|
| Status |
Public on Jan 13, 2016 |
| Title |
NRD1243 + WO4 input 2 |
| Sample type |
SRA |
| |
|
| Source name |
Total RNA for biological replicate 2 in the presence of tungstate (2 mM)
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
strain: NRD1243
antibody: none
|
| Treatment protocol |
Cells were lysed by with 0.1 mm glass beads, cell debris was removed by centrifugation, and immunoprecipitations were performed using anti-FLAG M2 resin (Sigma-Aldrich).
|
| Growth protocol |
Strains were grown in Luria broth at 37oC to an OD600 of ~1.0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from total cell extracts or immunoprecipitated samples by the hot phenol lysis method. RNA was subsequently precipitated with isopropanol at -80oC overnight and suspended in DEPC treated water.
The library was generated by removing DNA by DNase treatment, depleting rRNA with the Illumina Ribo-Zero rRNA removal kit for bacteria, and then performing sequencing with the Illumina TruSeq Stranded Total RNA Library Kit.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Total RNA
WO4-input-2_1
WO4-input-2_2
|
| Data processing |
Sequencing reads were aligned to the E. coli K-12 MG1655 genome by Axeq Technoloigies, Inc using Bowtie with the following comman line settings: > bowtie -S -I 30 –X 530 -p 24 --fr -m 1 --max sampleA_maxRead --un sampleA_unmappedRead -- chunkmbs 500 reference -1 sampleA_1.fastq -2 sampleA_2.fastq > sampleA.sam
RPKM calculations were performed by Axeq using a proprietary in-house script
Supplementary_files_format_and_content: Processed data files provided as an excel document.
|
| |
|
| Submission date |
Jun 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicholas De Lay |
| E-mail(s) |
[email protected]
|
| Phone |
713-500-6293
|
| Organization name |
University of Texas Health Science Center
|
| Department |
Microbiology and Molecular Genetics
|
| Street address |
6431 Fannin St
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL15010 |
| Series (1) |
| GSE69856 |
Polynucleotide phosphorylase can interact with small noncoding RNAs in both stabilizing and degradative modes |
|
| Relations |
| BioSample |
SAMN03774801 |
| SRA |
SRX1058230 |
