|
| Status |
Public on May 12, 2022 |
| Title |
Medio-Basal Hypohtalamus - January/Follicular phase - 2nd replicate |
| Sample type |
SRA |
| |
|
| Source name |
Brain - Hypothalamus
|
| Organism |
Capra hircus |
| Characteristics |
breed: Alpine
age: adult goat
time point: January/Follicular phase
tissue: Brain - Hypothalamus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriReagent
Libraries were constructed using the Truseq stranded mRNA sample prep kit (Illumina, San Diego, CA,USA) according to the manufacturer instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Foll_2
|
| Data processing |
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina). Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2.20). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
A splice junction mapper, TopHat 2.1.1 (using Bowtie 2.3.5.1), was used to align the RNA-Seq reads to the Capra hircus genome (NCBI, Capra hircus ARS1) with a set of gene model annotations (genes.gtf downloaded from NCBI on May 25 2020 ; release 103).
Final read alignments having more than 6 mismatches were discarded. Samtools (v1.9) was used to sort the alignment files. Then, the counting was performed with Featurecounts 2.0.0. As the data is from a strand-specific assay, the read has to be mapped to the opposite strand of the gene (-s 2 option).
Assembly: Capra hircus ARS1
Supplementary files format and content: tab-delimited text files include raw gene counts for every gene and every sample
|
| |
|
| Submission date |
May 09, 2022 |
| Last update date |
May 12, 2022 |
| Contact name |
Hugues Dardente |
| E-mail(s) |
hugues.dardente@inrae.fr
|
| Organization name |
INRAE
|
| Department |
INRAE - Centre Val de Loire
|
| Lab |
Physiologie de la Reproduction et des Comportements
|
| Street address |
INRA
|
| City |
Nouzilly |
| ZIP/Postal code |
37380 |
| Country |
France |
| |
|
| Platform ID |
GPL19149 |
| Series (1) |
| GSE202507 |
Transcriptome-wide impact of season and progesterone in the medio-basal hypothalamus of the goat |
|
| Relations |
| BioSample |
SAMN28159697 |
| SRA |
SRX15208738 |
