|
| Status |
Public on Jun 30, 2021 |
| Title |
Lung, Vehicle 0.15 NaCl, animal 1 |
| Sample type |
RNA |
| |
|
| Source name |
mRNA, lung after 28 days oral treatment
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain/gender/tissue: Fisher 344
gender: male
tissue: lung
treatment: Control
dose: 0
dose unit: mg/kg bw/day
way of administration: oral gavage
days of administration: 28
|
| Treatment protocol |
Rats were orally exposed to 6 structurally different pyrrolizidine alkaloids daily, after 28 d lung and kidney samples were gained, shock frozen and stored at 80°C prior isoation of RNA
|
| Growth protocol |
Rats were orally exposed to 6 structurally different pyrrolizidine alkaloids for 28 days (3.3 mg/kg body weight)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small pieces of the deep-frozen organs were homogenized with liquid nitrogen and transferred to RLT buffer (Qiagen, Hilden, Germany) containing 1 % β-mercaptoethanol. RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) in combination with QiaShredder (Qiagen, Hilden, Germany). Quality and quantity of the RNA were checked with an Agilent 2100 Bioanalyzer with an RNA Nano Lab chip and a Tecan M200 Pro spectrophotometer with a NanoQuant Plate at 260 nm and 280 nm.
|
| Label |
biotin
|
| Label protocol |
The samples were labeled with a GeneChip WT Plus labeling kit at Eurofins (Comp. No. 7230-GT0028).
|
| |
|
| Hybridization protocol |
hybridization to Gene Chip plate arrays
|
| Scan protocol |
staning and imaging on Gene Titan Multi-Channel Instrument
|
| Description |
gene expression data of lung of vehicle treated rats
|
| Data processing |
Data processing and statistical data evaluation was performed in the R environment. The raw data were normalized and summarized using the RMA (robust multi-array average) algorithm from the R package oligo version 1.54.1. The genes were associated with vendor-provided annotation information (Release 36, Thermo Fisher Scientific, https://sec-assets.thermofisher.com/TFSAssets/LSG/SupportFiles/Clariom_S_Rat.r1.na36.rn6.a1.transcript.csv.zip) and control genes were removed after background correction. Moreover, irrelevant genes with low or unchanged expression were removed (median < 4 or CV < 0.02, respectively) so that 12,699 genes remained. Differential gene expression (DGE) analysis was performed by the R package limma version 3.46.0: (Ritchie et al. 2015) linear models were fit and moderated t-statistics computed by the eBayes function. Afterwards, the Benjamini and Hochberg correction was applied to exclude false positive results and thus genes with an adjusted p-value < 0.1 were considered significantly differentially expressed. Besides, one-way analysis of variance (ANOVA) was performed to extract the top100 genes that were most affected in their expression by PA treatment.
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| |
|
| Submission date |
Feb 04, 2021 |
| Last update date |
Jun 30, 2021 |
| Contact name |
Heike Sprenger |
| E-mail(s) |
[email protected]
|
| Organization name |
German Federal Institute for Risk Assessment
|
| Department |
Food Safety
|
| Street address |
Max-Dohrn-Strasse 8-10
|
| City |
Berlin |
| ZIP/Postal code |
10589 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23040 |
| Series (1) |
| GSE166195 |
Gene expression changes in rat lung induced by six pyrrolizidine alkaloids |
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