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Transcriptomic profiles of mycobacteriophage D29, L5 and StarStuff
Internal Dataset

UID: 24

Author(s): Hatfull, Graham F.+, Dedrick, Rebekah M.*+, Mavrich, Travis N.+, Garlena, Becky+ * Corresponding Author + University of Pittsburgh Author
Description
This dataset contains twelve high throughput sequenced gene expression profiles of mycobacterium smegmatis infected with (1) mycobacteriophage D29 at 15min, 30min, 60min, and 150min, (2) mycobacteriophage StarStuff itself and at 15min, 30min, 60min, and 150min, and (3) mycobacteriophage L5 itself and at 30min and 150 min. Total RNA was isolated, depleted of rRNA, and library prepped.
Subject of Study
Mycobacterium phage

Species (Strain): StarStuff

Mycobacterium phage

Species (Strain): D29

Mycobacterium phage

Species (Strain): L5

Mycobacterium smegmatis
Keywords
Bacteriophage evolution
Evolution, Molecular
Gene Expression Profiling
Mycobacterium
Sequence Analysis, RNA
Access via NCBI GEO

Expression profiling by high throughput sequencing.
Accession #: GSE99182

Access via SRA

Raw data for 12 samples.
Accession #: SRP107805

Access via BioProject

Overall project information and data.
Accession #: PRJNA387480

Access Restrictions
Free to all
Access Instructions
The NCBI Gene Expression Omnibus, Sequence Read Archive, and BioProject databases provide open access to these files.
Associated Publications
Dedrick RM, Mavrich TN, Ng WL, Hatfull GF. Expression and evolutionary patterns of mycobacteriophage D29 and its temperate close relatives. BMC Microbiol. 2017 Dec 2;17(1):225. doi: 10.1186/s12866-017-1131-2. PMID: 29197343; PMCID: PMC5712189.
Data Type
Genetic/Genomic
Equipment Used
Illumina MiSeq
Software Used
Count

Evolutionary analysis of phylogenetic profiles with parsimony and likelihood

EvolView

Online tool for visualizing, annotating and managing phylogenetic trees

Mauve

Multiple Alignment of Conserved Genomic Sequence With Rearrangements

SeaView 4

Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

Dataset Format(s)
SOFT (.soft), MINiML (.miniml, .xml), TXT (.txt)
Resource Type(s)
Dataset
Grant Support
GM116884/National Institutes of Health
HHMI 54308198/Howard Hughes Medical Institute
NSF1247842/National Science Foundation
Data Catalog Record Updated
2022-04-04

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