|
Status |
Public on Jun 09, 2018 |
Title |
Planktonic 24h [S01_1P1_24] |
Sample type |
SRA |
|
|
Source name |
Cell culture
|
Organism |
Bacillus cereus ATCC 14579 |
Characteristics |
strain: ATCC14579 cell type: Planktonic 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 28ÂșC
|
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 |
S01_1P1_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 |
SAMN09383129 |
SRA |
SRX4184979 |