|
| Status |
Public on Nov 02, 2022 |
| Title |
delta-cyaA with 0.1mM cAMP rep1 |
| Sample type |
SRA |
| |
|
| Source name |
K-12 MG1655
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
strain: K-12 MG1655
genotype: delta-cyaA
growth phase: log phase
treatment: 0.1mM cAMP
|
| Treatment protocol |
Delta-cyaA E.coli cells were treated with 10 different concentrations of extracellular cAMP ranging from 0mM to 4mM. Cells were harvested when the population reached its maximum growth rate followed by mRNA isolation and sequencing.
Extracellular cAMP concentrations used: 0mM, 0.01mM, 0.05mM, 0.1mM, 0.3mM, 0.6mM, 0.8mM, 1.0mM, 2.0mM, 4.0mM
|
| Growth protocol |
Cells were grown in LB, with or without cAMP, at 37 degrees Celsius at 180rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the TRIzol-chloroform extraction methods, followed by removal of genomic DNA contamination. To enrich for mRNA 16S and 23S rRNA were depleted using Ambion Microbe Express Riboclean-up kits(AM1905).
Libraries for each sample were prepared using the NEB NextUltra directional RNA library prep kit followed by single end sequencing using Illumina HiSeq 2500 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
log phase bacteria grown in LB at 37 degree Celsius at 180rpm
|
| Data processing |
Illumina HiSeq-2500 for sequencing
BWA was used for indexing the reference genome and aligning the reads(q>20)
SAMtools(v1.2) and BEDtools(v2.25.0) were used to filter reads and determine the read counts per gene.
Normalisation and differential gene expression calling was done using EdgeR(3.28.1) and custom R scripts.
Assembly: Escherichia coli K12 MG1655 , Ref Seq: NC_000913.2
Supplementary files format and content: Tab-delimited text files containing read counts per gene(cyaA_readcounts.table).
Supplementary files format and content: Tab-delimited text files containing EdgeR(v3.28.1) normalised counts per million per sample(cyaA_logCPM_values.table).
|
| |
|
| Submission date |
May 09, 2022 |
| Last update date |
Nov 02, 2022 |
| Contact name |
Shweta Chakraborty |
| E-mail(s) |
[email protected], [email protected]
|
| Phone |
08023666506
|
| Organization name |
National Centre for Biological Sciences
|
| Lab |
Dr. Aswin Sai Narain Seshasayee
|
| Street address |
Rajiv Gandhi Nagar, Kodigehalli
|
| City |
Bangalore |
| State/province |
Karnataka |
| ZIP/Postal code |
560065 |
| Country |
India |
| |
|
| Platform ID |
GPL18956 |
| Series (1) |
| GSE202549 |
RNA-Seq of delta-cyaA E.coli mutant at 10 different cAMP concentration |
|
| Relations |
| BioSample |
SAMN28161117 |
| SRA |
SRX15211566 |
