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Sample GSM4952542 Query DataSets for GSM4952542
Status Public on May 08, 2021
Title 5-M74-C-Mucosa-Tx
Sample type SRA
 
Source name Uterine Cervix
Organism Equus caballus
Characteristics tissue: Cervical Mucosa
group: Placentitis
Treatment protocol Placentitis was induced in five mares at approximately 290d of gestation (placentitis group), four mares with gestationally age-matched (290 d) pregnancies did not receive any treatment (control group), and the remaining three mares were maintained until approximately 330 d of gestation (prepartum group). For induction of placentitis in the former group, Streptococcus equi subsp. zooepidemicus was introduced intracervically.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from all cervical mucosa 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 samples from the control and urea 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 Dec 01, 2020
Last update date May 08, 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)
GSE162465 Equine Cervical Remodelling during Prepartum Period and Placentitis: A Transcriptomic Approach (Mucosa)
Relations
BioSample SAMN16972450
SRA SRX9615699

Supplementary file Size Download File type/resource
GSM4952542_5-M74-C-Mucosa-Tx.fpkm_tracking.gz 890.8 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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