|
| Status |
Public on May 19, 2019 |
| Title |
Total SEnd-seq WT stationary phase rep3_part2 |
| Sample type |
SRA |
| |
|
| Source name |
E.coli cell
|
| Organism |
Escherichia coli |
| Characteristics |
growth stage: Stationary phase
treatment: 38 degrees C
genotype: wild type
|
| Treatment protocol |
Wild type E.coli RNA samples were collected once the growth stage reached to log phase or stationary phase. rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E.coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition.
|
| Growth protocol |
Escherichia coli K-12 MG1655 were cultured in LB media (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, pH 7.4) under aerobic conditions at 37 °C. The temperature-sensitive RNase E mutant E.coli strain [rne-3071(ts)] was cultured in LB media at 28 °C for normal culture and shift to 44 °C to deactive RNase E activity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
E. coli cells were quenched by adding 0.5 volume of cold Stop Buffer (5% phenol in ethanol) immediately to the culture medium before harvest and stay on the ice for 15 minutes. Cell pellets were collected by centrifugation (6,000 rpm, 5 minutes at 4 °C), thoroughly resuspended in 100 μl of lysozyme solution [2 mg/ml in TE buffer (10 mM Tris-HCl and 1 mM EDTA)], and incubated for 2 minutes. The cells were immediately lysed by adding 1 ml of TRIzol Reagent (Invitrogen, 15596) and the RNA was extracted following manufacture’s instruction.
A new RNA-seq method SEnd-seq was used to prepare the SEnd-seq library, and standard RNA-seq was prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101) following the manufacturer’s instructions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Processed data on GSM3307955
|
| Data processing |
Library strategy: SEnd-seq
Basecalls performed using CASAVA version 1.7
Paired-end reads were merged to single end fasta reads by usin FlASh software v1.2.11
Labled transcript 5' end and 3' end were extracted from merged single end reads and processed to paired-end reads again by custom program scripts
Extracted paired-end reads were mapped to E.coli genome (NC_00913.3) by using Bowtie2 v2.3.4.1, and single end full length sequence was generated by the paried-end data by custome transcripts and Bowtie2.
rRNA transcripts were removed and TSSs, TTSs and overlap TTSs were extracted from the remaining data.
Genome_build: Escherichia coli str. K-12 substr. MG1655, NC_000913.3
Supplementary_files_format_and_content: wig files
|
| |
|
| Submission date |
Jul 26, 2018 |
| Last update date |
May 20, 2019 |
| Contact name |
Xiangwu Ju |
| E-mail(s) |
xju@rockefeller.edu
|
| Phone |
212-327-8842
|
| Organization name |
The Rockefeller University
|
| Lab |
Liu Lab
|
| Street address |
1230 York Avenue
|
| City |
Newyork |
| State/province |
N.Y. |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL21222 |
| Series (1) |
| GSE117737 |
Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria |
|
| Relations |
| BioSample |
SAMN09724769 |
| SRA |
SRX4473921 |
