Overview
Name SMED30014788
Smed ID SMED30014788
Length (bp) 1050
Neoblast Clusters
Zeng et. al., 2018
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 SMED30014788 (SMED30014788) t-SNE clustered cells
Violin plots show distribution of expression levels for SMED30014788 (SMED30014788) 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 SMED30014788 (SMED30014788) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.
Violin plots show distribution of expression levels for SMED30014788 (SMED30014788) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.
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Anatomical Expression
PAGE et. al., 2020
SMED30014788
has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE
Expressed In Reference Transcript Gene Models Published Transcript Transcriptome Publication Specimen Lifecycle Evidence head region SMED30014788 SmedASXL_075382 SmedAsxl_ww_GCZZ01 PMID:27034770 Currie et al., 2016 Smed sexual biotype SMED30014788 SMESG000080313.1 SMESG000066842.1 SMESG000042931.1 SMESG000017493.1 SMESG000015917.1 SMESG000081995.1 SMESG000078665.1 SMESG000077025.1 SMESG000076395.1 SMESG000075858.1 SMESG000068623.1 SMESG000062442.1 SMESG000060496.1 SMESG000054975.1 SMESG000054276.1 SMESG000053832.1 SMESG000051957.1 SMESG000049162.1 SMESG000046165.1 SMESG000038724.1 SMESG000036894.1 SMESG000035648.1 SMESG000034762.1 SMESG000030069.1 SMESG000029693.1 SMESG000029692.1 SMESG000029599.1 SMESG000027993.1 SMESG000027217.1 SMESG000022058.1 SMESG000012961.1 SMESG000010709.1 SMESG000007675.1 SMESG000004166.1 SMESG000002239.1 Contig43903 uc_Smed_v2 PMID:29674431 Fincher et al., 2018 Smed sexual biotype SMED30014788 SMESG000080313.1 SMESG000066842.1 SMESG000042931.1 SMESG000017493.1 SMESG000015917.1 SMESG000081995.1 SMESG000078665.1 SMESG000077025.1 SMESG000076395.1 SMESG000075858.1 SMESG000068623.1 SMESG000062442.1 SMESG000060496.1 SMESG000054975.1 SMESG000054276.1 SMESG000053832.1 SMESG000051957.1 SMESG000049162.1 SMESG000046165.1 SMESG000038724.1 SMESG000036894.1 SMESG000035648.1 SMESG000034762.1 SMESG000030069.1 SMESG000029693.1 SMESG000029692.1 SMESG000029599.1 SMESG000027993.1 SMESG000027217.1 SMESG000022058.1 SMESG000012961.1 SMESG000010709.1 SMESG000007675.1 SMESG000004166.1 SMESG000002239.1 Contig43903 newmark_ests PMID:29674431 Fincher et al., 2018 Smed sexual biotype SMED30014788 SMESG000081995.1 SMESG000080328.1 SMESG000080048.1 SMESG000078665.1 SMESG000077025.1 SMESG000076395.1 SMESG000075858.1 SMESG000073751.1 SMESG000073596.1 SMESG000068623.1 SMESG000066691.1 SMESG000062442.1 SMESG000054975.1 SMESG000054276.1 SMESG000051957.1 SMESG000049162.1 SMESG000046165.1 SMESG000036051.1 SMESG000035648.1 SMESG000034762.1 SMESG000030928.1 SMESG000030069.1 SMESG000029599.1 SMESG000029355.1 SMESG000027993.1 SMESG000027217.1 SMESG000022058.1 SMESG000012961.1 SMESG000012903.1 SMESG000010709.1 SMESG000007675.1 SMESG000006952.1 SMESG000004166.1 SMESG000003706.1 SMESG000002239.1 SMESG000080313.1 SMESG000069906.1 SMESG000066842.1 SMESG000050392.1 SMESG000033095.1 SMESG000017493.1 SMESG000004603.1 SMESG000004121.1 Contig42477 