|
| Status |
Public on Jun 09, 2018 |
| Title |
Biofilm 24h [S03_1B1_24] |
| Sample type |
SRA |
| |
|
| Source name |
Cell culture
|
| Organism |
Bacillus cereus ATCC 14579 |
| Characteristics |
strain: ATCC14579
cell type: biofilm cells
time point: 24h
|
| Treatment protocol |
Planktonic cells were collected at 24h and biofilm cells at 24, 48 and 72 h. Planktonic cells were colected without disturbing submerged biofilm, taking only the 25% upper part of the medium of each well of a 24-well plate. From the same cultures, the medium was completely retired and the ring-shape biofilm was collected with a cotton swab and suspended in TY medium. Samples were inmediately centrifuged for 10 secs. at max. speed, the supernantant was discarded and tubes were inmediately freezed in liquid nitrogen.
|
| Growth protocol |
Cells were grown as standing cultures in TY medium in 24-well plates, 1 ml/well, at 28ºC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
cDNA library was prepared by employing a ScriptSeqtm Complete Kit for Bacteria
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
S03_1B1_24
|
| Data processing |
mapping of reads was done using: bowtie2 --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 cereus ATCC14579 | version NC_004722.1 GI:30018278 | 09-APR-2015
Supplementary_files_format_and_content: Tab delimited text file
|
| |
|
| Submission date |
Jun 08, 2018 |
| Last update date |
Jun 10, 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 |
GPL25160 |
| Series (1) |
| GSE115528 |
Time resolved transcriptome of isolated biofilm cells compared with planktonic cells |
|
| Relations |
| BioSample |
SAMN09383166 |
| SRA |
SRX4184981 |
