SMED30013611

Overview
NameSMED30013611
Smed IDSMED30013611
Length (bp)695
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 SMED30013611 (SMED30013611) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30013611 (SMED30013611) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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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Alignments
SMED30013611 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002216:53099..53792 -3342
v31.005221:25270..27744 -3075
v31.000483:160461..161108 -3016
v31.002776:59008..59732 +2956
v31.002042:92569..93216 -2926
v31.008500:13187..13834 -2917
v31.010859:17669..18317 +2913
v31.001806:20661..21309 +2913
v31.006195:27706..28347 -2887
v31.014000:1712..2437 +2878
v31.000838:19421..20059 -2864
v31.002456:35690..36338 -2859
v31.001188:87031..87686 +2841
v31.002255:22196..22843 +2836
v31.006028:14498..15144 +2819
v31.021328:3466..4178 -2784
v31.034589:4209..4856 -2780
v31.000008:43422..44071 -2745
v31.006149:8355..9016 -2743
v31.000118:37885..38549 -2735
v31.000211:17711..18432 -2717
v31.001655:74430..75042 -2708
v31.001357:57469..58153 +2705
v31.000767:55720..56357 -2695
v31.012703:13888..14525 +2685
v31.000736:32677..33362 -2684
v31.000076:157355..158068 +2677
v31.002496:43287..43923 -2673
v31.000833:65323..65959 +2673
v31.003145:33541..34254 -2671
v31.009715:12578..13240 +2664
v31.007895:21121..21771 +2662
v31.000724:57512..58225 -2661
v31.000116:120033..120744 -2659
v31.008381:6623..7289 -2656
v31.004228:32109..32745 +2653
v31.000879:71555..72189 +2642
v31.001080:32004..32717 -2637
v31.001917:50021..50731 -2629
v31.000019:193875..194584 +2628
v31.002374:61248..61959 +2621
v31.000069:192091..192802 +2619
v31.005088:21451..22087 -2608
v31.005255:23412..24061 +2602
v31.008460:6748..7428 -2595
v31.002587:38383..39032 -2590
v31.003559:27835..28548 +2587
v31.000361:36348..36984 -2583
v31.003684:13007..13718 +2575
v31.011507:12444..13168 -2563
v31.001838:71470..72090 -2563
v31.001313:34689..35335 -2561
v31.030604:814..1465 -2559
v31.009120:10697..11317 -2554
v31.002381:28091..28733 -2540
v31.008170:15985..16625 +2532
v31.031211:5596..6238 +2531
v31.011933:4864..5499 -2519
v31.007026:15399..16039 -2515
v31.011286:11897..12546 -2508
v31.010604:8762..9411 +2508
v31.000633:67071..67712 +2505
v31.010821:7290..7945 +2491
v31.003977:18062..18713 +2491
v31.038882:1095..1746 +2467
v31.037685:859..1510 +2467
v31.002350:20155..20806 +2458
v31.008370:9229..9889 +2449
v31.002362:81288..81940 -2444
v31.000090:65327..65968 +2434
v31.001602:21933..22582 -2427
v31.001880:69595..70247 +2426
v31.001821:1725..2385 +2421
v31.000602:9698..10406 +2417
v31.000024:216965..217624 -2417
v31.007467:14324..14970 -2414
v31.002198:69937..70636 -2410
v31.001314:14852..15511 -2408
v31.005580:57284..58011 -2402
v31.005358:35932..36588 +2394
v31.003401:25426..26077 +2391
v31.002596:32267..32926 +2390
v31.001158:72955..73592 -2389
v31.005195:35664..36309 -2388
v31.002363:23854..24507 +2384
v31.008913:22964..23609 +2379
v31.005077:18555..19263 -2378
v31.004555:18356..19014 +2372
v31.002456:43360..43982 -2372
v31.011651:13080..13783 -2370
v31.003057:45865..46591 +2365
v31.000183:141911..142565 -2362
v31.000043:62294..62971 +2356
v31.001838:28155..28835 +2352
v31.000081:149293..149943 -2350
v31.003557:20450..21083 +2349
v31.000447:18909..19571 -2343
v31.006931:3126..3858 +2341
v31.001391:25419..26111 -2337
v31.017166:2159..2824 +2266
v31.000525:46564..47137 -2263
v31.005456:14709..15374 -2223
v31.012574:3116..3781 -2214
v31.007685:3957..4625 +2208
v31.003369:11429..12033 +2198
v31.011190:10365..11033 -2187
v31.007321:16103..16677 -2185
v31.017241:4347..5037 +2166
v31.001327:15205..15831 -2164
v31.004089:30580..31252 -2161
v31.009293:18438..19106 -2160
v31.002369:57555..58130 -2157
v31.000396:136010..136586 -2153
v31.008003:13663..14330 -2107
v31.002784:61543..62168 -2104
v31.009886:7495..8197 +2099
v31.012985:11019..11651 -2057
v31.001406:31777..32380 -2033
v31.002822:37802..38475 -1978
v31.038773:598..1187 +1964
v31.011786:10342..11036 +1735
v31.005455:10987..11692 +1707
v31.003459:17970..18671 -1698
v31.000066:168569..169278 +1624
Homology
BLAST of SMED30013611 vs. Planmine SMEST
Match: SMESG000008330.1 (SMESG000008330.1)