uc_Smed_v2 PMID:29674431 Fincher et al., 2018 Smed sexual biotype SMED30014788 SMESG000081995.1 SMESG000080328.1 SMESG000080048.1 SMESG000078665.1 SMESG000077025.1 SMESG000076395.1 SMESG000075858.1 SMESG000073751.1 SMESG000073596.1 SMESG000068623.1 SMESG000066691.1 SMESG000062442.1 SMESG000054975.1 SMESG000054276.1 SMESG000051957.1 SMESG000049162.1 SMESG000046165.1 SMESG000036051.1 SMESG000035648.1 SMESG000034762.1 SMESG000030928.1 SMESG000030069.1 SMESG000029599.1 SMESG000029355.1 SMESG000027993.1 SMESG000027217.1 SMESG000022058.1 SMESG000012961.1 SMESG000012903.1 SMESG000010709.1 SMESG000007675.1 SMESG000006952.1 SMESG000004166.1 SMESG000003706.1 SMESG000002239.1 SMESG000080313.1 SMESG000069906.1 SMESG000066842.1 SMESG000050392.1 SMESG000033095.1 SMESG000017493.1 SMESG000004603.1 SMESG000004121.1 Contig42477 newmark_ests PMID:29674431 Fincher et al., 2018 nervous system SMED30014788 SMESG000081995.1 SMESG000080328.1 SMESG000080048.1 SMESG000078665.1 SMESG000077025.1 SMESG000076395.1 SMESG000075858.1 SMESG000066691.1 SMESG000062442.1 SMESG000060496.1 SMESG000054975.1 SMESG000054276.1 SMESG000051957.1 SMESG000049162.1 SMESG000046165.1 SMESG000036894.1 SMESG000035648.1 SMESG000034762.1 SMESG000030928.1 SMESG000030475.1 SMESG000030445.1 SMESG000030069.1 SMESG000029693.1 SMESG000029692.1 SMESG000029599.1 SMESG000029355.1 SMESG000027993.1 SMESG000027217.1 SMESG000022058.1 SMESG000020046.1 SMESG000014020.1 SMESG000012961.1 SMESG000010709.1 SMESG000007675.1 SMESG000006952.1 SMESG000004166.1 SMESG000003706.1 SMESG000002779.1 SMESG000002239.1 SMESG000001845.1 SMESG000080313.1 SMESG000066842.1 SMESG000050392.1 SMESG000048356.1 SMESG000042931.1 SMESG000033095.1 SMESG000018900.1 SMESG000017493.1 SMESG000015917.1 SMESG000004121.1 dd_Smed_v4_3574_2_1 dd_Smed_v4 PMID:29674431 Fincher et al., 2018 epidermis SMED30014788 SMESG000081995.1 SMESG000080328.1 SMESG000080048.1 SMESG000078665.1 SMESG000077025.1 SMESG000076395.1 SMESG000075858.1 SMESG000066691.1 SMESG000062442.1 SMESG000060496.1 SMESG000054975.1 SMESG000054276.1 SMESG000051957.1 SMESG000049162.1 SMESG000046165.1 SMESG000036894.1 SMESG000035648.1 SMESG000034762.1 SMESG000030928.1 SMESG000030475.1 SMESG000030445.1 SMESG000030069.1 SMESG000029693.1 SMESG000029692.1 SMESG000029599.1 SMESG000029355.1 SMESG000027993.1 SMESG000027217.1 SMESG000022058.1 SMESG000020046.1 SMESG000014020.1 SMESG000012961.1 SMESG000010709.1 SMESG000007675.1 SMESG000006952.1 SMESG000004166.1 SMESG000003706.1 SMESG000002779.1 SMESG000002239.1 SMESG000001845.1 SMESG000080313.1 SMESG000066842.1 SMESG000050392.1 SMESG000048356.1 SMESG000042931.1 SMESG000033095.1 SMESG000018900.1 SMESG000017493.1 SMESG000015917.1 SMESG000004121.1 dd_Smed_v4_3574_2_1 dd_Smed_v4 PMID:29674431 Fincher et al., 2018 cephalic ganglia SMED30014788 SMESG000081995.1 SMESG000080328.1 SMESG000080048.1 SMESG000078665.1 SMESG000077025.1 SMESG000076395.1 SMESG000075858.1 SMESG000066691.1 SMESG000062442.1 SMESG000060496.1 SMESG000054975.1 SMESG000054276.1 SMESG000051957.1 SMESG000049162.1 SMESG000046165.1 SMESG000036894.1 SMESG000035648.1 SMESG000034762.1 