ERC000011
ENA-CHECKLIST
2022-08-04T12:20:41Z
ENA-FIRST-PUBLIC
2022-08-04T12:20:41Z
ENA-LAST-UPDATE
SAMEA14375709
External Id
Institute of Animal Science, Physiology Unit, University of Bonn, 53115 Bonn, Germany Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany Department of Veterinary Medicine, Universita degli Studi di Milano, 26900 Lodi, Italy
INSDC center name
2022-08-04T12:20:41Z
INSDC first public
2022-08-04T12:20:41Z
INSDC last update
public
INSDC status
ERS11970084
SRA accession
E-MTAB-11725:Plasma, Bos taurus (cow), day 28, EFA, 97220
Submitter Id
Holstein
breed
ArrayExpress
broker name
cattle
common name
Protocols: Blood sampling and plasma separation Blood samples were collected immediately after morning milking and before feeding, using the Vacuette system (Greiner Bio-One International GmbH, Kremsmünster, Austria) containing 1.8 g potassium-EDTA (K3EDTA)/L of blood. The plasma fraction was extracted after centrifugation at 1,500 × g (4 °C) for 20 min and stored at −80 °C. A detailed description of the animal, study design, feeding Management, diet composition, fatty acid composition of diets, and performance can be found in (Vogel et al., 2020, https://doi.org/10.3168/jds.2019-18065, and Gnott et al., 2020, https://doi.org/10.3168/jds.2020-18735). Cows were daily abomasally supplemented from d 63 antepartum (AP) until d 63 postpartum (PP) with coconut oil, providing no ALA or CLA (CTRL, n = 9; Bio-Kokosöl #665, Kräuterhaus Sanct Bernhard KG, Bad Ditzenbach, Germany); a combination of linseed oil (Derby Leinöl #4026921003087, Derby Spezialfutter GmbH, Münster, Germany) and safflower oil (Gefro Distelöl, Gefro Reformversand Frommlet KG, Memmingen, Germany) to provide an n-6/n-3 FA ratio of 1:3 in the supplement mixture (EFA, n = 9); Lutalin (CLA treatment, n = 10; cis-9,trans-11 and trans-10,cis-12 CLA, 10 g/d each; BASF SE, Ludwigshafen, Germany); or a combination of EFA and CLA (EFA+CLA, n = 10). The amounts of daily infused supplements are given in Table 1. Treatments were infused using 60-mL catheter-tip syringes twice a day (2 equal portions) at 0700 and 1630 h. All supplements were liquified by heating to 38°C to allow infusion. The fatty acid compositions of the added lipids are shown in Supplemental Table S1 (https://doi.org/10.3168/jds.2019-18065). During the dry period, each dose was halved. Sampling started at wk 10 AP and was terminated at wk 9 PP. RNA extraction and quality measurement Total RNA was extracted using the QIAGEN miRNeasy serum/plasma kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s protocol (https://www.qiagen.com/de/resources/resourcedetail?id=46286f7e-0bee-4820-9af1-654b578c98c8&lang=en). The RNA yield and purity were assessed using an Agilent Small RNA kit on a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Library preparation and next-generation sequencing The QIAseq miRNA library kit (QIAGEN, Hilden, Germany) was used for library preparation following the manufacturer’s instructions for serum/plasma samples (https://www.qiagen.com/jp/resources/download.aspx?id=d3efdc53-9f98-4632-9bfe-cb2efab7db79&lang=en). Final libraries were checked Caliper (PerkinElmer, Waltham, MA). Libraries were then prepared for next-generation sequencing (NGS) and sequenced on single-end 100 bp mode on the NovaSeq 6000 (Illumina, San Diego, CA) on the respective platform of IGA Technology Services, Udine, Italy (https://igatechnology.com/). Raw-sequencing data was checked for quality (format conversion to FASTQ, demultiplexing, Adapter Trimming, and UMI Remova) using the Illumina Bcl2fastq2 Conversion Software (version 2.20).
description
adult
developmental stage
EFA
diet
normal
disease
wild type genotype
genotype
97220
individual
Bos taurus
organism
Bos taurus
organism
blood plasma
organism part
Bos taurus
scientific_name
female
sex
Plasma, Bos taurus (cow), day 28, EFA, 97220
title