Oxford Planarian Bioinformatics Community

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Jakke Neiro1 & Nathan Kenny2

  1. Aboobaker lab, University of Oxford, jakke.neiro@zoo.ox.ac.uk

  2. Solana lab, Oxford Brookes University, nkenny@brookes.ac.uk

This site includes code, files and other resources generated by the Oxford Planarian Bioinformatics Community.

Annotation of the Schmidtea mediterranea genome

A new expression-driven annotation of the sexual planarian genome (S. mediterranea) was generated based on total RNA-seq data from this species. The annotation is based on 183 planarian RNA-seq samples (see the sample list), the PlanMine sexual genome annotation (SMESG-high), and the PlanMine sexual genome (SMESG.1).

Notebook for annotation pipline

Download S. mediterranea annotation

Sample list (SRA ids) for creating the new annotation

Annotation of the Dugesia japonica genome

Similarly to the S. mediterranea annotation, the new expression-driven D. japonica annotation was generated based on 43 RNA-seq samples (see the sample list, the Augustus-derived annotation and the genome assembly at planarian.jp.

Download D. japonica annotation

rds files of analyses presented in ACME paper

These files allow easy uploading to R of the analyses presented in the García-Castro et al. 2020 ACME paper. Download link

Files

Expression values

Proportional expression values

ChIP-seq data

ATAC-seq data

Notebooks

1. Genome annotation

In the first section, a new expression-driven planarian genome annotation was created. This annotation was used to identify both coding and non-coding transcripts. Proportional expression values (X1:X2:Xins) were assigned to all transcripts.

1-1 Genome annotation

1-2 Genome annotation analysis

1-3 FACS expression

1-4 FACS expression analysis

1-5 Homology of new genes

1-6 Genome annotation visualization

2. Transcription factors

In the second section, putative transcription factors were identified computationally and then manually curated and assessed.

2-1 Transcription factors identification

2-2 Transcription factors literature review 2000-2009

2-3 Transcription factors literature review 2010-2014

2-4 Transcription factors literature review 2015-2021

2-5 Transcription factors motif inference

2-6 Transcription factors visualization

3. ChIP-seq analysis

In the third section, H3K27ac and H3K4me1 ChIP-seq data was used to identify enhancer-like regions.

3-1 ChIP-seq QC and alignment

3-2 ChIP-seq filtering and analysis

3-3 ChIP-seq annotation and analysis

3-4 ChIP-seq analysis and visualization

4. ATAC-seq analysis

In the fourth section, ATAC-seq data was used to assess chromosome accessibility and perform footprinting analysis.

4-1 ATAC-seq QC and alignment

4-2 ATAC-seq peak calling

4-3 ATAC-seq footprinting

4-4 ATAC-seq analysis

5. mbd34(RNAi)

In the fifth section, H3K4me1 and H3K4me3 ChIP-seq and RNA-seq data is analyzed from lpt(RNAi) worms (lpt is the homolog of mbd3/4).

5-1 Mbd3/4 RNAi H3K4me1 ChIP-seq QC and alignment

5-2 Mbd3/4 RNAi H3K4me3 ChIP-seq QC and alignment

5-3 Mbd3/4 RNAi H3K4me1/3 ChIP-seq analysis

5-4 Mbd3/4 RNAi RNA-seq

5-5 Mbd3/4 RNAi Differential gene expression analysis

6. Enhancer annotation

6-1 Enhancer annotation

6-2 Enhancer analysis

6-3 Enhancers genomic tracks

6-4 Gene regulatory networks

6-5 Enhancer analysis and visualization

7. Functional assessment

7-1 Transcription factor knockdown and RNA-seq

7-2 Transcription factor knockdown and differential gene expression analysis

7-3 Transcription factor knockdowns analysis

7-4 Transcription factor enrichment visualization

7-5 Knockdown target genes and genome tracks

Publications

Identification of enhancer-like elements defines regulatory networks active in planarian adult stem cells

Jakke Neiro, Divya Shridhar, Anish Dattani, Aziz Aboobaker

Planarians have become an established model system to study regeneration and stem cells, but the regulatory elements in the genome remain almost entirely undescribed. Here, by integrating epigenetic and expression data we use multiple sources of evidence to identify enhancer elements active in the adult stem cell populations that drive regeneration. We have used ChIP-seq data to identify regions with histone modifications consistent with enhancer identity and activity, and ATAC-seq data to identify accessible chromatin. Overlapping these signals allowed for the identification of a set of high confidence candidate enhancers predicted to be active in planarian adult stem cells. These enhancers are enriched for conserved transcription factor (TF) binding sites for TFs and TF families expressed in planarian adult stem cells. Foot-printing analyses provided further evidence that these potential TF binding sites are occupied in adult stem cells. We integrated these analyses to build testable hypotheses for the regulatory function of transcription factors in stem cells, both with respect to how pluripotency might be regulated, and to how lineage differentiation programs are controlled. Our work identifies active enhancers regulating adult stem cells and regenerative mechanisms.

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

Helena García-Castro, Nathan J. Kenny, Marta Iglesias, Patricia Álvarez-Campos, Vincent Mason, Anamaria Elek, Anna Schönauer, Victoria A. Sleight, Jakke Neiro, Aziz Aboobaker, Jon Permanyer, Manuel Irimia, Arnau Sebé-Pedrós & Jordi Solana

Single-cell sequencing technologies are revolutionizing biology, but they are limited by the need to dissociate live samples. Here, we present ACME (ACetic-MEthanol), a dissociation approach for single-cell transcriptomics that simultaneously fixes cells. ACME-dissociated cells have high RNA integrity, can be cryopreserved multiple times, and are sortable and permeable. As a proof of principle, we provide single-cell transcriptomic data of different species, using both droplet-based and combinatorial barcoding single-cell methods. ACME uses affordable reagents, can be done in most laboratories and even in the field, and thus will accelerate our knowledge of cell types across the tree of life.