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| Status |
Public on Jul 14, 2021 |
| Title |
NPN-4 |
| Sample type |
SRA |
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| Source name |
Uterus
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| Organism |
Equus caballus |
| Characteristics |
tissue: Chorioallantois
group: Nocaridioform Placentitis normal-appearing region
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| 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).
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| 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.
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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 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 |
Jul 17, 2020 |
| Last update date |
Jul 14, 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) |
| GSE154637 |
Transcriptomic Analysis of the Chorioallantois of Mares with Nocardioform Placentitis |
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| Relations |
| BioSample |
SAMN15568133 |
| SRA |
SRX8755832 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4676181_NPN-4_fpkm_tracking.xlsx |
1.6 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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