 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 20, 2023 |
| Title |
control_943 |
| Sample type |
SRA |
| |
|
| Source name |
White blood cell
|
| Organism |
Bos taurus |
| Characteristics |
breed: Holstein
Sex: Female
cell type: White blood cell
treatment: Control
time: Day 7 after calving
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Blood extraction from jugular vein later preserved in RNAlater (Thermo Fisher Scientific, USA) and stored at -80 °C until processing by RNA-sequencing analysis
RNA extraction with assay and hemoglobin depletion. RNA quality was verified with an Agilent bioanalyzer (Agilent, CA, USA).
After quality control procedures, the samples were sequenced in a NovaSeq 6000 sequencing platform (Illumina Inc, CA, USA) and the paired-end 150b (PE150) strategy
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw data were filtered to remove low-quality and adapter sequences
nf-core/RNAseq project pipeline was used to perform RNA-seq analysis
This workflow includes the following analyses: quality control of reads with FastQC, STAR software for alignment to reference genome and featureCounts software for counting reads. Reads not having in average 10 total reads in SG and CG were filtered to delete non-expressed genes and transcripts with low expression levels
To identify differentially expressed genes (DEG), the DESeq2 software in R was applied using the Benjamini and Hochberg method implemented in this package
Transcripts with an adjusted p value < 0.05 were considered to have DGE, as identified by the Ensembl database
Assembly: ARS-UCD1.2 version as the reference bovine genome
Supplementary files format and content: Count matrix. Content including Raw count matrix, filtered matrix average>10, Deseq2 analysis results
Supplementary files format and content: Calcaterra_et_al_biochemichal_determinations_and_productive_data.xlsx: Excel file contains measurements of different parameters in the samples (Osi, GSHpx and SOD activity, AC, Tbars) and milk production on day 30
Supplementary files format and content: metadata.docx
|
| |
|
| Submission date |
May 02, 2023 |
| Last update date |
Feb 20, 2024 |
| Contact name |
Guillermo Giovambattista |
| E-mail(s) |
guillermogiovambattista@gmail.com
|
| Phone |
02214211799
|
| Organization name |
CONICET-UNLP
|
| Department |
Facultad de Ciencias Veterinarias
|
| Lab |
IGEVET
|
| Street address |
Calle 60 y 118 S/N
|
| City |
La Plata |
| State/province |
Buenos Aires |
| ZIP/Postal code |
1900 |
| Country |
Argentina |
| |
|
| Platform ID |
GPL26012 |
| Series (1) |
| GSE231491 |
Effect of Parenteral Trace Element Supplementation on RNA-sequencing Profile of Peripheral Blood in Peripartum Dairy Cows |
|
| Relations |
| BioSample |
SAMN34535755 |
| SRA |
SRX20189804 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
