SMED30030665

Overview
NameSMED30030665
Smed IDSMED30030665
Length (bp)524
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 SMED30030665 (SMED30030665) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30030665 (SMED30030665) 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 SMED30030665 (SMED30030665) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30030665 (SMED30030665) 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



SMED30030665

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
reproductive organSMED30030665SMESG000055629.1 SMESG000066348.1 SMESG000050918.1 Contig45882newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30030665SMESG000055629.1 SMESG000066348.1 SMESG000050918.1 Contig45882uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30030665 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006629:15809..16383 +2442
v31.018745:5137..5726 +1733
v31.015210:10321..10879 +1715
v31.000306:123716..124209 -1702
v31.001803:74889..75400 +1692
v31.011611:5309..5810 +1689
v31.000461:87111..87684 -1689
v31.009694:9745..10263 -1688
v31.024326:12621..13138 +1687
v31.002890:33093..33663 +1687
v31.014732:14826..15417 +1686
v31.050732:191..748 -1683
v31.026951:6884..7469 +1678
v31.023177:8370..8955 +1678
v31.006273:12078..12558 -1678
v31.000166:202993..203571 +1678
v31.000621:17371..17849 +1672
v31.019538:2764..3330 -1666
v31.012081:11479..12007 +1666
v31.000407:60662..61457 -1661
v31.023406:9474..9951 -1658
v31.001399:60074..60633 +1657
v31.011429:10890..11459 +1656
v31.009174:21322..21816 +1651
v31.002459:21253..21847 -1648
v31.002732:36176..36783 -1644
v31.000180:31426..31946 -1643
v31.005638:9948..10531 -1640
v31.006636:28472..28965 +1638
v31.003838:31606..32170 -1638
v31.020592:11488..11966 -1632
v31.036089:3658..4184 -1628
v31.006542:19173..19656 -1625
v31.000088:278184..278762 -1621
v31.003625:28946..29528 -1614
v31.008023:9564..10070 +1613
v31.025182:8661..9160 +1611
v31.001318:28508..29074 +1607
v31.009374:14801..15256 +1603
v31.020975:3734..4206 -1600
v31.006159:6505..7012 -1596
v31.000763:54723..55214 -1590
v31.000200:127637..128232 +1583
v31.000985:7175..7684 +1580
v31.011809:2864..3402 +1579
v31.000074:196208..196765 -1571
v31.013857:11804..12307 -1567
v31.011429:12588..13119 -1567
v31.010345:11348..11854 +1564
v31.003826:12545..13098 +1559
v31.002020:30420..32923 +1557
v31.001806:17978..27792 -1556
v31.001350:23745..24362 +1556
v31.003180:49658..50101 -1550
v31.003395:17469..17975 +1549
v31.001086:60279..60771 +1537
v31.006361:23199..23701 +1518
v31.000717:18373..18832 +1514
v31.003232:35868..36330 -1509
v31.009369:7335..7860 +1505
v31.003469:36276..36767 +1501
v31.022083:6190..6684 -1494
v31.001673:42656..43162 -1423
v31.010739:29053..29539 -1419
v31.005463:3497..4031 +1411
v31.001810:29504..30037 +1409
v31.009731:1817..2346 +1406
v31.020865:9729..10284 -1400
v31.039319:404..967 +1390
v31.001257:31578..32097 +1386
v31.032499:3368..4051 +1382
v31.006172:10424..10894 -1370
v31.000255:14450..14949 -1367
v31.002598:50643..51208 -1362
v31.000124:260591..261085 +1359
v31.002945:2094..2609 +1302
v31.003760:5748..6260 -1301
v31.011053:22052..22489 +1300
v31.003562:50658..51095 +1282
v31.000096:303709..304124 -1237
v31.000241:193985..194534 -1236
v31.015384:3542..4097 -1235
v31.022304:1765..2290 -1197
v31.000623:34297..34729 -1174
v31.001864:12969..13447 +1172
v31.000515:29732..30183 -1153
v31.010343:51347..51881 -1118
v31.000515:29775..30242 +526
Homology
The following BLAST results are available for this feature:
BLAST of SMED30030665 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 SMED30030665 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 SMED30030665 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 SMED30030665 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 SMED30030665 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 SMED30030665 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 SMED30030665 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 SMED30030665 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 SMED30030665 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 SMED30030665 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 SMED30030665 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 SMED30030665 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 SMED30030665 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 SMED30030665 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030665 ID=SMED30030665|Name=SMED30030665|organism=Schmidtea mediterranea sexual|type=transcript|length=524bp
TTTGTGGATTTTTTTGTGGCTCATGAAATTTCAGACGTTTTGATTTTGGT
TCTTCATTCGATTTAAGTTGGCTAAGCCTACTTAAGAACAAACAAGTAAG
ATAAAAATACTTCGAGATTTTTAATTATTATTTATTAGTAGTTGTAACCA
GGCTTGCCAGACCTCCCGATTTCGTGGGAGTCTCCCGATATGGAACGCAT
ATTCCCGTCATCCCGATATATGAACCGTAACTCCCGATATTGAACAGTTT
TAGATTTTGAGTAGATTTTACCCATCATGAAAGGATTTTTTAAAAAAACC
ATAAAATAAACGAAACTAAGAAAAATAGAGAAATTATATTTCTATATTAC
TGATTGCTCGCTATTTTTACCATAGGGATTTGTGATTTCACCTTTTCCTT
ATGGATTGGTGTTACATTTAATTTCAAAATGACGTGCAATGAGTTTCAGG
CATTCTTAAAAAACAGAAAATGCACAAGGAATACTTTTTTTACGTTAACA
AAACTGAAGACTTATTTTTTTGTT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