|
| Status |
Public on Apr 24, 2015 |
| Title |
Carrot_21day_7 |
| Sample type |
RNA |
| |
|
| Source name |
Carrot juice, 24 hours at 30°C + 21 days at 4°C
|
| Organism |
Lactiplantibacillus plantarum |
| Characteristics |
strain: C2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was done by using QIAGEN RNeasy mini kit (Cat#74106) as per the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using WT primer with a T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality was assessed for yields and specific activity using the Nanodrop ND-1000.
|
| |
|
| Hybridization protocol |
2000ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Custom Lactobacillus Gene Expression 8x15k Array (AMADID: 067475). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)
|
| Scan protocol |
Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 5 micron resolution.
|
| Description |
Gene expression data from Carrot juice at growth condition 24 hours at 30°C + 21 days at 4°C
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters. 'gMedianSignal' column was taken as foreground intensity and 'gBGMedianSignal' column was taken as background intensity. Data was background corrected and Quantile normalized using the functions present in 'limma' package of R. If a gene has more than one probe, average intensity value of all the probes was taken to represent the gene
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| |
|
| Submission date |
Apr 23, 2015 |
| Last update date |
Apr 24, 2015 |
| Contact name |
pasquale filannino |
| E-mail(s) |
pasquale.filannino1@uniba.it
|
| Organization name |
Università degli Studi di Bari “Aldo Moro”
|
| Department |
Dipartimento di Scienze del Suolo
|
| Lab |
della Pianta e degli Alimenti - Di.S.S.P.A
|
| Street address |
Via Amendola, 165/A
|
| City |
BARI |
| ZIP/Postal code |
70126 |
| Country |
Italy |
| |
|
| Platform ID |
GPL20099 |
| Series (1) |
| GSE68188 |
From transcriptomics to phenomics to reveal adaptation response of Lactobacillus plantarum C2 in plant substrates |
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