DOI: 10.20350/digitalcsic/14498
title: Dataset for the paper "Mart??n, Alba; Gir??ldez, F. Javier; Montero, O.; Andr??s, S. 2022. Dietary administration of L-carnitine during the fattening period of early feed restricted lambs modifies liver transcriptomic and plasma metabolomic profiles. Animal Feeed Science and Technology"

description: [Description of methods used for collection/generation of data] Liver samples stabilized in RNAlater were homogenized using RLT (Qiagen), Lysing Matrix D and a FastPrep-24 instrument (MP Biochemicals); RNA purification was performed with the RNeasy Mini kit and RNase-Free DNase Set kit (Qiagen). "Poly(A)+ mRNA fraction was isolated from total RNA and cDNA libraries were obtained following Illumina??s recommendations. Briefly, poly(A)+ RNA was isolated on poly-T oligo-attached magnetic beads and chemically fragmented prior to reverse transcription and cDNA generation. The cDNA fragments then go through an end repair process, the addition of a single ???A??? base to the 3??? end and then ligation of the adapters. Finally, the products are purified and enriched with PCR to create the indexed final double stranded cDNA library. The quality of the libraries was analyzed in Bioanalyzer 2100, High Sensitivity assay; the quantity of the libraries was determined by real-time PCR in LightCycler 480 (Roche). The pool of the libraries was sequenced by paired-end sequencing (100 ?? 2) in an Illumina HiSeq 2500 instrument."
description: [Methods for processing the data] Basecalls performed using bcl2fastq 1.8.4 BBDuk version 36.30 (BBMap tools) was applied to raw fastq files for quality trimming (Phred &gt;= 20), filtering short reads (min length = 30) and removing adapter sequences BBMap version 36.30 was used to map the trimmed reads onto the reference genome; parameters: "maxindel=200k ambig=random intronlen=20" Bioconductor packages GenomicFeatures (v 1.24.5), GenomicAlignments (v 1.8.4) and the Oar_rambouillet_v1.0 annotation were used to calculate per gene read counts. Bioconductor package mygene was used to obtain the Entrez ID Differential expression analysis was conducted with the bioconductor package DESeq2 (v 1.12.4). TPM values were calculated according to Wagner et al. (2012; PMID 22872506) using DESeq2-normalized read counts GCF_002742125.1 The processed data file contains the results of the DESeq2 differential expression analysis, the TPM values for each sample/biological replicate and the Entrez annotation.
description: [Purpose] The present study was designed to identify both differentially expressed (DE) genes in the liver tissues of fattening Merino lambs and differences in metabolites accumulated in plasma, thus trying to identify modified metabolic pathways as a consequence of dietary L-carnitine administration during the fattening period of early feed restricted lambs.
description: [Methods] Twenty-two male Merino lambs, all of them milk restricted during the suckling period, were assigned to 2 different groups (n=11 per dietary treatment). The first group (CARN, carnitine group) were fed a completed pelleted diet ad libitum formulated with 3 g of L-carnitine/kg diet, and the control group (CTRL) received the same diet with no additive included. All the lambs were slaughtered with 34 kg. For transcriptomic analysis, 4 liver samples representative from each group (8 samples in total) were selected for RNA sequencing methodology (RNA-seq).
description: [Results] 104 DE annotated genes were identified by RNA-seq, with 36 DE genes being down-regulated and 68 up-regulated in the liver of CARN relative to the CTRL group (P &lt; 0.05). In general, those genes and pathways related to ribosomes and translation, cholesterol, ATP-binding and ATPase activity, and ABC transporters were up-regulated in the CARN group, thus suggesting a an improved metabolism of the muscle and a reduced absorption and increased excretion of cholesterol in these lambs.
description: [Conclusions] According to the data obtained, the administration of 3 g of L-carnitine carnitine/ kg diet during the fattening period of early feed restricted lambs increases the expression of genes related to ribosomes and traslation and also those involved in the excretion of cholesterol into bile acids or a reduced cholesterol absorption in the intestine.
description: File List: DESeq2_Results_TPM_AbundanceValues.xlsx; SM004296_1_S1_L001_R2_001.fastq.gz; SM004296_8_S8_L003_R2_001.fastq.gz; SM004296_3_S3_L001_R2_001.fastq.gz; SM004296_4_S4_L001_R2_001.fastq.gz; SM004296_2_S2_L001_R2_001.fastq.gz; SM004296_6_S6_L003_R2_001.fastq.gz; SM004296_1_S1_L001_R1_001.fastq.gz; SM004296_8_S8_L003_R1_001.fastq.gz; SM004296_3_S3_L001_R1_001.fastq.gz; SM004296_4_S4_L001_R1_001.fastq.gz; SM004296_2_S2_L001_R1_001.fastq.gz; SM004296_6_S6_L003_R1_001.fastq.gz; SM004296_5_S5_L003_R2_001.fastq.gz; SM004296_5_S5_L003_R1_001.fastq.gz; SM004296_7_S7_L003_R2_001.fastq.gz; SM004296_7_S7_L003_R1_001.fastq.gz. Liver samples of lambs slaughtered with 34 kgs of live body weight.