|
| Status |
Public on Mar 08, 2018 |
| Title |
Bacillus amyloliquefaciens; B4140_T0B |
| Sample type |
SRA |
| |
|
| Source name |
Cell culture
|
| Organism |
Bacillus amyloliquefaciens |
| Characteristics |
strain: B4140
genotype: Wild type
growth stage: T0
|
| Treatment protocol |
Samples were followed in time during the sporulation process
|
| Growth protocol |
Bacterial cells were grown in M17 broth (containing 0,5% (w/v) glucose ) at 30°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
Standard library preparation kit for IonProton
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
B4140_T0B
Processed_data_rpkm.txt
|
| Data processing |
mapping of reads was done using: bowtie2 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Bacillus subtilis subsp. subtilis str. 168 chromosome, complete genome NC_000964.3
Genome_build: Bacillus amyloliquefaciens sB4140 sGCF_001587325.1sLQYO00000000sPRJNA270600
Genome_build: Bacillus subtilissB4146 sGCF_000830645.1sJXHR00000000s
Genome_build: Bacillus amyloliquefaciens sB425 sGCF_001587435.1sLQYP00000000sPRJNA270600
Genome_build: Bacillus subtilis HR3sB4417sGCF_001619535.1sASM161953v1s
Genome_build: Bacillus subtilissB4067 sGCF_000828495.1sJSXS00000000s
Genome_build: Bacillus subtilissB4072 sGCF_000830595.1sJXHO00000000s
Genome_build: Bacillus subtilissB4143 sGCF_000832195.1 sJXLQ00000000s
Supplementary_files_format_and_content: Tab delimited text file
|
| |
|
| Submission date |
Jan 02, 2018 |
| Last update date |
Mar 08, 2018 |
| Contact name |
Anne de Jong |
| E-mail(s) |
anne.de.jong@rug.nl
|
| Phone |
+31 50 363 2047
|
| Organization name |
university of Groningen
|
| Department |
Molecular Genetics
|
| Street address |
Nijenborgh 7
|
| City |
Groningen |
| ZIP/Postal code |
9747 AG |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL24453 |
| Series (1) |
| GSE108659 |
Analysis of differential gene expression during Bacillus subtilis spore outgrowth |
|
| Relations |
| BioSample |
SAMN08284964 |
| SRA |
SRX3526619 |
