|
| Status |
Public on Jun 10, 2014 |
| Title |
rne-3071 ts |
| Sample type |
SRA |
| |
|
| Source name |
E. coli cell cultures
|
| Organism |
Escherichia coli |
| Characteristics |
strain: N3431
analysis: in vivo
genotype: rne-3071 (ts)
incubation time: n/a
|
| Treatment protocol |
Cultures for samples 1 and 2 were incubated at 44°C for 45 min after growth.
|
| Growth protocol |
All cultures grown up to 0.6 OD600 with shaking at 200 rpm. Samples 1,2,5 and 6 were grown at 30°C whereas samples 3 and 4 were grown at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated as desribed in Kime et al., 2008
Libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls were performed using CASAVA.1.8
Sequence reads were trimmed for adaptor reads and mapped to E. coli K12 MG1655 genome using CLC Genomics Workbench 6.0.1
Genome_build: U00096.2
Supplementary_files_format_and_content: Processed files are in tab delimited format. Separate files are provided for the forward and reverse strands. The start and end coordinates should be the same. Each line in the data set represents the position of the first nucleotide at the 5' end of a sequence that could be mapped to the E. coli genome.
|
| |
|
| Submission date |
Jun 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Kenneth McDowall |
| E-mail(s) |
K.J.McDowall@leeds.ac.uk
|
| Organization name |
University of Leeds
|
| Department |
Faculty of biological sciences
|
| Lab |
McDowall
|
| Street address |
Clarendon way
|
| City |
Leeds |
| ZIP/Postal code |
LS2 9JT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL14548 |
| Series (1) |
| GSE58285 |
Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli |
|
| Relations |
| BioSample |
SAMN02847879 |
| SRA |
SRX582025 |