SMESG000030928.1 SMESG000030475.1 SMESG000030445.1 SMESG000030069.1 SMESG000029693.1 SMESG000029692.1 SMESG000029599.1 SMESG000029355.1 SMESG000027993.1 SMESG000027217.1 SMESG000022058.1 SMESG000020046.1 SMESG000014020.1 SMESG000012961.1 SMESG000010709.1 SMESG000007675.1 SMESG000006952.1 SMESG000004166.1 SMESG000003706.1 SMESG000002779.1 SMESG000002239.1 SMESG000001845.1 SMESG000080313.1 SMESG000066842.1 SMESG000050392.1 SMESG000048356.1 SMESG000042931.1 SMESG000033095.1 SMESG000018900.1 SMESG000017493.1 SMESG000015917.1 SMESG000004121.1 dd_Smed_v4_3574_2_1 dd_Smed_v4 PMID:29674431 Fincher et al., 2018 neoblast SMED30014788 SMESG000081995.1 SMESG000080328.1 SMESG000080048.1 SMESG000078665.1 SMESG000077025.1 SMESG000076395.1 SMESG000075858.1 SMESG000066691.1 SMESG000062442.1 SMESG000060496.1 SMESG000054975.1 SMESG000054276.1 SMESG000051957.1 SMESG000049162.1 SMESG000046165.1 SMESG000036894.1 SMESG000035648.1 SMESG000034762.1 SMESG000030928.1 SMESG000030475.1 SMESG000030445.1 SMESG000030069.1 SMESG000029693.1 SMESG000029692.1 SMESG000029599.1 SMESG000029355.1 SMESG000027993.1 SMESG000027217.1 SMESG000022058.1 SMESG000020046.1 SMESG000014020.1 SMESG000012961.1 SMESG000010709.1 SMESG000007675.1 SMESG000006952.1 SMESG000004166.1 SMESG000003706.1 SMESG000002779.1 SMESG000002239.1 SMESG000001845.1 SMESG000080313.1 SMESG000066842.1 SMESG000050392.1 SMESG000048356.1 SMESG000042931.1 SMESG000033095.1 SMESG000018900.1 SMESG000017493.1 SMESG000015917.1 SMESG000004121.1 dd_Smed_v4_3574_2_1 dd_Smed_v4 PMID:29674431 Fincher et al., 2018 parenchymal cell SMED30014788 SMESG000081995.1 SMESG000080328.1 SMESG000080048.1 SMESG000078665.1 SMESG000077025.1 SMESG000076395.1 SMESG000075858.1 SMESG000066691.1 SMESG000062442.1 SMESG000060496.1 SMESG000054975.1 SMESG000054276.1 SMESG000051957.1 SMESG000049162.1 SMESG000046165.1 SMESG000036894.1 SMESG000035648.1 SMESG000034762.1 SMESG000030928.1 SMESG000030475.1 SMESG000030445.1 SMESG000030069.1 SMESG000029693.1 SMESG000029692.1 SMESG000029599.1 SMESG000029355.1 SMESG000027993.1 SMESG000027217.1 SMESG000022058.1 SMESG000020046.1 SMESG000014020.1 SMESG000012961.1 SMESG000010709.1 SMESG000007675.1 SMESG000006952.1 SMESG000004166.1 SMESG000003706.1 SMESG000002779.1 SMESG000002239.1 SMESG000001845.1 SMESG000080313.1 SMESG000066842.1 SMESG000050392.1 SMESG000048356.1 SMESG000042931.1 SMESG000033095.1 SMESG000018900.1 SMESG000017493.1 SMESG000015917.1 SMESG000004121.1 dd_Smed_v4_3574_2_1 dd_Smed_v4 PMID:29674431 Fincher et al., 2018 muscle cell SMED30014788 SMESG000081995.1 SMESG000080328.1 SMESG000080048.1 SMESG000078665.1 SMESG000077025.1 SMESG000076395.1 SMESG000075858.1 SMESG000066691.1 SMESG000062442.1 SMESG000060496.1 SMESG000054975.1 SMESG000054276.1 SMESG000051957.1 SMESG000049162.1 SMESG000046165.1 SMESG000036894.1 SMESG000035648.1 SMESG000034762.1 SMESG000030928.1 SMESG000030475.1 SMESG000030445.1 SMESG000030069.1 SMESG000029693.1 SMESG000029692.1 SMESG000029599.1 SMESG000029355.1 SMESG000027993.1 SMESG000027217.1 SMESG000022058.1 SMESG000020046.1 SMESG000014020.1 SMESG000012961.1 SMESG000010709.1 SMESG000007675.1 SMESG000006952.1 SMESG000004166.1 SMESG000003706.1 SMESG000002779.1 SMESG000002239.1 SMESG000001845.1 SMESG000080313.1 SMESG000066842.1 SMESG000050392.1 SMESG000048356.1 SMESG000042931.1 SMESG000033095.1 SMESG000018900.1 SMESG000017493.1 SMESG000015917.1 SMESG000004121.1 dd_Smed_v4_3574_2_1 dd_Smed_v4 PMID:29674431 Fincher et al., 2018