HSP 1 Score: 140.969 bits (354), Expect = 2.161e-69
Identity = 65/73 (89.04%), Postives = 66/73 (90.41%), Query Frame = 1
Query:  238 QFSKRFDKFVFTGFWMDESRITMRFPSHSAAKCRQAMWDEGYSISPVRKARFERQDDMEDAERPYIAIKREPG 456
             F  +FDKFVFTGFWMDESRITMRFPSHSAAKCRQAMWDEGYSISPVR  RFERQDD E AERPYIAIKREPG
Sbjct:   49 HFELQFDKFVFTGFWMDESRITMRFPSHSAAKCRQAMWDEGYSISPVRTVRFERQDDTEVAERPYIAIKREPG 121          

HSP 2 Score: 140.198 bits (352), Expect = 2.161e-69
Identity = 68/80 (85.00%), Postives = 71/80 (88.75%), Query Frame = 3
Query:  456 RNPARELRGRAEDILARLEAHQRKTNREVNRAHQHLKQINKDIATGLIPSTGGYAPSYGISFELDDPRVNQPIPPMTVSV 695
            RNP RELR RAEDILARLEAHQ+KTNREVNRA QHLKQINKDIA GLIPST GYAP+YGI FELDDP +NQ I PMTVSV
Sbjct:  122 RNPTRELRERAEDILARLEAHQQKTNREVNRARQHLKQINKDIAAGLIPSTDGYAPAYGILFELDDPHMNQSILPMTVSV 201          
BLAST of SMED30013611 vs. Planmine SMEST
Match: SMESG000075969.1 (SMESG000075969.1)

HSP 1 Score: 122.865 bits (307), Expect = 7.990e-53
Identity = 57/80 (71.25%), Postives = 68/80 (85.00%), Query Frame = 3
Query:  456 RNPARELRGRAEDILARLEAHQRKTNREVNRAHQHLKQINKDIATGLIPSTGGYAPSYGISFELDDPRVNQPIPPMTVSV 695
            RNPARELR R E+ILAR EAHQR+TN++V +A + L+Q N+DIA GLIPST GY PSYGISF+LDDPRVNQP+  MTVS+
Sbjct:   70 RNPARELRSRVEEILARPEAHQRRTNKQVEKARRQLEQTNEDIAAGLIPSTDGYTPSYGISFQLDDPRVNQPVQAMTVSM 149          

HSP 2 Score: 102.834 bits (255), Expect = 7.990e-53
Identity = 44/64 (68.75%), Postives = 52/64 (81.25%), Query Frame = 1
Query:  265 VFTGFWMDESRITMRFPSHSAAKCRQAMWDEGYSISPVRKARFERQDDMEDAERPYIAIKREPG 456
            +    W+DESRITMRFPSHSA +CRQAMWD G+SISPVR++RF RQ   ED E P++AIKREPG
Sbjct:    6 ILIDSWVDESRITMRFPSHSAVRCRQAMWDAGFSISPVRESRFGRQGGTEDVELPFVAIKREPG 69          
BLAST of SMED30013611 vs. Planmine SMEST
Match: SMESG000004613.1 (SMESG000004613.1)

HSP 1 Score: 108.227 bits (269), Expect = 6.354e-42
Identity = 46/65 (70.77%), Postives = 52/65 (80.00%), Query Frame = 1
Query:  262 FVFTGFWMDESRITMRFPSHSAAKCRQAMWDEGYSISPVRKARFERQDDMEDAERPYIAIKREPG 456
            F+    W+DESRITMRFPSH AA+CRQAMWD  YSISPVR++ FERQ   ED E PY+AIKREPG
Sbjct:    3 FISIDSWVDESRITMRFPSHPAARCRQAMWDARYSISPVRESLFERQGGAEDVELPYVAIKREPG 67          

HSP 2 Score: 80.8777 bits (198), Expect = 6.354e-42
Identity = 34/49 (69.39%), Postives = 45/49 (91.84%), Query Frame = 3
Query:  456 RNPARELRGRAEDILARLEAHQRKTNREVNRAHQHLKQINKDIATGLIP 602
            RNPAR+LRG+AE+I ARLEAHQR+T+++V +A + L+QIN+DIATGLIP
Sbjct:   68 RNPARKLRGQAEEIFARLEAHQRRTDKQVEKARRQLEQINEDIATGLIP 116          
BLAST of SMED30013611 vs. Planmine SMEST
Match: SMESG000004613.1 (SMESG000004613.1)

HSP 1 Score: 108.227 bits (269), Expect = 6.354e-42
Identity = 46/65 (70.77%), Postives = 52/65 (80.00%), Query Frame = 1
Query:  262 FVFTGFWMDESRITMRFPSHSAAKCRQAMWDEGYSISPVRKARFERQDDMEDAERPYIAIKREPG 456
            F+    W+DESRITMRFPSH AA+CRQAMWD  YSISPVR++ FERQ   ED E PY+AIKREPG
Sbjct:    2 FISIDSWVDESRITMRFPSHPAARCRQAMWDARYSISPVRESLFERQGGAEDVELPYVAIKREPG 66          

