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Sample GSM4988180 Query DataSets for GSM4988180
Status Public on Jan 12, 2022
Title TYESA-Blood_b
Sample type RNA
 
Source name Bacteria
Organism Flavobacterium psychrophilum
Characteristics strain: OSU THCO2-90
blood: TYSEA blood
Treatment protocol Colonies grown in the presence of blood. Starting cultures were diluted 500 times in TYES broth and incubated with vigorous shaking (200 rpm and 5:1 flask-to-volume ratio) at 18°C until OD600nm of 2. Twenty µL of culture were then striked on TYES agar plates with an overlay of 10% defibrinated horse blood-agar [TYESA-Blood] or on plates made with 10% defibrinated horse blood solidified with 1.5% agar [Blood]. Plates were inubated at 18°C until colonies appeared and cells were then harvested, 4 and 10 days after inoculation for [TYESA-Blood] and [Blood], respectively.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted as described in Rochat T. et al (2019) (PMID:30635380).
Label Cy3
Label protocol 10 µg of DNase-treated RNA were converted into Cy3-labeled cDNA using Fairplay III Microarray labelling kit (Agilent technologies) with random priming and 50 µg/mL actinomycin D as described for strand-specific hybridization (Rasmussen et al., 2009).
 
Hybridization protocol Samples (1.2 µg) were hybridized on SurePrint G3 Custom GE 8x60K microarrays (Agilent technologies, design n° 071137) at 65°C using Agilent's GE Hybridization kit. Washes were conducted as recommended by the manufacturer using Agilent's Gene Expression Wash Pack.
Scan protocol Slides were scanned after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides. Spot intensities and other quality control features were extracted with Agilent's Feature Extraction software version 10.7.3.1.
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 071137_D_F_20141113) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The “gProcessedSignal” produced by Agilent Feature Extraction software served as probe-level raw expression values. An aggregated raw expression value was computed for each feature as the median of probe-level values. CDS expression values were quantile-normalized between all experiments (64 hybridizations data) using the R package ‘limma’ and this transformation was propagated to all other types of regions.
 
Submission date Dec 24, 2020
Last update date Jan 12, 2022
Contact name Cyprien Guérin
E-mail(s) [email protected]
Phone +33-1-3465-2896
Organization name INRAE
Lab MaIAGE
Street address INRAE - Domaine de Vilvert
City Jouy-en-Josas
ZIP/Postal code F-78350
Country France
 
Platform ID GPL29531
Series (1)
GSE163842 Transcriptome architecture and regulation at environmental transitions of the fish pathogen Flavobacterium psychrophilum

Data table header descriptions
ID_REF
VALUE qnorm_all_probes_values_log2

Data table
ID_REF VALUE
CDS_-_1004237_1005373_1019-1061 3.9093
CDS_-_1004237_1005373_190-234 9.1213
CDS_-_1004237_1005373_22-72 7.6931
CDS_-_1004237_1005373_243-286 8.0363
CDS_-_1004237_1005373_287-333 6.0818
CDS_-_1004237_1005373_393-448 6.8315
CDS_-_1004237_1005373_526-581 7.4822
CDS_-_1004237_1005373_668-724 3.8807
CDS_-_1004237_1005373_710-756 6.4908
CDS_-_1004237_1005373_754-805 7.4396
CDS_-_1004237_1005373_813-872 7.1027
CDS_-_1004237_1005373_867-909 6.2608
CDS_-_1004237_1005373_924-975 7.0489
CDS_-_1004237_1005373_978-1037 3.8921
CDS_-_1004237_1005373_99-158 5.0091
CDS_-_1006906_1007832_119-176 8.3577
CDS_-_1006906_1007832_175-228 8.2909
CDS_-_1006906_1007832_236-277 8.2646
CDS_-_1006906_1007832_301-359 7.9339
CDS_-_1006906_1007832_345-391 9.5606

Total number of rows: 61157

Table truncated, full table size 2357 Kbytes.




Supplementary file Size Download File type/resource
GSM4988180_257113710008_201702231211_S01_GE1_107_Sep09_1_2.txt.gz 10.6 Mb (ftp)(http) TXT
Processed data included within Sample table
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