|
| Status |
Public on Aug 09, 2024 |
| Title |
Conceptus_E1_EM_S5_1 |
| Sample type |
SRA |
| |
|
| Source name |
n/a
|
| Organism |
Bos taurus |
| Characteristics |
cell type: Conceptus
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 |
Conceptus_E1_UMD3.1_RNA-seq_Counts
Conceptus_E1_S5
|
| 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 |
SAMN35369475 |
| SRA |
SRX21416304 |
