|
| Status |
Public on Aug 31, 2018 |
| Title |
473 ILW backfat, mRNA |
| Sample type |
SRA |
| |
|
| Source name |
backfat
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Italian Large White
gender: female
tissue: backfat
backfat deposition: low
age: 247 days
weight: 150-160 kg
|
| Treatment protocol |
Backfat sample was collected in a commercial slaughterhouse. The sample was immediately frozen in liquid nitrogen and stored at -80C in a deep freezer until RNA isolation.
|
| Growth protocol |
All animals were housed in the same environment and fed the same diet.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Trizol (Invitrogen) according to the manufacturer's instruction. Results of the extraction were quantified using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies) and the quality of the extracted RNA was assayed using an Agilent 2100 BioAnalyzer (Agilent Technologies).
The mRNA library was prepared using the TruSeq Small RNA kit (Illumina) and version 3 of the reagents, following the manufacturer's suggested protocol.
The libraries were individually tagged and sequenced on an Illumina GAII as 100 bp long single-end reads using two samples per lane.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
pig_backfat_473
Sample_473U966
processed data file: raw_counts_variants.txt
processed data file: normalized_counts_variants.txt
|
| Data processing |
Reads with an overall sequence mean Phred quality lower than 30, reads with more than two nt (nucleotides) with quality lower than 20 and reads with uncalled bases were also discarded. Reads between 15 and 30 nt long were selected by means of the HTSEQ package.
The selected reads were mapped using BOWTIE v.0.12.7. We used the Sscrofa 10.2 genome as a reference.
Cleaned sequencing data were processed by the MIR&MORE software pipeline. The two branches of the pipeline are devoted to perform the quantification and the characterization of known miRNAs and the discovery of mature miRNAs in known precursor sequences.
MiRDeep2 v 0.0.5 was then run using default parameters. miRDeep2 predictions were filtered restricting to precursors with miRDeep2 score greater than 1.0, length greater than or equal to 50 nt and predicted probability of being a miRNA greater than 60%.
Read counts were normalized across all the samples according to the DESeq2 (v1.4.5) approach. Small RNAs represented by less than ten normalized reads considering all samples were excluded from further analysis. Short RNA differential expression was assessed by DESeq2, considering significant those variations with FDR < 0.05.
A custom target prediction was performed by the application of the MIRANDA )v 3.3a) method using the transcript sequences detected on the same samples.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: raw_counts_variants.txt: Semicolon-delimited text file formatted as a matrix table of raw reads.
Supplementary_files_format_and_content: normalized_counts_variants.txt: Semicolon-delimited text file formatted as a matrix table of normalized reads.
|
| |
|
| Submission date |
Jan 05, 2018 |
| Last update date |
Aug 31, 2018 |
| Contact name |
Roberta Davoli |
| E-mail(s) |
roberta.davoli@unibo.it
|
| Phone |
+390512096024
|
| Organization name |
Bologna University
|
| Department |
DISTAL
|
| Lab |
Livestock Genomics
|
| Street address |
Viale G. Fanin, 46
|
| City |
Bologna |
| State/province |
Bologna |
| ZIP/Postal code |
40127 |
| Country |
Italy |
| |
|
| Platform ID |
GPL10945 |
| Series (1) |
| GSE108829 |
Identification of differentially expressed small RNAs and prediction of target genes in Italian Large White pigs with divergent backfat deposition |
|
| Relations |
| BioSample |
SAMN08299298 |
| SRA |
SRX3537830 |
