|
| Status |
Public on Dec 03, 2019 |
| Title |
S_nbB_5 [STAT_nbB5] |
| Sample type |
SRA |
| |
|
| Source name |
Expressing non binding HMfB_17 hrs after induction
|
| Organism |
Escherichia coli |
| Characteristics |
genotype/variation: Expressing non binding HMfB
timepoint: 17 hours after induction
molecule subtype: Total RNA depleted for ribosomal RNA
|
| Treatment protocol |
Expression of HMf histones was triggered by Rhamnose induction to a final working concentration of 15mM. The cells were harvested in late exponential and stationary phase, which means 2 hours and 17 hours after induction, respectively.
|
| Growth protocol |
Escherichia coli cells were obtained from DSMZ (https://www.dsmz.de/) and grown at 37C in LB medium under constant agitation (180rpm).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Induced cells were harvested at the precise time point, centrifuge to remove the medium and the pellet snap frozen in liquid nitrogen. Protoplasts were obtained by incubating the pellet in Y1 buffer () for 1 hours at 37C. Total mRNA was extracted using RNeasy Mini Kit. Illumina Ribo-zero rRNA removal reagent was used to deplete the samples of rRNA before library preparation.
For the RNA samples paired-end reads were prepared using TruSeq Stranded RNA LT Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
S_nbB_5_S99_L006
|
| Data processing |
Basecalls performed using CASAVA 1.8.4
Paired-end 100bp reads were quality trimmed using trimgalore (standard parameters).
Trimmed reads were mapped to non mRNA species' index using Bowtie2 (--un-conc) and unmapped reads were extracted.
Surviving paired end reads were then mapped to the E. coli NC_000913.3 genome using Bowtie2 (--no-discordant --no-mixed).
Raw count matrices were computed using the summarisedOverlaps function (mode="Union",singleEnd=F,ignore.strand=F,fragments=T) from the GenomicAlignments R package and then the differential expression analysis was performed with the R package DESeq2.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: cvs file containing gene information, basMean, log2FoldChange and padj for each condition.
|
| |
|
| Submission date |
May 07, 2019 |
| Last update date |
Dec 03, 2019 |
| Contact name |
Tobias Warnecke |
| E-mail(s) |
molecular.systems.laboratory@gmail.com
|
| Organization name |
Imperial College
|
| Street address |
Du Cane Road
|
| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18133 |
| Series (2) |
| GSE127680 |
The role of archaeal histones in gene expression - a synthetic biology perspective |
| GSE130799 |
The role of archaeal histones in gene expression - a synthetic biology perspective [Escherichia coli RNA-seq] |
|
| Relations |
| BioSample |
SAMN11585702 |
| SRA |
SRX5800921 |
