|
| Status |
Public on Dec 31, 2019 |
| Title |
Bacteria_rG4seq_M_Li_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
liquid culture in LB (Luria-Bertani) medium
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
genotype: Wild-type
rts reaction buffer: Li
|
| Growth protocol |
grow until mid-log phase in LB
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To examine the effect of rG4 sites on the transcriptome of E. coli, 2 ml of mid-log-phase (OD600= 0.6) bacterial LB (Luria-Bertani) cultures (Escherichia coli str. K-12 substr. MG1655 strains) were collected by centrifugation (12,000 rpm, 4℃). An RNeasy minikit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the Ribo-ZeroTM rRNA Removal Kit (Bacteria) (Epicentre), mRNA was used to generate the cDNA library according to the TruSeq RNA sample prep kit protocol (Illumina), which was then sequenced using the HiSeq 2000 system (Illumina). Bacterial rG4-seq reads were mapped to the E. coli str. K-12 substr. MG1655 genome (NC_000913.3) by using TopHat (version 2.0.0), with two mismatches allowed. Only the uniquely mapped reads were kept for the subsequent analyses. GO enrich-ment analyses were conducted on all differentially transcribed genes using DAVID before data sets were imported into Cytoscape with an Enrichment Map plugin. The each sample inrG4-seq assay was repeated twice.
TruSeq RNA sample prep kit protocol (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Ecoli_K_hits.bed
single-ended rG4-seq data of Escherichia coli str. K-12 substr. MG1655 in Li+ rich buffer
instrument model: MiSeq V3 (Illumina).
|
| Data processing |
Bacterial rG4-seq reads were mapped to the P. auruginosa genome by using TopHat (version 2.0.0), with two mismatches allowed
Only the uniquely mapped reads were kept for the subsequent analyses.
Calculate the coverage of each base
Calculate the reverse transcriptase stalling sites
Genome_build: Pseudomonas aeruginosa PAO1 (NC_002516.2) and Escherichia coli str. K-12 substr. MG1655 (NC_000913.3)
Supplementary_files_format_and_content: bed file containing the significant RNA reverse transcriptase stalling sites
Column names: Refseq, W_Start, W_End, hgnc, RTS_Score, strand, P_Value, genomic_location, hgnc_genomic_location.
RTS_Score was used to measure the RNA reverse transcriptase stalling degree.
|
| |
|
| Submission date |
Apr 03, 2019 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Xin DENG |
| E-mail(s) |
[email protected]
|
| Phone |
852-34425693
|
| Organization name |
City University of Hong Kong
|
| Department |
Department of Biomedical Sciences
|
| Lab |
Dr Xin DENG's Lab
|
| Street address |
1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong
|
| City |
Hong Kong |
| ZIP/Postal code |
000000 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL17439 |
| Series (1) |
| GSE129281 |
rG4-seq for P. aeruginosa and E. coli |
|
| Relations |
| BioSample |
SAMN11332885 |
| SRA |
SRX5630348 |
