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Sample GSM4676177 Query DataSets for GSM4676177
Status Public on Jul 14, 2021
Title NPL-4
Sample type SRA
Source name Uterus
Organism Equus caballus
Characteristics tissue: Chorioallantois
group: Nocaridioform Placentitis Lesion
Treatment protocol Chorioallantois (CA) samples were collected from the margin of the NP lesion (NPL, n=4) and grossly normal region (NPN, n=4). Additionally, CA samples were collected from normal postpartum mares (Control; CRL, n=4).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from all CA samples using RNeasy Mini Kit (#74104; Qiagen), and DNA digestion was performed on-column using RNase-free DNase I (#79254: Qiagen), followed by cleanup procedures. All procedures were performed according to the manufacturer’s instructions. After extraction, RNA concentration and quality were analyzed using Nanodrop 2000 spectrophotometer (#ND-2000; Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer® (Agilent, Santa Clara, CA, USA). All samples had a 260/280 ratio >2.0 and RNA integrity number (RIN) > 8.0.
A TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA) was used to prepare libraries for mRNA sequencing. Libraries were loaded onto an Agilent DNA 1000 chip and validated on an Agilent 2100 Bioanalyzer (Agilent). Quantitation was performed with the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems. Libraries were run on a NextSeq 500 v2 (Illumina) 300cycles High Output kit in a 2x150 base pairs with paired-end reads.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing The Fastq files were evaluated for read quality using FastQC 0.11.4
Trim Galore 0.4.1 was used for adapter and read quality trimming (Phred score threshold of 30).
Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using STAR 2.5.3a (Dobin, Davis et al. 2013)
Reads were annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1
Fragments per kilobase per million (FPKM) were used to determine the expression level of genes
Cuffdiff 2.2.1 was used to calculate differentially expressed genes (DEG) between groups
Significance level was set at FDR-adjusted p-value of the test statistic < 0.05 using a Benjamini-Hochberg correction
Genome_build: EquCab 3.0
Supplementary_files_format_and_content: Normalized abundance measurements- Cufflink Gene.FPKM.Tracking
Submission date Jul 17, 2020
Last update date Jul 14, 2021
Contact name Barry A. Ball
Organization name University of Kentucky
Department Veterinary Scinece
Lab Reproduction
Street address 108 Gluck Equine Research Center,
City Lexington
State/province Kentucky
ZIP/Postal code 40546-0099
Country USA
Platform ID GPL21401
Series (1)
GSE154637 Transcriptomic Analysis of the Chorioallantois of Mares with Nocardioform Placentitis
BioSample SAMN15568137
SRA SRX8755828

Supplementary file Size Download File type/resource
GSM4676177_NPL-4_fpkm_tracking.xlsx 1.6 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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