|
| Status |
Public on Dec 31, 2021 |
| Title |
EvoCrp3_2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria grown in M9+ glucose + 40 mM MOPS
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
genotype: Adaptively evolved mutant of <delta>crp
media: Glucose minimal media
growth phase: Exponential
|
| Growth protocol |
Escherichia coli cells grown in a bioreactor under aerobic conditions with M9+glucose+ 40mM MOPS at 37 degree Celsius and 700 rpm till exponential phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted at exponential phase.
Total RNA extraction was done using the TRIzol-chloroform method. DNase treatment was done to remove any DNA contamination after which enrichment for mRNA was done using the MicrobExpress Kit.
Single-end, strand specific libraries for RNA sequencing were prepared using NEBNext Ultra II Directional RNA library kit. The sequencing was carried out on HiSeq 2500 Rapid Run Mode using 1x50 bp single-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Evocrp3_S2
processed data file: Raw_counts.txt
|
| Data processing |
Illumina Hi-seq 2500 used for sequencing.
CUTADAPT used for removing adapter sequence and low-quality reads (q >= 20).
BWA used for read mapping and alignment to reference genome (GenBank accession no. NC_000913.3).
Samtools used for compressing alignment files and sorting.
FeatureCounts used for assigning counts at gene level.
EdgeR used for differential gene expression analysis.
Genome_build: Reference genome used: E.coli K12 MG1655, accession number : NC_000913.3
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited .txt file containing raw reads count.
|
| |
|
| Submission date |
Jun 10, 2020 |
| Last update date |
Dec 31, 2021 |
| Contact name |
Ankita Pal |
| E-mail(s) |
[email protected]
|
| Phone |
08879536816
|
| Organization name |
Uppsala University
|
| Department |
Medical Biochemistry and Microbiology
|
| Lab |
Dan I. Andersson
|
| Street address |
Husargatan 3
|
| City |
Uppsala |
| ZIP/Postal code |
75321 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL18956 |
| Series (1) |
| GSE152214 |
Global pleiotropic effects in adaptively evolved Escherichia coli lacking CRP reveal molecular mechanisms that define growth physiology |
|
| Relations |
| BioSample |
SAMN15201477 |
| SRA |
SRX8521108 |
