77.78%), Postives = 159/189 (84.13%), Query Frame = 2
Query:   32 TRIIER*INCLLLQNAIEDKDIKREIKMRNISNVXXXXXXXXXXXXXXXXXXXXXXAAMKPFKRSYANVVQNQSQYLDXXXXXXXXXXXXXXXXXXXXXENTLTRREPFRNNNRFLDQRSLPSRPSVLPTQNRSDFSNSYERSNRRYE*LRSN**WGCKEV*LIRVQCPNIKCSHCKKASHLKFQCFDL 598
            TRIIE+ +   LLQ+AIEDKD+KREIKMRNI NVKEI+EIITKIEEINKEMKN+DIAAMKPFKR+Y+NVVQNQ+QYL       + RQ    QQHQRFRENTL +REPFRNNNRFLDQRSLPSRPS LPTQNRSDFSNSYERSNRRYE       WGCKEV  IR QCPNIKCSHCKKA HLKFQCF+L
Sbjct:  310 TRIIEKKLTAFLLQDAIEDKDVKREIKMRNIFNVKEIEEIITKIEEINKEMKNKDIAAMKPFKRTYSNVVQNQNQYL-----VQQYRQSQPTQQHQRFRENTLPQREPFRNNNRFLDQRSLPSRPSGLPTQNRSDFSNSYERSNRRYEQC-----WGCKEVGQIRAQCPNIKCSHCKKAGHLKFQCFNL 488          
BLAST of SMED30026854 vs. Planmine SMEST
Match: SMESG000064279.1 (SMESG000064279.1)

HSP 1 Score: 179.874 bits (455), Expect = 8.819e-57
Identity = 121/173 (69.94%), Postives = 130/173 (75.14%), Query Frame = 2
Query:  113 MRNISNVXXXXXXXXXXXXXXXXXXXXXXAAMKPFKRSYANVVQNQSQYLDXXXXXXXXXXXXXXXXXXXXXENTLTRREPFRNNNRFLDQRSLPSRPSVLPTQNRSDFSNSYERSNRRYE*LRSN**WGCKEV*LIRVQCPNIKCSHCKKASHLKFQCFDLRGTQSYRYQQN 631
            MRNISNVKEIKEIITKIEEINKE KNEDIAAMKPFKRSYANV +     ++        + Q    +        + RREP RNNNRFLDQ+SLPSRPSVLP QNRSDFSNSYE+SNRRYE LRS   WGCKEV  IR Q PNIK SHCKK+ H KFQCFD RGTQSYRYQQN
Sbjct:    1 MRNISNVKEIKEIITKIEEINKERKNEDIAAMKPFKRSYANVKKLSKIKINIYLNNIDNQNQDNNIKDFE----KILRREPIRNNNRFLDQKSLPSRPSVLPIQNRSDFSNSYEQSNRRYELLRSKQRWGCKEVGHIRAQYPNIKSSHCKKSGHFKFQCFDRRGTQSYRYQQN 169          
BLAST of SMED30026854 vs. Planmine SMEST
Match: SMESG000009301.1 (SMESG000009301.1)

HSP 1 Score: 164.081 bits (414), Expect = 1.635e-53
Identity = 79/105 (75.24%), Postives = 84/105 (80.00%), Query Frame = 2
Query:  329 ENTLTRREPFRNNNRFLDQRSLPSRPSVLPTQNRSDFSNSYERSNRRYE*LRSN**WGCKEV*LIRVQCPNIKCSHCKKASHLKFQCFDLRGTQSYRYQQNWQQL 643
            +NTL RREPFRNNNR L +R LPSR S+LP QNRSD SNSYERSN+RYE LRS   WGCKEV  IR Q PNIKCS CKKA H KFQCFDLRGTQSYRYQQN   +
Sbjct:  546 KNTLPRREPFRNNNRLLSERILPSRSSLLPIQNRSDISNSYERSNKRYEQLRSKQCWGCKEVEHIRAQYPNIKCSQCKKAGHFKFQCFDLRGTQSYRYQQNMAAI 650          

HSP 2 Score: 64.3142 bits (155), Expect = 1.635e-53
Identity = 29/35 (82.86%), Postives = 31/35 (88.57%), Query Frame = 1
Query:  631 LAAITDQGDDENMMSDSEYLNGNAPTHEEVIGTID 735
            +AAI DQGDDENMMSDSEY NGNAPT EEVIG I+
Sbjct:  647 MAAIIDQGDDENMMSDSEYPNGNAPTEEEVIGAIN 681          
BLAST of SMED30026854 vs. Planmine SMEST
Match: SMESG000037636.1 (SMESG000037636.1)

