|
| Status |
Public on Jun 18, 2021 |
| Title |
RNAseq of Camelus dromedarius: adult male kidney / medulla dehydration 3 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney medulla
|
| Organism |
Camelus dromedarius |
| Characteristics |
tissue: Kidney medulla
age: 4-5 years
Sex: Male
treatment: 20 days dehydration
individual: D3
|
| Treatment protocol |
The camels were supplied with alfalfa hay as feed and ranch-housed in the United Arab Emirates. Veterinary supervision was provided throughout the experimental period and no signs of distress or illness were identified. After a short adaptive period, the camels were divided into 3 groups, control (n=5), dehydrated (n=8) and rehydrated (n=6). The control group had free access to food and water during the entire experimental period. The dehydrated group was water-deprived but had ad libitum access to food for 20 days. Meanwhile the rehydrated group was subjected to the same protocol as the dehydrated animals followed by ad libitum water supply for 3 additional days. After the experimental period, the camels were sacrificed in the local central abattoir for human consumption in April 2016. Kidney samples were harvested within 1 hour after killing the animals, immediately frozen in liquid nitrogen and kept at -80°C for later physiological, histological, morphological and molecular analysis. Samples were shipped frozen on dry ice to the University of Bristol under the auspices of a DEFRA Import Licence (TARP/2016/063). This study was approved by the Animal Ethics Committee of the United Arab Emirates University (approval ID: AE/15/38) and the University of Bristol Animal Welfare and Ethical Review Board.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from fresh frozen kidney medulla and cortex of 5 control, 5 dehydrated and 5 rehydrated camels (for a total of 30 samples). These 15 animals were randomly selected out of the 19 animals included in the experimental set up while the remaining 4 were used for preliminary analyses only. Frozen tissue was added to a pre-cooled mortar containing a small volume of liquid nitrogen. Tissue was then grounded to a fine powder using a pestle and the nitrogen was allowed to evaporate. The powdered tissue was placed into pre-chilled tubes on dry ice and stored at -80°C. For RNA extraction, 1ml of Qiazol (79306, Qiagen) was added to 100mg of powdered tissue, then immediately vortexed for 2 minutes, then incubated on ice for 10 minutes. Lysed samples were spun at 12000xg for 10 minutes at 4°C and the supernatant was transferred to a new tube. 1/5 volume Chloroform (22711.244, VWR) was added to each sample and vortexed for 15 seconds. Samples were then spun at 12000xg for 15 minutes at 4°C. 350ml of the upper phase was removed and mixed with an equal volume of absolute ethanol. RNA was extracted using ZymoTM Direct-Zol RNA miniprep (Zymo Research) as per the manufacturer’s instructions. Total RNA concentration and 260/280 ratios were measured using a Nanodrop 2000c (Thermo Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ArabianC_kidney_MD3
23.MD3
RNAseq polyA selection
|
| Data processing |
Merge fastq files (Linux command line).
Sort fastq files (Linux command line).
Trim adapter regions (Linux command line).
Align reads against reference genome (Linux command line; Rsubread package).
Run QC of the alignments (Linux command line).
Run feature counts (Linux command line).
Run QC of feature counts (Linux command line).
Analyse differential gene expression (DESeq2 1.31.18 in Rstudio 1.3.1073).
Genome_build: CamDro2 (Camelus_dromedarius.CamDro2.dna.toplevel.fa.gz)
Supplementary_files_format_and_content: FeatureCountsCamelKidneyRsubread.txt: Tab-delimited text file includes Feature counts for all transcripts identified in the analysis.
Supplementary_files_format_and_content: CamKidRNA_DESeq2NormalisedExpressionDataWithGeneInfo.csv: Comma-separated text file includes raw data of differential gene expression for all identified genes.
|
| |
|
| Submission date |
Apr 30, 2021 |
| Last update date |
Jun 18, 2021 |
| Contact name |
Fernando Alvira Iraizoz |
| E-mail(s) |
f.alvirairaizoz@gmail.com
|
| Phone |
07498580362
|
| Organization name |
University of Bristol
|
| Department |
Bristol Medical School
|
| Lab |
Molecular Neuroendocrinology Group
|
| Street address |
Dorothy Hodgkin Building, University of Bristol, Whitson Street
|
| City |
Bristol |
| ZIP/Postal code |
BS1 3NY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL30063 |
| Series (1) |
| GSE173683 |
Multiomic analysis of the Arabian camel (Camelus dromedarius) kidney reveals a role for cholesterol in water conservation |
|
| Relations |
| BioSample |
SAMN18747124 |
| SRA |
SRX10725089 |
