|
| Status |
Public on Jul 10, 2012 |
| Title |
CDMenriched vs MRSenriched |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
grown in CDM
|
| Organism |
Lactiplantibacillus plantarum |
| Characteristics |
strain: WCFS1
rna subtype: enriched mRNA
|
| Treatment protocol |
Harvested cultures were immediately pelleted at 4570xg and 4˚C
|
| Growth protocol |
Cultures were grown in CDM and MRS at 37˚C without agitation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were lysed by beat-beating and total RNA was isolated by subsequent phenol-chloroform extraction, followed by RNA purification and mRNA enrichment
|
| Label |
Cy5
|
| Label protocol |
Total RNA and enriched mRNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label
|
| |
|
| Channel 2 |
| Source name |
grown in MRS
|
| Organism |
Lactiplantibacillus plantarum |
| Characteristics |
strain: WCFS1
rna subtype: enriched mRNA
|
| Treatment protocol |
Harvested cultures were immediately pelleted at 4570xg and 4˚C
|
| Growth protocol |
Cultures were grown in CDM and MRS at 37˚C without agitation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were lysed by beat-beating and total RNA was isolated by subsequent phenol-chloroform extraction, followed by RNA purification and mRNA enrichment
|
| Label |
Cy3
|
| Label protocol |
Total RNA and enriched mRNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label
|
| |
|
| |
| Hybridization protocol |
Hybridization buffer (Agilent In Situ Hybridization Kit Plus) was added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers at 65 degrees Celcius for 17 h. After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)
|
| Data processing |
scanned slides were Lowess normalised using Prep (van Hijum, Applied Bioinformatics 2003 2(4):241-244). Interslide scaling was performed using Postprep (van Hijum, Applied Bioinformatics 2003 2(4):241-244).
|
| |
|
| Submission date |
Feb 13, 2012 |
| Last update date |
Jul 10, 2012 |
| Contact name |
Michiel Wels |
| E-mail(s) |
michiel.wels@nizo.com
|
| Organization name |
NIZO food research
|
| Street address |
Kernhemseweg 2
|
| City |
Ede |
| ZIP/Postal code |
6718 ZB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL13984 |
| Series (1) |
| GSE35754 |
Comparative analysis of bacterial transcriptome using DNA microarray and next generation sequencing technologies |
|
