|
| Status |
Public on Mar 29, 2021 |
| Title |
control1_2h [RNAseqHU4] |
| Sample type |
SRA |
| |
|
| Source name |
whole cells
|
| Organism |
Bacillus subtilis |
| Characteristics |
strain: PY79
treatment: vehicle control
timepoint: 2 hours
|
| Treatment protocol |
25 mM HU or water (vehicle control) was incubated with cells for 1 and 2 hours post-treatment
|
| Growth protocol |
PY79 was grown to an OD600 of 0.2 in LB medium at 30oC and supplemented with 25 mM HU for 1 and 2 hours before collecting cell pellets for nucleic acid extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-SNAP from Stead et al. 2012
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
84968_GTCCGC_S4_L004
RNAseqHU4_sort.bam
|
| Data processing |
align files to reference genome using BWA
samtools to generate a fast QC report for quality assessment
checking mapped vs. unmapped reads using samtools
calculate RPKMs in R, then used limma implementation to detect differential expression
generated top tables with a p-value cut off at 0.05
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000497485.1/
Supplementary_files_format_and_content: .csv files generated detailing differential expression
|
| |
|
| Submission date |
Mar 24, 2021 |
| Last update date |
Mar 29, 2021 |
| Contact name |
Lyle A. Simmons |
| E-mail(s) |
lasimm@umich.edu
|
| Organization name |
University of Michigan
|
| Department |
Molecular, Cellular, & Developmental Biology
|
| Street address |
1105 N. University Ave.
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48105 |
| Country |
USA |
| |
|
| Platform ID |
GPL29515 |
| Series (2) |
| GSE169563 |
RNA-seq of hydroxyurea treated Bacillus subtilis cells |
| GSE169565 |
RNA-seq,Tn-seq, and whole genome sequencing of hydroxyurea treated Bacillus subtilis cells |
|
| Relations |
| BioSample |
SAMN18474856 |
| SRA |
SRX10437540 |
