|
| Status |
Public on Jul 01, 2015 |
| Title |
L06 |
| Sample type |
SRA |
| |
|
| Source name |
Mammary gland, control
|
| Organism |
Capra hircus |
| Characteristics |
breed: Alpine
tissue: mammary gland
physiology: peak of lactation (48 ± 2 days post-partum)
treatment: control
|
| Treatment protocol |
The goats were fed an orchard grass hay-based diet with a 35:65 forage to concentrate ratio during a 2-week pre-experimental period. For 48 h before slaughtering, 4 goats consumed this diet ad libitum (Control) and the 6 others were food deprived (FD). Goats were milked at 0800 and 1600. Goats were housed in individual stalls, had free access to water, and were fed twice daily (except during the deprivation) just after milking.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were isolated from ~150 mg of goats mammary gland using TRIzol® Reagent (Life Technologies) and further purified with the SV Total RNA Isolation system (Promega) to eliminate contaminating genomic DNA.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Total RNA was extracted from ~150 mg of mammary tissue collected and frozen at the slaughterhouse.
Control: Fed ad-libitum during a 2-week pre-experimental period and during the 48 hours experimental period.
Small RNA-seq using Solexa's Illumina technic.
|
| Data processing |
Images analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2.
Sequenced reads were trimmed for poly-A stretches, then filtered for their size (17-28 nt). The cleaned sequences were clustered into unique reads and then mapped to the goat genome (CHIR1.0) using the mapper.pl module from miRDeep2 with default parameters.
Novel miRNA and precursors were identified using miRDeep2 core module miRDeep2.pl using default parameters. Potential miRNA dataset was created by adding known goat miRNA (miRBase v21) to miRNA corresponding/associated to predicted precursors with a miRDeep2 score≥ 0. The same operation was done to create the dataset of potential precursors.
Quantification was achieved using quantifier.pl module from miRDeep2 with default parameters using the unique reads, potential miRNA and precursors datasets.
Results were then filtered with a custom Perl script parse_miRDeep2_outputs.pl (https://mulcyber.toulouse.inra.fr/projects/bioinfoutils/) to eliminate redundancy between known and putative novel miRNA.
Genome_build: CHIR1.0 (http://goat.kiz.ac.cn/GGD/index.htm)
Supplementary_files_format_and_content: Quantification files (*_quantification.txt) are the resulting files generated by the quantifier.pl module of miRDeep2. These tab-delimited text files include for each miRNA its associated precursor, raw abundance measurements, normalized abundance, and sequence.
Supplementary_files_format_and_content: Prediction file (chi_novel_miRNAs_miRDeep2_prediction.txt) is the resulting file generated by the miRDeep2 prediction process (miRDeep2.pl). This tab-delimited text file includes predicted miRNA and precursors, associated miRDeep2 scores, and their genome location.
|
| |
|
| Submission date |
Sep 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Sylvain Marthey |
| E-mail(s) |
abridge@inra.fr
|
| Organization name |
INRA
|
| Department |
Animal Genetics
|
| Lab |
Animal Genetics and Integrative Biology
|
| Street address |
Domaine de Vilvert Bat 320
|
| City |
Jouy-en-Josas |
| ZIP/Postal code |
78352 |
| Country |
France |
| |
|
| Platform ID |
GPL19149 |
| Series (1) |
| GSE61025 |
A food deprivation affects the miRNome in the lactating goat mammary gland |
|
| Relations |
| BioSample |
SAMN03015774 |
| SRA |
SRX695003 |
