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Sample GSM7028109

Query DataSets for GSM7028109

Status

Public on Dec 01, 2023

Title

Skin, susceptible, after infestation, bovine 1

Sample type

SRA

Source name

skin

Organism

Bos taurus

Characteristics

breed: Braford
tissue: skin
tick resistance_phenotype: susceptible
time point: After infestation

Treatment protocol

Thirty-nine Braford cattle were artificially infected with approximately 20,000 cattle tick larvae (Rhipicephalus microplus). Skin biopsy samples were collected before infestation and 24 hours after infestation.

Extracted molecule

total RNA

Extraction protocol

Skin biopsies were mechanically crushed with 7 mm metallic beads in the TissueLyser equipment (Qiagen), and total RNA harvested using the RNeasy Fibrous Tissue kit (Qiagen)
Sequencing libraries were prepared individually using TruSeq RNA Sample Preparation kit v2 guide (Illumina, San Diego, CA) with standard protocols, clustered using TruSeq PE Cluster Kit v3-cBot-HS kit (Illumina, San Diego, CA)
Sequencing libraries were sequenced in a paired-end mode (2 x 100 bp) on a HiSeq1500 equipment (Illumina, San Diego, CA)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 1500

Description

125posIA

Data processing

Sample RNA quality check was performed with the FastQC (v. 0.11.8)
Reads were aligned to the bovine reference genome using Hisat2 (v. 2.1.0), with the annotation from RefSeq assembly accession GCF_002263795.1
Sample counts were sorted using Samtools v 1.9 and grouped with the FeatureCounts (v. 1.6.4)
Using DESEQ2 (v. 4.0.3), gene counts were normalized and differential expression analyzes at the gene level were performed using the generalized linear model: Yijkl = TIMEj + TYPEk + TIME*TYPE(jk) + TYPE*ANIMAL(kl) + eijkl.
The 237preIA sample was removed from the final analysis due to its discrepancy with the other data, when the PCA and heatmap analysis was performed
Assembly: bovine reference genome (ARS-UCD1.2, GCA_002263795.2; 2018
Supplementary files format and content: featureCounts_total.txt - table with gene counts per sample
Supplementary files format and content: normalized_counts.txt - table with gene counts normalized according to the generalized linear model used

Submission date

Feb 06, 2023

Last update date

Dec 01, 2023

Contact name

Robert Domingues

E-mail(s)

robert.domingues@embrapa.br

Phone

53 3240 4650

Organization name

Embrapa