|
| Status |
Public on Aug 23, 2022 |
| Title |
PL-7 dehydrated camel supraoptic nucleus |
| Sample type |
SRA |
| |
|
| Source name |
Supraoptic nucleus
|
| Organism |
Camelus dromedarius |
| Characteristics |
tissue: Supraoptic nucleus
gender: Male
treatment: free access to food and no access to water
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Unilateral supraoptic nucleus samples were isolated from hypothalamus of male dromedary camels under control (water ad libitum) and dehydrated (water deprivation for 20 days) conditions (n=5 per group). Total RNA was extracted using a Direct-zol™ RNA MiniPrep kit (Zymo research, R2052) following the manufacturer’s instructions. Average RNA Integrity Number (RIN) of samples processed for sequecing (n=10) was 6.27. Ribosomal depleted sequencing libraries were produced using TruSeq® Stranded Total RNA library preparation kit (illumina). Libraries were sequenced on Illumina NextSeq500 platform using NextSeq 500 High Output v2.5 (2 x 75 bp run) Kit (Illumina; 20367064).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The paired end sequencing files (.fastq) were merged and trimmed for adaptor sequences using BBDuk tool.
All samples passed the FastQC check and were aligned to the reference dromedary camel genome Camdro2 (GCA_000803125.2) using STAR aligner.
The mapped reads aligned to each gene were counted using FeatureCounts.
Differential expression analysis were performed using DESeq2.
Assembly: Camdro2 (GCA_000803125.2)
Supplementary files format and content: Matrix table with raw read counts for each gene and every sample
Supplementary files format and content: Matrix table with DESeq2-normalized (median of ratios method) read counts for each gene and every sample
|
| |
|
| Submission date |
Mar 14, 2022 |
| Last update date |
Aug 23, 2022 |
| Contact name |
Panjiao Lin |
| E-mail(s) |
panjiao.lin@outlook.com
|
| Organization name |
University of Bristol
|
| Department |
Bristol Medical School
|
| Lab |
David Murphy's neuroendocrinology lab
|
| Street address |
Dorothy Hodgkin Building, Whitson Street
|
| City |
Bristol |
| ZIP/Postal code |
BS1 3NY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL30063 |
| Series (1) |
| GSE198577 |
Transcriptomic plasticity of the hypothalamic osmoregulatory control centre of the Arabian dromedary camel |
|
| Relations |
| BioSample |
SAMN26656407 |
| SRA |
SRX14461809 |
