SMED30024880

Overview
NameSMED30024880
Smed IDSMED30024880
Length (bp)529
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 SMED30024880 (SMED30024880) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30024880 (SMED30024880) 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 SMED30024880 (SMED30024880) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30024880 (SMED30024880) 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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Alignments
SMED30024880 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000594:48030..48558 +2645
v31.000049:210235..210764 -2540
v31.012823:2190..2720 +2530
v31.000578:1822..2351 +2513
v31.003105:36307..36849 +1243
v31.008375:9592..10141 -1224
v31.003290:839..1341 -1212
v31.002629:23716..24207 +1212
v31.002735:46525..46985 -1192
v31.030732:2172..2660 +1191
v31.018144:9083..9545 +1185
v31.005092:8659..9102 +1185
v31.001118:13220..13702 -1185
v31.000058:234581..235011 +1177
v31.002348:29275..29739 +1171
v31.029163:9261..9688 -1167
v31.016864:5064..5530 -1166
v31.000314:97348..97763 -1159
v31.014482:3965..4400 +1158
v31.009243:22768..23301 -1158
v31.006715:21146..21597 -1149
v31.002629:39689..40178 -1149
v31.001324:67105..67594 -1149
v31.000276:146159..146615 -1146
v31.000057:150478..151016 -1143
v31.012246:8397..8865 -1139
v31.018962:8312..8746 -1134
v31.000309:93600..94073 +1127
v31.002911:31175..31706 -1126
v31.006026:25887..26332 -1123
v31.002491:6233..6790 +1123
v31.035265:1352..1791 -1122
v31.020934:12639..13066 -1118
v31.003121:27847..28296 +1117
v31.020621:12921..13355 -1115
v31.042565:342..849 +1111
v31.001597:40951..41424 -1110
v31.002109:2644..3166 -1104
v31.010314:12521..12979 +1102
v31.000732:104882..105347 +1096
v31.010362:10390..10890 +1095
v31.000118:185292..185760 -1094
v31.007862:7405..7880 -1092
v31.000795:39967..40442 -1092
v31.012094:13213..13669 +1089
v31.008118:29643..30160 +1084
v31.019607:13829..14299 +1068
v31.008429:3708..4229 -1065
v31.033844:3553..4044 -1064
v31.022139:395..821 -1055
v31.047828:291..715 -1038
v31.011723:5947..6371 -1038
v31.003263:10749..11239 -1033
v31.011445:7930..8384 +1031
Homology
The following BLAST results are available for this feature:
BLAST of SMED30024880 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 SMED30024880 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 SMED30024880 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 SMED30024880 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 SMED30024880 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 SMED30024880 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 SMED30024880 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 SMED30024880 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 SMED30024880 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 SMED30024880 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 SMED30024880 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 SMED30024880 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 SMED30024880 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 SMED30024880 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

>SMED30024880 ID=SMED30024880|Name=SMED30024880|organism=Schmidtea mediterranea sexual|type=transcript|length=529bp
TTAATTGAAATATAATGTGTTTTAGTAAGTTCAAGACAGATTAGGTGATA
ATCAGAATTCTAAAAGTAATTATTTTGATTTGTCCGTGTGAAAAATAGCG
TAAAAATTATTTGGAAGATTTTCATGAAAAATAAAGAACATAATTGATTG
CATAAAGAGAAGAAATGCTGTCATCAACCCTTTCACTGTGCAATGTTTTG
AGATTTCGTGTTCGATGTGCGCAAATCTTTCGATTATTGTTCCTTACAGA
TGCACAAAATTCCGATTTTACAATACTAAAAGTGAAACATCATTTTAGGA
TTTTTGTACCTGACTTGTTTGAATACTCTGTGTGAATAGTTGTGTTGAAC
CAGGAAGAATTCGGAGCGTATGGGTCATTCATATTGTGCGAGTATATACG
GCTTGAGCAGTGAAAGGGTTAAAGTGTTGGGTTTAATTATAGAAAGTCGG
TACTTAGGTCTGACTCCTTGGCGTCCTTCTTTAATCGATTTAATTAACCC
AACACAATAAGATTTATTGCCAATTTATA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0000421tail