|
| Status |
Public on Jul 14, 2016 |
| Title |
fusA_topA_2 |
| Sample type |
SRA |
| |
|
| Source name |
fusA_topA_exponentially growing cells
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
mutation(s): FusAA608E - TopAS180L
growth phase: Exponentially growing cells
molecule subtype: rRNA depleted RNA
|
| Treatment protocol |
No treatment; only the growth of strains in Luria-Bertani broth.
|
| Growth protocol |
For RNA extraction, cells were grown in Luria-Bertani broth and harvested at the point of maximal growth rate after addition of stop solution to stabilise cellular RNA and stop transcription. Two biological replicates were harvested for each strain.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using hot phenol-chloroform. DNase treated RNA was depleted of ribosomal RNA using the Ambion Microbe Express Kit (AM1905). RNA was checked for quality using Bioanalyzer (Agilent).
DNase treated RNA was depleted of ribosomal RNA using the Ambion Microbe Express Kit (AM1905). RNA was checked for quality using Bioanalyzer (Agilent). Checked RNA was used for library preparation and sequencing. Briefly, 100 ng of qubit quantified RNA was used for library preparation using the NEXTflex Rapid Directional RNA-Seq kit (5138-08 Bioo Scientific). The library was quantified using qubit and its quality was checked using Agilent Bioanalyzer before proceeding for sequencing on the Illumina NextSeq 500 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Replicate 2
|
| Data processing |
Adapters from FASTX filtered reads were trimmed using Cutadapt.
Trimmed reads were aligned to the E. coli reference genome (NC_000913.3) using BWA, -q 30 flag was used for quality trimming.
Number of reads mapping to each gene were obtained from samfiles using custom Python scripts (only reads with mapping quality > 20 were considered).
Genome_build: NC_000913.3
Supplementary_files_format_and_content: tab delimited text files with gene names and the number of reads mapping to each gene.
|
| |
|
| Submission date |
Jun 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Aalap Mogre |
| E-mail(s) |
aalap.ncbs@gmail.com
|
| Organization name |
National Centre for Biological Sciences
|
| Street address |
NCBS, GKVK, Bellary Road
|
| City |
Bangalore |
| State/province |
Karnataka |
| ZIP/Postal code |
560065 |
| Country |
India |
| |
|
| Platform ID |
GPL21117 |
| Series (1) |
| GSE82343 |
Modulation of global transcriptional regulatory networks as a strategy for increasing kanamycin resistance of EF-G mutants |
|
| Relations |
| BioSample |
SAMN05213447 |
| SRA |
SRX1828504 |
