|
| Status |
Public on Jun 30, 2022 |
| Title |
Fig2bc_Customized |
| Sample type |
SRA |
| |
|
| Source name |
RNA-seq data in Fig. 2b, c, using our customized rRNA depletion method
|
| Organism |
Escherichia coli BW25113 |
| Characteristics |
strain: BW25113
|
| Growth protocol |
Single colony was picked up from a stock LB agar plate and was grown aerobically with shaking at 220 rpm in LB medium overnight (typically 12 hours) as the seed culture. A subculture was established by firstly washing the bacteria once using M63B1 medium (centrifuge by 7000 g, 3 minutes) and resuspension; and then cultivating the seed culture into fresh M63B1 medium (4% volume) and grown for 10 hours with shaking at 220 rpm to reach exponential stage (OD600 ~ 0.6).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial RNA was obtained utilizing the RNAClean XP beads (Beckman, A63987). Lysate was prepared using lysozyme and proteinase K
miniBac-seq, a customized bacterial RNA-seq library construction method, see description of our paper for details
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
E. coli K12 BW25113
|
| Data processing |
quality trimming step using cutadapt (v2.10) command with a quality threshold of 20
the pooled sample was demultiplexed according to the anchored barcode of the first seven nucleotides at the 5’-end from the first read
internal adaptor sequence embedding in some second reads with too short insert was also trimmed
a minimum length threshold of 20 bp for both the first and second reads was used to filter out those pair-end reads with too short insert
bowtie2 (v2.4.1) to align the second read to a reference genome (NC000913.3) (default setting)
Feature counting was carried out using R method summarizeOverlaps from GenomicAlignments package (v1.26.0) in a strand-specific manner, giving rise to a read count table for each gene.
Genome_build: NC000913.3
Supplementary_files_format_and_content: gene raw count data, comma-delimited matrix table
|
| |
|
| Submission date |
Sep 17, 2021 |
| Last update date |
Jun 30, 2022 |
| Contact name |
Tianmin Wang |
| E-mail(s) |
wangtm@shanghaitech.edu.cn
|
| Organization name |
ShanghaiTech University
|
| Department |
School of Life Science and Technology
|
| Lab |
Tianmin Wang Lab
|
| Street address |
Huaxia Middle Road, 393
|
| City |
Shanghai |
| ZIP/Postal code |
201210 |
| Country |
China |
| |
|
| Platform ID |
GPL27123 |
| Series (1) |
| GSE184365 |
Development of miniBac-seq to profile bacterial transcriptome from ultra-low input RNA amount |
|
| Relations |
| BioSample |
SAMN21482127 |
| SRA |
SRX12221649 |
