|
| Status |
Public on Jul 31, 2022 |
| Title |
8.LE-16We-m1-S8-all-R1-001 |
| Sample type |
SRA |
| |
|
| Source name |
LE dairy cows 16 weeks after calving (animals were fed with LE since one month before calving)
|
| Organism |
Bos taurus |
| Characteristics |
breed: Prim Holstein
cow status: primiparous
diet: LE (low energy diet) since one month before calving
time point: 16 weeks after calving
tissue: subcutaneous adipose tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from the fat tissue of three cows per group was extracted using a RNeasy Midi kit (Qiagen®, Courtaboeuf, France) and purified using a DNAfree kit (Invitrogen by Life Technologies), according to the manufacturer’s recommendations.
Directional RNA-Seq libraries were constructed using the TruSeq Stranded Total RNA library prep kit (Illumina), following the manufacturer’s instructions, using 750 ng of total RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Image analysis, base calling and demultiplexing were performed using RTA 2.4.6 and bcl2fastq 2.15.0
Adapter sequences were trimmed with Cutadapt-1.3, only reads longer than 10 bp were kept for analysis
Sequences were aligned to the cow genome (bosTau8.fa) with TopHat2 using default parameters
Mapped reads were assigned to features with htseq-count (intersection-nonempty mode)
Differential expression analysis was performed with DESeq2,
Genome_build: bosTau8.fa
Supplementary_files_format_and_content: tabulated .txt file containing DESeq2 results
|
| |
|
| Submission date |
Jul 31, 2019 |
| Last update date |
Jul 31, 2022 |
| Contact name |
joelle dupont |
| E-mail(s) |
joelle.dupont@inra.fr
|
| Phone |
33247427789
|
| Organization name |
INRA
|
| Street address |
Centre Val de Loire
|
| City |
Nouzilly |
| ZIP/Postal code |
37380 |
| Country |
France |
| |
|
| Platform ID |
GPL23055 |
| Series (1) |
| GSE135162 |
RNAseq bovine subcutaneous adipose tissue in periparturient stage |
|
| Relations |
| BioSample |
SAMN12404573 |
| SRA |
SRX6619969 |
