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| Status |
Public on Jul 24, 2020 |
| Title |
Majorera Restricted 3 [C6] |
| Sample type |
SRA |
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| Source name |
Majorera experimental_mammary gland
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| Organism |
Capra hircus |
| Characteristics |
breed: Majorera
treatment: underfed; restricted
tissue: Mammary gland
replicate no.: Biological Replicate #3
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| Treatment protocol |
Samples were excised from the mammary gland, preserved in RNA later following manufacturer's instructions and kept at -80ºC until further analysis
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| Growth protocol |
Conditions for animal experimentation have been thoroughly described in Lerias et al. (2013). Body live weight and milk production parameters in the Majorera and Palmera goat breeds from the Canary Islands: influence of weight loss. Trop Anim Health Prod. 2013 Nov;45(8):1731-6. doi: 10.1007/s11250-013-0423-2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the tissue using the E.Z.N.A. Total RNA Kit II (Omega Bio-Tek Inc., Norcross, Georgia, USA). About 30 mg of tissue was finely grinded in liquid nitrogen and used with the kit following manufacturer’s instruction to extract total mRNA. A DNAse digestion step was carried out after extraction to remove contaminating genomic DNA using an Ambion® TURBO™ DNase (Life Technologies, Carlsbad, CA, U.S.A.) following manufacturer´s instructions. A quantitative and qualitative assessment of the isolated RNA was performed using a NanoDrop® 2000c Spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, U.S.A.). Purity was also estimated based on the absorbance ratios of the RNA samples at 260/280 nm and 260/230 nm. For pure RNA, ratios should be of about 2.0 and 2.0-2.2, respectively (T042‐Technical Bulletin, Thermo Scientific). RNA integrity was assessed by an electrophoresis in a 2.0% agarose gel. Good quality RNA should present well defined 28S and 18S bands. RNA quality was also analysed using a RNA Nano Kit Chips from the Agilent 2100 Bioanalyzer System (Agilent Technologies, Santa Clara, CA, U.S.A.). Using this approach, a good RNA sample should present well defined peaks corresponding to 28S and 18S bands and a RNA Integrity Number (RIN) above 7. The absence of DNA in RNA treated samples was verified by standard polymerase chain reaction (PCR).
RNA Sequencing was conducted by LC-Sciences (Houston, TX, USA) following the TruSeq® Stranded mRNA Sample Preparation Guide (Illumina)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Bowtie2 v2.2.3
RSEM v1.2.17
edgeR v3.2.4
DAVID (Database for Annotation, Visualization and Integrated Discovery) v6.7
Genome_build: CHIR_1.0
Supplementary_files_format_and_content: Raw number of reads and statistical analysis of each gene, with accession number, between Majorera (M), Palmera (P), Control and Experiemntal as indicated in the file names
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| Submission date |
Jun 01, 2020 |
| Last update date |
Aug 24, 2020 |
| Contact name |
Andre Martinho de Almeida |
| Organization name |
Instituto Superior de Agronomia / University of Lisbon
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| Department |
DCEB
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| Lab |
Animal Production
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| Street address |
Tapada da Ajuda
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| City |
Lisboa |
| ZIP/Postal code |
1349-017 |
| Country |
Portugal |
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| Platform ID |
GPL19149 |
| Series (1) |
| GSE151599 |
Understanding seasonal weight loss tolerance in dairy goats: a transcriptomics approach |
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| Relations |
| BioSample |
SAMN15078586 |
| SRA |
SRX8451885 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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