Table 1 RNA-seq data used for the blood transcriptome assembly
From: A high-quality annotated transcriptome of swine peripheral blood
Study accession | Sample description | Read length | Layout | Total raw read count | Breed | Source | Run accession | Reference |
|---|---|---|---|---|---|---|---|---|
PRJEB5250 | 16 pigs (7Â weeks old) were infected with Salmonella enterica serovar Typhimurium. Whole blood was sampled before infection (day 0) and day 2 post infection. Globin was depleted from the total RNA. | 51 | SE | 1,611,707,563 | Yorkshire crossbred | ENA | ERR413315 - ERR413346 | [35] |
PRJNA189967 | Whole blood from 3 individual healthy pigs | 51 | SE | 106,157,368 | unknown | ENA | SRR747924-SRR747926 | [36] |
Swine Genome Sequencing Consortium | Whole blood from one healthy pig | 83 | SE | 48,973,230 | Duroc | ENSEMBL(ftp://ftp.ensembl.org/pub/release-83/bamcov/sus_scrofa/genebuild/whole_blood_merged_sorted.bam) | Unknown | http://www.ensembl.org/info/genome/genebuild/2012_04_sus_scrofa_genebuild.pdf |
PRJEB12300 | Whole blood was sampled from 31 post-weaning (5 ~ 6 weeks old) pigs from lines divergently selected for residual feed intake. Globin was depleted from the total RNA. | 100 | PE | 2 × 632,557,790 | Yorkshire | ENA | ERR1199492-ERR1199522 | [34] |
PRJEB20136 | 28 pigs (~ 63 kg of body weight) from lines divergently selected for residual feed intake were muscularly injected with E. coli LPS or saline at time 0, and 48, 96 h and 144 h post the first injection. Whole blood was sampled immediately before first injection and 2, 6, 24 and 168 h post first injection. Globin was depleted from the total RNA. | 49 | PE | 2 × 1,509,173,972 | Yorkshire | ENA | ERR1898446-ERR1898477 | H. Liu, K. Feye et al., unpublished |