|
| Status |
Public on Dec 31, 2021 |
| Title |
IG116-Δcrp_1 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria grown in M9+ glucose + 40 mM MOPS
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
genotype/variation: IG116-{delta}crp
culture/growth condition: batch exponential phase
molecule type: Ribo-depleted mRNA
|
| Growth protocol |
Escherichia coli cells grown in a bioreactor under glucose-limited chemostat condition and batch condition with M9+glucose+ 40mM MOPS at 37 degree Celcius and 700 rpm and total RNA extracted after 3-5 residence times in steady state and at exponential phase, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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 |
IG116-crp_S1
processed data file: counts_new.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 reads mapping and alignment to reference genome (GenBank accession no. NC 000391.3)
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 K-12 MG1655, accession number : NC_000913.3
Supplementary_files_format_and_content: tab delimited .txt file containing raw reads count (counts_new.txt)
|
| |
|
| Submission date |
Apr 06, 2021 |
| Last update date |
Dec 31, 2021 |
| Contact name |
Ankita Pal |
| E-mail(s) |
ankita.pal@imbim.uu.se
|
| 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 |
SAMN18632235 |
| SRA |
SRX10519930 |
