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Status |
Public on Sep 02, 2024 |
Title |
adipose, vitamin E rep 3 |
Sample type |
SRA |
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Source name |
adipose
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Organism |
Sus scrofa |
Characteristics |
tissue: adipose genotype: Iberian pig treatment: VE
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Treatment protocol |
50-100 mg samples of each tissue were ground in liquid nitrogen with mortar and pestle.
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Growth protocol |
Subcutaneous adipose tissue was collected within 15 min postmortem, snap-frozen in liquid nitrogen, and then stored at -80° C until processing.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from 50-100mg samples of adipose tissue using the RiboPure TM of High Quality total RNA kit (Ambion, Austin, TX, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-100 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The quality of the RNA was evaluated using the RNA Integrity Number (RIN) value from the Agilent 2100 Bioanalyzer device (Agilent technologies, Santa Clara, CA, USA). Sequencing libraries were made using the mRNA-Seq sample preparation kit (Illumina Inc., Cat. # RS-100-0801) according to manufacturer’s protocol. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end mode with the read length 2x76bp on a on a NovaSeq 6000 (Illumina, Inc). Images from the instrument were processed using the manufacturer’s software to generate FASTQ sequence files.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Data processing |
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to assess the quality of raw sequencing data. TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to quality trim data with default settings and to remove the sequencing adaptors and poly A and T tails (stringency of 6 bp, -s 6) keeping only paired-end reads where both pairs were longer than 40 bp. Filtered reads were mapped against the pig reference genome (Sscrofa11.1) using HISAT2 applying default settings except that reads were first aligned to the ENSEMBL (11.1.90) transcriptome annotation (-G option), and the distance between both pairs was set to 100 bp (inner-mean distance) and the standard deviation to 150 bp. HTseq-counts was used to calculate transcript abundances. Differential expression was analysed with Deseq2 Assembly: Sscrofa 11.1 Supplementary files format and content: Processed data file includes read counts for all genes in all 24 samples
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Submission date |
Dec 08, 2023 |
Last update date |
Sep 02, 2024 |
Contact name |
Cristina Ovilo |
E-mail(s) |
ovilo@inia.csic.es
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Organization name |
INIA-CSIC
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Street address |
Ctra Coruña km 7.5
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City |
Madrid |
ZIP/Postal code |
28040 |
Country |
Spain |
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Platform ID |
GPL26351 |
Series (1) |
GSE249774 |
Maternal dietary antioxidants enrichment regulates weaned piglets’ adipose tissue functionality |
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Relations |
BioSample |
SAMN38735002 |
SRA |
SRX22835896 |
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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