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Homology
BLAST of SMED30014788 vs. Planmine SMEST
Match:
SMESG000080313.1 (SMESG000080313.1)
HSP 1 Score: 57.7658 bits (138), Expect = 7.896e-10
Identity = 26/26 (100.00%), Postives = 26/26 (100.00%), Query Frame = -2
Query: 90 LLGQHTNSLENCLNASVIQHENPAPR 167
LLGQHTNSLENCLNASVIQHENPAPR
Sbjct: 142 LLGQHTNSLENCLNASVIQHENPAPR 167
BLAST of SMED30014788 vs. Planmine SMEST
Match:
SMESG000030276.1 (SMESG000030276.1)
HSP 1 Score: 50.8322 bits (120), Expect = 4.444e-7
Identity = 39/113 (34.51%), Postives = 55/113 (48.67%), Query Frame = 3
Query: 363 ILTIRERHSKRMFK----HDYPEFVKSDLSSHQFHVYRNDEIKTSLDLRSTVKISHSRQQDPEAVISYQILEPMTSMTS------------CVTQFLKSEHQKFNFFQKQKLP 653
++ +R+ S + FK PEFVK D+S H+FH Y NDE+K SL ++ V+ RQQ+ ++E S TS C T + KF FF+ QKLP
Sbjct: 137 VIWLRDHFSGKCFKRVRRGISPEFVKRDISVHKFHAYINDEMKISLVVKLMVETPQPRQQE--------VMETQNSSTSVEYWTDDFSDEICHT-VPQVGTTKFKFFRYQKLP 240
The following BLAST results are available for this feature:
Analyses
This transcript is derived from or has results from the following analyses
Sequences
The following sequences are available for this feature:
transcript sequence
>SMED30014788 ID=SMED30014788|Name=SMED30014788|organism=Schmidtea mediterranea sexual|type=transcript|length=1050bp TTTATTTTTATGTTTTTGATTTTATATTTATTTATATTCTCTCAGATTTT AAAGTGTTTAATTGGTGTTGTATATTGTATTTTAAGTTATCTTGGTGCTG GGTTTTCGTGCTGTATTACTGATGCATTTAAACAATTCTCAAGGCTATTT GTGTGCTGGCCCAACAGTGGTAAATCGGTATTTAATTCCCGCAGTTACGT TTGCGGGACGTTGACGTGTCGATTTATCATTTTCTACTCCTCGGAGTCTG CTGGGACTGGTCAGCTTTCTACTGATAGCGAAAGTAAGACTCCACTGGAC TTCACCGCAGCGTTCATGAATGGTGGGTGGAGCAGTAACTAAATCAAAAT CACGGGAAGATCATTTTGACTATAAGGGAACGACATTCAAAAAGAATGTT TAAGCATGACTATCCAGAGTTTGTAAAATCGGATCTCTCATCGCACCAGT TCCATGTCTATAGAAACGATGAAATAAAAACCAGTTTAGACCTTCGATCA ACGGTGAAAATATCACACTCTCGACAGCAAGACCCAGAAGCCGTCATCTC CTATCAGATATTAGAACCGATGACTTCGATGACGAGCTGTGTCACTCAGT TCCTCAAGTCGGAACATCAAAAATTCAATTTCTTCCAAAAACAGAAACTC CCAGTTGATATAGATGAGGATACCCGAGATATTCTCATGGACTTGAGCGA ACTTTTAGACGAATAGGAATCCTGTCAATTATCTCGTTTTTCTTTTTGAC GCATCATTTTGTTCTATTCAATTCTAAGTTTTCTTTTTGGTGTATGTTAA TTGTTTTTTCTTTTCGAATAAATAGTTTTAGTATTGTTAATAATTGTTGT CGAATGTAATGTAGTAATAGTAAAAATATAATAGTTTGATTGTGCTGTGA ATGAGATTAATTACATAAGGAAGCTGTAATAGGGAATGCGCCAGGTTCCG ATAAGGCAATTTAAGGGATTTATAAGAGGTTTCCGGGAAGCAGAGCGTTG ATTTAATTAAAAGGCAGGAAGTAAACCCGAATTTATTTACATTGATTCCC back to top protein sequence of SMED30014788-orf-1
>SMED30014788-orf-1 ID=SMED30014788-orf-1|Name=SMED30014788-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=107bp
MFKHDYPEFVKSDLSSHQFHVYRNDEIKTSLDLRSTVKISHSRQQDPEAV ISYQILEPMTSMTSCVTQFLKSEHQKFNFFQKQKLPVDIDEDTRDILMDL SELLDE* back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
Term Definition
PLANA:0000099 neuron
PLANA:0000418 head