|
| Status |
Public on Jan 20, 2021 |
| Title |
GfpOn_1 |
| Sample type |
SRA |
| |
|
| Source name |
GfpOn
|
| Organism |
Bacillus subtilis |
| Characteristics |
growth phase: Exponential growth
strain: bSS339
|
| Treatment protocol |
Cells was directly sorted by BD FACSAriaTM III flow cytometer into GFP-on/off subsets.
|
| Growth protocol |
Cells were cultured in 10 ml CH medium in 125 ml flasks to an OD660 of 0.5 and quickly cooled by adding 10 ml ice-cold PBS with 4 M NaCl, which preservers the mRNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
GFP-on/off cells were respectively broke using glass beads (0.1 mm) and RNA was extracted using 25:24:1 phenol/chloroform/isoamyl alcohol (P/C/I) mixture, and Dnase I was used to remove DNA from the RNA samples.
1 μl 1:1000 diluted ERCC RNA Spike-In mix 1 (Invitrogen) was added to 50 ng total RNA and the mixed RNA was subjected to sequencing library construction using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Raw data were analyzed on the web-based platform Galaxy
Trimmomatic was applied to remove adaptors and filter bad reads
Bowtie2 was used to aligned trimed reads to reference genome fasta (NC_000964.3 + ERCC92)
featureCounts was used to count reads for the gene features base on annotation GFF3 file (NC_000964.3 + ERCC92) and using "locus_tag" as the GFF gene identifier
Genome_build: NC_000964.3 and ERCC92
Supplementary_files_format_and_content: tabular files include raw counts for each gene/RNA features
|
| |
|
| Submission date |
Jan 06, 2021 |
| Last update date |
Jan 24, 2021 |
| Contact name |
Biwen Wang |
| E-mail(s) |
B.wang@uva.nl
|
| Organization name |
University of Amsterdam
|
| Department |
Swammerdam Institute for Life Science
|
| Lab |
Bacterial Cell Biology
|
| Street address |
Work, Science Park 904,1098 XH,Amsterdam,The Netherlands
|
| City |
Amsterdam |
| ZIP/Postal code |
1098 XH |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL28092 |
| Series (1) |
| GSE164348 |
Different resource allocation in a Bacillus subtilis population displaying bimodal motility |
|
| Relations |
| BioSample |
SAMN17228350 |
| SRA |
SRX9794139 |
