|
| Status |
Public on May 28, 2014 |
| Title |
wt_noleu_mono |
| Sample type |
SRA |
| |
|
| Source name |
whole cell lysate_ribosome profiling
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
strain: leuB::kan
stress condition: leucine starvation
sample type: whole cell lysate
molecule subtype: Monosome protected mRNA
|
| Treatment protocol |
Either amino acid rich medium (control) or 30 minutes of starvation for leucine or serine
|
| Growth protocol |
30C, 200rpm shaking
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rapid filtration followed by flash freezing of intact cells, cell lysis by glass bead beating, Micrococcal nuclease digestion of polysomes, purification of monosomes/disomes by sucrose-gradient centrifugation. Total mRNA was purified from the cell lysate by phenol-chloroform method, rRNA-subtracted (MicrobeExpress, Ambion) and heat fragmented for use in sequencing library preparation.
A modified small RNA protocol (Subramaniam et al., in preparation) was used for both the construction of both ribosome-protected and total mRNA sequencing libraries.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
extracted at OD600 = 0.6, after 30 min of leucine starvation
|
| Data processing |
PolyA tails were trimmed by identifying a continuous run of 10 or more As
Reads aligning to genome were trimmed by 8nt on either side, weighted by the inverse length of the fragment and assigned to the genomic coordinate
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Each line in the processed file has three columns: Col 1: Genomic coordinate based on NC_000913.3.fna, Col 2: Strand, Col 3: Total read weight assigned to the coordinate, Only genomic coordinates with non-zero read weight are included in the text file.
|
| |
|
| Submission date |
May 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Arvind R Subramaniam |
| E-mail(s) |
rasi@fredhutch.org
|
| Phone |
6174968433
|
| Organization name |
Harvard University
|
| Department |
Molecular and Cellular Biology
|
| Street address |
52 Oxford St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL15010 |
| Series (1) |
| GSE51052 |
An Integrated Approach Reveals Regulatory Controls on Bacterial Translation Elongation |
|
| Relations |
| BioSample |
SAMN02801781 |
| SRA |
SRX554706 |
