|
| Status |
Public on Jan 09, 2017 |
| Title |
RNAseq_delAr1_glycerol_NH4Cl_O2_1 |
| Sample type |
SRA |
| |
|
| Source name |
E. coli K12 MG1655
|
| Organism |
Escherichia coli |
| Characteristics |
strain: Crp_delAr1
|
| Treatment protocol |
Gene expression analysis was performed using a strand-specific, paired-end RNA-seq protocol using the dUTP method (Levin et al., 2010). Total RNA was isolated and purified using the Qiagen Rneasy Kit with on-column DNase treatment.
|
| Growth protocol |
Cells were grown in shake flasks to mid-exponential phase under either aerobic or anaerobic conditions depending on the sample. M9 minimal media supplement with either glucose, fructose, or glycerol as the sole carbon source was used depending on the sample.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was depleted of ribosomal RNAs using Epicentre’s RiboZero rRNA removal kit.
rRNA depleted RNA was then primed using random hexamers and reverse transcribed using SuperScript III (Life Technologies).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
The MiSeq Reporter MiSeq Reporter 2.4.60.8 was used for basecalling and demultiplexing
bowtie2 v2.2.3 was used for alignment
Reads were mapped to the NC_000913.2 reference genome using the default settings in bowtie2 (Langmead and Salzberg, 2012). Datasets were quantified using cuffdiff in the cufflinks package to generate FPKM (Framents Per Kilobase per Million reads mapped) values for all genes (Trapnell et al., 2013).
Genome_build: NC_000913.2
Supplementary_files_format_and_content: Processed data is presented in a cuff diff analysis format
|
| |
|
| Submission date |
Jan 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Haythem Latif |
| Organization name |
University of California San Diego
|
| Lab |
Latif
|
| Street address |
417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093-0412 |
| Country |
USA |
| |
|
| Platform ID |
GPL16085 |
| Series (2) |
| GSE64848 |
Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq] |
| GSE64849 |
Integrated analysis of molecular and systems level function of the Crp regulon |
|
| Relations |
| BioSample |
SAMN03280591 |
| SRA |
SRX837321 |
