 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 15, 2016 |
| Title |
487 ILW backfat, mRNA |
| Sample type |
SRA |
| |
|
| Source name |
backfat
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Italian Large White
gender: male
phenotype: castrated
tissue: backfat
age: 241 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 RNA sample preparation kit (Illumina) and version 3 of the reagents, following the manufacturer's suggested protocol (oligo-dT selection). The library was sequenced on an Illumina HiSeq 2000 as 100 bp long paired-end reads using half lane per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw read fragments with quality Phred score lower than 30 were trimmed using the DynamicTrim script of the SolexaQA v2.1. Reads shorter than 50nt were discarded along with their mate. Clean read were mapped to the Sscrofa10.2 genome using Tophat v2.0.8, which used Bowtie v2.1.0.0, with default parameters and transcriptome inference from annotation enabled Ensembl Sscrofa10.2 v70.
Gene annotation for the reference genome was retrieved from Ensembl (BioMart) using the biomaRt R package. Read alignments were processed by Cufflinks v2.1.1 to identify and discover expressed genes and transcripts, and to quantify their expression. Expression data were indicated as Fragments per Kilobase of transcript per Million mapped reads (FPKM). Differential expression was assessed for genes and transcripts resulting from the filtered Cufflinks predictions. Two different methods, Cuffdiff2 and DESeq2, were used for the genes. For transcript DE test only Cuffdiff2 was used as long as the DESeq2 model is not suitable for the analysis of transcript predictions.
Genome_build: Sscrofa10.2
|
| |
|
| Submission date |
Apr 17, 2015 |
| Last update date |
May 15, 2019 |
| 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 |
GPL11429 |
| Series (1) |
| GSE68007 |
Long RNAs expression profiling of 20 Italian Large White pig backfat |
|
| Relations |
| BioSample |
SAMN03490536 |
| SRA |
SRX998809 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
