|
| Status |
Public on Sep 10, 2019 |
| Title |
ΔrnhAΔdnaArrnD-rrnC 1 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria grown in LB Media
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
growth phase: Single colony grown in LB media and sequenced at exponential phase
genotype: {delta}rnhA{delta}dnaArrnD-rrnC
|
| Treatment protocol |
Escherichia coli str K-12 substr MG1655 cells were grown in Luria broth media till exponential phase of growth at 37 degrees Celsius at 200 rpm were used to isolate total RNA .
|
| Growth protocol |
Escherichia coli str K-12 substr MG1655 cells were grown in Luria broth media till exponential phase of growth at 37 degrees Celsius at 200 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from bacteria using Trizol method and subjected to purification and removal of genomic DNA contamination. Ribosomal RNA was depleted to obtain enriched mRNA for library preparation.
Fragmentation and random priming of samples was done for each mRNA sample. First and second strand cDNA synthesis was carried out using NEBNextUltra Directional RNA library prep kit for Illumina according to manufacturer’s protocol. Equimolar quantities of all libraries were pooled and sequenced in a high throughput run on the Illumina HiSeq 2500 sequencer using 1X50 bp single-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina HiSeq-2500 for sequencing
BWA (0.7.12-r1039) was used for indexing the reference genome and aligning the reads (q >= 20)
SAMTOOLS (0.1.19-96b5f2294a) was used to filter out multiply mapped reads
BEDTOOLS(2.25.0) was used to calculate the read counts per gene
Normalisation and differential gene expression analysis was done using EdgeR
Genome_build: Reference genome used : E.coli K12 MG1655, accession number : NC_000913.3
Supplementary_files_format_and_content: tab delimited .txt file containing raw reads count (raw_data_counts.txt)
|
| |
|
| Submission date |
Aug 12, 2019 |
| Last update date |
Sep 10, 2019 |
| Contact name |
Aswin Sai narain Seshasayee |
| E-mail(s) |
[email protected]
|
| Phone |
08023666059
|
| Organization name |
National Centre for Biological Sciences
|
| Department |
Bioinformatics
|
| Lab |
Bugbears
|
| Street address |
GKVK campus Bellary road
|
| City |
Bengaluru |
| State/province |
Karnataka |
| ZIP/Postal code |
560065 |
| Country |
India |
| |
|
| Platform ID |
GPL18956 |
| Series (1) |
| GSE135706 |
Laboratory Evolution Experiments Help Identify a Predominant Site of ΔrnhA-dnaA Constitutive Stable DNA Replication Initiation |
|
| Relations |
| BioSample |
SAMN12560184 |
| SRA |
SRX6699520 |