HSP 1 Score: 145.976 bits (367), Expect = 9.991e-44
Identity = 72/93 (77.42%), Postives = 78/93 (83.87%), Query Frame = 2
Query:  365 NNRFLDQRSLPSRPSVLPTQNRSDFSNSYERSNRRYE*LRSN**WGCKEV*LIRVQCPNIKCSHCKKASHLKFQCFDLRGTQSYRYQQNWQQL 643
            NN+FLDQ+SLPSRPSVLPTQNRS+FSNSYERSNRRYE LRS   W  KEV  IR Q PNIKCS+CKKA HLKF CFDLRGT+SYRYQQN   +
Sbjct: 1127 NNQFLDQKSLPSRPSVLPTQNRSNFSNSYERSNRRYEQLRSKQCWRYKEVGHIRAQYPNIKCSYCKKAGHLKFHCFDLRGTESYRYQQNMAAI 1219          

HSP 2 Score: 49.2914 bits (116), Expect = 9.991e-44
Identity = 21/32 (65.62%), Postives = 26/32 (81.25%), Query Frame = 1
Query:  631 LAAITDQGDDENMMSDSEYLNGNAPTHEEVIG 726
            +AAI  QGDD+ MMSDS+Y N NAPT EE++G
Sbjct: 1216 MAAIAYQGDDKKMMSDSKYQNANAPTQEELLG 1247          
The following BLAST results are available for this feature:
BLAST of SMED30026854 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 SMED30026854 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 SMED30026854 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 SMED30026854 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 SMED30026854 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 SMED30026854 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 SMED30026854 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 SMED30026854 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 SMED30026854 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 SMED30026854 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 SMED30026854 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 SMED30026854 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 SMED30026854 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 SMED30026854 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000029285.17.024e-6877.78SMESG000029285.1[more]
SMESG000029285.11.076e-6777.78SMESG000029285.1[more]
SMESG000064279.18.819e-5769.94SMESG000064279.1[more]
SMESG000009301.11.635e-5375.24SMESG000009301.1[more]
SMESG000037636.19.991e-4477.42SMESG000037636.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026854 ID=SMED30026854|Name=SMED30026854|organism=Schmidtea mediterranea sexual|type=transcript|length=745bp
TAATTGATCGATTGGCAGAAAATATCTTAAGACACGAATTATCGAAAGAT
AAATCAACTGCCTTTTATTGCAAAATGCGATAGAAGATAAAGATATAAAA
AGAGAAATAAAGATGAGAAATATTTCCAATGTCAAAGAGATTAAGGAGAT
TATTACAAAGATAGAAGAAATTAATAAAGAAATGAAAAACGAAGATATTG
CTGCTATGAAGCCATTCAAAAGAAGTTATGCAAATGTGGTCCAAAATCAA
AGTCAATATTTAGATCAACAATATCGACAATCACGACCAAGACAGCAACA
TCAAAGACAACAACATCAAAGATTTCGAGAAAACACCCTTACACGAAGAG
AACCATTTCGAAATAATAATAGATTTCTAGATCAAAGGAGTTTACCTAGT
CGACCTTCAGTTCTACCGACACAAAACAGATCGGATTTTTCAAATTCTTA
TGAGCGGTCAAATAGAAGATACGAATAACTACGATCAAATTAATGATGGG
GATGCAAAGAAGTATGACTTATAAGAGTCCAATGTCCGAACATAAAATGT
TCTCATTGCAAGAAGGCAAGCCATCTAAAATTCCAATGCTTCGATCTAAG
AGGAACTCAGAGCTACAGATATCAACAGAATTGGCAGCAATTACAGATCA
AGGAGATGATGAGAACATGATGTCCGACAGCGAATACCTAAATGGGAACG
CTCCAACACATGAGGAAGTGATTGGAACGATAGACTAAATGTAAC
back to top

protein sequence of SMED30026854-orf-1

>SMED30026854-orf-1 ID=SMED30026854-orf-1|Name=SMED30026854-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=122bp
MRNISNVKEIKEIITKIEEINKEMKNEDIAAMKPFKRSYANVVQNQSQYL
DQQYRQSRPRQQHQRQQHQRFRENTLTRREPFRNNNRFLDQRSLPSRPSV
LPTQNRSDFSNSYERSNRRYE*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0002089reproductive organ