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Sample GSM2699490 Query DataSets for GSM2699490
Status Public on Aug 01, 2018
Title Day 1 Neinke 2014 foal
Sample type SRA
Source name peripheral blood mononuclear cells
Organism Equus caballus
Characteristics age: day 1
Sex: male
breed: Warmblood
Extracted molecule total RNA
Extraction protocol Peripheral blood mononuclear cells (PBMC) were isolated from blood samples and stored at -80C. RNA was isolated with the RNeasy kit including on-column DNase I digestion, as directed (Qiagen, Valencia CA).
RNA libraries were prepared as directed by the Illumina TruSeq Stranded mRNA Library Prep Kit. Samples were barcoded for multiplexing with the following adapters: day 1 Inga foal index 2; day 1 Konstance foal index 4; day 1 Wild Rose foal index 5; day 1 Neinke 2014 foal index 6; day 42 Inga foal index 7; day 42 Konstance foal index 12; day 42 Wild Rose foal index 13; day 42 Neinke 2014 foal index 14; Inga mare index 15; Holly mare index 16; Wild Rose mare index 18; Neinke mare index 19
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing FASTQC software used for quality check
Sequenced reads were trimmed for adaptor sequence, filter low-quality sequence
Trimmed reads were aligned to the equine genome sequence (NCBI reference assembly EquCab2.0) with TopHat version 2.1.1
Cuffdiff version 2.2.1 was used to get raw read count at gene level
edgeR was for normalization and statistical analysis for identifying differentially expressed genes
Genome_build: NCBI reference assembly EquCab2.0
Supplementary_files_format_and_content: abundance measurements
Submission date Jul 10, 2017
Last update date May 15, 2019
Contact name Wojciech Pawlowski
Organization name Cornell University
Department Plant Breeding and Genetics
Street address Bradfield Hall, Room 403
City Ithaca
State/province NY
ZIP/Postal code 14853
Country USA
Platform ID GPL21401
Series (1)
GSE101117 Dynamic immune gene expression in young foals
BioSample SAMN07340757
SRA SRX2994644

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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