|
Status |
Public on Mar 29, 2021 |
Title |
control2_1h [RNAseqHU2] |
Sample type |
SRA |
|
|
Source name |
whole cells
|
Organism |
Bacillus subtilis |
Characteristics |
strain: PY79 treatment: vehicle control timepoint: 1 hour
|
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 |
84966_GTGGCC_S2_L004 RNAseqHU2_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 |
SAMN18474858 |
SRA |
SRX10437538 |