|
| Status |
Public on Nov 01, 2023 |
| Title |
WT+A1-2 |
| Sample type |
RNA |
| |
|
| Source name |
PCC7120, WT+Phage A1,replicate 2
|
| Organism |
Nostoc sp. PCC 7120 = FACHB-418 |
| Characteristics |
condition: WT + Phage A1
|
| Treatment protocol |
WT culture was split into two cultures of the same size. Cyanophage A1 was added to one of the cultures with a multitude of infection (MOI) of 2. The cultures incubated 1 hour under the same conditions.
|
| Growth protocol |
Liquid culture in BG11 medium under standard illumination at 30 centigrades.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using a hot phenol-based protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer.
|
| Label |
Cy3
|
| Label protocol |
DNase-treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol. Further details of the labeling and hybridization protocol were published in: Voß,B. and Hess,W.R. (2014) The identification of bacterial non-coding RNAs through complementary approaches. In Handbook of RNA Biochemistry. WILEY-VCH, Weinheim, Germany, Vol. 2, pp. 787–800.
|
| |
|
| Hybridization protocol |
The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays
|
| Scan protocol |
Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 for Cy3 labelled arrays
|
| Description |
Gene expression in wild type after 1h Phage A1 infection
|
| Data processing |
Raw data were processed with the R package Limma. Median signal intensities were normexp background substracted (offset=50) and quantile normalized.
|
| |
|
| Submission date |
Sep 07, 2021 |
| Last update date |
Nov 01, 2023 |
| Contact name |
Marcus Ziemann |
| E-mail(s) |
marcus.ziemann@biologie.uni-freiburg.de
|
| Organization name |
Albert-Ludwigs-Universität Freiburg
|
| Street address |
Schänzlestraße 1
|
| City |
Freiburg |
| State/province |
Baden württemberg |
| ZIP/Postal code |
79104 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25601 |
| Series (1) |
| GSE183630 |
Anabaena PCC7120 infection with Cyanophage A1 |
|
