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Status |
Public on Dec 01, 2023 |
Title |
Skin, susceptible, after infestation, bovine 17 |
Sample type |
SRA |
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Source name |
skin
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Organism |
Bos taurus |
Characteristics |
breed: Braford tissue: skin tick resistance_phenotype: susceptible time point: After infestation
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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.
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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)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 1500 |
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Description |
9128posIA
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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
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Submission date |
Feb 06, 2023 |
Last update date |
Dec 01, 2023 |
Contact name |
Robert Domingues |
E-mail(s) |
robert.domingues@embrapa.br
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Phone |
53 3240 4650
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Organization name |
Embrapa
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Department |
Animal health
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Street address |
Av. General Osório 1737/302
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City |
Bagé |
State/province |
Rio Grande do Sul |
ZIP/Postal code |
96400101 |
Country |
Brazil |
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Platform ID |
GPL22316 |
Series (1) |
GSE224634 |
Genetic factors underlying immune response to tick infestation of resistant and susceptible cattle unrevealed by omics data integration |
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Relations |
BioSample |
SAMN33141515 |
SRA |
SRX19292473 |
Supplementary data files not provided |
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Raw data are available in SRA |
Processed data are available on Series record |
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