|
| Status |
Public on Mar 31, 2015 |
| Title |
Glucose time course, 336 hour time point, biological replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
REL606_glucose-limited minimal medium_336 hr
|
| Organism |
Escherichia coli |
| Characteristics |
strain: REL606
time point: 336 hours
molecule subtype: rRNA-depleted total RNA
|
| Growth protocol |
Escherichia coli B strain REL606 was revived from a freezer stock via overnight growth in 10 ml Davis Minimal medium supplemented with limiting glucose at 0.5 g/l (DM500) in a 50 ml Erlenmeyer flask. This culture was diluted 100-fold into 50 ml fresh DM500 in a 250 ml Erlenmeyer flask and incubated for 24 hours. To initiate the experiment, these preconditioned cultures were diluted 100-fold into 50 ml fresh DM500 in multiple 250 ml Erlenmeyer flasks and grown for the specified times until harvesting cells for total RNA isolation. All growth steps were conducted with incubation at 37°C and orbital shaking at 120 r.p.m. over a one-inch diameter.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAsnap followed by RiboZero rRNA removal kit for gram-negative bacteria (Epicentre)
RNA was fragmented using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). Then, RNA was phosphorylated using T4 polynucleotide kinase and prepared using the NEBNext Small RNA Library Prep Set for Illumina (Multiplex Compatible). DNA fragments greater than 100 bp were excised from a 4% agarose gel after library preparation and recovered using the Zymoclean Gel DNA Recovery Kit (Zymo Research).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
AG3C-105
|
| Data processing |
Trimmed adaptor sequences from reads using Flexbar 2.31
Mapped R1 reads in single-end mode using Bowtie2 2.1.0 with the –k 1 option
The number of R1 reads mapping to each gene were counted using HTSeq 0.6.0
Exact details for the full computational pipeline are available at https://github.com/wilkelab/AG3C_starvation_tc_RNAseq.
Genome_build: NC_012967.1 plus small RNAs as annotated in Rfam 11.0 database
Supplementary_files_format_and_content: Read counts aligned to genes and noncoding Rfam features in CSV format
|
| |
|
| Submission date |
Mar 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeffrey E. Barrick |
| Organization name |
The University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Street address |
2500 Speedway, Stop A4800
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712-1639 |
| Country |
USA |
| |
|
| Platform ID |
GPL14548 |
| Series (1) |
| GSE67402 |
Controlled measurement and comparative analysis of cellular components in E. coli reveals broad regulatory changes under long-term starvation |
|
| Relations |
| BioSample |
SAMN03450873 |
| SRA |
SRX971957 |