HSP 2 Score: 80.8777 bits (198), Expect = 6.354e-42
Identity = 34/49 (69.39%), Postives = 45/49 (91.84%), Query Frame = 3
Query:  456 RNPARELRGRAEDILARLEAHQRKTNREVNRAHQHLKQINKDIATGLIP 602
            RNPAR+LRG+AE+I ARLEAHQR+T+++V +A + L+QIN+DIATGLIP
Sbjct:   67 RNPARKLRGQAEEIFARLEAHQRRTDKQVEKARRQLEQINEDIATGLIP 115          
BLAST of SMED30013611 vs. Planmine SMEST
Match: SMESG000027872.1 (SMESG000027872.1)

HSP 1 Score: 105.916 bits (263), Expect = 9.483e-42
Identity = 49/80 (61.25%), Postives = 62/80 (77.50%), Query Frame = 3
Query:  456 RNPARELRGRAEDILARLEAHQRKTNREVNRAHQHLKQINKDIATGLIPSTGGYAPSYGISFELDDPRVNQPIPPMTVSV 695
            RNPARE+RG+A+ +LARLE HQR+T +++ RA +HL +IN+DIA GLIPST GYAP Y  SF LDDPR N+P   + V V
Sbjct:   70 RNPAREIRGQAKHLLARLEEHQRQTAQQIRRAQRHLDEINRDIAVGLIPSTNGYAPPYNTSFNLDDPRFNRPTEAINVVV 149          

HSP 2 Score: 82.8037 bits (203), Expect = 9.483e-42
Identity = 35/59 (59.32%), Postives = 49/59 (83.05%), Query Frame = 1
Query:  280 WMDESRITMRFPSHSAAKCRQAMWDEGYSISPVRKARFERQDDMEDAERPYIAIKREPG 456
            W+D SR+T+RFP+HSAA+CRQAMWD  +SISPVR+++ + Q   +D + P++AIKREPG
Sbjct:   11 WIDASRVTLRFPAHSAARCRQAMWDAEFSISPVRESQGKDQKISDDVDLPFVAIKREPG 69          
The following BLAST results are available for this feature:
BLAST of SMED30013611 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 SMED30013611 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 SMED30013611 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 SMED30013611 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 SMED30013611 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 SMED30013611 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 SMED30013611 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 SMED30013611 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 SMED30013611 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 SMED30013611 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 SMED30013611 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 SMED30013611 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 SMED30013611 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 SMED30013611 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000008330.12.161e-6989.04SMESG000008330.1[more]
SMESG000075969.17.990e-5371.25SMESG000075969.1[more]
SMESG000004613.16.354e-4270.77SMESG000004613.1[more]
SMESG000004613.16.354e-4270.77SMESG000004613.1[more]
SMESG000027872.19.483e-4261.25SMESG000027872.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013611 ID=SMED30013611|Name=SMED30013611|organism=Schmidtea mediterranea sexual|type=transcript|length=695bp
GAAATACAGAAATACTATTAAAAATTATTACTTGACTCCCATCAGATTTG
ACTTGATAAGACCCATTACGAAAACTTAATTCACCTATAGGTTGATGCAT
GGTCTAATAACTCTACGCGAACAATTTATTCAACAATCTAATTAATTTTT
CCTTGTAATGAATATTAACTCTATCAGTTCACTATAACTGCTACAAACGA
ATTATCTGTTGCACATGTTAACTCCATATGAACGATTCAGTTTAGTAAAC
GATTTGATAAATTTGTATTCACAGGTTTTTGGATGGACGAATCTCGTATC
ACGATGAGATTCCCATCCCACTCCGCCGCAAAATGTCGACAGGCGATGTG
GGATGAGGGGTATTCTATCTCCCCGGTACGAAAGGCCAGATTCGAAAGGC
AGGATGACATGGAGGACGCCGAACGGCCATATATTGCCATCAAACGGGAG
CCCGGCGAAACCCGGCTCGCGAACTTCGAGGAAGGGCAGAAGATATCCTA
GCCCGACTCGAAGCTCACCAACGGAAAACCAACAGAGAGGTAAATCGGGC
TCACCAACATCTCAAACAAATAAACAAAGATATCGCGACTGGCTTGATCC
CGAGCACGGGTGGGTATGCCCCTTCGTATGGCATCTCATTCGAGCTCGAT
GATCCGCGGGTGAATCAGCCAATTCCTCCAATGACGGTATCGGTG
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protein sequence of SMED30013611-orf-1

>SMED30013611-orf-1 ID=SMED30013611-orf-1|Name=SMED30013611-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=100bp
MRGILSPRYERPDSKGRMTWRTPNGHILPSNGSPAKPGSRTSRKGRRYPS
PTRSSPTENQQRGKSGSPTSQTNKQRYRDWLDPEHGWVCPFVWHLIRAR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland