 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 08, 2022 |
| Title |
Pineal Gland, active, animal 4 [28_PG_A] |
| Sample type |
SRA |
| |
|
| Source name |
Pineal Gland
|
| Organism |
Ovis aries |
| Characteristics |
tissue: Pineal Gland
age: Adult ram
breed: Rasa Aragonesa
sexual behaviour_state: Active
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples from HT, PT and PG tissues were isolated and rapidly frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from tissue samples using RNeasy Lipid Tissue mini kit (QIAGEN, Madrid, Spain) according to the manufacturer’s instructions
Sequencing was carried out at the CNAG (Centro Nacional de Análisis Genómico, Spain; https://www.cnag.crg.eu/). The RNA-Seq library was prepared with KAPA Stranded mRNA-Seq Illumina Platforms Kit (Roche) following the manufacturer´s recommendations using Illumina platform compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies). The final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on NovaSeq 6000 (Illumina) with a read length of 2x151bp following the manufacturer’s protocol for dual indexing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
All transcripts were analysed with bioinformatics tools implemented within OmicsBox v2.0.36 from BioBam
Checking quality control of the sequence with FastQC
Sequence reads were trimmed for adaptor sequence/low-quality sequence using the Sliding Window Trimming option with a window size of 40 and a required quality of 20. The filtering configuration of reads was set to 20 and 35 for the average quality and the minimum length respectively
Clean reads were mapped against the ovine reference genome using STAR v2.7.8a
Mapped reads were assembled by HTSeq. Gene quantification levels were analysed using the Union model.
Identification of differentially expressed genes with EdgeR
Assembly: Oar_rambouillet 1.0 (GCA_002742125.1)
Supplementary files format and content: Raw_gene_counts_matrix.txt: tab-delimited text file with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
May 26, 2022 |
| Last update date |
Nov 08, 2022 |
| Contact name |
Kenza Lakhssassi |
| E-mail(s) |
kenza.lakhssassi@inra.ma
|
| Organization name |
CITA
|
| Street address |
Av Montañana, 930,
|
| City |
Zaragoza |
| State/province |
Zaragoza |
| ZIP/Postal code |
50059 |
| Country |
Spain |
| |
|
| Platform ID |
GPL27721 |
| Series (1) |
| GSE204861 |
Exploring differentially expressed genes in hypothalamic (HT), pars tuberalis (PT) and pineal gland (PG) transcriptomes in different sexual behaviour phenotypes in rams using RNA-seq |
|
| Relations |
| BioSample |
SAMN28679591 |
| SRA |
SRX15470056 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
