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| Status |
Public on May 08, 2021 |
| Title |
6-K56-C-Mucosa-Prg |
| Sample type |
SRA |
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| Source name |
Uterine Cervix
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| Organism |
Equus caballus |
| Characteristics |
tissue: Cervical Mucosa
group: Control
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Dec 01, 2020 |
| Last update date |
May 08, 2021 |
| Contact name |
Barry A. Ball |
| Organization name |
University of Kentucky
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| Department |
Veterinary Scinece
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| Lab |
Reproduction
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| Street address |
108 Gluck Equine Research Center,
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| City |
Lexington |
| State/province |
Kentucky |
| ZIP/Postal code |
40546-0099 |
| Country |
USA |
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| Platform ID |
GPL21401 |
| Series (1) |
| GSE162465 |
Equine Cervical Remodelling during Prepartum Period and Placentitis: A Transcriptomic Approach (Mucosa) |
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| Relations |
| BioSample |
SAMN16972449 |
| SRA |
SRX9615700 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4952543_6-K56-C-Mucosa-Prg.fpkm_tracking.gz |
913.2 Kb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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