Ashley Seifert Lab Introduction

Research activities in the Seifert lab related to bioinformatics: Regeneration is a process where an organism regrows a lost or damaged part. A key characteristic of epimorphic regeneration is the formation of a heterogeneous mass of lineage-restricted progenitor cells which accumulates from local tissues and is known as blastema. Blastema cells are able to re-enter the cell cycle and proliferate to form new tissue. This type of regenerative process is rarely observed in mammals. Spiny mice (Acomys) can regenerate ear pinna tissue through epimorphic regeneration whereas an identical injury in other rodents like the common laboratory mouse (Mus) results in fibrotic repair with a scar (Seifert et al., 2012; Gawriluk et al., 2016). Cellular senescence is a process that regulates cell cycle progression and proliferation by arresting cell cycle re-entry and inducing cell death. Interestingly, cell cycle progression and proliferation were found only in Acomys, not in Mus. Insight from recent work in our lab showed that fibroblasts from regenerating mammals are very resistant to external stressors like hydrogen peroxide and gamma radiation (Saxena et al., 2019). Moving forward, we intend to compare healing ear tissue during regeneration and fibrotic repair in an attempt to isolate pathways that differentially regulate cell cycle progression and the cellular stress response using RNA-seq data.

Ashley Seifert Lab DLX usage

Bioinformatics related to regeneration in Acomys and Mus

Students

Shishir Biswas - Grad
Sruthi Purushothaman - Grad
Adam Cook - Grad
Tom Gawriluk - Postdoc

Sandeep Saxena - Fellowship

Brennan L Riddell - Fellowship, Added on 09/06/2022 on MCC resources

Ajoy Aloysius, Postdoc, Added 09/29/2022 on LCC cluster

Software

RSEM
blast
bowtie
bwa
minia package
Trinity

Collaborators

(and possible collaborators who have not yet generated data) – N/A

Assembly of small/low complexity Acomys genome

Students

Chanung Wang - Grad

Brianda Lopez Avina, Grad, Added on MCC cluster, 05/31/2022

Software

RSEM
blast
bowtie
bwa
minia package
Trinity

Collaborators

Grants

Publications

Project:

Our lab currently has four different RNAseq datasets that we would like to analyze using the cluster. The first dataset follows complex tissue in the ear as it undergoes healing across a time series (Day 0, 5, 10, 15 and 20) for Acomys and Mus. Using this dataset, we are looking at raw levels of gene expression (transcripts per million) as well as gene expression dynamics (fold change) to identify gene expression patterns that differentiate regeneration from scarring at the transcriptional level.

Students:

Shishir Biswas (graduate student)

Project:

Second, we are using this dataset in conjunction with the mitochondrial genomes from these animals to examine mitochondrial function and metabolic dynamics during regeneration.

Students:

Sandeep Saxena (graduate student), Added 11/10/2020

Project:

The third dataset is from macrophages harvested from Acomys and Mus that have been activated using standard treatments to investigate how macrophages from different species may influence wound healing in our regeneration model.

Students:

Shishir Biswas (graduate student)

Fatemeh Safaee (graduate student)

Jennifer Simkin (former post-doc)

Project:

The fourth dataset is a time series (D0, D7, D14, D21, D30) from Acomys only and was generated using laser-capture microdissection to isolate the epidermis and mesenchyme, as well as deconstructing the mesenchyme into multiple compartments, to identify signaling and gene expression gradients specific to tissue type.

Students:

Shishir Biswas (graduate student)

Computational Methods:

We will primarily be processing and mapping RNAseq reads onto genomes and de novo assembled transcriptomes to quantify gene expression. We will also be using BLAST to align gene sequences from different species. All of the packages to analyze our data are currently freely available.

Software:

Software’s each individual project will be using. Currently, all of our projects employ multiple software packages centered around analyzing RNA-seq data as well as identifying gene orthologs between species using their genomes and transcriptomes. To analyze RNAseq data, our lab uses the following software packages:

Trinity

Bowtie2

RSEM

EBSeq

Tophat

Cufflinks

Hisat2

Stringtie2

DESeq2

To compare genomic and transcriptomic sequences across species our lab uses the following software packages:

BLAST

NCBI

Collaborators:

John Gensel, PhD is a collaborator at UK on the Macrophage RNAseq project.

David Thybert, PhD is a non-UK collaborator at the European Bioinformatics Institute and is a collaborator on the bulk RNAseq project.

Gustavio Tiscornia, PhD is a non-UK collaborator PI at the University of Algarve and is a collaborator on the LCM RNAseq project.

(None of these collaborators require access to the cluster.)

Students

Shishir Biswas - Grad
Sruthi Purushothaman - Grad
Adam Cook - Grad
Tom Gawriluk - Postdoc

Sandeep Saxena - Fellowship, Added 11/10/2020

Chanung Wang - Grad

Grants:

Publications:

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