Open Access Research

Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNA-seq, RNA interference and irradiation approach

Jordi Solana1*, Damian Kao1, Yuliana Mihaylova1, Farah Jaber-Hijazi1, Sunir Malla2, Ray Wilson2 and Aziz Aboobaker12*

Author Affiliations

1 Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK

2 Deep Seq, Faculty of Medical and Health Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK

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Genome Biology 2012, 13:R19  doi:10.1186/gb-2012-13-3-r19

Published: 22 March 2012

Additional files

Additional file 1:

Dynamics of Smed-nb.21.11e-positive cells after irradiation. (a-d) WMISH of Smed-nb.21.11e in non-irradiated (a) and irradiated animals 1 (b), 3 (c) and 6 (d) days after irradiation. Smed-nb.21.11e-positive cells are still detected 1 day after irradiation, but strongly decline in numbers after 3 days (b) and are not detectable after 6 days (d). Anterior is to the left. Scale bars: 500 μm.

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Additional file 2:

Dynamics of Smed-agat-1-positive cells after irradiation. (a-d) WMISH of Smed-agat-1 in non-irradiated (a) and irradiated animals 3 (b), 5 (c) and 10 (d) days after irradiation. Smed-agat-1-positive cells are depleted from the anterior region of the worm 3 days after irradiation, strongly decline in numbers after 5 days (b) and are not detectable after 10 days (d). Anterior is to the left. Scale bars: 500 μm.

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Additional file 3:

Dynamics of expression of Smed-mcm2 and Smedwi-3 in Smed-H2B(RNAi) animals. (a-h) WMISH of Smed-mcm2 (a,c,e,g) and Smedwi-3 (b,d,f,h) in control(RNAi) (a,b) and Smed-H2B(RNAi) animals 1 (c,d), 3 (e,f) and 5 (g,h) days after RNAi. Most signals located in NBs disappear progressively for both markers (c-h). Almost no signals are detected 5 days after RNAi for the NB-specific marker Smed-mcm2 (g). The expression in the CNS of Smedwi-3 (h) is not eliminated by Smed-H2B RNAi and becomes more apparent after 5 days of RNAi (h). Some expression is detected in two rows of dorsal cells (g,h). Anterior is to the left. Scale bars: 500 μm.

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Additional file 4:

Dynamics of Smed-nanos-positive cells after Smed-H2B RNAi. (a-d) WMISH of Smed-nanos in control(RNAi) (a) and Smed-H2B(RNAi) animals 1 (b), 3 (c) and 5 (d) days after RNAi. Smed-nanos-positive cells are distributed as two rows of NB-like dorsal cells, and are still detected, although severely reduced, 5 days after Smed-H2B RNAi (d). Anterior is to the left. Scale bars: 500 μm.

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Additional file 5:

Summary of mapped reads.

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Additional file 6:

Transcriptomic data after low expression filter.

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Additional file 7:

Mapping of category 1 transcripts described by Eisenhoffer and co-workers [24].

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Additional file 8:

Mapping of transcripts downregulated by irradiation by Rossi and co-workers [25].

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Additional file 9:

Mapping of known neoblast markers compiled from the literature.

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Additional file 10:

Category 1, 2, 3 and 4 transcripts described by Eisenhoffer and co-workers [24].

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Additional file 11:

Validation of peaking transcripts. (a) Dynamics of validated peaking transcript expression in irradiated samples (left) and Smed-H2B(RNAi) samples (right) relative to non-irradiated (left) and control(RNAi) (right) samples. (b-d) WMISH of the transcripts AAA.454ESTABI.18948 (Smed-argininosuccinate-synthase) (b), AAA.454ESTABI.18310 (Smed-soxF) (c) and AAA.454ESTABI.16120 (Smed-histone-H1-gamma) (c) in non-irradiated and animals 2, 4 and 7 days after irradiation. Smed-argininosuccinate-synthase (b) and Smed-soxF (c) signals are lost progressively after irradiation, in a pattern similar to progeny markers. Smed-histone-H1- gamma signals are distributed in a pattern reminiscent of NBs and the majority of signals are lost after 2 days of irradiation.

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Additional file 12:

Combined list of 1,270 transcripts downregulated in both irradiated and Smed-H2B(RNAi) samples.

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Additional file 13:

List of 823 NB-expressed transcripts.

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Additional file 14:

Summary of GO term annotation and enrichment analysis of NB-expressed transcripts.

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Additional file 15:

Summary of domain annotation and enrichment analysis of NB-expressed transcripts.

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Additional file 16:

Summary of KEGG pathway annotation and enrichment analysis of NB-expressed transcripts.

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Additional file 17:

Compiled list of chromatin associated components.

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Additional file 18:

Compiled list of putative CB components.

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Additional file 19:

Compiled list of cell division machinery components.

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Additional file 20:

Compiled list of transcription factors.

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Additional file 21:

Compiled list of RNA associated transcripts.

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