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Sample GSM7429414 Query DataSets for GSM7429414
Status Public on Aug 09, 2024
Title Endometrium_E1_S15_1
Sample type SRA
 
Source name n/a
Organism Bos taurus
Characteristics cell type: Endometrium
group: Embryo Mortality
time: D16
Extracted molecule total RNA
Extraction protocol RNA was extracted using TRIzol reagent following the manufacturer’s instructions. Remaining DNA was removed by treatment with Qiagen-RNase free DNase and -RNAeasy MinElute Cleanup Kit 50.
Total RNA from tissues were shipped to be processed by Zoetis Inc. (Kalamazoo, MI, USA) for construction of cDNA libraries using Illumina’s TruSeq Stranded mRNA Library Prep Kit.
For experiment 1, there were 100 bp paired-end reads. For experiment 2, there were 75 bp single-end reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Endometrium_E1_UMD3.1_RNA-seq_Counts
Endometrium_E1_S15
Data processing Sequence reads were trimmed by Zoetis.
Trimmed sequence reads were aligned for respective bovine genome assembly (E1: UMD 3.1 and E2: ARS-UCD 1.2) by Zoetis using CLC Genomics Workbench.
RNA-Seq data were exported to Excel Spreedsheets, organized (R package: dplyr and plyr) and filtered (R package: edgeR) to exclude samples with less than 10 mRNA raw counts.
Use of DESeq2 package in R controlled for potential false discovery using an adjusted p-value and the Benjamini-Hochberg method.
Assembly: Experiment 1: UMD 3.1; Experiment 2: ARS-UCD 1.2
Supplementary files format and content: tab-delimited text files include raw counts for each sample.
 
Submission date May 25, 2023
Last update date Aug 09, 2024
Contact name Carolina Lucila Gonzalez-Berrios
Organization name USDA-ARS
Street address 243 Fort Keogh Road
City Miles City
State/province Montana
ZIP/Postal code 59301
Country USA
 
Platform ID GPL15749
Series (1)
GSE233492 Embryo Mortality with an Impaired Interferon-Tau Release Mounts a Massive T-Helper Immune Response in Lactating Holstein-Friesian cows
Relations
BioSample SAMN35369465
SRA SRX21416314

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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